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Infectious Diseases
HARVEY COURSE 2018/19
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Index
Topic Pages
Viral Hepatitis 2-14
MONDELLI

Infections of the CNS 15-26

Tuberculosis 27-32
Infectious Heart Diseases 33-39
BRUNO

Urinary Tract Infections 57-62

Sexually-Transmitted Diseases 62-68
The Febrile Patient 69-72
Sepsis 73-76
AIDS and Opportunistic Infections 77-90
Infection control
Infections in Pregnancy (TORCH) 91-93
MERONI

Toxoplasma Gondii 93-96

Parvovirus B19 96-98
Syphilis 99-102
Rubella 102-104
Cytomegalovirus 105-108
Skin and Osseous Tissue Infections 49-56
BRUNETTI

Syphilis (part of STDs)

Invasive Fungal Infections 109
Parasitic Infections
Antibiotic Stewardship
MALFITANO/FILICE

Gastrointestinal Infections 40-48

• Disease elimination – complete control, maintained by vaccination Five acute medical infectious
• Disease eradication – not observing new cases of the disease for years emergencies:

• Probability – a thing may happen, more likely than not happening 1. Meningococcal meningitis
• Possibility – a thing may happen, but it is unknown how likely 2. Endocarditis
3. Necrotizing fasciitis
4. Sepsis → septic shock
Answer for a clinical case: hypothesis, DDx and, if needed, therapy 5. C. difficile colitis
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Viral Hepatitis
Clinical Manifestations
Jaundice
The most frequent manifestation of acute infection is jaundice – yellow discoloration of the skin and
mucosal layers, best visualized in the sclerae. It occurs mostly (see differential diagnosis) due to
increase in serum bilirubin – conjugated (direct) and unconjugated (indirect). Jaundice is classified to
three types:
• Pre-hepatic jaundice: aka hemolytic jaundice. Can also occur due to increase in RBC synthesis (e.g.
polycythemia). Expressed as increased unconjugated bilirubin.
• Hepatic jaundice: due to hepatitis or genetic disorders. Can be expressed by the increase of both
un/conjugated bilirubin.
• Post-hepatic jaundice: aka obstructive (tumor, gallstones)/surgical jaundice. Can also occur by
inflammation at the sphincter of Oddi that results in obstruction of the biliary tree. Expressed by
conjugated bilirubin (was handled by the liver, but its secretion is blocked).
However, it is not a pathognomonic sign of hepatitis – can appear in different pathologies (differential
diagnosis of jaundice):

↑ Unconjugated bilirubin ↑ Conjugated Bilirubin Other causes of

(usually increases in post-hepatic yellow discoloration
jaundice)
Mechanisms: Mechanisms:
↑ Production ↓ Conjugation Impaired Biliary obstruction
excretion
Physiological – e.g. in Gilbert syndrome – Hepatitis Carotenoderma – due to
prolonged starvation mutation of the UGT- excess ingestion of
state (increase in 1A gene that causes carotenes, acquired from
catabolism which decreased production carrots, other orange
increases bilirubin) of the enzyme fruits/vegetables or
green-leafy vegetables.

Not evenly distributed on

the palms, soles,
forehead and nasolabial
folds.
Hemolysis – since Crigler-Najarr Rotor/Dubin- Choledocholithiasis Quinacrine/Mepacrine –
bilirubin is the syndrome – mutation Johnson syndrome - an anti-protozoan drug
product of heme in the UGT-1A gene genetic defects of that causes yellow
group catabolism that yields a liver proteins (OATP discoloration (in 4-37% of
completely and MDRP2, the cases).
dysfunctional enzyme respectively)
Hematoma Hyperthyroidism Metabolic disorders Biliary atresia
Polycythemia – due Prematurity (neonatal Tumor of the head
to tobacco smoking jaundice) of the pancreas
or hematological
diseases
(polycythemia vera)
Sepsis
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Histopathology
In acute infection:
• Periportal accumulation of lymphocytes and monocytes (not extensively)
• Hepatocyte swelling (ballooning) – hydropic formation that causes the cells to lose their hexagonal
shape, become rounder.
• Councilman bodies – due to lobular hepatocyte apoptosis (more eosinophilic, also called
acidophilic bodies)
• Cholestasis – expressed as the browning of the bile ducts
Disease progression under a histological point-of-view:
1. Liver is normal in appearance
2. Inflammation (accumulation of lymphocytes)
3. Fibrosis – begins in accumulation of blue material (collagen) around the lobules. In more advanced
stages there is much more fibrotic material.
4. Cirrhosis – appearance of nodules due to regeneration of the parenchyma over the damaged
reticular connective tissue.
Today biopsy is less used in the clinical practice, since there are new diagnostic tools which are sensitive
in detecting the disease.

Laboratory Tests
Detection of liver enzymes in serum:
Enzyme Tissue specificity Other conditions (rather than hepatitis)
AST Liver and cardiac/skeletal muscles • Higher value than ALT in cirrhosis
• Together with ALT – more sensitive test of acute liver disease
• Together with γGT - high in chronic alcohol use
ALT Liver and some other tissues (the most
specific marker)
ALP Liver and bones • Together with γGT indicate cholestasis
• Bone degradation
γGT Liver and some other tissues (also a very • Increase in alcoholism
specific marker) • Using psycho-active drugs
• Metabolic disorders
Viremia: more accurate in detection of hepatitis, especially in chronic patients.

Epidemiology
The deaths due to viral hepatitis are mostly by HBV (66%), other than that - 30% is by HCV, 3.3% by HEV
and 0.8% are by HAV.
While in most diseases a decline in morbidity has been demonstrated, in viral hepatitis there are more
cases of death every year. Out of yearly 1.34 million deaths – about 50% are due to decompensated
cirrhosis, and about a third due to hepatocellular carcinoma.

HBV Infections
• 3.5% of the world population suffers from a chronic HBV infection
• 68% of all infections in Africa and West-Pacific
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• About 1% are coinfected with HIV

• Prevalence in minorities: Amazonas, Andaman and Nicobar Islands, Maori (New-Zealand),
Aborigines and Torres strait islanders (Australia), Roma people (Europe).
Elimination Strategy of HBV
Interventions 2030 targets
Three-dose 90%
hepatitis B vaccine
Prevention of 90%
mother-to-child
transmission1
Service Blood and injection 100% screened blood donations
coverage safety 90% reuse-prevention devices2
Harm reduction 300 injection sets/PWID3/year
Treatment 90% diagnosed patients –
improve the diagnosis4
80% eligible treated – increase
the number of treated patients5
Incidence reduction 90% less cases
Impact Mortality reduction 65% less cases of death

HCV Infections
• 1% of the world suffers from a chronic HCV infection
• Prevalence (in descending order): the Mediterranean and Arabian regions, some European regions,
Africa, India and China. In Italy: patchy distribution (prevalence increases Southwards).
• About 3% are coinfected with HIV
• Prevalence in minorities: indigenous communities and prevalent within immigrants
WHO Guidelines on HCV Testing
• There are only few evidence-based guidelines in countries with lower mean income (correlation
with higher probability for acquiring the infection)
• In countries with high mean income the testing is according to risk factors (IVDU, men who have
sex with men, HIV carriers, incarcerated people, hemodialysis patients etc.).
• Testing of every individual is recommended only in Japan
• Testing of Baby-boomers in the US (1948-1963)

Agents
Virus Family Genus Genome
HAV Picornaviridae Heparnavirus RNA
HBV Hepadnaviridae Orthohepadnavirus DNA
HCV Flaviviridae Hepacivirus RNA
HDV Deltaviridae Deltavirus RNA
HEV Hepeviridae Orthohepevirus RNA

1 Prevention of mother-to-child transmission (PMTCT) – sometimes vaccination is not enough to prevent vertical transmission
due to high viral load. It is possible to decrease the chances by administration of gamma-globulins.
2 Risk of acquiring the disease from a contaminated syringe or needle: HBV – 30%, HCV – 3% and HIV – 0.3%.
3 PWID = people who inject drugs. Note that any tool (of the paraphernalia) can transmit HBV, HCV or HIV – e.g. needles, syringes,

spoons, filters (e.g. cotton), water or alcohol swabs.

4 Currently diagnosed patients (estimated) – HBV: 9%, HCV: 20%
5 Currently treated patients (estimated) – HBV: 8%, HCV: 7.4%
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Hepatitis B Virus (HBV)

Generalities
Structure:
• Genome of circular, partially double-stranded DNA
• DNA polymerase
• Nuclear protein – HBcAg (core antigen)
• HBeAg – made from the same gene of HBcAg but found
between the core and the surface antigens.
• Envelope – HBsAg (surface antigen – can be divided into
three types: large, medium and small. The latter is mostly represented)
Life-cycle:
1. The virus binds to its receptor on a hepatocyte
2. Entry of the viral content to the cytoplasm and migration of the genome towards the nucleus
3. Synthesis of complementary RNA segments that can turn into-
a. DNA – turning the genome to fully dsDNA -> covalently closed circular DNA (cccDNA)
b. mRNA – for protein synthesis, among them a RT (viral polymerase with RT activity)
c. Pre-genomic RNA -> migrates to the cytoplasm
4. Replication of DNA out of the pre-genomic RNA within the capsid
5. Addition of the HBsAg
6. Exit the cell
Genotypes: (A-I)
• A – common in Northern Europe, India and South Africa
• B and C – common in Asia
• D – common in the Mediterranean region and the Arabian Peninsula
# Other genotypes are less common
# Vaccination is against serotype adw2
Transmission:
• Sexual
• Parenteral – blood transfusions, IV drug users (contaminated needles)
• Perinatal
Presence in biological fluids:
• High – blood and exudates
• Moderate – seminal fluid, vaginal secretions, saliva
• Low/absent – urine, stool, sweat, tears, maternal milk
Clinical Presentation
Features:
• Incubation period (mean): 60-90 days (range between 45-180 days)
• Jaundice: in infants (<5 years old) – less than 10%. In older patients – 30-50%.
• Chronic infection: depends on the age (more common in younger ages)
• Mortality from chronic liver disease: 15-25%
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Serological markers:
HBsAg
IgM anti-HBc The most significant marker of acute disease
Acute HBV DNA
disease: HBeAg Appears in B and C serotypes (Chinese variants). Associated with high viral
replication but does not necessarily indicate the severity of the disease.
ALT (increase) in adults. DDx – hepatotoxic drugs (applies for all types of hepatic infections)
HBsAg If the infection was not recovered, persists in high amounts in the serum
IgG anti-HBc
Chronic
HBV DNA
disease:
HBeAg
Anti-HBe antibodies the disease lasts long enough (passed sensitization phase)
In immunized
Anti-HBs IgG
individuals:
In recovered Anti-HBc IgG Early
patients: Anti-HBs IgG Late

Acute disease Chronic disease

Immune Immune clearance Low/non-replicative Reactivation phase

tolerance phase
High viral 107-108 units/mL <105 units/mL DNA concentration
concentration increases
(109-1010 Florid liver damage
units/mL)
without
significant liver
damage
↑ALT – can fluctuate6 No fluctuation of ALT Mild fluctuation
Cirrhosis can evolve Cirrhosis can evolve
• Inactive carrier
state
Acute disease • Resolution (HBsAg Chronic infection
negative, anti-
HBsAg positive)

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Trends in ALT:
• Peaks and normalizations – higher risk for liver damage, deposition of scars that can evolve to cirrhosis
• Relatively constant – low propensity of evolving into liver damage
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Natural History: Acute infection

• More than 90% of infected children will develop
chronic disease
• Less than 5% of infected adults (who are
immunocompetent) will develop a chronic disease

Chronic infection
Inactive carrier
• Decompensation – development of ascites due to
impaired albumin synthesis (↓ chances of survival)

Liver failure Cirrhosis Liver cancer (HCC)

• After 5 years of cirrhosis, in • 30% of chronically HBV-infected patients • 5-10% of chronically
23% of patients • 5-year survival: 86% (28% after infected patients
• About 3% of patients with decompensation). • About 3% of patients with
cirrhosis every year cirrhosis every year
• Increased risk after
Liver transplant decompensation (~2 fold)
• Increased risk with increase
Death in viral load

Factors that influence the progression of HBV infection:

• Demographics – age, gender or family history (e.g. of HCC)
• Environmental (metabolic) – alcohol intake, aflatoxin7, NAFLD or tobacco smoking
• Host immune response
• Viral factors – polymorphism in HBc promoter, associated with progressed HBV infection
Treatment
Antivirals:
• Nucleotide analogs (NUC): nowadays, the drugs in use are entecavir (ETV) and tenofovir (TDF).
o Other drugs are not used anymore due to resistance
o Used for longer period as a suppressive treatment (similar to anti-HIV drugs)
o Almost always the first treatment choice (with respect to PegIFN)
• Pegylated interferon α2a (PegIFN): polyethylene glycol and IFN, administered subcutaneously.
o Short-term curative treatment
o Side-effects: fever, myalgia (flu-like symptoms)
o Contraindications: high viral replication, low aminotransferases
o Rarely used in clinical practice (in about 1% of the patients)
Vaccine:
• Provides immunity against HBsAg (no synthesis of anti-HBc antibodies, which occurs only in
recovered patients)
• In the beginning of the 90’s there was a change in strategy regarding the age of administration:
now, the vaccine is given in infancy to enhance its efficacy.

7 Aflatoxin – found in pistachio, a co-carcinogen

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Hepatitis D Virus (HDV)

Generalities
Structure:
• Small genome (~1.7Kbp), -ssRNA
• The delta antigen can be classified into large and small
Life-cycle:
• Usually infects plants
• A satellite virus - when incorporated into HBsAg it becomes pathogenic (appears as a
co/superinfection of HBV)
Transmission:
• Requires current replication of HBV
• Mucosal exposure – sexual contacts
• Percutaneous exposure – in IV drug users
Clinical Presentation
Pattern of disease:
• HBV-HDV coinfection:
o Severe acute hepatitis
o Relatively low risk of developing a chronic disease
• HDV superinfection (of a chronic HBV carrier):
o High risk for development of a chronic liver disease
o High risk for chronic co-infection (prolonged replication of both viruses)

Serological markers:
• In co-infection: ALT increases with appearance of HBsAg in serum
• In super infection: ALT peaks in the beginning of the infection and then decreases (not entirely,
and can fluctuate).
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Note: the δ antigen can be expressed regardless the presence of HBsAg – for example in transplanted
liver. This can be prevented by administration of immunoglobulins anti-HBsAg before the procedure.
Therapy and Prophylaxis
Drugs: currently in testing.
Prohylaxis:
• Primary: contraception, screening of blood transfusions, using individual needles (in IVDU) etc.
• Secondary: hepatitis B vaccine, which prevents also HDV infection.

Hepatitis C Virus (HCV)

Generalities
Structure:

C E1 E2 p7 NS2 NS3 NS4a NS4b NS5a NS5b

Nucleocapsid Envelope Auto-protease NS3 protease RNA-dependent

(Core) proteins cofactor RNA polymerase
• Serine protease
Functions in viral
• Helicase replication
• NTPase

• Non-structural proteins (NS) are crucial components of the replication cycle.

Genotypes:
• The virus has 7 genotypes and 67 subtypes
• The most common genotypes are 1 to 4, where 4 is the most prevalent in the Middle East.
Transmission:
• Mother-to-child – (average risk of ~4%)
o The first cause of HCV infection in developed countries
o About one third of transmissions occur in the uterus
o Factors which increase the probability for infection: high viral load (the threshold is unknown),
untreated HIV and drug use.
o May be prevented by administration of immunoglobulins at birth
• Sexual intercourse – risk factors:
o More common in anal intercourse (men who have sex with men)
o Past syphilis
o Reinfection can occur = no immunity
Clinical Presentation
Symptoms and features:
Incubation period: 15-150 days (mean: 30-50 days)
Jaundice: Rare, less than 10% of the cases
Chronic evolution: 60-80% in adults (always asymptomatic until the development of cirrhosis/HCC)
Cirrhosis: 10-20% of the cases
Liver-related mortality: 1-5% after more than 20 years. Depends on the mode of transmission and the viral
load at exposure
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• Cryoglobulinemia – purpura and vasculitis due to the deposition of cryoglobulins in small

capillaries. Cryoglobulins are antibodies that precipitate in lower temperatures (= hence the name
“cryo”-cold in Greek) eliciting inflammation and/or occlusion of small vessels. It occurs due to the
high mutation rate of the virus, forcing the body to synthesize many useless antibodies, since they
cannot find their antigen, which eventually precipitate in the vessels.
o More common in the limbs (due to lower temperature)
o Peripheral neuropathy
o Ulcerations and systemic vasculitis may develop.
o DDx: lymphoproliferative disorder.
Serological markers:
• The large mass of antibodies develops relatively late, after the presence of RNA in the blood.
• Core antigen detection – not a sensitive test.
• RNA in blood – tested in blood transfusions (more sensitive than test of anti-HCV antibodies in
the serum).

Natural history:

Acute Chronic infection Chronic Cirrhosis HCC

infection • About 60-80% of the patients Hepatitis • 10-20% of the • 1-4% of the
• Can last over 30 years patients patients every
• Risk factors of slow- year
progression: female sex,
younger age at infection

• The progression of the diseases can be speeded up (less than 20 years until the progression of
cirrhosis) by alcohol abuse (steatosis), coinfections, older age, male sex.
Therapy
Sustained virologic response (SVR) – is defined when HCV is not detected in the serum during the
treatment, and for 12 weeks after completing it. The benefits of achieving SVR are decreased
transmission and improved clinical outcomes both hepatic (less intense disease progression) and
extrahepatic (improved quality of life and reduction of all-cause mortality)
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Therapy has become more effective, because:

• There are new drugs which attack specific viral targets
• The HCV genome does not integrate in the host cell genome (unlike HBV)

Note: all patients (no matter the stage of the disease) must be considered for therapy.

Drugs: DDAs (direct-acting antivirals)-

• NS3/4 inhibitors – inhibition of serine protease which is responsible for post-transcriptional
modifications (polyprotein processing). Suffix -previr, e.g. Voxilaprevir (VOX), Glecaprevir (GLE).
• NS5a inhibitors – inhibition of viral replication and assembly. Suffix -asvir e.g. Velpatasvir (VEL),
Pibrentasvir (PIB).
• NS5b inhibitors – inhibition of the RNA polymerase, thus blocking an essential step of viral
replication. Suffix -buvir. Can be classified into two groups:
o Nucleotide inhibitors (NUC) – nucleotide analogs which upon integration with the enzyme
cause its inhibition; e.g. Sofosbuvir (SOF).
o Non-nucleotide inhibitors – bind the catalytic site and block the enzymatic activity; e.g.
Dasasbuvir (DSV).

Current treatment options – combination regimens, to achieve high rates of SVR and minimize the
chances of resistance:
1. Sofosbuvir and Velpatasvir for 12 weeks
2. Pibrentasvir and Glecaprevir for 8-12 weeks
3. Sofosbuvir, Velpatasvir and Voxilaprevir for 12 weeks
4. Addition of Ribavirin – in case of cirrhosis or patients who underwent treatment, meant to amplify
the responses of the combinations. Contraindication: pregnancy.

Note: the regimen can be shortened to 8 weeks in naïve, non-cirrhotic patients.

To date:
• Almost every infection (~100%) is curable
• No evidence of non-human reservoir (and the virus cannot HCV elimination is possible
replicate in the environment) (without a vaccine!)
• Simple and accurate diagnostic tools

Prevention:
• A vaccine in development, targeted against the viral non-structural proteins. Currently it prevents
only chronic infections (prevents high viral load).
• Increasing the awareness, calling people to get tested and behavioral changes (sex education etc.)
• Reaching treatment to all patients (the partner study – patients that are being treated did not
transferred HIV to their partners after intercourse).
• Treatment as prevention will help in reaching the WHO goals by 2030 (an annual net cure of 7%),
but not in all countries.
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Hepatitis E Virus (HEV)

Generalities
Genotypes: the ones which affect humans and their geographic prevalence-
• Genotype 1: Asia, Africa
• Genotype 2: Mexico, Africa
• Genotype 3: western countries; zoonotic Genotypes 3 and 4 are found in animals such as pigs,
• Genotype 4: Asia, Europe; zoonotic boars, deer and rabbits; all are asymptomatic.

Transmission: there is no solid evidence for an exact mode of transmission

• Fecal-oral route via infected water (major health issue in developing countries).
• Blood transfusion
• Liver transplant (chronic HEV3 infection in transplant patients)
Epidemiology: common in travelers (especially young adults, except for HEV3 which is irrelevant for
traveling and affects older males), less seen in western countries.
Clinical Presentation
Symptoms:
• Often asymptomatic
• Acute illness is similar to HAV,
self-limiting
• Can be highly lethal to pregnant
women (25% mortality, except
for HEV3)
• Chronicity is only for HEV3 –
cirrhosis is rapidly progressing
Serological markers: (right)
• Incubation period of 2-6 weeks
• Can be also perceived from CSF
Extrahepatic manifestations: (associated conditions)
• Neurological disorders – may occur both in acute and chronic infections (described in HEV1 and
HEV3):
o Guillain-Barré syndrome – post infectious, immune-mediated polyradiculopathy.
o Bell’s palsy
o Neuralgic amyotrophy (HEV3)
o Acute transverse myelitis
o Meningoencephalitis
• Kidney injury
• Thyroiditis
• Myocarditis
• Cryoglobulinemia
• Pancreatitis (HEV1)
• Hematological disorders: aplastic anemia, thrombocytopenia
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Treatment
Vaccine: currently in testing
Drug: ribavirin was not proven as efficient since there is an increase in viral load after therapy stops.

Hepatitis A Virus (HAV)

Generalities
Transmission:
• Person-to-person – intrafamilial, sexual, kindergarten
• Contaminated food or water – especially seafood (clams/mussels)
• Blood exposure – e.g. transfusion, very rare
Presence in biological specimens: (ordered highest to lowest abundance)
• Stool
• Serum – present for a limited amount of time
• Saliva
Epidemiology:
• More prevalent in the south portion of the globe
Genotypes: the two major ones are I and II.
Clinical Presentation
Serological markers:

Features:
• Incubation period: 15-50 days (mean is 30 days)
• Does not evolve to chronic infection
• Jaundice – prevalence increases with age:
o <6 years-old: <10% of the cases
o 6-14 years-old: 40-50%
o >14 years-old: 70-80%
Complications:
• Cholestasis
• Long-term fluctuations of ALT and virus shedding
• Fulminant hepatitis (rare)
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Treatment
Prophylaxis:
• With the improvement of the hygiene status (safe water supply) – less cases appear
• Post-exposure – normal immunoglobulins anti-HAV
Vaccine:
• 4 different types of inactivated vaccine (and one with a combination of a vaccine against HBV)
• Should be vaccinated: children (over 1-year-old) and travelers in endemic areas, food-workers,
military forces, medical staff, men who have sex with men.

Hepatitis – Differential Diagnosis

1. Drug-induced Liver Injury (DILI) – common in elderly, 13% of the patients also have HEV3 (always
test presence of viral RNA in blood)
2. Autoimmune hepatitis
3. Acute HEV
4. Seronegative hepatitis
5. EBV hepatitis
6. Acute HBV infection
7. HAV infection (always acute)
8. Acute HCV infection
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Infections of the CNS

There are three types of CNS infections, classified according to the infected structure:

• Meningitis – inflammation of the meninges, in most cases by a viral infection which is more benign
(has better prognosis) than bacterial infection. More than 75% of the cases are medical emergencies
due to the proximity to the brain and spinal cord.
• Meningoencephalitis – mixed presentation, common in viral infections as well.
• Encephalitis – inflammation of the brain parenchyma. Predominantly by viruses but can also occur
in acute bacterial infection.

Meningitis
Pathogenesis (Bacterial meningitis)
The infection typically begins by a bacterium which colonizes the
pharynx:
• Neisseria meningitidis - its pili adhere to mucosal receptors
• Haemophilus influenzae - can infiltrate through gap junctions (more
common in children (though almost eradicated thanks to a vaccine)

Penetration through the mucosal layer

Bacteremia (and sepsis)

Crossing of the BBB - note that the antibiotics must be able to

pass to yield effective treatment.
• Release of endotoxins and pro-inflammatory mediators
Meningitis
Increased vascular permeability and likelyhood of thrombosis
• Blood congestion (distinguished in autopsy)
• Exudation
The result – cerebral edema that increases the intracranial
pressure. The condition deteriorates because the brain is less
perfused and can eventually become infarcted.
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Causes of Meningitis
The severity of the infection depends on the agent that causes it, therefore, it is crucial to know the
exact cause of the meningitis.
Turbid CSF
Bacteria: (in bold – nasopharyngeal flora) Fungi:
• Haemophilus influenza • Candida
• Neisseria meningitidis (meningococcus)8 • Mucor
• Streptococcus pneumonia (pneumococcus) • Naegleria – rare, found in ponds/fresh
• Escherichia coli – very common in neonates water
(0-30 days old) • Acanthamoeba
• Staphylococci
• Streptococci (Groups A and B)

Clear CSF
Bacteria: Aseptic: due to physical injury or cancer
• Mycobacterium tuberculosis
Viruses:
• Treponema pallidum (syphilis)
• Enterovirus (Echovirus, Coxsackie virus)
• Brucella spp. (Maltese fever)
• Arbovirus (mosquito-borne diseases)
• Listeria monocytogenes – sometimes
• Polio virus
present with a turbid CSF. Common in the
• Mumps (parotitis)
elderly; acquired by eating contaminated
• Measeles
food
• Herpesviridae (HSV1/HSV2, VZV, EBV, CMV)
• Leptospirae
• HIV
• Rickettsiae – Rocky Mountain spotted fever
• Parvovirus
• Chlamidiae
Parasites:
Fungi: especially in immunocompromised
patients. • Toxoplasma
• Histoplasma capsulatum • Trypanosoma
• Cryptococcus neoformans/gattii – AIDS- • Plasmodium malariae – creates thrombi in
defining illness brain vessels

Modes of Transmission
Transmission usually occurs by close contact with nasopharyngeal carriers (see above), yet people can
only become carriers (in a healthy state).
Mortality According the Etiological Agent
Meningitis Sepsis
Meningococcus ~20% ~85%
Pneumococcus ~15% ~30%
Other etiologies ~20% ~30%

8
Men C-cc11 strain of N. meningitidis is highly invasive, not commensal
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Epidemiology
Bacterial Meningitis
Incidence of 3-12 cases in every 100,000 people each year. Most cases are by N. meningitidis (common
in first 5 years of life), where the second most common agent is S. pneumoniae (affects all ages).
Agents can be classified according to the age-specific risk:

• Premature babies and newborns (<3 months old)

o Group B streptococci – can be found in the birth canal
o E. coli – due to the proximity to the anus
o L. monocytogenes – serotype IVb
o S. Pneumoniae – from one month old (up to 4 years of age)
• Older children
o H. influenzae – with capsule antigen type B, in children between the ages of 6 months to 4
years, mostly as a complication of middle ear infection. Nowadays can be easily prevented by
the Hib vaccine.
o N. meningitidis – most common in children under 2 years old. Adolescents are the ideal target
vaccination population (to avoid the use of boosters).
o S. pneumoniae – serotypes 6,9,14,18 and 23.
• Adults
o N. meningitidis and S. pneumoniae – 80% of all bacterial meningitis cases. 10% of the people
are healthy nasopharyngeal carriers of N. meningitidis.
o L. monocytogenes – the risk increases with age (common in older adults, >50 years old)

Another classification, according to risk factors that predispose particular patients to meningeal
infection:

• Immunodeficiency – S. pneumonia, P. aeruginosa9, N. meningitidis, L. monocytogenes

• Skull fracturs – S. pneumoniae (+++), H. influenzae
• Shunts, trauma – Staphylococcus spp.10 (+++), P. aeruginosa
• Neurosurgery – Staphylococcus spp. (+++), P. aeruginosa, E. coli
• Following splenectomy / functional asplenia – increased risk of N. meningitidis infection
(11/100,000)
• Complement defects/hypogammaglobulinemia – N. meningitidis

Viral Meningitis
Incidence of 5-35 cases in every 100,000 people each year = more common than bacterial meningitis.
Children, adolescents and young adults (up to 30 years old) are mostly affected. Most infections occur
in children under the age of 5.

Most cases of viral meningitis are due to enteroviruses, which can also cause intestinal illness. Viral
meningitis may be associated with symptoms and signs of encephalitis (meningoencephalitis).

9
Pseudomonas aeruginosa – nosocomial infection
10
Remember that staphylococci normally colonize the skin, so their migration to different tissues creates infection
 19

Agent Characteristics
Hemophilus Influenza
• Gram-negative, aerobic bacterium
• Part of the normal throat flora
• Capsule antigen type B causes meningitis
• Complications: subdural effusion, deafness, learning disability
Neisseria Meningitidis (Meningococcus)
• Gram-negative diplococcus
• Membrane LPS characterize 13 serogroups, 6 of them are responsible for fatal diseases: A, B, C,
Y, W135 and X.
Serotype Further epidemiological data
A More frequent in Africa
B More frequent in children (aged 0-4), and in Europe and America
More frequent in adults in Europe and America,
C
strain Men C-cc11 (found in Tuscany) is highly invasive, not commensal
W135 A clone has been identified in Canada
Y Increasing incidents in adolescents

• The LPS bind TLR4 on macrophages → leads to sepsis (some patients are more sensitive)
• Manifestation typical of meningococci – petechiae (but can occur also in pneumococcal infection)
• Clinical presentation:
o Typical meningitis: 68%
o Meningitis with sepsis: 14%
o Isolated sepsis: 16%
o Other: 2%
Streptococcus Pneumoniae (Pneumococcus)
• Gram-positive diplococcus
• 70% of people are healthy nasopharyngeal carriers (part of the flora)
• Infection may originate from the middle ear (otitis media) or mastoid
• Mortality: 30% in children, 80% in elderly
Listeria Monocytogenes
• Gram-positive rods
• The most common serotypes (80%) – Ia, IIa and IVb
• Mortality of 30%, especially in elderly
• Risk factors:
o Young and old age
o Alcohol consumption
o Cirrhosis
o Immunosuppression and autoimmune diseases
o Pregnancy (last trimester)
• Typical symptoms: seizures, ataxia, tremors, behavioral alterations
• Complications: cerebritis, abscesses, paralysis, nystagmus
 20

Borrelia Burgdorferi (Lyme Disease)

Always suspect in a peculiar clinical picture. Borrelia burgdorferi is a spirochete transferred by a tick
bite = higher prevalence in campers/hikers. The tick’s eggs hatch in the spring and in the summer,
they become larvae. Therefore, this is the period of the year when most infections occur.
The stages of the disease:
1. Early localized: 3-30 days since the bite
• Flu-like symptoms, sometimes with neck stiffness
• “Bull’s-eye” – skin reaction with peculiar morphology, can last up to 4 weeks
• Erythema migrans – rash that spreads throughout all the skin (not-specific for Lyme disease)
2. Early disseminated: weeks to months since the bite
• Rash
• Neuralgia, facial paralysis
• Dyspnea, palpitations
3. Late disseminated: months to years since the bite
• Arthritis – particularly in big joints (sampling – aspire fluid from synovial joints)
• Paresthesia – abnormal dermal sensation (tingling, burning, numbness etc.)
• CNS disorders – meningitis (clear CSF), facial paralysis, neurocognitive disorders
• Arrhythmias
Full adult larvae are easier to detect, so always perform laboratory tests according to the following
algorithm:

First test Second test

Signs or symptoms
Positive result
≤ 30 days IgM and IgG
Enzyme
Immunoassay (EIA) Western Blot
or
Signs or symptoms
Immunofluorescence Negative result
Assay (IFA) >30 days IgG Western Blot
only

Consider alternative diagnosis

Or
If the patient has symptoms/signs of Lyme
disease (less than 30 days) → consider
obtaining a convalescent serum

Viral Meningitis
• Incubation period: 3-6 days
• Duration of the illness: 7-10 days
• Milder than bacterial meningitis
• Herpes meningitis/meningoencephalitis: as a primary infection (associated with labial or genital
herpes11) or reactivation of a latent infection. Severe sequalae are very common.

11
If there are neurological symptoms – administer acyclovir
 21

Tuberculous Meningitis (Chronic Meningitis)

Epidemiology: increasing incidence
• 75% of the cases are in immigrants
• More frequent in children and young-adults
• Risk factor: HIV infection
Clinical presentation:
• Localization of tuberculosis is usually secondary (coming from other foci) and takes time to grow.
• Frequent cranial nerve localization
• Differential diagnosis: cerebral abscesses (more common), fungal lesions and meningioma
Complications:
• Hydrocephalus (fluid congestion)
• Epilepsy
• Mental retardation
• Cranial nerve paralysis
Diagnosis: (in the brain) by imaging – multiple round cerebral lesions surrounded by edema =
tuberculomas.
Therapy: a combination of at least 3-4 drugs (depends on the strain and its antibiotic resistance)
 22

Clinical Presentation
Onset
• Acute – within less than 24 hours (can be hyperacute – within few hours). 25% of bacterial
meningitis.
• Subacute – within 1-7 days. 75% of bacterial meningitis and all viral meningitis cases.
• Chronic – weeks to months after the infection
Symptoms and Signs
• Headache – severity depends on the increase in ICP.
• Fever
• Vomiting – projectile, not preceded by nausea. Due to ↑ICP.
• Neck stiffness – the patient is unable to move the neck. In
children – may not be able to raise the head
• Ocular disorders – photophobia, papilledema (swelling of the
optic disc, due to ↑ICP)
• Phonophobia
• Seizures
• Drowsiness/altered mental status → lethargy (fatigue)→
coma
• Petechiae – skin lesions and purpura, typical in septicemic N.
meningitidis infections but can also appear in pneumococcal
infection.
• Muscle spasm (in severe infection) – arched back and neck
retraction
• Bulging of the bregma fontanelle – in newborns (fontanelle
close in the 3rd/4th month after birth)
Signs of physical examination (patient is lying supine):
• Kernig’s sign – with the hip flexed, the patient cannot extend the knee joint
• Brudzinski’s sign – flexing the neck causes involuntary flexion of the knees and hips
Note: rhinorrhea of CSF (“runny-nose”) in recurrent S. pneumoniae infection (due to fracture in the
cribriform plate)
Complications
• Brain abscess
• Cranial nerve paralysis
• Hearing loss
• Hydrocephalus – especially in pneumococcal / tuberculosis infection due to increased production
of fibrin, which eventually blocks the ducts between the ventricles, increasing the pressure.
• In Hemophilus influenzae infection – subdural effusion, deafness, learning disability
• Disseminated intravascular coagulation (DIC) – in about 6% of affected infants
• Brain damage – due to penetration to the brain parenchyma (CNS involvement).
• Seizures – a bad prognostic sign
 23

Diagnosis
1. CT Scan
Better to perform this exam before sending the patient to lumbar puncture, especially if the
setting is a well-facilitated hospital.
(1) Cerebral infarction
(hypodense area)
(2) Hydrocephalus (enlarged
ventricles, note the
hyperdense wall of the right
ventricle minute
ventriculitis)
(3) Heavily inflamed ependymal
cells with ventricular
involvement = ventriculitis.
(4) Cerebral abscess
(hyperintense border)
(5) Diffuse brain edema
(6) Frontal subdural effusion (H.
influenza infection)
2. Lumbar Puncture – CSF Examination
Examination of the CSF includes:
• Cell count, glucose and protein → differentiate the type etiological agent
• Gram stain, other stains (Ziehl-Nielsen – for mycobacteria) → detect the specific bacteria
• PCR, NASBA, LAMP (if viruses/TB are suspected) → molecular assays that have high sensitivity,
to identify the specific agent
Method – Lumbar Puncture
1. The patient is lying on his flank, the back must lean forward as much as possible
2. Application of local anesthetic
3. Insertion of a long needle between the spinous processes of the lumbar vertebrae (usually
L3 and L4)
4. If the intrathecal pressure is increased, the CSF should leak fast. If not – CSF is dropping
slowly.
Analysis of the Results
Normal CSF: clear
− Pressure: 35-45cmH2O (sitting) / 15-20cmH2O (lying to the side)
− Protein concentration: 20-30mg/dL (mostly albumin)
− Glucose concentration: 40-70mg/dL
− Chloride concentration: 700mg/dL
− Cells: <5/μL
 24

Abnormal results: (turbidity of the CSF – in infections of the previously mentioned agents)
Glucose Proteins Cells
Acute Bacterial Meningitis Low High – cell debris Predominantly PMNs
(often >300/mm3)
Viral Meningitis Normal Normal/high Predominantly
(depends on the Ig lymphocytes <300mm3
synthesis location)
Tuberculous Meningitis Very low High (cell debris and Lymphocytes and PMNs
fibrin) <300/mm3
Fungal Meningitis Low High <300/mm3
Malignant (aseptic, mostly Low High Usually lymphocytes
cerebral lymphomas)
Note: consider the timing of the sample from biological fluids, since viruses my not be present in
significant amounts.
FilmarrayTM
New machine that can detect up to 14 pathogens:
• Yeasts – C. neoformans/gattii
• Bacteria – E. coli (K1 - antigen on the capsule), H. influenzae, L. monocytogenes,
meningococci, pneumococci, S. agalactiae.
• Viruses – CMV, HSV1/2, HHV-6, VZV, parechovirus, enterovirus
3. Blood Tests
Blood examination includes:
• Blood culture –
o Chocolate agar – (brown color due to heating of blood) detection of N. meningitidis and
H. influenzae. Colonies appear as purple spots (oxidase positive).
• Markers of inflammation – CRP, PCT, CBC
• Electrolytes – especially in in severe bacterial meningitis (hyponatremia is common)

Treatment
Prescribe antibiotics immediately after taking samples for laboratory assessment.
➢ Meningococcal Disease
Antibiotics:
• Ceftriaxone – 2g IV (twice a day i.e. BID)
o Advantages: rapid sterilization of CSF, decreases carriage
o Disadvantages: might be toxic in children
• Cefotaxime – 2g IV (four times a day i.e. QID, up to 24g/day)
o Advantages: low toxicity
o Disadvantages: slower sterilization, no evidence of decreasing carriage
 25

Prophylaxis: for people in close contact with patients (decreases with time away from exposure)
• Ciprofloxacin 500mg (single dose) – for adults. Not to be used by pregnant women and children.
• Rifampin (Rifampicin) 600mg (twice a day, for two days) – for children.
Vaccine:
• Tetravalent (A, C, W135 and Y) – for all population (aged over 2 years old)
• Monovalent – against serotype C, and a new vaccine against serotype B. Applicable for all ages
(75% efficacy)
➢ Pneumococcal Disease
Antibiotics:
• Vancomycin + 3rd generation cephalosporin (cefotaxime/ceftriaxone)
Vaccine:
• Polysaccharide vaccine – against 23 serotypes (contains purified antigens)
• Conjugated vaccine – against less serotypes, but confer also mucosal immunity
➢ Escherichia Coli
Antibiotics: 3rd generation cephalosporin (cefotaxime/ceftriaxone)
➢ Hemophilus Influenza
Antibiotic: rifampin (rifampicin)
Vaccine: HIB – anti-capsule antigen B
➢ Listeria Monocytogenes
Antibiotic: amoxicillin/ampicillin or penicillin G. Consider the addition of aminoglycoside
➢ Streptococci spp.
Antibiotic: amoxicillin/ampicillin or penicillin G.
Note: Steroids in acute bacterial meningitis
There is evidence that in some cases the addition of steroids can help reducing the
complications of meningitis (but not the overall mortality), since they reduce inflammation and
edema.
• Dexamethasone – significantly reduced hearing loss and neurological sequalae. Useful in
treating meningitis but has no effect in sepsis. Start up to 4 hours after the first
administration of antibiotics.
o Adults dosage: 10mg, QID for 4 days
o Children dosage: 0.15mg/kg, QID for 4 days
Contraindication: do not prescribe to neonates, due to the effect of the drug on cartilages.
 26

Meningoencephalitis/Encephalitis
Etiology
Viral Fungal
Most frequent: • Cryptococcus
• HSV • Coccidiodes
• Enterovirus (Coxsackievirus, Echovirus) • Histoplasma
• Mumps • Mucormycosis
• Rabies • Aspergillus (Galactomannan – invasive
• Japanese B encephalitis virus Aspergillosis)
• St Louis encephalitis virus • Candida (yeasts)
• La Crosse encephalitis virus
Parasitic
Intermediate frequency:
• Angiostongylus
• CMV, VZV
• Toxoplasma
• Poliovirus
• Hydatid
• Measles
• Amoeba
• HIV1
• Plasmodium
• Western equine encephalitis virus
• Cysticercosis
• Murray valley virus
• Tick borne encephalitis (TBE) virus
Least frequent:
• EBV
• Dengue virus
• West Nile virus
• Adenovirus
• Colorado tick fever virus
• Eastern equine encephalitis virus
• Venezuelan equine encephalitis virus
• Influenza virus
• Lymphocytic choriomeningitis
• Chikungunya

Agent Characteristics
Dengue Virus
The most pathogenic virus, since the antibodies against it facilitate the entry of other viruses. The
result – decremental prognosis in case of a second viral infection.
West Nile Virus
Usually it is expressed by a benign demyelinating disease. In immunocompromised/elderly patients it
can be very lethal.
Common especially in the summer months.
 27

Chikungunya Virus
Disease is characterized by fever and severe muscle pain
Cryptococcus Neoformans/Gattii
Very common in immunocompromised patients (an AIDS-defining illness) or drug users. The fungus
proliferation in the fissures causes the accumulation of a gelatinous material, which increases the ICP.
As a result, the patient experiences intense headache, cranial and/or peripheral paralysis.
Diagnosis:
• Cryptococcal antigens in CSF (in more than 85% of the cases) or together with serum sampling
(combination of the two in 94% of the cases.
• CSF staining by India ink – shows the typical refractive cell wall of the fungus
Therapy:
• Liposomal Amphotericin B IV/intrathecally
• Prophylaxis: Fluconazol/Itraconazol PO 200mg/day
 28

Tuberculosis
Agent Characteristics
Classification of Mycobacteria:
• Tuberculous bacilli – Mycobacterium Tuberculosis (humans), M. Bovis (cows), M. Microti (rats)
o Infection of tonsils, cervical lymph nodes (→scrofula) or the intestines
• Lepromatous bacilli – M. leprae (humans), M. lerpae murium (rats)
• Atypical Mycobacteria (Runyon Groups) – photochromogens, Non-photochromogen (M. avium),
Scotochromogen
o Show no caseous necrosis
o Form of rods found inside macrophages
o Distributed in soil, water and domesticated animals
Features: (of M. tuberculosis)
• Aerobes – infect organs and tissues which are highly oxygenated (e.g. lungs)
• Fastidious – cannot proliferate below 25˚C (usually grows at 37˚C), at pH of 6.4-7.0
• Non-motile
• Do not form spores
• Slowly-growing (generation time of 12-18h)
• Hydrophobic - due to high lipid content (mycolic acid) in the cell wall, which is impermeable to some
basic dyes (unless phenol is used) = the mycobacteria are called “acid-fast bacilli”.
Transmission:
• Mainly via the respiratory system - infectious droplets by coughing, sneezing or talking. Each action
can emit 3000 bacteria to the air.
• M. Bovis – by non-pasteurized milk (uncommon these days), usually infection of the ileo-cecal
region.
• Atypical Mycobacteria – acquired directly from the environment

Epidemiology
• Atypical Mycobacteria – common in immunocompromised patients, in immunocompetent produce
a chronic pulmonary disease.
• M. Tuberculosis –
o The leading cause of death in the world due to bacterial infection.
o About 25% of the world population has been exposed to TB.
o Common in immigrants
o Endemic in Russia and Eastern Europe
Risk factors:
• Genetic – N-RAMP1 polymorphism (provides resistance to the bacteria against immune response)
• Ethnicity – black, Asian
• Age – children or elderly
• Nutrition
• Immunosuppression – AIDS (about 13% of the cases are HIV-related, in Africa there is almost always
association to TB), chemotherapy, steroids, biological drugs, diabetes, chronic renal failure.
 29

Pathogenesis
Course of Infection
•Primarily, infection of alveolar macrophages
•Intracellular replication (asymptomatic patient/mild flu-like symptoms) - without toxin
Early phase production
of 1˚ •Can complicate to bacteremia
infection

•3 weeks after the infection, Th1 cells secrete cytokines, especially IFNγ, stimulating macrophages to
contain the proliferation of the bacteria - cell-mediated immunity (type IV hypersensitivity)
Sensitization • Activated macrophages produce TNFα → monocyte recruitment
phase

•Formation of granulomas and caseous necrosis:

•The Th1 cells contribute to the development of TC cells that will eliminate the infected cells
Granuloma •The recruited monocytes differentiate into histiocytes, a component of the granulomas
formation

•An a-vascular granuloma

Tubercle •Contains: M. Tuberculosis bacilli, lymphocytes, giant cells, fully/partially activated macrophages
with caseous •Discharge of the tubercule leads to further spreading of the bacteria
necrosis

•In most cases, the infection is contained without significant tissue destruction
Course of •The infection can progress or reactivate later in life (risk factors - elderly/immunocompromised)
disease

Resistance of M. Tuberculosis:
• Can survive in sputum 10-30 minutes
• Killed at 60˚C for 15-20-minute exposure
• Resistance against chemicals: 5% phenol, 15% Sulfuric acid, 3% Nitric acid, 5% oxalic acid, 4%
sodium-hydroxide.
• Sensitive to glutaraldehyde, formaldehyde and ethanol (on superficial lesions)

Clinical Presentation
Tissue Appearance
Primary tuberculosis:
• Granulomatous inflammation +/- caseation – multinucleated giant cells (Langerhans cells)
surrounded by lymphocytes and fibroblasts rim. The nuclei of Langerhans cells are located along
the edge of the cell.
• Ghon focus – area of consolidation due to caseous necrosis (1-1.5cm, grey-white)
Progressive pulmonary tuberculosis:
• Expansion of the area of caseation → evacuation of the caseous center
• Erosion of bronchi and blood vessels → hemoptysis
• In pleural involvement: effusion, empyema or obliterative fibrous pleurisy
 30

Secondary tuberculosis: (85-90% of the cases occur in the lungs)

• Cavitation of the lungs – typical for large granulomas and more common in the upper lobes (classic
location – the apex of one or both lungs). Extensive necrosis in larger bronchi can drain out and
leave a cavity.
• Lymph node enlargement (complication)
Natural History Reinfection

Healed lesions Latent Lesions Reactivation

• In 95% of patients • Dormant bacteria in the lungs/other
• A scar is left tissues Secondary
• No protective immunity (possible Tuberculosis
reinfection or reactivation) except for BCG • Localized caseating
Progressive primary TB
destructive lesions
• Typically occurs in immunocompromised
• Developed by 5% of
patients, malnourished children and
Primary Complex primary TB patients
elderly.
• Typically localized next to the fissure
• Acute pneumonia-like disease:
between two lobes, close to the pleura
(where oxygenation is best)
consolidation, pleural effusion / empyema Progressive
and lymphadenopathy. secondary TB
• Drainage of bacilli into lymph nodes forms
• Discharge of tubercles can lead to further
granulomas
complications (in case of spreading):
Healing
Primary infection • Immuno-
Isolated organ TB Miliary TB
• Occurs in unexposed individuals competent
• Involvement of kidneys, • Dissemination of the bacteria
(especially immunocompromised patients) patients
bones, meninges, by venous circulation to liver,
• 5% will develop a severe disease
adrenals or adnexa kidneys, spleen etc.

The bacillary load is correlated with the probability to develop a secondary infection.
Complications
• Meningitis – through dissemination, frequent cranial nerve localization. Sequalae: hydrocephalus,
epilepsy, mental retardation and cranial nerve paralysis. In CT scan – lesions surrounded by edema.
• Pleurisy – in penetration of the pleura, can deteriorate to pneumothorax.
• GI infections
• Kidney infection
• Pott’s spine – localization of Mtb in the bodies of the vertebrae.
• Osteomyelitis, arthritis
• Lymphadenitis – scrofula (at the cervical lymph nodes), around the ileocecal valve or any other
nodal site (filled by colliquation)
• Miliary tuberculosis
Signs and Symptoms
# Localized tuberculosis can be asymptomatic.
• Low-grade remittent fever (in the evening), night sweats, malaise, anorexia and weight loss
• Sputum: mucous → purulent
• Hemoptysis (50% of the cases, DDx with tumors/pulmonary edema)
• Pleuritic pain
• Crepitus upon auscultation (“walking on snow”)
 31

Diagnosis
1. History-taking, physical examination
Pay attention to the epidemiology, immunocompetence, typical symptoms and signs.
2. Radiological findings – consolidation and cavitation (1), scrofula (2) and brain tuberculomas (3)

3. Laboratory diagnosis
Type of specimens: stained by Ziehl-Neelsen (acid-fast) stain or taken for PCR
• Sputum and BAL – the most common
• Aspiration
o Pleura - in case of pleural effusion
o Stomach – in case of cold abscesses
o Lymph nodes – in case of involvement (e.g. scrofula)
• Stool – in case of GI infection (e.g. M. bovis)
• CSF – in case of suspected meningitis
• Blood – in case of disseminated tuberculosis
• Urine
Methods:
• Identification of the acid-fast bacilli in culture of sputum – by immunofluorescence or electron
microscopy. Disadvantage – can take up to 6 weeks (PCR is much faster).
• Sputum smear - three consecutive smears are required both to diagnose (positive smears) and
discharge (negative smears) a patient with TB.
o Advantages: cheap, fast, easy to perform, high predictive value and high specificity.
o Disadvantages: low sensitivity (there must be enough bacteria to make the test positive)
and less immunocompetent patients (e.g. elderly) may not produce sputum with Mtb.
• Tuberculin PPD (skin) Test (TST/Mantoux) – subcutaneous injection of bacteria. If an immune
reaction occurs, the test is positive = strong cellular immunity against the bacteria.
o Disadvantages: TB-positive patients may develop reactivated TB, TB-negative patients are
at risk to develop a primary infection. Moreover, cannot differentiate between immunized
and affected patients.
o False-positives: infections with non-tuberculous mycobacteria
o False-negatives: military TB, patients taking steroids, malnutrition, immunodeficiency,
infants.
 32

• IFNγ-based Assays – test the CD4+ cellular reaction: in-vitro exposure of Th1 cells to specific
antigen of MTB, which meant to release IFNγ. Can differentiate immunized/infected patients
o QuantiFERON-TB gold and gold in-tube – 2 ELISA tests. In case of high bacterial load – the
test is as sensitive as TST. In case of low TB prevalence – lower sensitivity.
o 1 ELISPOT test – more sensitive and specific than TST.
• CSF sample (lumbar puncture) – in tuberculous meningitis
• PCR – see below
4. Molecular typing – PCR amplification of M. tuberculosis DNA
PCR identifies the genus of the mycobacterium in a rapid (3-4 hours) and highly sensitive
procedure. Endonucleases are added to the specimen to extract DNA fragments of different
lengths. The fragments are amplified, and strain-specific primers are added to find the strain that
caused the disease – and can be further assessed in epidemiological studies.

Treatment
Treatment methods ordered according to the time of introduction:
1. Sanatorium – the TB patients were concentrated in buildings where they received nourishment, a
place of rest and supportive therapy only. They were neglected when drug therapy was introduced.
2. Directly-observed Treatment of Short-course (DOTS) – a control strategy suggested by the WHO.
Cases were detected by sputum smear under a microscope. Throughout all the drug therapy period,
all cases were observed, recorded and assessed (regimen lasted 6-8 months) until complete healing.
• Effects: higher prevalence of cured patients, money is saved, and new infections were avoided.
3. BCG (Bacillus Calmette–Guérin) Vaccine - the vaccine is produced from live M. bovis bacteria and
given at birth (without TST) intra-dermally, since it was proven to be more efficient in younger ages
of inoculation. The vaccine is far from being 100% efficient (immunity lasts for 10-15 years, with
60% of efficiency), but it can prevent skeletal, meningeal and military forms of tuberculosis.
4. Drugs used against MTB – as a principle: always better to prescribe at least two drugs
concomitantly, to lower the probability of resistance.
1st Line Drugs (ESSENTIAL) 2nd Line Drugs 3rd Line Drugs (uncertain efficacy)
Isoniazid Injectable: Clofazimin
Rifampicin • Kanamycin Linezolid
Pyrazinamide • Capreomycin Amoxycillin/Clavulanate
Ethambutol • Amikacin Imipenem/Cilastatin
• Streptomycin12 Clarithromycin
Fluoroquinolones13:
• Moxifloxacin
• Levofloxacin
• Ofloxacin
Bacteriostatic:
• Cicloserin
• Para-amino Sialic (PAS) acid
• Terizidone
• Ethionamide

12 Streptomycin – the first antibiotic after penicillin proven to cure MTB infections (today there might be resistance)
13 Fluoroquinolones – adverse effect is rupture of tendons = do not administer in children.
 33

Standard treatment:
• Rimstar (commercial name) - a combination of all 4 first-line drugs for the first two months,
• Rifinah - two-drug combination (rifampicin and isoniazid) for four months.
Drug-Resistance
As mentioned earlier, the frequency of drug resistance is greatly reduced in a regimen of at least
two drugs, for example: in the case of isoniazid and rifampicin combination, the probability is
reduced by 108-fold.
The machine that tests the resistance of the different strains is called Gene Xpert. The results allow
to classify the strain in the following manner:
• TB with any drug resistance
• MDR-TB: strains resistant to isoniazid and rifampicin (at least)
• XDR-TB: multi-drug resistant TB with additional resistance to fluoroquinolones/injectable
second-line drugs
• TDX/XXDR-TB: resistance to all drugs (there is no standardized definition)
Treatment of MDR-TB:
1. Begin with any first line drug to which the bacteria are sensitive + fluoroquinolone + injectable
drug.
2. Add second-line drug (oral), up to 6 drugs combined.
3. If there is no sensitivity for 4-6 drugs from the categories above, consider a third-line drug by
consulting with an expert.
# Try to use at least 3 previously unused drugs (not only these three)
# Never add a single drug to a failing regimen – change completely the composition of the
regimen
# As for non-MDR-TB, if possible, continue injection for at least six months after the first
specimen culture
 34

Infectious Heart Diseases

Infective Endocarditis (IE)
IE is an infection of the endothelial layer lining the inner surface of the heart – the walls, valves or on a
septal defect.
Relapse – IE reappears less than six months after the initial disease, caused the same pathogen
Reinfection – IE reappears more than six months after the initial disease, caused by the same/different
pathogen

Generalities
Epidemiology:
• Incidence of 3-10 cases/100,000 people per year
• Common in IV drug users (right heart i.e. tricuspid valve) – infections by S. aureus, fungi, P.
aeruginosa and other gram-negative bacteria. Can be polymicrobial.
• The most common IE is on heart valves
• The most common etiological agents vary between geographic areas
Risk Factors:
• Prosthetic valves – 1%/one year per patient
• Poor dental hygiene (or dental infection)
• Degenerated valves – e.g. aortic stenosis (in elderly patients), mitral valve prolapse/regurgitation
• Healthcare-associated IE – nosocomial (>48h of hospitalization), non-nosocomial (IV catheters,
pacemaker electrodes, hemodialysis, chemotherapy), HSC/solid organ transplantation
• Congenital heart diseases – PDA, VSD, ToF, bicuspid valves or any native/surgical high-flow lesion
• In rheumatic valvular disease – usually the mitral valve is affected and then aortic valve
• Marfan syndrome
• Syphilis (rarely)
Classification:
• Native valve endocarditis (NVE) – acute/subacute
o Acute NVE usually has an aggressive course (no matter the health status of the patient)
o Subacute NVE usually affects abnormal valves, with more indolent course (several months)
• Prosthetic valve endocarditis (PVE) – early/late
o Early PVE – within one year following the valve replacement surgery, due to spread of
aggressive pathogens in the sewing material.
o Late PVE – more than one year after surgery, similar presentation to NVE
• Intravenous drug abuse (IVDA) endocarditis
• Infectious endocarditis due to pacemaker/implantable cardioverter-defibrillator (ICD) electrodes –
IE close to the electrodes, most likely by Staphylococcus aureus.
 35

Pathogenesis
Degenerative changes / electrodes / prosthetic materials If the infection is on a valve:
/ catheters
→ high inflammatory
Injury of the endocardial surface and endocardial content on the vegetation
damage
→ stiffness of the tissue
Exposure of the the collagen of the ECM
→ turbulent flow
Factor III initiates the coagulation cascade, platelet → murmur.
aggregation

Fibrin-platelet vegetation (sterile) → increased risk of

bacterial colonization

Possible agents:
Common bacteria Rarer bacteria (HACEK) Fungi Intracellular pathogens
• Staphylococci • Hemophilus influenza • Candida • Coxiella
• Streptococci • Actinobacillus • Aspergillus • Bartonella
• CA-Enterococci • Cardiobacterium • Chlamydia
• Pseudomonas • Eikenella • Mycoplasma
• Kingella • Legionella
• Treponema

Clinical Presentation
Symptoms and signs may vary between patients:
• Fever (in 95% of the cases)
• Signs and symptoms of systemic disease (nausea, weight loss)
• Heart murmur (in 85% of the cases) – e.g. regurgitation in PVE
• Septic arterial embolization (left heart) in 20-50% of the cases, associated with the size of the
vegetations (usually more than 10mm) – to the brain, kidneys, spleen or lungs. Peripheral
microembolization is less common.
• In IVDA endocarditis (more common on the tricuspid valve): increased risk of recurrences, septic
lung embolization → cough/hemoptysis, pulmonary abscesses
Diagnosis
Blood Culture: Echography:
• Take three samples from different sites and • TTE has low sensitivity, but TEE (esophageal
at different times approach) has much better sensitivity
• Therapy should be started after the sampling • Detects vegetations (see image), valvular
• 85-90% of the cultures are positive (mostly perforation, new partial dehiscence of
to Strep/Staph/Enterococci), the remaining prosthetic valve and abscesses
10% appear negative, mostly due to therapy • With color doppler it is possible to assess
by antibiotics. regurgitation
Physical examination: signs of embolization – can be neurological (like in stroke e.g. alexia, altered
cognitive status) or on the skin (hematomas or even as small as black spots on the nails).
# Fever + murmur → immediately suspect endocarditis
 36

Duke criteria:
Major Criteria Definite IE
• Microbiology: blood culture positive for IE – • Pathological criteria- microorganisms
o 2 separate cultures – with the bacteria mentioned above demonstrated in histology/culture
o 3 persistently positive cultures – performed in different times • Clinical criteria
o Single blood culture positive for Coxiella burnetii14 o 2 major criteria
• Imaging: positive for IE o 1 major and 3 minor criteria
o Echo positive for the findings mentioned above o 5 minor criteria
o Abnormal activity around the site of prosthetic valve Possible IE
implantation (PET/CT) • 1 major and 1 minor criteria
o CT positive for definite paravalvular lesions • 3 minor criteria
Minor Criteria Rejected IE
• Predisposing condition: valve replacement / IVDU • Firm alternative diagnosis
• Fever > 38˚C • Resolution of symptoms without
• Vascular phenomena (due to embolization) antibiotic therapy for less than 4 days
• Immunological phenomena • No evidence in pathological examination
• Microbiological evidence (which does not meet the major criteria)
Treatment
Drugs:
• Antibiotics – consider first empirical therapy (should focus on S. aureus), then after culture results
arrive change the regimen
o Streptococci: penicillin / cephalosporin + gentamycin, vancomycin (in MDR bacterial infections)
o Staphylococci: methicillin / oxacillin + gentamycin
o Enterococci: penicillin15 / cephalosporin + gentamycin, vancomycin
o HACEK/early PVE: consult with an ATB expert
o Late PVE (>6 weeks): rifampicin
• Antifungals (in fungal infection) – consult with an ATB expert
• Diuretics – to prevent decompensation from the rupture of the cords

14 Not part of the normal flora i.e. all other cultures can be positive due to contamination.
15 Note there is a common penicillin resistance among enterococci
 37

Instructions:
• Therapy usually lasts 4-6 weeks (regardless of surgery)
• TTE follow-up (after less than 2 weeks)
• Stop treatment when: normal CRP (for one week), no embolization (for 2 weeks), favorable TTE
absence of focus (location suitable) for potential reinfection
Surgery:
• Performed on patients in high risk – age, comorbidities, PVE (more often than native valve
replacement), heart failure, shock, high risk agents (S. aureus, fungi), antibiotic treatment failure
or risk of embolization (>10mm)
• Prevention (or dampening) of prosthetic valve senescence: restrictive approach, surgery a high-
risk-patients only
• Prevention of IE in high-risk-patients: prophylaxis before high-risk dental procedures

Myocarditis
Myocarditis is defined as the inflammation of the muscular layer of the heart.
Generalities
Epidemiology: usually manifests in health people
Etiology:
• Infection (most common are viruses)
Bacteria Viruses Fungi Parasites
• Borrelia spp. • Adenovirus • Aspergillus spp. • Trypanosoma cruzi
• Mycobacterium spp. • Coxsackievirus • Candida spp. • Larva migrans
• Mycoplasma pneumoniae • HHV-6, EBV • Coccidioides spp. • Schistosomiasis
• Streptococcus spp. • HCV • Cryptococcus spp.
• Treponema pallidum • HIV • Histoplasma spp.
• Influenza A
• Parvovirus B19

• Autoimmune disorders and other immunological syndromes

• Exogenous agents – drug hypersensitivity, toxins (e.g. cocaine)
• Idiopathic – in 50% of the cases
Pathogenesis:
• In the acute phase (first two weeks) – direct cytotoxic effect and cell-mediated toxicity
• In the chronic phase (after two weeks) – mainly autoimmune
↓
• Destruction of cardiac cells can lead to acute disorders such as arrhythmias or AV block
• Chronic defects: dilated cardiomyopathy and heart failure
Clinical Manifestations
Signs and symptoms: range from minor to severe presentation
• Flu-like symptoms: fever, malaise, arthralgias
• Chest pain, palpitations, dyspnea, sweats
• Upper respiratory tract infection: pharyngitis, tonsillitis
• Signs of heart failure/cardiogenic shock
• In severe cases: syncope or sudden cardiac death
 38

Diagnosis
• Blood tests: CBC, ESR, CRP, rheumatological screening, cardiac biomarkers (TnI, TnT)
• Viral antibody titers: controversial use (low specificity, delayed rising and no impact on therapeutic
decisions
• ECG: detection of arrhythmias (sinus tachycardia, ST changes, AV blocks – all are non-specific)
• Imaging
o TTE: estimation of damage and ruling-out other causes
o Coronary artery angiography (CAG): rule out CAD
o MRI (+gadolinium as contrast agent): nonspecific, assesses the extent of inflammation and
cellular edema
• Endomyocardial biopsy (EMB): mandatory in rapidly-progressing heart failure (to rule out giant-
cell myocarditis), but rarely useful in other cases (due to side effects)
Prognosis:
• Patients who survive fulminant myocarditis usually have good prognosis
• 30% of the patients will develop DCM, the others will recover completely
• Giant cell myocarditis has very bad prognosis (disease course of 6 months until death)
Treatment
• Standard treatment of heart failure e.g. diuretics, inotropics, ACE inhibitors etc.
• Rest (avoid physical stress for several months)
• Immunosuppression: only in giant-cell myocarditis/systemic autoimmune disease (SLE,
rheumatoid arthritis)
• Follow up: especially in chronic infections, patients with history of myocarditis

Pericarditis
Inflammation of the pericardium.
Generalities
Etiology:
• Idiopathic (50% of the cases)
• Infections: (also of the lungs)
o Viral (second-highest cause) – enterovirus, echovirus, parvovirus
o Bacterial (commonly by Mtb) or fungal (Candida)
• Immune disorders: rheumatoid arthritis, SLE, scleroderma, rheumatic fever, Reiter syndrome,
dermatomyositis
• Organ failure: renal failure, hypothyroidism
• Cardiovascular disorders: AMI, Dressler syndrome
• Iatrogenic: post-cardiotomy syndrome, catheterization
• Neoplasms (also paraneoplasms)
• Drugs, irradiation
• Trauma
• Pulmonary infarction
 39

Clinical Manifestations
Myocarditis and pericarditis evolve from each other.
Signs and symptoms:
• Chest pain is the main symptom, characterized by:
o Location: retrosternal, can radiate to the back, neck, left shoulder or arm
o Quality: pleuritic (can be sharp, burning or dull)
o Intensity: higher when lying supine, inspiration, swallowing or with body motion. It can be
relieved when leaning forward
• ECG changes
• Pericardial friction rub (upon auscultation) – due to effusion of liquids to the pericardial cavity
• Intermittent fever
• Dyspnea (tachypnea)
• Cough, dysphagia
Complications:
• Recurrence – in 15-30% of the cases
• Constrictive pericarditis – deposition of fibrin in the pericardial cavity during pericardial effusion,
which leaves further inflammation, fibrotic scarring, calcification and restricted cardiac filling
(↓cardiac output)
• Cardiac tamponade – acute pericardial hemorrhage / large chronic malignant effusions which
interfere with ventricular filling → decrease in cardiac output and hemodynamic compromise.
Symptoms depend on the severity of the effusion or the underlying disease:
o Pericarditis symptoms – dyspnea, tachypnea, chest pain, fever, dysphoria
o Hypotension, tachycardia
o Pulsus paradoxus
o Elevated jugular vein pressure
Diagnosis
• Physical examination: chest pain and pericardial friction
rub
• ECG changes (new ST elevation, PR depression)
• Imaging:
o To view the effusion: Chest X-ray (enlarged heart of
the effusion is >250mL) or TTE (see image)
o CT (view of calcifications), MRI
• Laboratory:
o CBC (especially the inflammatory cells)
o ESR, CRP
o Cardiac TnI/TnT
o Electrolytes, BUN, creatinine
o Thyroid hormones
o Specific testing (rheumatoid factor etc.)
 40

Treatment
Drugs:
• Treat accordingly the cause of the inflammation (for bacterial infection use antibiotics etc.)
• Symptom relief:
1. NSAIDs for 7-14 days (600-800mg ibuprofen/day), consider proton-pump inhibitors
2. Colchicine – if the infections progresses over 14 days or in the case of recurrence (1mg/day)
3. Corticosteroids
– If there is no response to NSAIDs or colchicine
– Never as an initial therapy, unless the mechanism is autoimmune
• Pericardiocentesis – in case of large effusions or cardiac tamponade
Surgery:
• Indicated when there is recurrence or in the case of large effusions
• Pericardiectomy in constrictive pericarditis
 41

Gastrointestinal Infections
GI infections are one of the most encountered group of infectious diseases. They are classified according
to the Rome criteria:

Diarrhea
Acute or chronic diarrhea are the most significant symptoms of gut infections, and one of the leading
causes of death in developing countries. They are caused by a wide range of pathogens which can be
divided according to the course of disease:
• Acute diarrhea – caused mostly by bacteria
• Chronic diarrhea – caused mostly by parasites
• Diarrhea in immunocompromised host – different disease than in immunocompetent patients,
caused by parasites
The routes of transmission are:
• Fecal-oral route: through food or contaminated water
• Person-to-person
The differences between the routes relies upon the degree of the pathogen’s survival in the GI tract
(e.g. acid-stable or sensitive).
Risk factors:
• Anti-acid therapy or gastrectomy – reduce the necessary inoculum of bacteria needed to produce
an infection
• Antibiotic therapy – affects also the gut flora, which constitutes another line of defense against
pathogenic bacteria (prevent their proliferation)
• Compromised immune system – in patients with HIV, following a transplantation or undergoing
chemotherapy

Acute Diarrhea
Definition: abrupt onset of three or more loose stools per day which lasts for 14 days. The definition
can be flexible – can be 15 days, but must have each day three or more loose stools
Etiology: Consider also the epidemiology (pathogens endemic to certain areas, nosocomial infections
– increase the risk).
Bacteria
Viruses Parasites
Invasive Enterotoxigenic Toxic
• EIEC • ETEC • Clostridium difficile • Rotavirus • Giardia spp.
• Shigella spp. • Klebsiella spp. • Adenovirus • Cryptosporidium spp.
• Campylobacter spp. • Clostridium perfringes • Calicivirus • Entamoeba histolytica
• Yersinia spp. • Cholera spp. • Astrovirus
• Aeromonas spp. • Vibrio spp. • Norovirus
• Plesiomonas spp.
Common in adult, immunocompetent patients Common in Common in
children and immunocompromised
infants patients
 42

Bacterial Diarrhea
Salmonella, Shigella and Campylobacter infections are very difficult to be distinguished clinically – so
the diagnosis is base upon the isolation of the bacterium from a stool culture.
• Salmonella
o Microbiology: aerobic gram-negative bacilli, motile, does not ferment lactose
o Classification (clinically): typhoidal (typhi and paratyphi) or non-typhoidal (enteritidis,
typhimurium and choleraesuis)
o Pathogenesis: large inoculum (~106 bacteria), which is associated with more severe disease
and shorter incubation period. Salmonella causes an invasive infection, similar to Shigella.
• Shigella
o Microbiology: aerobic gram-negative bacilli, immotile, does not ferment lactose
o Pathogenesis: the bacterium is acid-resistant, so only a small inoculum (~200 bacteria) can
produce a disease. The most important virulence factor is the Shiga toxin, which has a
cytotoxic effect and can be easily transmitted between cells → invasive bowel disease, causing
superficial ulcers in the mucosa and result in bloody stools.
• Campylobacter (C. jejuni)
o Microbiology: micro-aerophilic gram-negative rods, grow best at 42°C.
o Pathogenesis: acid-sensitive (requires large inoculum of at least ~104 bacteria), can reside in
monocytes as well as the gut epithelium → produces similar symptoms to Shigella.
Other important bacterial strains:
• Escherichia coli
o Microbiology: gram-negative facultative anaerobic rods, lactose fermenters. Serotyping (O+H
antigens) helps in distinguishing between the strains- some can be part of the normal flora
o Pathogenesis: depends on the strains – which can be divided into five groups:
Cholera-like toxin Produce relatively mild inflammation – result in
Enterotoxigenic (ETEC) watery diarrhea aka traveler’s diarrhea
(heat-stable)
Enteroaggregative (EAEC) Enterotoxin
Enteropathogenic (EPEC) Usually results in watery diarrhea
Large inoculum Produces moderate inflammation – inflammatory
Entero-invasive (EIEC) (108 bacteria) colitis similar to Shigella infection
Produces the most severe inflammation, infection of
serotype O157:H7 can complicate to:
Enterohemorrhagic (EHEC) Shiga-like toxin • Hemorrhagic inflammatory colitis
• Hemolytic uremic syndrome (HUS)
• Vibrio cholera/parahaemolyticus
o Microbiology: gram-negative facultative anaerobes, curved-rod shape, acid sensible
o Cholera: exotoxin which binds a receptor on endothelial cells → increase in intracellular cAMP
→ increased secretion of electrolytes and water → massive watery diarrhea (not mucous and
not bloody). Can become dormant (which cannot be cultured), and produces biofilms
(protection against disinfectants)
o Parahaemolyticus: enterotoxin → moderate inflammation
• Yersinia enterolytica
o Microbiology: gram-negative bacilli
o Pathogenesis: large inoculum needed (109 bacteria), invade the mucosa of the terminal ileum
– DDx with appendicitis
 43

• Clostridium difficile
o Microbiology: gram-positive, obligate anaerobe, spore-forming
o Pathogenesis: exotoxins A and B with cytotoxic effect → ulcerations of the mucosa, formation
of pseudo-membranes (composed of exudate and inflammatory debris) which thickens the
wall of the gut. In severe conditions the lumen can be occluded (little or absence of diarrhea).
Epidemiology:
• Salmonella – common even in developed countries (1 million new infections of salmonella in the
US). Acquired infections from eating contaminated food (eggs, meat, cheese, fruits and
vegetables) or through contact with animal feces.
• Shigella – humans are the only hosts hence the transmission is by person-to-person only (e.g.
toilet seats, contaminated water, daycare centers). Common in developing countries. There are 1
million deaths and 165 million new cases worldwide each year.
• Campylobacter – transmission via contaminated food (dairy products, meat, eggs, fruits and
vegetables).
• E. coli – ETEC, EAEC, EPEC and EIEC are found in developing countries, transferred by ingestion of
contaminated food or person-to-person (EPEC – common in nurseries). EHEC can be found
especially in raw meat, mayonnaise and can be transmitted in daycare centers or nursing homes.
• Vibrio
o V. cholera – can survive in aquatic environments (attached to seaweed and shellfish)
o V. parahaemolyticus – prefers salty environment (found in raw fish and shellfish)
• Yersinia enterolytica – common worldwide (except for N. America), prevalent in children and
during the winter. The infection is transmitted via contaminated meat products.
• Clostridium difficile infection – risk factors include elderly patients, severe comorbidities, post-
surgery, anti-cancer chemotherapy, patients with enteral feeding. Can spread from person to
person (KEEP HYGIENIC ENVIRONMENT IN THE HOSPITAL)
Symptoms and signs:
• Enterocolitis / gastroenteritis – diarrhea and abdominal pain
• Fever – 38-39°C
• Increased peristalsis
• Symptoms and signs related to fluid loss – hypotension and electrolyte abnormalities
Stools
Incubation period
Watery Bloody Purulent and mucous
• Salmonella: 8-24h Increased secretion of Invasive infection which forms Abnormal host
• Shigella: 36-72h fluids from enterocytes ulcerations in the mucosa inflammatory response
↓ ↓ ↓
• EHEC: 4 days ETEC, EAEC, EPEC, Vibrio Shigella, Campylobacter, EIEC Shigella
and EHEC
• Enteric (typhoid) fever – by S. typhi or paratyphi
o 1st week: flu-like symptoms, anorexia, lethargy, mild abdominal discomfort and constipation
o 2nd week: bloody diarrhea, fever, severe abdominal pain, mental status alteration, small rose-
colored maculo-papular dots on the chest and upper abdominal wall.
o 3rd week: tender and distended abdomen, splenomegaly, hemorrhagic anemia, moderate
leukopenia, temperature-pulse dissociation.
− In 10%: complicate to septic shock or perforation → death
 44

• Pseudomembranous colitis – by C. difficile

o Can begin due to ingestion of spores from contaminated food or following antibiotic therapy.
o Watery diarrhea without colitis, bilateral pain in lower abdomen, fever, leukocytosis
o Detection of the pseudo-membrane in colonoscopy, thickening of the gut wall (in CT scan)
o Can complicate into fulminant colitis (2-3% of the patients) – high mortality, due to bowel
perforation (can also occur during the colonoscopy).
Diagnosis: the following factors must be taken into consideration-
• Stool characteristics: consistency, color, volume and frequency of defecation
Small Intestine Large Intestine
Appearance Watery Mucoid and/or bloody
Volume Large Small
Frequency Increased Much more increased
Blood Might be positive (but never gross bleeding) Positive (very common gross bleeding)
pH <5.5 >5.5
WBCs <5/hpf– high power field >10/hpf
Serum WBCs Normal Possible leukocytosis / Bandemia
• Other symptoms: nausea or vomiting, fever and abdominal pain
• Behavioral factors:
o Eating raw or contaminated food (especially seafood)
o Water exposure – swimming pools, lakes, rivers or the sea
o Travel history – depends on the agents which are endemic to the areas of travel
o Animal exposure – stray animals or puppies
o Unsafe sexual behavior
• In children – use of daycare increases the likelihood of infection by several pathogens (e.g.
calicivirus, astrovirus, rotavirus)
• Iatrogenic causes of diarrhea – hospitalization (nosocomial infection), antibiotic or use of proton-
pump inhibitors.
o The most severe/important complication of use of antibiotics is Clostridium difficile infection
(pseudomembranous colitis) – this situation can be avoided by correct stewardship.
• The patient’s immune status (immunocompromised or not)
• Hydration status 0-5% Dehydration 5-10% dehydration ≥ 10% Dehydration
evaluation → (mild) (moderate) (severe)
• Physical examination – General feeling Well Restless Lethargy, fatigue
Eyes Normal Sunken Severely sunken
increased fremitus /
Tears Moist eyes Dry eyes Dry eyes
bowel sounds Mouth Moist Dry Very dry
Thirst Absent Present Present
Skin Pinch retracts fast Pinch retracts slowly Pinch stays folded
• Laboratory tests
o Culture of blood (the longer the disease – the less frequently it is used) – take three samples
o Culture of stools (if the disease is disabling and lasts for more than 48h) on appropriate media.
PCR can be useful for further investigations.
o Antigens in stools:
− O+H-: somatic antigen is positive, so bacteria are present = active/acute infection,
− O-H+: only the flagella is positive, so it can be a past infection
o Fecal PMN check – very rarely performed, only if there is already presence of blood or mucus
 45

Management:
• Significant part of the therapy is fluid and electrolytes restoration
• Antibiotics – if the disease is longer than 48h and disabling (administer after samples for culture
were taken). They are recommended for a short use (3-4 days)
o Antibiotic-associated Diarrhea by C. difficile (less commonly by S. aureus, Candida spp. and
Klebsiella oxytoca) – production of a toxin that causes perforation of the gut (a life-
threatening situation associated with high mortality)
o Probiotics can help preventing antibiotic-associated diarrhea
o Immediately treat typhoid fever – primarily fluoroquinolone or 3rd generation cephalosporine
o For non-typhoid diarrhea: administer to patients at risk - neonates, people over 50 years old,
immunocompromised
o For C. difficile – metronidazole (1st) or vancomycin (in severe disease)
o Antibiotics are contraindicated in EHEC infection – can exacerbate HUS
# Do not prescribe or stop therapy by drugs that slow peristalsis. Loperamide is useful in decreasing
the amount of diarrhea but does not solve the problem (better to take the drug if the patient is
traveling with no option to use the toilet).
Viral Diarrhea
The most common agents are:
• Norovirus (caliciviridae)
o Microbiology: +ssRNA virus
o Pathogenesis: highly contagious, less than 100 virions are required to produce a disease
• Adenovirus (enteric serotypes F and G, dsDNA virus)
• Astrovirus (ssRNA virus)
• Rotavirus
o Microbiology: dsRNA virus
o Pathogenesis: loss of absorption by the villi and cause lactase deficiency
• Ebola virus
o Microbiology: -ssRNA virus (filoviridae family)
o Pathogenicity: cytopathic effect
Epidemiology:
• Norovirus – each year causes 19-21 million cases of acute gastroenteritis, it is the leading cause
of the disease in US infants (under 5 years old). More common during the winter. Transmission is
by raw seafood, contaminated fruits and vegetables. Waterborne outbreaks are common in
community settings.
• Adenovirus – second most frequent cause of viral gastroenteritis. More common in the summer.
• Astrovirus – affects mostly infants and elderly.
• Rotavirus – affects mostly infants and usually during the winter
• Ebola virus – there are other four viruses in the genus, all endemic in Africa16, while in Congo it is
quite prevalent. Bats are the likely hosts of the virus. Its transmission is primarily via direct contact
with lesions on the skin, secondly via body fluids or contact with infected animals. Most infections
are caused due to lack of personal hygiene.

16 Zaire, Sudan, Tai Forest, Bundibugyo and Reston – the latter caused a disease only in primates
 46

Clinical manifestations: in most cases viruses cause minimal symptoms, but there can be more severe
manifestations, for example: due to extensive loss of water. The disease is usually self-limiting.
• Severe nausea, vomiting
• Abdominal cramps
• Headache
• Myalgia
• Fever (<39°C)
Ebolavirus disease (EVD)- appear on average 8-10 days after exposure (up to 21 days)
• Fever above 38.6°C
• Severe headache
• Muscle pain and weakness
• Diarrhea and abdominal pain
• Vomiting
• Unexplained hemorrhage
Diagnosis: in the case of viral diarrhea the diagnosis can be quite useless – the diagnostic tests are
expensive, especially when the disease can be cured before the results arrive.
Samples Methods
• Stool sample • Stool smear – leukocytes are absent
• Vomitus specimen • Cultures – negative for bacteria
• PCR – for norovirus
• ELISA – for rotavirus
When vomiting is quite significant, viral infection might be the cause (incubation of 24-48h, while food
poisoning is 2-7h)
Therapy: there is no specific treatment against viral gastroenteritis.
• Rehydration and electrolytes balance are the most important actions of management
o Usually oral administration of fluids, IV in more severe cases
• Antiviral therapy is less significant than rehydrating the patient
• Immunocompromised patients – need specific therapy
• Ebola virus – treatment of the symptoms (IV fluids…), taking care of the hygiene at the
surroundings of the patient

Chronic diarrhea
Definition: patient presenting with three loose stools per day for more than 4 weeks. Note that
diarrhea which is present between the acute and chronic setting is often called “persistent diarrhea”.
Etiology: the most common agents are parasites – very frequent in developing countries.
• Infections similar to bacterial diarrhea: Entamoeba histolytica –a parasite which invades the
mucosal layer, hence bloody diarrhea may be present if there is ulceration. The most important
complication – the parasite can enter the portal circulation and reach up to the liver, there it can
cause amoebic liver abscess (ALA). This disease is a medical emergency since it is rapidly
progressing.
• Infections similar to viral diarrhea (yet they are not self-limiting): Giardia lambia – can appear in
two forms (cysts or trophozoites – the latter have a unique shape of binucleated cell. The cysts can
survive without a host for a long period
 47

Epidemiology:
• Entamoeba histolytica – common in developing countries, areas with poor sanitary conditions and
among MSM. The amoeba can survive in cysts for months without a host (acid stable).
• Giardia – worldwide spread, more common in developing countries
Clinical manifestations:
• Amoebiasis
o Superficial bowel infection – watery diarrhea, abdominal pain…
o Invasive infection – bloody diarrhea, abdominal pain, tenesmus, abdominal tenderness, fever
o Amoebic liver abscess – RUQ pain, hepatomegaly…
• Giardiasis (usually for 4-6 weeks)
o Abdominal cramps and diarrhea
o Anorexia
o Nausea
Diagnosis:
• The causes of chronic diarrhea are in many cases iatrogenic – due to radiotherapy, medications or
surgery (do not require further investigation). Therefore, it is important to inquire well the medical
history of the patient.
• Differential from irritable bowel syndrome (IBS) – in IBS there are peaks of abdominal pain before
defecation, whereas in infection the pain is more constant.
• Amoebiasis -
o Ameba Under microscopy – trophozoites and cysts in the stool. Finding only one cell is enough
for the diagnosis
o Low PMN in stools
o Increased liver enzymes in chronic liver disease
• Giardiasis -
o Microscopy of the stools
o ELISA or immunofluorescence
o No PMN in stool smear
Treatment:
• Amoeba – metronidazole (750mg, every 8h for 10 days). Iodoquinol/paromomycin for carriers.
• Giardia – metronidazole (250mg, every 8h for 5-7 days)

Diarrhea in Immunocompromised Host

Etiology: all are parasites = cause chronic diarrhea (manifestations and diagnosis are similar)
• Cryptosporidium – a parasite that can survive and replicate within the intestinal mucosal cells.
Acquired from oocysts found in contaminated water.
• Microsporidium – obligate intracellular parasite
• Isospora belli – a parasite that causes villous atrophy, can reach the biliary tract and cause
cholangitis.
Therapy:
• Cryptosporidium: nitazoxanide (children and chronically symptomatic adults)
• Isospora belli: trimethoprim-sulfamethoxazole
• Microsporidium: fumagillin
 48

Peritonitis
Primary Peritonitis
Etiology: develops only in patients with cirrhosis and ascites. The disease has high mortality (60-70%),
also because of other comorbidities. The most common agents are:
• E. coli (in most cases)
• K. pneumoniae, S. pneumoniae, Enterococci, S. aureus and anaerobes
Pathogenesis: bacteria can enter the peritoneum via hematogenous spread, lymphatic spread or
directly penetrate through it.
Clinical manifestations:
• Fever and chills
• Diffuse abdominal pain
• Diarrhea
• Hepatic encephalopathy
• Abdominal distension without guarding.
Diagnosis:
• Paracentesis – aspiration of 10mL of ascitic fluid. PMN > 250/mm3 is highly suggestive
• Blood tests – total proteins, albumin, LDH, glucose and amylase
Therapy:
• It is important to administer life-long prophylaxis for patients at risk – by trimethoprim-
sulfamethoxazole or ciprofloxacin (less recommended)
• Immediate treatment by ceftriaxone or cefotaxime + metronidazole if secondary peritonitis is
suspected.

Secondary Peritonitis
Etiology: acute inflammation of abdominal organs, bowel neoplasm, trauma at the abdomen or arterial
insufficiency. The most common agents are: E. coli, Candida (very dangerous), anaerobes, Klebsiella,
Proteus, Enterobacter, S. viridans
Pathogenesis: spillage of bacteria into the peritoneum → exudation and increased permeability →
more likely for the bacteria to enter the bloodstream → sepsis (acidosis, shock and MOF) → death.
Clinical manifestations: similar to primary peritonitis.
Diagnosis: the difference between primary and secondary peritonitis is by checking the abdominal
distension – tender, present with guarding. Abdominal sounds are decreased or absent. Etiology is also
an important factor in the differential diagnosis.
• High leukocytosis
• X-ray: in the thorax look for basilar pneumonia, in the abdomen look for free air (better with US or
CT scan).
Therapy: right after taking all the samples for laboratory diagnosis start empiric therapy – cover both
gram positive and negative but know that the results are not always satisfying.
• Mild disease – 2nd generation cephalosporin or piperacillin-tazobactam.
 49

• Severe disease – combination of two drugs:

o 2nd generation cephalosporin + gentamycin
o Metronidazole + 3rd generation cephalosporin
o Metronidazole + fluoroquinolone
o Clindamycin + aztreonam

Hepatic Abscess
Etiology: abscess can originate from many underlying conditions – biliary tract infections, sepsis,
appendicitis, diverticulitis, abdominal surgery, immunocompromised patients and alcohol consumption.
In general-
• Bacterial abscess – (most common are anaerobes and gram-negative) in industrialized countries
• Fungal abscess – in immunocompromised patients
• Amoebic abscess – in developing countries
Pathogenesis: the right lobe is more common site (in 80% of the cases) because it is directly in front of
the flow coming from the portal circulation (today it is more common to use the classification of
segments).
• Brucellar abscess – usually has a calcification
• Amoebic abscess – very large, rapidly growing
Clinical manifestations:
• RUQ pain, typically can radiate to the right shoulder
• Fever
Diagnosis:
• Laboratory: markers of inflammation (leukocytosis, ESR) and liver enzymes (elevated)
• US – several agents have typical appearance (see above)
o Abscess with focal hyperechoic lesions – is usually gas produced by bacteria (anaerobes)
• Fine needle aspiration guided by US (and CT) – for drainage (therapeutic) and culture
Therapy:
• Needle aspiration (guided by US) and antibiotics
• Surgery is performed in very limited number of cases.

Pancreatic Abscess
A complication of pancreatitis, usually a polymicrobial infection – can lead to necrosis of the pancreas.
Usually requires surgical drainage of the lesion, and treatment is by broad-spectrum antibiotics.

Cholecystitis
A polymicrobial infection occurs in more than half of the cases. The common agents are E. coli,
Klebsiella, Enterococci and anaerobes.
Signs and symptoms: Charcot’s triad - RUQ pain, high fever, jaundice
Diagnosis: US - inflammation = thickened wall, elevated liver enzymes (ALP, GGT) and bilirubin
Treatment: broad-spectrum antibiotics (ampicillin and gentamycin, imipenem, metronidazole and
levofloxacin), ERCP (imaging method which can also remove stones) or surgery.
 50

Skin and Soft Tissue Infections (SSTI)

Generalities
Risk factors:
• Type 2 diabetes – an important risk factor due to:
o Increase in subcutaneous glucose – bacteria can thrive
o Microangiopathy – in long term diabetes oxygen supply is impaired → makes the tissue more
prone to infections (most commonly on the feet)
o Neuropathy – diabetic patients are less likely to feel pain at the lesions
• Vasculopathy – atherosclerosis, heavy smoking
• Poor personal hygiene
• Alcoholism – predisposing factor to cellulitis, probably due to skin trauma and poor hygiene
• IV drug users – commonly infected by Staphylococcus aureus
• Venous or lymphatic lesions – thrombophlebitis, trauma or due to surgery
• Congestive heart failure – contributes to venous stasis
Epidemiology:
• The most common infection leading to hospitalization is cellulitis
• The most severe complication of STI is necrotizing fasciitis
• Most common agents are group A Streptococci (GAS) and Staphylococcus aureus (including
community-acquired MRSA)

The red line is the threshold limit for the severity of the infection – if the infections is deeper it means
that it is a medical emergency.
 51

Classification and Manifestations

The infections are classified according to depth – superficial/deep. The superficial infections rarely
require hospitalization, but as they penetrate deeper through the skin they can be caused by more
aggressive microorganisms. Thus, incorrect or delayed therapy can have fatal consequences.

Superficial Infections
Erysipelas
Erysipelas are superficial cellulitis infections.
Epidemiology:
• Common in young children and older adults
• Almost always caused by GAS (less frequently by groups C, G or B)
Clinical manifestations:
• Swelling of the skin, with sharp boundaries between normal and infected areas
• Often there is visible lymphatic involvement
Clostridial Cellulitis
A superficial infection (limited to the epidermis and dermis) caused by Clostridium perfringens. It is
usually preceded by a local trauma or surgery.
Clinical manifestations:
• Presence of gas superficially (deeper structures are spared)
Differential diagnosis: clostridial myonecrosis (deeper infection)

Deep Infections
Cellulitis
An infection caused by a combination of aerobic and anaerobic bacteria.
Risk factors: about 50% of the patients do not have a prior condition that increases the risk of infection
Clinical manifestations:
• Gas production in the tissues – has a foul odor.
• In the cervical area: Ludwig’s angina – a severe type of cellulitis, characterized by rapidly-
progressing inflammation in the submandibular/sublingual spaces
Necrotizing Fasciitis
A rare and fatal soft tissue infection, which occurs at the superficial fascial layers of the extremities,
abdomen or perineum. There is an extensive tissue loss of fascia and fat, but the superficial skin may
be unaffected.
Epidemiology: most cases are community-acquired, but there is an increase in the cases of
nosocomial infections.
Etiology: usually begins by trauma of the skin, also by simple bruise, burn or insect bite. Can be also
due to bacterial superinfection during a VZV infection. Should be considered in diabetic patients with
cellulitis and systemic symptoms (tachycardia, leukocytosis, hyperglycemia, acidosis).
 52

Classification:
• Type I – occurs due to multiple concomitant bacterial infections (usually 4-5 bacteria)
o Agents: gram (+)- Staphylococcus aureus, Streptococcus pyogenes, Peptostreptococcus |
gram (-)- E. coli | anaerobes - Clostridium, Bacteroides, Prevotella, Porphyromonas
o Risk factor: highly associated with diabetes mellitus
• Type II – occurs due to a single organism
o Agents: a classical example is GAS (Streptococcus pyogenes) – the infection was previously
called “streptococcal gangrene” or “streptococcal toxic shock syndrome (STSS)”. Another
emerging agent is Klebsiella pneumoniae.
Signs and symptoms:
• Severe pain (earliest symptom)
• Septic appearance
• Tachycardia
Variants:
• Fournier’s gangrene – necrotizing fasciitis of the perineal area/genitalia. The infection starts with
severe pain and can progress through the pelvic area to the abdominal wall, gluteal muscles (in
males: to the scrotum and penis).
Diagnosis: most of the approach is empiric – it is less common to take swabs for culture, but it is useful
to aspirate with a needle some of the content of the lesion to check if the infection is caused by a
methicillin-sensitive strain.
• Laboratory tests:
o CPK – found in muscles, helps to determine if muscle necrosis occurs
o Bacterial culture
o All parameters under LRINEC
• Imaging: CT scan or MRI
(the latter is more
sensitive). In the image
on the right it is clear
that the fascia of the
right thigh is affected.
In the left image –
Ludwig’s angina.

Prognosis
LRINEC (laboratory risk indicator for necrotizing fasciitis) – a scoring system for the risk due to the
infection.
The score can be used as a complement for diagnosed necrotizing fasciitis, but not as the diagnostic
tool. This is because it has sensitivity of about 77%, which means that it can miss the diagnosis in more
than 20% of the cases. The diagnosis is made by CT/MRI scan, confirmed by surgery. Because of the low
sensitivity, the scoring system was updated to serve as a better diagnostic tool.
 53

Older LRINEC Updated LRINEC

Parameter Range Score Parameter Range Score
>13.5 0 >13.5 0
Hb (g/dL) 11-13.5 1 Hb (g/dL) 11-13.5 1
<11 2 <11 2
<15 0 <1590/mm3 0
WBC 15-25 1 WBC 1590-2650/mm3 1
>25 2 >2650/mm3 2
Sodium <135 2 RBC <4∙109/L 1
Creatinine >1.41 2 Creatinine <135mM 2
Glucose >10 1 Fibrinogen >750mg/dL
CRP (mg/dL) >150 4 CRP (mg/dL) >150 4
Scores: ≤5 low risk, 6-7 – intermediate risk and ≥8 Mild/none 0
high risk. Pain Intermediate 1
Strong 2
≤37.5 0
Fever 37.6-37.9 1
≥38 2
Tachycardia >100 bpm 1
No 0
Signs of acute kidney injury
Yes 1
≥8 strong suspicion for NF, 6-7 – suspicion and ≤5 no suspicion

Therapy
Cellulitis:
• 2nd generation penicillin (penicillinase-
resistant) – oxacillin, nafcillin
• 1st generation cephalosporin – cefazolin
• Vancomycin – for patients allergic to
penicillin or against CA-MRSA
Necrotizing fasciitis:
• Surgery – removal of the affected area
• Supportive therapy – fluid administration and
vasopressors
• For type II NF – penicillin + clindamycin (against
GAS)
• For type I NF – ticarcillin +clavulanate, piperatazo,
carbapenem, in case of CA-MRSA use vancomycin
• In severe cases – immunoglobulin administration

Muscle Tissue Infections

Myonecrosis
Myonecrosis, aka necrotizing myositis is a rare infection of a muscular tissue which develops rapidly,
causing a life-threatening situation – early diagnosis and treatment is crucial. Like necrotizing fasciitis,
the infections usually start due to trauma, surgery, post-abortion or spontaneously from hematogenous
seeding of muscle.
Most of these infections are caused by Clostridium spp., producing gas gangrene.
Spontaneous gangrenous myositis is not with a traumatic origin and occurs due to GAS or C. septicum
infection, with features similar to necrotizing fasciitis.

Pyomyositis/Tropical myositis
An infection which results in a primary muscle abscess, commonly occurs in tropical areas. The most
frequent agent is Staphylococcus aureus. Vibrio vulnificus is another common agent (found in coastal
areas) which causes muscle infections (also of the skin and fascia).
 54

Osseous Tissue Infections

There are many biological processes which occur in the bone, hence an infection in an osseous tissue is
not as simple as one may think. Primarily, the destruction of bones leads to problems with posture (in
the back or legs) or dexterity (in the hands and arms).

Osteomyelitis (OM)
Osteomyelitis is a progressive infectious process that can involve one or more components of the bone.
It is characterized by inflammatory destruction of the bone, which leads to necrosis, and new bone
formation.
Generalities
Etiology:
• Traumatic injury – deep wounds make it more likely for bacteria to penetrate bones
• Penetration injury (contiguous tissue) – for example:
o Due to complicated necrotizing fasciitis
o Acute purulent frontal sinusitis which penetrates the bone (results in edema of the forehead –
Pott’s puffy tumor)
o Due to dental root infection which penetrates the bone
o Deep pressure sores (usually at the sacrum and by several microbes)
• Orthopedic surgery
• Hematogenous spread of bacteria (mostly in children and elderly)
Risk factors:
• Diabetes / other forms of ischemic or neuropathic ulcer
• Age of the patient (hematogenous spread is more common in children and elderly)
Epidemiology:
• The most common pathogens of hematogenous according are according to age group-
o Neonates – E. coli, group B Streptococci and S. aureus
o Children and adults – S. aureus (predominantly), E. coli and Serratia spp.
o Elderly – following bacteremia by gram-negative organisms, S. aureus
• IVDU – P. aeruginosa
• IV catheters and immunocompromised patients – common complication is fungal osteomyelitis
• The most common microbes of contiguous OM (descending order):
o S. aureus
o Streptococci
o Enterobacteriaceae
o P. aeruginosa – in chronic OM
o Anaerobes – in animal bites, mandible OM, pressure sores OM
Pathogenesis:
• As for long bones (more common in hematogenous osteomyelitis in children)
1. The metaphyseal capillaries are diverged due to the infection, having sharp turns – the bacteria
are trapped
2. Blood flow in the bone becomes slower and more turbulent
 55

3. Blood flow moves to paths with the least degree of resistance (Haversian and Volkmann canal)
4. Local cortical necrosis
• As for the vertebral bodies (more common in hematogenous osteomyelitis in adults)
o Usually two adjacent vertebral bodies are affected because the vertebral arteries bifurcate
next to these boney structures.
o Since the vertebrae are drained by a unique venous plexus17 the pathogen(s) can be
transmitted if there is a genitourinary infection.
o The most commonly affected segment is the lumbar region, then the thoracic and the least
involved area is the cervical spine.

Clinical Manifestations
Hematogenous OM:
• Long bones:
o Fever, chills and malaise
o Soft tissue swelling and pain (elevation of the periosteum due to pus)
• Vertebrae:
o Back pain and localized tenderness
o Fever – may appear in more chronic cases
• Contiguous infection:
o Mild fever
o Increasing pain
o The wound blushes with slight discharge
• Diabetic OM: (almost always in the lower extremities, develops insidiously)
o Ulcer – usually painless (neuropathy – develops in patients with intermittent claudication) but
excruciatingly painful in acute bone destruction
o Cellulitis – may be minimal

17 Baston’s plexus – venous network without valves, which drains the bladder and the pelvic region as well.
 56

Diagnosis
# Since symptoms are non-specific, it is useful to consider osteomyelitis in the DDx of back pain
# Anemia may be present (normochromic and normocytic) in prolonged cases.
Laboratory tests:
• Increase in inflammatory markers (ESR, CRP)
• Peripheral WBC count is normal in most cases
• Bone film – demineralization within 2-3 weeks of infection
• Tissue biopsy – for culture and histopathology (only when blood cultures are negative)
Imaging: the main diagnostic tool
• Bone scan (scintigraphy)
o Can detect early disease but false positives are common
• X-ray
o Reduction of bone calcium – can be detected only after 50% is lost (low sensitivity early in the
course of disease)
o Vertebrae – abnormalities are usually visible 6-8 weeks after the onset of infection. Moreover,
unlike in neoplastic processes, in vertebral osteomyelitis almost always two vertebral bodies
are involved.
• MRI
o More sensitive in the detection of sequestra18 than CT scan (early detection)
o Hypointense signals from the infected disc and vertebral bodies (in T2-weighted images)
Treatment
Try to avoid empiric therapy!
Hematogenous OM and OM secondary to contiguous infection:
• S. aureus
o Methicillin-sensitive: nafcillin/oxacillin, ciprofloxacin-rifampicin
o Methicillin-resistant: vancomycin
• Streptococci – penicillin G
• Gram-negative organisms – oral ciprofloxacin
• Serratia/P. aeruginosa – piperacillin-tazobactam/imipenem
• Anaerobes – clindamycin/metronidazole
# Surgery – by removal of the necrotic tissue or drainage of soft tissue abscess. It may be considered
especially in vertebral osteomyelitis (to avoid spinal cord compression)
Diabetic/neuropathy ischemic osteomyelitis:
• Revascularization
• Consider amputation
• Antibiotics – for 2-6 weeks (see instructions above)

18 Sequestrum – a piece of dead bone that has been sequestered within the necrotic process
 57

Epidural Abscess
One of the most life-threatening infectious conditions due to its rapid progression, hence a failure in
diagnosis or delay in surgical treatment can result with very severe implications.
Risk factors:
• Diabetes
• IVDU
• Immunocompromised patients
• Spinal abnormalities
• Surgery
Pathogenesis:
1. Formation of an abscess between the dura and the vertebral column
2. Compression of the CNS
3. Paralysis (often seen as bladder incontinence)
Clinical manifestations: (rarely all of them are expressed together)
• Fever
• Spinal pain
• Neurological impairment
Diagnosis:
• Primarily by MRI – since it requires a very specific imaging tool
• Markers of inflammation (CRP and ESR)
Treatment: surgical drainage
 58

Urinary Tract Infections (UTIs)

UTIs are symptomatic disorders due to the presence of microorganisms in the kidneys, ureters, bladder
or the urethra. In short, they are the consequence of inflammation in any organ of the urinary tract. UTIs
have significance due to their pathogenesis: the increased permeability of vessels due to the
inflammation makes the infection more likely to be spread in an hematogenous manner.

Classification
Terminology
Bacteriuria:
• Significant – presence of at least 105 bacteria/mL of urine
• Asymptomatic – bacteriuria with no symptoms
Complexity:
• Uncomplicated – primary disease, a UTI without an underlying renal/neurologic disease
• Complicated – UTI with an underlying renal/neurological disease
Return of infection:
• Recurrence – more than three symptomatic UTIs within 12 months after therapy
• Reinfection – another incidence of UTI but with a different pathogen
• Relapse – another incidence of UTI which caused by the same infectious agent and within two
weeks of therapy

Location
Lower UTI
Urethritis – infection of anterior urethra. Accompanied by dysuria (painful/difficult urination),
urgency and frequency of urination.
Cystitis – infection of the urinary bladder. Accompanied by dysuria, frequency and urgency, polyuria,
pyuria (pus in urine) and hematuria (in hemorrhagic cystitis). Abdominal pain/pelvic discomfort as
well.
Upper UTI
Pyelonephritis –
• Acute – infection of one/both kidneys, sometimes also involves the lower urinary tract.
Accompanied by pyuria + WBC casts, fever, chills and painful urination. Non-specific symptoms:
nausea and vomiting, back pain and suprapubic tenderness.
• Chronic – different type of kidney pathology (loss of tubular function) which may be unrelated to
infection (marked by increased serum creatinine). Accompanied by polyuria and nocturia that can
develop to hypertension and nephrotic syndrome.
• Interstitial
Abscess –
• Renal
• Perirenal
 59

Epidemiology and etiology are key factors in empiric therapy, before the results of urinalysis arrive.

Epidemiology
Age: seen in all age groups, but there is increased incidence with age (10% of males and 20% of females)
Prevalence:
• Males are much less prone than females (which are at greater risk): prevalence of 0.04% and 40-
50% respectively.
• 10% of women have recurrent UTI in their life
• 7 million new cases of lower UTI/year
• 1 million hospitalizations/year

Etiology
Common Agents
Acute uncomplicated UTIs:
• Escherichia coli – in 80% of the cases
• Gram-negative:
o Klebsiella pneumonia – note that there is increased
antibiotic-resistance in recent years
o Proteus mirabilis
• Gram-positive: (increase in prevalence in recent years)
o Streptococcus faecalis
o Staphylococcus saprophyticus – especially in young, sexually-active females
o Staphylococcus aureus – its prevalence as an etiologic agent increases over time
Complicated UTIs:
• Pseudomonas aeruginosa
• Enterobacter
• Serratia

Risk Factors
1. Aging/degeneration of the urinary system
• Diabetes mellitus – bacteria can proliferate in excess of glucose
• Urine retention – inability to empty the bladder (i.e. urine stasis due to neurological disorders)
• Impaired immune system
2. Females
• Shorter urethra
• Sexual intercourse
• Contraceptives – increase the pH of the vagina
3. Males
• Prostatic hypertrophy (note: almost always in elderly patients → affects the DDx)
• Bacterial prostasis
4. Iatrogenic
• Hospital-acquired infections
• Catheterization
 60

Pathogenesis
There are four mechanisms in which bacteria
can enter the urinary tract:
1. Ascending infection – the most common
route of infection. Organisms which
colonize in the periurethral region can enter
the tract, adhere to the epithelium and
gradually ascend to the bladder or the
kidneys. Common agents are:
• E. coli, Proteus and Enterobacter
2. Blood-borne (hematogenous) spread –
entry to the kidneys due to bacteremia.
Common agents are:
• Staphylococcus, E. coli
3. Lymphogenous spread – different between
the sexes:
• Males – via rectal/colic lymphatic
vessels to the prostate and bladder
• Females – via peri-uterine lymphatics to
the urinary tract
4. Direct extension from other organs –
examples:
• Pelvic inflammatory disease (PID)
• Genito-urinary tract fistulas
• Gut barrier dysfunction – increase in
intestinal permeability leads to leaky
gut, and microorganisms can enter the
bloodstream.

Clinical manifestations depend on the age of the patient:

• In newborns and infants: growth retardation, fever, apathy and diarrhea
• In children: dysuria, urgency, frequency, hematuria, acute abdominal pain and vomiting
• Adults:
o Lower UTI – frequency, urgency, dysuria, hematuria
o Upper UTI – fever, rigor and lion pain + symptoms of lower UTI
• Elderly: mostly asymptomatic, but should be considered due to the increase in incidence with age

Pseudo-algorithms presented in class - suspicion of infections according to symptoms:

• Vomiting + dys/hematuria → renal disorder in children
• Hematuria in the beginning of micturition → lower UTI
• Hematuria throughout all micturition → upper UTI
 61

Diagnosis
Urine sample – uncontaminated (preferably), midstream, can be collected by:
• Sterile urine bag
• Urethral catheterization (CATH)
• Suprapubic aspiration (SPA) – the most sterile method (gold-standard), but it is invasive
There are four tests of diagnosis:
1. Urine Microscopy
Search for bacteria (with appropriate staining) / blood cells.
2. Urinalysis
Normal findings Abnormal findings
pH 4.4-7.4 Relevant to UTI – alkaline pH
Turbidity Clear Cloudy – due to pus
Color Pale to amber yellow Relevant to UTI - Deep amber, red
Odor Aromatic Foul odor
RBCs Negative Positive
Leukocyte esterase Negative Positive
WBCs Negative Positive
Bacteria Negative Positive (significant/asymptomatic)
Nitrite Negative Positive (pink color)

3. Urine Culture (not a rapid test)

Used in suspected pyelonephritis: WBC differential with increased neutrophils (pus).
4. Imaging Techniques – CT and MRI
Mostly by CT, MRI takes longer so it is less frequently used. US and cystoscopy are useful diagnostic
tools in males for every UTI. Moreover, cystoscopy is performed in children with recurrent
infections to check for congenital abnormalities.
Diagnostic Algorithm
Urinalysis
Urine microscopy and culture

Any sex -
Adult female
Male, any UTI complicated UTIs Children, any UTI
lower UTI
/ Pyelonephritis

Treat without Blood cultures, CT

US and Cysto-
further scan, renal
cystoscopy urethrography
investigation function tests

Management
The goals of therapy:
• Elimination of the infectious agent
• Relief of the acute symptoms
• Prevention of recurrence and long-term complications
 62

Non-Specific Therapy
Increase in water intake (to avoid urine retention) and maintenance of urine acidity by cranberry juice
or orange juice – both rich in acids.
Drug Therapy
Factors that should be considered in antibiotic administration:
• Adequate coverage over E. coli – since it is a major etiological agent
• Concentration in urine – the drug needs to be eliminated by the kidneys to pass in the urinary tract
• Concentration in blood – important in pyelonephritis19
• Duration of therapy – long enough to eliminate the infection, but short enough to avoid resistance
• Cost
• Low adverse effects profile
Single-dose therapy: for uncomplicated UTIs (not to
Advantages: Disadvantages:
patients with history of recurrent/complicated UTI and
Compliance, Increased chances
infections by antibiotic-resistant bacteria).
cost, less side for recurrence or
1. Trimethoprim-sulfamethoxazole (Bactrim™): 160mg
effects and less relapse
TMP + 800mg SMZ
resistance.
2. Amoxicillin-clavulanate
3. Ciprofloxacin / Norfloxacin 400mg20
Three-day course: has similar efficacy to 7-day course but with less side effects. Usually administered
in lower UTIs
1. Nitrofurantoin – has high concentration in urine, with very low systemic adverse effect
2. Quinolones (ciprofloxacin/norfloxacin) – 500mg for uncomplicated UTI, 1000mg for complicated
infection
3. Trimethoprim-sulfamethoxazole
4. Beta-lactams – amoxicillin
Seven-day course: usually for complicated UTIs, relapses, during pregnancy (to prevent hematogenous
spread) and UTI with other risk factors (structural abnormalities)
1. Cephalexin
2. Nitrofurantoin
3. Amoxicillin
10-14-day course: for complicated UTIs with high risk of mortality (e.g. pyelonephritis with
hematogenous spread) and treatment failure of relapses
1. Ceftazidime
2. Meropenem
3. Piperacillin-tazobactam
6-week course: for children with structural abnormalities corrected by surgery, adults with continuous
symptoms and high risk of renal damage

19Use parenteral antibiotics: Ceftriaxone 1g / Gentamycin 80-120g IV Q12h / Ciprofloxacin 200mg IV Q12h
20Fluoroquinolones: have severe adverse effects (e.g. on cartilage in children, aneurism in adults), hence should be used as the
last-resort drugs in milder infections.
 63

Agent-specific treatment:
Pathogen Treatment Options
Escherichia coli Ceftriaxone 50mg/Kg IV/IM 4 time a day
Pseudomonas aeruginosa Ciprofloxacin / Meropenem
Klebsiella spp., Enterobacter spp., Proteus spp. Ceftazidime 100-150mg/Kg/day IV Q8 hours
Enterococcus Ampicillin 100-200mg/Kg/day Q6 hours

Asymptomatic Bacteriuria
• Children- treat the same as for symptomatic bacteriuria
• Adults – treat in cases of pregnancy / in patients with obstructive-structural abnormalities
Prophylaxis of UTI
• Single dose of Trimethoprim-sulfamethoxazole 100mg / Nitrofurantoin 50mg (for women – also
after sexual intercourse)
• Try to change the susceptibility of the patients (non-specific therapy)
• Catheterized patients – remove the catheter before treatment is beneficial
Surgical Treatment
• Surgical removal of renal or bladder calculi
• Ureteroplasty
• Reimplantation of ureters if VUR (vesico-urethral reflux) is present

Sexually-Transmitted Diseases (STDs)

General Concepts
STDs are a group of very common diseases, all transmitted by sexual intercourse whether it is normal,
oral or anal. According to the WHO, a relatively large fraction of the world population is infected by at
least one disease. The reason for this is due to the decreased production of IgA/IgE there is increased
likelihood for an agent to be integrated in the mucosa, and there are several agents infecting the same
patient.
STDs are the main cause of infertility in both males and females and in general males are more
symptomatic than females. Being caused by exogenous agents, it is easy to expect that they can be
eradicated. However, because most of STDs are asymptomatic, people are not aware that they are
infected, so they can further transmit the infection.
STDs can have implications on issues other than health status such as the financial burden of treatment,
psychological effect and problems in relationships (divorce/abandonment).
Epidemiology:
• Higher prevalence in urban residents who are unmarried and young adults
• Differences between countries and regions are due to the socio-economic status of the individuals
and depend on cultural factors and level of access to healthcare
• Highly associated with HIV infection – affect similar populations due to the same route of
transmission.
 64

Complications:
• Infertility
• Neoplasms (e.g. HPV)
• Spread to other systems (e.g. syphilis)
• Considerable morbidity
• Facilitation of HIV infection
It is important to distinguish between the fates of these diseases –
Curable Treatable
• Gonorrhea • Herpes
• Chlamydia • HPV
• Syphilis • HIV
All caused by bacteria, so they can be Difficult to eliminate the virus because there is no specific
eliminated by antibiotics. therapy. In the case of Herpes – integration in the host
genome makes it even more impossible to eliminate.
Gonorrhea
Microbiology
Agent characteristics: Neisseria gonorrhea (Gonococcus)
• Gram-negative bacteria
• Incubation period of 1-30 days
Transmission: can be transmitted even without symptoms
• Sexual intercourse of all forms (also anal, oral)
• Vertical transmission

Clinical Manifestations
Signs and symptoms:
• In males:
o Some infections are asymptomatic
o Burning sensation during urination
o White/yellow/green discharge from the urethra
• In females:
o Most infections are asymptomatic
o Painful urination / (depends on the extent of inflammation) painful sexual intercourse
o Abnormal bleeding
Complications:
• Epididymitis – swelling of the scrotum and severe pain
• Pelvic inflammatory disease (PID) – infection of the uterus, fallopian tubes and the ovaries
• Infertility

Diagnosis
Gram-stain of the discharge material reveals many PMNs and cocci.
Treatment - According to the CDC, treatment against gonorrhea includes ceftriaxone (IM) and azithromycin (PO).
 65

Chlamydia
Microbiology
Agent characteristics:
• Gram-negative intracellular bacteria
• Incubation period of 1-3 weeks
Transmission: can be transmitted even without symptoms
• Sexual intercourse of all forms (also anal, oral)
• Vertical transmission

Clinical Manifestations
Signs and symptoms: aka “the silent disease”, in 50% of males and 75% of females the disease is
asymptomatic. If symptoms occur, they usually appear several weeks after exposure.
• In males:
o Penile discharge (noted usually as staining of the underwear)
o Crusting of the meatus
o Pain during urination
• In females:
o Abnormal vaginal discharge
o Pain during sexual intercourse
Complications: (same as in gonorrhea)
• Epididymitis – swelling of the scrotum and severe pain
• Pelvic inflammatory disease (PID) – infection of the uterus, fallopian tubes and the ovaries
• Infertility

Diagnosis
• Nucleic acid amplification tests (NAATs) – frequently used in the clinical practice, “gold standard”
o Detection of plasmid DNA or rRNA
o Much more sensitive than other tests
• Non-NAATs
o Direct-fluorescent antibody (DFA) – variety of possible specimens, can be used to determine
the quality of endocervical specimens
o EIA
o Nucleic acid hybridization (also for N. gonorrheae)
• Serology – results are difficult to interpret, hence this method is rarely used
• Culture of the discharge material - variable sensitivity but high specificity, not useful as a screening
tool (used mostly in legal investigations

Treatment
Macrolides – have high intracellular concentration
 66

Syphilis
Microbiology
Agent characteristics: Treponema pallidum
• Gram-negative (theoretically) bacteria, a spirochete, very thin (cannot be visualized by standard
microscopy)
• Characterized by slow growth (30 hours of doubling time)
• Incubation period of 10-90 days, on average 21 days (blood tests appear negative)
• Cannot be cultured
Transmission:
• Sexual intercourse by contact with a lesion (chancre)
• Vertical transmission
• Direct contact
• Blood transmission is rare

Clinical Manifestations
Signs and symptoms:
• Primary syphilis:
o A painless sore = chancre, marks the entry of the bacteria to the body
− In MSM the chancre will be located next to the anus, where it is difficult to see. It is often
misdiagnosed as trauma, fissure or hemorrhoids. Therefore, syphilis in this population is
usually recognized in later phases.
o Lasts 1-5 weeks, throughout which the bacteria are highly transmissible
o The chancre heals without treatment
• Secondary syphilis:
o Rash appears mostly on the palms or the soles of the feet, but can be on any part of the body
− Similar to the rash pattern caused by several drugs, but the latter does not occur on the
palms (DDx).
− Does not tend to itch
o Condyloma lata – merging of lesions in moist areas (e.g. the groins) creates highly-infectious
plaques, which are painless, red and then grey-white.
− DDx with condyloma accuminata due to HPV infection – looks like cauliflower lesions while
syphilis lesions look flatter, but still elevated from the skin.
o Lasts 2-6 weeks (4 weeks on average)
o The disease is less transmissible (unless there is direct contact with the lesions, very rare)
o Symptomatic secondary disease occurs in 30% of the patients: can be accompanied by fever,
lymphadenopathy (commonly the epitrochlear nodes), headache, hair loss (alopecia) and
myalgia
o In addition to the symptoms above, any organ can be affected and manifest with symptoms
accordingly:
− Basilar meningitis → deficits of CN III, VI, VII, and VIII → pupillary abnormalities, diplopia,
facial weakness, hearing loss or tinnitus.
− Anterior uveitis
 67

− Immune complex glomerulonephritis

− Hepatitis
− Synovitis and periostitis
• Latency – after the dissemination, the infection remains in the body but does not manifest
clinically. This stage can last for years, but the disease is still curable.
• Tertiary syphilis: damage to internal organs which evolves very rapidly and eventually leads to
death. The main syndromes of this phase:
o Late Neurosyphilis – in most cases the brain will be involved, causing neurological symptoms:
muscles discoordination (ataxia), numbness, dementia or seizures.
− Consider meningovascular syphilis in younger patients who suffer from CVA (uncommon
before the middle age)
− Dementia – most common symptom (perform lumbar puncture for the diagnosis).
− General paresis: personality disorder, psychiatric disturbances and neurological
abnormalities. Usually develop 15-20 years after exposure
− Tabes dorsalis: demyelination of the posterior spinal cord up to the dorsal root ganglions
→ loss of sensation and reflexes
o Cardiovascular syphilis (arise 15-30 years after primary infection in 10% of untreated patients)
− Arteritis of the vasa vasorum → dilation of the aorta → congestive heart failure
− Asymptomatic saccular aneurism of the thoracic aorta (less common)
o Later benign gummas (= granulomatous lesions on soft tissue/bones, very rare except for AIDS
patients)
− Bone gummas appear in long bones → tenderness, bone destruction
− Visceral gummas can be found in every organ (usually at the cerebral cortex, liver and
gastric antrum)

Diagnosis
1. Clinical History
• History of syphilis – typical signs or symptoms of syphilis in the past 12 months
• Assess if there was contact to an early case of syphilis
• Ask the most recent serologic test for syphilis
2. Physical Examination
• Oral cavity
• Lymph nodes
• Skin of torso, palms and soles
• Genitalia and perineal area
• Neurologic examination
3. Laboratory diagnosis
See syphilis under “TORCH infections”

Treatment
Benzathine penicillin is the main drug in the therapy of syphilis, but there is no discrete dosage and
therapy duration documented.
• Minimal therapy: 2 weeks, concentration of 0.03μg/mL, intramuscular injection.
 68

• For primary and secondary syphilis: Benzathine penicillin G of 2.4 million units (3 injections over 2
weeks) / doxycycline for two weeks
• For early latent syphilis: single weekly dose of IM benzathine penicillin G / (in case of allergy)
doxycycline for four weeks
• For late latent syphilis: three weekly doses of IM benzathine penicillin G /(allergy) doxycycline for
four weeks
• For tertiary syphilis: aqueous penicillin G, 12-24 million units, every 4 hours for 10-14 days (+ oral
probenecid 500mg every 6 hours for 10-14 days)
• HIV patients should be treated as for tertiary syphilis at any stage of disease
• Because there must be a constant serum concentration, which may not be achieved by IM
administration, the patients must be tested by follow up after the treatment (6 months and 1 year).
o Treatment failure/reinfection: appearance of symptoms and NTT titers increase 4-fold → re-
administer the drug.
• Jarisch-Herxheimer reaction – systemic reaction to treatment of syphilis (mostly reported in
secondary syphilis but can happen in any stage) accompanied by fever, chills, muscle aches,
headache and shock-like signs.
• In case of allergy to penicillin: use doxycycline or tetracycline for two weeks

Herpes Virus
Microbiology
Agent characteristics:
• dsDNA-virus, linear genome, enveloped
Transmission: can be transmitted even without symptoms
• Sexual intercourse of all forms (also anal, oral)
• Saliva
• Vertical transmission

Clinical Manifestations
Signs and symptoms: herpes genitalis (HSV2, but can also be due to HSV1), may reoccur
• Small red sores or blisters on the genitalia/anus
o Appearance: “dew drops on rose petals”, initially as a rash then can be ulcerous or crusted
o The blisters are painful. There might be itching or burning sensation.
o Painful urination (more common in females)
• Sometimes accompanied by flu-like symptoms: (more common in females)
o Fever, headache, malaise
o Gradually increase and decrease over a week period

Diagnosis
Culture of the lesion/PCR.

Treatment
Acyclovir, Famciclovir, Valacyclovir.
Note that the infection is not-curable, and transmission can occur regardless the use of medications.
 69

Human Papilloma Virus (HPV)

Microbiology
Agent characteristics:
• dsDNA virus
• There are more than 100 types of HPV, from which 30 types can affect the genital area
Epidemiology: one of the most common STDs
Transmission: direct skin-to-skin contact (not in the act of sexual intercourse)

Clinical Manifestations
Signs and symptoms:
• In most cases, genital HPV infection is transient, asymptomatic and resolves without treatment.
• Genital warts (especially in AIDS patients)
o Single or multiple fleshy growths, flesh/white color
o May itch, bleed or burn
o Usually benign, can be very small (undistinguishable)
Complications:
• Regrowth of the warts
• The warts can become neoplastic – HPV (16, 18, 31, 33, 45) is highly associated with cancer:
oropharyngeal, cervical
• Infertility

Diagnosis
• Pap smears – the best diagnostic tool
• Biopsy – indicated when the wart is unusual in appearance

Vaccine
There are three types of vaccines:
• Cervarix – bivalent vaccine against types 16 and 18 which are associated with cervical cancer
• Gardasil – tetravalent vaccine against types 6 and 11 which cause genital warts, and against 16 and
18 which are associated with cervical/vulvar/vaginal/anal cancer
• Gardasil 9 – nine-valent vaccine against types 6, 11, 16, 18, 31, 33, 45, 52, 58
Indications:
• Every vaccine is recommended for females aged 11-12 years (but can be administered at the age
of 9 or 10)
• Gardasil/Gardasil 9 are recommended also for males aged 11-12 years
• Also match the criteria – females up to the age of 26, males up to the age of 21, MSM up to the
age of 26
Instructions:
• Three-doses of the vaccine must be administered IM and over a six-months period
• Females who are vaccinated should continue routine cervical cancer screening.
 70

The Febrile Patient

Fever is one of the most common signs in medicine, hence it is important to know the principles of the
approach to patients with fever. Elevation of body temperature can be divided into two different
definitions:
• Fever – aka pyrexia, “elevation of body temperature above the normal circadian range as a result of
a change in the thermoregulatory center” i.e. excessive production of heat.
Fever is a beneficial function of the body because it increases the survival rate of infectious diseases:
o Enhances the phagocytic and bactericidal activity of neutrophils – cytokines summon them to
fight the infection
o Enhances the cytotoxic effects of lymphocytes
o Impairs the growth and virulence of some bacteria
• Hyperthermia – “elevation of the core body temperature without the elevation of the hypothalamic
set point”, so the cause for the increase in temperature is inadequate heat loss. For example:
o Heat stroke
o Intracerebral hemorrhage
o Induced by drugs – e.g. tricyclic antidepressants or other psychiatric drugs

Thermoregulation – Physiology
Body temperature is controlled by the hypothalamus, which is sensitive to changes in the core
temperature. A set point of core temperature is 37°C and ranges 0.5°C either below or above this point.
This is done to ensure the function of many enzymes and other metabolic processes.
The hypothalamus controls the balance between heat production and loss -
↓ ↓
Body temperature is generated by: Body temperature is lost by:
• Basal metabolic activity • Conduction
• Muscle movement • Convection – increased by wind
• Evaporation – increased by sweating
Febrile Response
Mechanism of Action
Stimulus:
• Exogenous - microorganisms, their products or toxins (e.g. LPS of gram-
negative bacteria - endotoxins)
• Endogenous - pyrogenic cytokines: IL1, IL6, TNFα and IFNγ

Mactophages are triggered to release more cytokines

Activation of the arachidonic acid pathway by the enzyme

phospholipase A2

Synthesis of prostaglandin E2 (PGE2) in the cyclo-oxygenase

pathway
 71

Clinical Presentation
Variation of fever:
• Diurnal variation: in the middle of the day (16:00) the body temperature is 0.5°C higher than in the
morning, then decreases again. In case of fever, it follows this pattern of variation.
• Location of measurement: rectal temperature is about 0.6°C higher than oral temperature (more
precise measurement).
Symptoms:
• Feeling hot can be mistakenly perceived as fever – in fact, it occurs due to increase in cytokines
release
• Chills – due to the rising of the body temperature
o Profound chills (with chattering of the teeth) are due to a rapid increase in body temperature.
Occurrence: Brucellosis, Malaria, sepsis with abscess and lymphomas
• Excessive sweating – occurs usually at night, attempts of the body to cool itself
o Night sweats are prevalent in tuberculosis infection and lymphoma
• Headache – (due to vasoconstriction) other causes include emboli/encephalitis, and headache with
neck stiffness and photophobia may suggest meningitis
• Delirium – confusion, frequent finding in children and elderly. Use the GCS to assess the condition
• Muscle pain – especially in influenza or other viral infections (normally due to increase in cytokines
and activation of the cyclo-oxygenase pathway) Malaria and Brucellosis
Absence of fever:
• Severely ill newborns
• Elderly patients
• Uremic patients
• Severely malnourished patients
• Patients under antipyretic therapy

Fever Patterns
Continuous fever – fever which follows the diurnal Typhoid fever, meningitis
variation and remains above the baseline
throughout the day
Intermittent fever - episodes of fever between Deep infection (visceral leishmaniasis, malaria,
hours of normal temperature sepsis, EBV), malignancy, drug-induced
• Quotidian – daily bouts of fever (P. Knowlesi)
• Tertian – every 48h (P. vivax/ovale)
• Quartan – every 72h (P. malariae)
Remittent fever - a fever with daily variation of Tuberculosis, viral infections, infectious
more than 1˚C, but still remains above the normal endocarditis and Brucellosis
Relapsing fever - episodes of fever every 5-7 days Borrelia infections
Pal-Epstein fever - continuous/remittent fever Hodgkin lymphoma, tuberculosis
followed by afebrile period of variable number of
days (3-10)
 72

# Fever with extreme degree: gram-negative bacteremia, Legionnaire’s disease and complicated
pyelonephritis (bacteremia)
# Fever cannot be diagnostic when the patient is administered with antipyretics, steroids and
antibiotics

Fever of Unknown Origin (FUO)

FUO is usually diagnosed by exclusion, since after all possible investigations there is no explanation
why the patient is pyretic. The definition of FUO:
• Fever of >38.3°C measured several times
• The fever lasts for at least three weeks
• Uncertain diagnosis after one week of hospitalization

Approach to Fever
History-taking
The most important diagnostic mean is the thorough assessment of the patient’s history:
• Chronology of the symptoms – put them in order
• Check if the patient is taking drugs – which may
o Interfere with the true appearance of the fever
o Induce fever themselves (e.g. penicillin, cephalosporins, sulfonamide, anti-tuberculous agents
and anticonvulsants – phenytoin)
o Produce an allergic reaction
• Surgical or dental procedures – if the patient took prophylactic means, or if was implanted with
prothesis
• Occupational history – exposure to animals, toxic materials etc.
• Residence – the geographic area can affect the diagnosis
• Travel history – destination, activities, duration
• Behavior – diet, sexual practice, IVDU, alcoholism
• Family history – of infectious diseases or genetic defects
• Ethnicity – in the case of familial Mediterranean fever

Examination
Always exclude factitious fever – manipulation of the measurement of body temperature by the
patient, which is completely healthy (drinking hot water, ingestion of chalks etc.)

• Inspection:
o Look for rash: erythematous (becomes white on pressure, due to measles, rubella etc.),
petechial (always remains red, usually due to meningococcal septicemia) or vesicular (herpes
zoster infection).
o Mouth and pharynx:
– Streptococcus/coxsackie: vesicular lesions, tonsillar exudate
– HIV: hairy leukopenia or oropharyngeal candidiasis (immunodeficiency)
o Eyes:
– Conjunctival petechiae: meningococcal meningitis
– Jaundice: hepatitis
 73

o Lymph nodes: >1cm in size is a pathologic finding

– Tonsillar: acute pharyngitis/tonsillitis
– Cervical: infectious mononucleosis or HIV infection
– Axillary: infection, leukemia or lymphoma
o Joint: look for redness, swelling, heat → may suggest arthritis
• Laboratory tests:
o CBC with differential
– Neutropenia → typhoid, brucellosis, viral infection or vasculitis in SLE
– Lymphocytosis → tuberculosis, brucellosis, viral infection
– Monocytosis → tuberculosis, typhoid and brucellosis
– Eosinophilia → hypersensitivity, Hodgkin lymphoma or adrenal insufficiency
o Blood smear (susp. Malaria)
o Blood chemistry
o Microbiology: samples of body fluids
o Urinalysis
o Stool inspection – culture / occult blood / O&P
• Radiology – chest X-ray for patients with significant febrile illness

Treatment
In low-grade fever there is no need to use antipyretic drugs, except for pregnant women (1st trimester)
or infants with seizures – where fever can be dangerous
Hyperthermia – cool immediately the patient by cold shower, in adults use also ice (but only on the
extremities).
Drugs – use in case of high-grade fever. Antipyretics (paracetamol) lower the temperature but do not
treat the underlying cause (if it is bacterial – use antibiotics).
 74

Sepsis
Sepsis is a complication of an infection that results in a life-threatening situation. It occurs when
metabolites of the infectious agent/s migrate into blood vessels. As a response, the body activates an
abnormal systemic inflammatory response that can affect the entire body and may lead to damage of
organs or systems. The sepsis can furtherly progress into septic shock, even more dangerous state where
the blood pressure decreases dramatically and can rapidly cause death.

Generalities
Definitions
Infection – a microbial phenomenon characterized by inflammatory response to presence or invasion
of microorganisms to a normally sterile host tissue.
Bacteremia – presence of bacteria in the bloodstream. The term “sepsis/septicemia” is no longer used
to describe this condition. The old definition of sepsis was based on:
Systemic inflammatory response • Body temperature >38°C or <36°C
syndrome (SIRS) – a dysregulated
• Heart rate >90bpm
inflammatory response, which can
• Respiratory rate of > 20 breaths per minute or
occur even without infection. SIRS with
PaCO2 < 32mmHg
presumed or confirmed infection is
• WBC>12,000/mm3 or <4000/mm3
considered sepsis. The criteria of SIRS
• More than 10% immature forms
are: (to the right)
# WBC increase is typical in gram-negative infections (e.g. E. coli).
New criteria for sepsis diagnosis:
Quick Sequential organ failure assessment • Glasgow Coma Scale (GCS) < 15 (instead of
(qSOFA) score – may identify patients with altered mentation)
suspected infection who are at greater risk for a
• Respiratory rate of ≥ 22 breaths/minute
poor prognosis outside the intensive care unit.
• Systolic blood pressure ≤ 100mmHg
Patients presenting with two of the criteria are
# Serum lactate > 2mM (good prognostic marker
considered to have sepsis. – increases usually in later stages due to
# Measurement of lactate is by hemogas analysis. microvascular occlusion = ischemia)

Epidemiology
There is no particular risk for sepsis – it can occur in all individuals. Early detection and treatment can
significantly improve the chances of survival. Conditions in which sepsis becomes more likely:
• Elderly or immunocompromised patients (immunodeficiency, transplant and chemotherapy
patients)
• Multi-drug resistant bacteria (an emerging problem throughout the world, which also increased
the incidence of sepsis in the past years)
The list of most common agents varies a lot, depending on the country, size of the hospital, time of the
year etc.
 75

Etiology
It is important to know, or at least to infer, the Another important preliminary information is
causative agent of sepsis to start a correct about the location of the primary infection that
empirical treatment. In general, the most caused the sepsis. Common infections that can
common agents that induce sepsis are: lead to sepsis: (ordered according to frequency)
• Staphylococcus aureus (including MRSA, a • Lung infections
multi-drug resistant bacteria) • UTIs (in particular – kidney infections)
• Escherichia coli • GI tract infections
• Enterococci • Skin infections
• Klebsiella pneumonia (a multi-drug resistant
bacteria)
• Group A Streptococci (S. pyogenes)
Potential risk factors leading to sepsis:
• Community factors: travel, disease outbreaks, contacts and specific exposure
• Hospital factors: duration of hospitalization (longer = high probability of sepsis), department of
hospitalization, local antibiotic resistance rates, outbreaks
• Procedures: urinary catheters, IV cannulas and wound dressings
• Surgery: wounds, type of procedure – upper (“clean”) / lower (“dirty”) than the diaphragm,
emergency/elective and prosthetic material
• Intrinsic factors: age, comorbidities, immunosuppression, vaccination, nutrition (glucose-rich →
bacterial proliferation, lipid-rich → fungal infections, contamination of the IV line that supplies
nutrition to the patient) and mucosal integrity (destroyed under chemotherapy)

Pathogenesis
Gram negative bacteria Gram positive bacteria
Lipopolysaccharide (LPS) – the O antigen of the bacterium, Teichoic acid and lipoteichoic
aka endotoxin. They are released as a response for cell lysis. acid – surface antigens

Endothelia, neutrophils and monocytes

Free radicals Synthesis of pro-inflammatory Lipid mediators

cytokines and chemokines: TNFα,
IL-1, IL-6, PAF (platelet activating
factor), Tissue Factor, NO

Neutrophils Platelets Endothelia T cells

Activation, Extravasation, Activation, aggregation Vasodilation, increased permeability Release of IL-2, IFNγ,
degranulation (release of and metabolism of arachidonic acid colony stimulating factor
radicals and proteases) → thromboxane, prostaglandins, (CSF2)
leukotrienes → coagulopathy

Microvascular occlusion Vascular instability

Sepsis
 76

The decrease in blood pressure leads to hypoperfusion, which is one of the main contributing factors
for organ failure. For example – in the kidneys, acute hypoperfusion can rapidly lead to renal failure.
The involvement of a system during sepsis depends on the microorganism. The most common
dysfunctions at the moment sepsis is recognized (in descending order) are: respiratory tract, renal,
metabolic, coagulation and DIC. Furthermore, the number of the systems involved in sepsis is directly
proportional to the increase in mortality.

Diagnosis
Direct Diagnosis - Blood Culture
The process of blood culture is meant to detect the specific causative agent/s of sepsis, to state a
prognosis and consider more precise therapy (and avoid antibiotic resistance) than the empiric drugs.
Instructions for the extraction of blood:
• Only if the patient has fever of more than 38˚C (best when the temperature begins to increase)
• Before antimicrobial treatment has started
• Test two samples taken at different times for confirmation
• 20mL of blood in adults, 1-2mL in children
• In children and neonates – collect blood from a peripheral vein (not from the umbilical vein)
Blood is injected into two bottles with growth medium → colonization means a positive exam, which
is further examined for its content.

Indirect Diagnosis
Procalcitonin (PCT)
Procalcitonin is the precursor molecule of the hormone calcitonin, normally synthesized by the
thyroid gland. PCT is an acute phase protein, since its synthesis is stimulated in all body tissues as a
part of the inflammatory response: LPS → stimulate the release of IL-1β and TNF. These cytokines
signal to all body tissues to synthesize PCT (but it is not furtherly processed to calcitonin) so it is
released extensively to the bloodstream.
In contrast, viral infection → stimulate the release of IFNγ → inhibition of PCT release (rule out
bacterial infection – remember that the NPP is 90%, so if PCT is negative you can almost always rule it out).
Therefore, integration of PCT with other parameters is useful because:
• Higher accuracy in the diagnosis of bacterial infection or sepsis
o Fever is highly non-specific sign, which can be the result of malignancy or an autoimmune
disease. Increase in PCT levels indicates that the source of fever is a bacterial infection.
o In comparison to other biomarkers of inflammation (such as CRP, IL-6 and lactate), PCT has
the best statistical value in the diagnosis of sepsis
• Improved clinical decision (due to better prognostic picture) and patient management
o The level of PCT is correlated with the severity of sepsis (directly proportional)
Reference range: in healthy subjects, <0.5μg/L
ACCP/SCCM Definitions
Mentioned in Laboratory medicine of last year, but not in this class. May be useful list in the future.
 77

• Altered mental status • Acute oliguria (>2 hours)

• Edema or increased fluid balance – resulting from the low
blood pressure
• Decreased capillary refill or matting – press the nails to check
if the capillaries fill immediately.
Shunts (functional/micro-anatomic) – impaired
microcirculatory vasomotor control.
• Hypotension
• Increased CRP or PCT – respectively: an acute phase protein
and a good biomarker for sepsis (released excessively by
macrophages).
• Coagulopathy (INR>1.5) – prothrombin time (international
normalized ratio). Checks liver function.
• Increased SvO2 – mixed venous oxygen saturation. Measured
preferably by a catheter in the pulmonary artery. Normal levels:
65-70%, lower levels indicate on higher consumption, but
increased levels indicate on hypoperfusion.
• Arterial hypoxemia (PaO2/FiO2 < 300)
• Thrombocytopenia (<100,000/uL) – low platelet count
• Increased serum creatinine (>0.5mg/dL) – indicates on an acute
renal injury
• Ileus – absent bowel sounds
• Hyperglycemia – where diabetes is absent, cortisol is secreted as
a response to stress, but due to the impaired perfusion the
glucose cannot be uptaken by cells.
•
• Hyperlactatemia (>1mM) – citric acid cycle defect with
anaerobic glycolysis/ aerobic glycolysis with lactate production
Found an article with the cutoff of 2.5mM, and in the next slides
it is written 4mM.
• CI>3.5L/min/m2 – cardiac index. Calculations of the perfusion
with respect to body surface area.
• Hyperbilirubinemia (>40mg/dL or 70mM) and elevated levels
of liver enzymes in serum (ALP, AST, ALT)

Principles of Management
Time
Early recognition and management of patients with severe sepsis lead to improved outcomes, the same
principle as in ACS, stroke or trauma patients. Untreated sepsis can rapidly deteriorate to shock state,
where the prognosis is highly unfavorable.
1. Time zero (at admission) – perform blood culture and then prescribe antibiotics (see empirical
therapy). Measure blood lactate level.
2. 3 hours past admission –
• Repeat the test of blood lactate
• Administration of 30mL/Kg of crystalloid (Ringer/saline) for patients with: mean arterial
pressure (MAP) < 65mmHg or lactate ≥ 4mM.
• Administer vasopressors for patients unresponsive to the crystalloid infusion / Hydrocortisone
200mg/day (not a 1st line drug, but can assist in restoring normal blood pressure)
• Measure other parameters which may indicate a system in decompensation
“Delays in administering all four guidelines recommendations, even when they did not exceed 3 hours,
were associated with a significant increase in-hospital mortality”.

Empirical Therapy
Start empirical therapy by antibiotics within one hour from admission, considering the location of the
infection and the possible causative agent. Choose an antibiotic therapy that cover all the spectrum of
bacteria that match the reasoning – sometimes several drugs are necessary.
The factors that should be considered when choosing an antibiotic are efficacy (spectrum, patterns of
resistance, PK and PD), toxicity and cost (see the chapter about antibiotic stewardship)
E.g. Vancomycin – used against gram-positive infections but does not have high penetrance. Therefore,
if it is used to treat pneumonia, the therapy may fail.
 78

AIDS and Opportunistic Infections

HIV infections are spread world-widely, hence it is crucial to be aware of them as a physician. They are
one of the causes of immunocompromising patients, so they can cause severe deterioration of the health
status and expose these patients to diseases which rarely occur in immunocompetent subjects.

Microbiology
Classification
HIV, the human immunodeficiency virus, belongs to the Retroviridae family and the Lentivirus genus.
The virus can be classified into two groups:
• HIV-1
o HIV-1M (major) – the cause of the current worldwide epidemic
− Eleven identified clades (A-K): each is predominant in a particular geographic region.
Different clades have different clinical and biologic behavior.
− Recombinant clades (e.g. A/G and A/E)
o HIV-1O (outlier), HIV-1N and HIV-1P (Cameroon) – rarer groups
• HIV-2 – antigenically different that HIV-1

History
HIV evolved from the Simian Immunodeficiency Virus (SIV), which is prevalent only among African
monkeys and has many different subgroups – each infects a different species. SIV possibly transferred
to humans who handled or hunted chimpanzees (specifically HIVcpz). The transmission of the different
clades is estimated: 1908 for HIV-1M and 1932 for HIV-2
The timeline of HIV discovery and investigation:
• 1959 – the oldest human sample. HIV probably emerged quickly throughout the population due to
the increase in urbanization and international travelling.
• 1981 – HIV was first reported among 5 gay men
• 1982 – the term “AIDS” was first coined, first cases in women and due to transfusion were reported
• 1983 – first isolation of HIV (a retrovirus from a patient with AIDS)
• 1985 – FDA approves the first commercial antibody test
• 1986 – NIH establishes the AIDS clinical trials group
• 1987 – AZT, the first antiretroviral, was approved by the FDA

Pathogenesis
Viral proteins:
• Envelope (Env) – gp160, which is cleaved into:
o Gp41: trans-membrane protein – responsible for membrane fusion
o Gp120: outer glycoprotein – binds to chemokine receptors (CCR5/CXCR4) / CD4
• Core and matrix proteins (Gag) – the capsid protein (p24) and others
• Polymerase (Pol) – fulfills three functions:
o Reverse transcriptase: has high error rate = increased likelihood of mutations
o RNase H: cleaves DNA-RNA hybrids
o Integrase: integrates the vDNA in the host cell genome
 79

• Essential regulatory elements

o Tat – activates reverse transcription
o Rev – regulator of virion, allows the export of non-spliced transcripts from the nucleus
• Accessory regulatory elements
o vif – (viral infectivity factor) inhibits host APOBEC3G/3F
o nef – increases the efficiency of transmission (promotes T cell activation and down-regulation
of MHC-1 and CD4)
o vpu – degrades cellular Tetherin, enhancing the viral budding
o vpr – assists in replication (aids in transferring the pre-integration complex into the nucleus)
Life cycle:
1. HIV approaches a human CD4+ macrophage/T-lymphocyte.
2. Binding: HIV binds with glycoproteins to a CD4 receptor and either a CCR5 (on macrophages – slow
loss) or CXCR4 (Th cells – rapid loss) co-receptor protein.
3. Fusion: the virus fuses to the host cell and releases RNA into the cell.
4. Reverse transcription: the HIV enzyme reverse transcriptase converts viral ssRNA into dsDNA.
5. Integration: HIV DNA enters the hosts nucleus and is integrated into the host genome using an
enzyme called integrase creating a provirus.
6. Transcription: the provirus becomes active and uses RNA polymerase to create copies of HIV
genomic material, as well as mRNA. The mRNA is used to make long chains of HIV proteins
7. Assembly: the enzyme protease cuts the long chains of HIV into individual proteins and assemble
a virus particle containing HIV RNA.
8. Budding: the virus buds assemble in the host cell, using the cell’s plasma membrane. The envelope
formed is a mixture of protein and carbohydrates (composing the viral glycoproteins).
9. The immature virus breaks free of the infected cell
10. Maturation: protease completes cutting the HIV protein chains into individual proteins and the
newly formed copy of HIV can now infect other cells.
Neurotropic – the virus is concentrated
in the brain and can cause
meningoencephalitis (the drug to treat
this condition must cross the BBB).
Loss of CD4 cells in the gut makes the
gut more permeable for infections and
more prone for microbial translocations
(constant stimulation of the immune
system which weakens it faster).
The condition can be stabilized by
specific drugs (making it a chronic
infection) but it can be accelerated
when the rate of CD4+ cells destruction
is higher than the rate of their
synthesis21.

21 Clade D (East Africa) is associated with faster disease progression

 80

Epidemiology and Transmission

There are 34-46 million infected subjects all over the world. HIV-2 is highly prevalent in West Africa
while HIV-1 is more common worldwide. AIDS, the clinical manifestation of the virus, is the leading cause
of death among men aged 25-44 and 4th leading cause of death among women in the same age group.
Modes of transmission: contact of the following biological fluids with mucosal membranes-
• Blood – through transfusions, shared needles or in utero (TORCH)
• Semen – makes the disease transmittable also by anal sex
• Vaginal secretions – transmittable also during labor
• Breast milk
# HIV is not transmitted by other ways such as hugging, shaking hands, sharing food, public pools or
toilets. Inform the patients about the ways of transmission to eliminate wrong opinions about
infected subjects.
Factors that influence the transmission:
• Viral load – primary infections (high viral load) account for about half of all new HIV infections
worldwide. Patients without heavy replication of the virus cannot transmit the virus.
• Other STDs – cause mucosal damage (reduction of IgA synthesis) thus higher likelihood of
transmitting HIV.
• The type of exposed mucosa – the most probable transmission is rectal, then cervicovaginal and
lastly penile.
• Circumcision – decreases the transmission by 2-fold among heterosexual males
• Oral contraceptives or pregnancy – increased risk of infection
• The duration of relationship with the partner – sexual intercourse with occasional partners
increases the risk of transmission more than habitual sex partner (local immunity to his/her
antigens)

Clinical Manifestations
1. Acute Retroviral Syndrome
Clinically overt in two thirds of patients. It begins 2-6 weeks after initial infection and lasts about
2-4 weeks. The presentation can be confused with influenza or mononucleosis since symptoms are
very non-specific (lymphadenopathy, fever and rash) but it is self-limited.
During this period the virus is replicating vigorously so the CD4 count decreases. It ends when the
body compensates by synthesizing more cells until the immune system recovers.

2. Clinical Latency
The virus replicates in lower levels and CD4 count is maintained in normal range (500-1300/μL),
but the virus is still transmissible. The host can feel well for years, but in the end of this period
there can be several conditions: bacillary angiomatosis22, vulvovaginal candidiasis, PID, cervical
dysplasia, hairy leukoplakia, herpes zoster.
Symptoms which can develop: fever or chronic diarrhea

22 Bacillary angiomatosis - skin lesions caused by infection of a gram-negative bacterium

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3. Acquired Immunodeficiency Syndrome (AIDS)

AIDS is the state when the infection caused severe damage to the immune system of the host, so
s/he is more prone for opportunistic infections. Higher viral load – more CD4 cells are destroyed
and rapid progression of AIDS.
Definition
AIDS is defined when either (or both) of the conditions are found:
• The patient has a CD4 cells count under 200/μL
• The presence of one or more opportunistic infection (AIDS-defining illnesses)

AIDS-Defining Illnesses
Note that there is a correlation between the CD4 count level and the severity of the infection, for
example: CD4 = 200/μL pneumonia due to pneumocystis, and in CD4 < 50/μL more severe
infections by opportunistic pathogens. According to the CDC, these infections are:
• Burkitt's Lymphoma, immunoblastic or primary brain
• Candidiasis of bronchi, trachea, lungs or the esophagus
• Cervical cancer (invasive)
• Coccidioidomycosis, disseminated or extrapulmonary
• Cryptococcosis, extrapulmonary
• Cryptosporidiosis, chronic intestinal for longer than 1 month
• CMV disease (other than liver, spleen or lymph nodes)
• Encephalopathy (HIV-related)
• HSV: chronic ulcer(s) for more than 1 month, bronchitis, pneumonitis or esophagitis
• Histoplasmosis, disseminated or extrapulmonary
• Isosporiasis, chronic intestinal (for more than 1 month)
• Kaposi's sarcoma (HHV-8)
• Mycobacterium avium complex (MAC, the most common) or other species: disseminated or
extrapulmonary
• Pneumonia: recurrent or due to Pneumocystis carinii
• Progressive multifocal leukoencephalopathy (PML) – by JK virus
• Salmonella septicemia (recurrent)
• Toxoplasmosis of the brain
• Tuberculosis
• Wasting syndrome due to HIV
Stage Definition
CD4 Cell Categories Clinical Categories
A B C
(Asymptomatic) (Symptomatic) (presence of AIDS-
defining illness)
>500/μL (≥29%) A1 B1 C1
200-499/μL (14-29%) A2 B2 C2
<200/μL (<14%) A3 B3 C3

In grey – presence of AIDS

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Diagnosis
Methods
ELISA
Uses antibodies against the viral proteins p24, gp120, gp41 and gp160
• Easy to perform, highly sensitive and specific
• Used in: screening, diagnosis, monitoring, research
Western Blot
Uses a lysate prepared from an HIV virion, requires the presence of the proteins: p17, p24, p31, gp41,
p51, p55, p66, gp120 and gp160. The sample is separated into strips, each is represented by a different
protein.
• Some proteins appear in different stages of the infection:
o Earliest – p24 and p55 (then decrease or disappear)
o Later – gp31, gp41, gp120 and gp160 (then present always)
• Used in: confirmation of ELISA – positive test (according the CDC) is when there are two bands of
either p24, gp41, gp120 or gp160.
PCR
Uses a blood sample and checks for viral RNA (mostly) or reversely-transcribed DNA
• The most sensitive test but it is very costly
• Used in: checking the viral load, monitoring the efficacy of ART
• Genetic material is detectable as soon as 1 week past the exposure
CD4 Count
Reflects the immune function of the patient. Normal values range between 500-1300 cells/μL
• Used in: staging of disease progression, determining the risk of opportunistic infection
• If the count is below 200 cells/μL – use prophylaxis against toxoplasma, pneumocystis carinii

Timing
Routine screening for:
• Patients aged 13-64
• Patients initiating treatment against tuberculosis
• Patients who seek cure for STDs
• Pregnant patients
Repeat screening for:
• Patients at high risk – annual testing
• Patients before starting new sexual relationship
• When clinically indicated
• After occupational exposure
 83

Treatment
Antiretroviral therapy (ART)23
The “cocktail, a combination of three drugs. Greatly reduced the overall mortality from AIDS and made
it a “chronic disease” (just like diabetes, hypertension, asthma etc.). The goals of the therapy:
• To prevent disease progression – keeping the viral load as low as possible
• To prevent transmission of infections – related to the viral load as well
• To improve the quality of life – the body can still have a functional immune system
• To reduce hospitalizations and deaths from AIDS
Antiretrovirals are classified into classes, according to the way the drug Drug name Abbr.
attacks the virus. When choosing the optimal regimen for your patient, follow Lamivudine 3TC
the next instructions: Abacavir ABC
• The regimen should be selected by an experienced healthcare worker Dolutegravir DTG
• Always use three or more different drugs – to avoid resistance Elvitegravir EVG
• Check for drug-drug interactions - especially with the drugs against Raltegravir RAL
tuberculosis – both are metabolized by CYTP450 in the liver Tenofovir TDF

Patients must take regularly the drugs to maintain constant their level in the blood. Any deviation from
the regimen can result in lower efficacy of the drugs. In addition to ART – use means of prevention
against opportunistic infections by drugs/vaccination/avoiding exposure to pathogens.
Immune Reconstitution Syndrome - ART should not be administered during an opportunistic infection
since it may exacerbate the symptoms or be followed by symptoms of new opportunistic infection.
This may occur in the following infections:
• Mycobacterial infections – in TB there are paradoxical reactions (↑CD4 count, ↓HIV RNA)
• Fungi: Pneumocystis jiroveci, Cryptococcus
• Parasitic infections: toxoplasmosis
• Viruses: HBV, HCV, CMV, VZV, JC virus (PML)
Resistance
There are two ways in which resistance can occur:
• HIV mutations – due to the high error rate of the reverse transcriptase
• Skipping doses – increases the susceptibility of mutations formation
The resistance can be tested in two ways:
• Genotype – amplification of the genome and its sequencing to look for mutations associated with
resistance.
o Recommended in the beginning of therapy (to choose the most effective regimen)
o The test is sensitive if the viral load is >1000copies/mL
• Phenotype – synthesis of virions in vitro from a template, to check the activity of the drug over
them.
o Recommended for patients who have shown to have virions with multidrug resistance
o The process takes 2-3 weeks and it is very expensive

23 AKA antiretrovirals (ARV), highly active antiretroviral therapy (HAART)

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Opportunistic Infections
Mycobacteria
M. tuberculosis (MTB)
Epidemiology:
• High risk in IVDU, people who work in close quarters, endemic countries
• Primary TB can be also in non-infected people, but it is still very prevalent among HIV carriers (any
CD4 count)
• Reactivation of TB is more likely in HIV-infected people – also in extrapulmonary locations
• Patients with TB have high viral loads and faster progression of HIV
Clinical manifestations: due to advanced immunosuppression TB may be a systemic disease – fever,
rapid progression and dissemination (→ sepsis).
Treatment: see under the chapter “tuberculosis”
M. avium Complex (MAC) Disease
Epidemiology:
• Incidence of 20-40% among AIDS patients who are using ineffective ART or prophylaxis.
• Common in patients with CD4 count of <200cells/μL
• Increased risk in high viral load (>105 copies), prior opportunistic infections or prior colonization
of MAC
Clinical manifestations:
• Absence of ART: disseminated organ failure (i.e. sepsis) – fever, night sweats, weight loss, fatigue,
diarrhea and abdominal pain.
• Presence of ART:
o Immune reconstitution syndrome – see above
o Localized manifestations – lymphadenitis (cervical or mesenteric), pneumonia, pericarditis,
osteomyelitis, SST abscesses, genital ulcers or CNS infection
Diagnosis: it is important to isolate, identify and differentiate the species from “normal” TB out of
body fluid samples (of normally sterile tissues)
• Physical exam/imaging: hepatosplenomegaly or lymphadenopathy (usually paratracheal,
retroperitoneal or paraaortic)
• Laboratory tests: anemia, increased ALP
Treatment:
• Initial treatment – for ≥12 months, by at least two active drugs
o Preferred: clarithromycin 500mg PO (once a day) + ethambutol 15ng/Kg of body weight PO
(QD)
o Alternative: azithromycin 500-600mg PO (QD) + ethambutol
o Consider the addition of rifabutin 300mg PO (QD), especially in cell count <50 (alternatives –
fluoroquinolones, amikacin)
• Chronic maintenance therapy – by ART (to minimize the risk of immune reconstitution syndrome
start therapy 1-2 weeks after the therapy against MAC. In case of moderate-severe symptoms –
consider NSAIDs or short-term glucocorticoids).
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Fungi
Pneumocystis jiroveci Pneumonia (PCP)
Epidemiology:
• Ubiquitous in the environment – initial infection usually occurs in early childhood, then the
infection can be reactivated in immunocompromised patients
• For immunosuppressed patients it can spread airborne
• There is a decline in incidence (in developed countries) due to available prophylaxis and ART
• Most cases are common in patient who are unaware of their condition (and not in care) or in
advanced AIDS (CD4 count <100cells/μL)
• Increased risk in recurrent bacterial pneumonia, unintentional weight loss and high viral load
Clinical manifestations: subacute onset, worsens over days-weeks
• Progressive exertional dyspnea, fever, non-productive cough, chest discomfort
• Extrapulmonary disease is rare, but can occur in every organ (associated with aerosolized
pentamidine prophylaxis)
Diagnosis: the organism cannot be cultured
• Physical exam: lung auscultation can be normal or with diffuse dry rales
• Imaging: chest X-ray (non-specific), bronchoscopy (+ BAL)
• Laboratory tests:
o Hypoxemia (pO2 <70mmHg or gradient >35mmHg)
o LDH >500mg/dL (common finding)
o Histology – after transbronchial / open lung biopsy (use silver stain)
Treatment: regimen lasts 21 days
• Preferred: TMP-SMX
o Trimethoprim 15-20mg/Kg/day + sulfamethoxazole 75-100mg/Kg/day (IV, divided to doses
every 8 hours)
o TMP-SMX DS 2 tablets PO (twice a day)
• Alternative (in mild-moderate PCP): Atovaquone 750mg PO (BID)
• Adjunctive: corticosteroids (for moderate-severe disease) e.g. prednisone
• Secondary prophylaxis (chronic maintenance therapy) for life, preferably by TMP-SMX
Mucocutaneous Candidiasis
Clinical manifestations:
• Oropharyngeal – thrush
o Pseudomembranous: painless, creamy white and scrapable plaques on the mucosal layer
o Erythematous: red patches on the tongue or upper palate
o Angular cheilitis/cheilosis – infection of both corners of the mouth
• Esophageal –
o Retrosternal burning sensation or discomfort
o Pain while swallowing (odynophagia)
o Fever
• Vulvovaginal –
o Creamy discharge
o Mucosal burning and itching
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Diagnosis:
• Oropharyngeal candidiasis: usually clinical, otherwise by KOH preparation and culture.
• Esophageal candidiasis: clinical with empirical therapy. Imaging – endoscopy with histology and
culture
• Vulvovaginal: clinical diagnosis, KOH preparation
Treatment: (preferred treatment for oropharyngeal candidiasis)
• Fluconazole 100mg PO (QD)
o If contraindicated – itraconazole / Amphotericin B suspension or IV
• Itraconazole 200mg oral solution (QD)
• Clotrimazole troches 10mg PO (5 times per day)
• Nystatin suspension 4-6mL PO (QD) or 1-2 flavored pills (4-5 times per day)
Cryptococcosis
Epidemiology:
• Incidence is greatly reduced due to usage of ART
• Most cases are among patients with CD4 count <50
Clinical manifestations: meningitis/meningoencephalitis
• Acute: nuchal rigidity, seizures, focal neurologic signs (common in developing countries)
• Subacute: most common presentation
o Fever, headache, photophobia
o Malaise, lethargy, altered mental status, rarely – personality changes
• Disseminated disease:
o Pulmonary involvement – cough, dyspnea, lung consolidation (X-ray)
o Skin lesions – papules, nodules, ulcers, infiltrated plaques
Diagnosis:
• Blood tests:
o Cryptococcal antigen (CrAg)
o Blood culture
• CSF test: for CrAg
o Proteins – mildly elevated
o Glucose – normal or slightly low
o Lymphocytes (a few)
o Increased pressure
• BAL: may be negative for CrAg
Treatment:
• Amphotericin B + flucytosine / liposomal amphotericin B + flucytosine
• Lung consolidation: fluconazole
• Chronic maintenance: fluconazole (lower dose)
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Parasites
Toxoplasma gondii Encephalitis
Epidemiology:
• In AIDS patients – a disease is usually due to reactivation of latent tissue cysts
• Seroprevalence ranges between 15-75% in developed countries (even higher in developing
countries)
• Transmission is by ingestion of undercooked meat or cysts from cat feces in soil, water or food.
There is no person-to-person transmission.
Clinical manifestations:
• Focal encephalitis – headache, confusion, motor weakness and fever. Can progress to seizures,
altered mental status and coma.
• Dissemination – retinochoroiditis, pneumonia or other organs
Diagnosis: definitive diagnosis by physical examination (clinical), imaging and biopsy
• Serology – since most cases are due to activation of latent cysts, IgG will be usually positive (IgM
will be seropositive in case of recent primary infection). For more information – see Toxoplasmosis
under “TORCH infections”. (PCR of a CSF sample is not a sensitive test)
• Imaging –
o CT/MRI – multiple lesions seen clearly in the brain, often surrounded by edema
o PET/SPECT – can distinguish the lesions from lymphomas
• Biopsy – detection of the organism. Make empiric diagnosis and start therapy, if the latter fails –
perform the biopsy.
Differential diagnosis: CNS lymphoma, TB, fungal infection, Chagas disease, cerebral abscess, PML
Treatment:
• Preferred: pyrimethamine (first large dose and then small doses QD) + sulfadiazine + leucovorin
o For more than 6 weeks (the more extensive is the disease – the longer is the regimen)
• Alternative:
o Pyrimethamine (as in above) + clindamycin + leucovorin
o Pyrimethamine + azithromycin + leucovorin
o Pyrimethamine + trimethoprim-sulfamethoxazole
o Trimethoprim-sulfamethoxazole
o Atovaquone +/- sulfadiazine
• Additional drugs:
o Corticosteroids – in case of mass effect (monitor closely and stop the treatment ASAP)
o Anticonvulsants (anti-epileptics) – in case of seizures (continue at least throughout the acute
disease)
• Life-long chronic maintenance therapy (secondary prophylaxis): consider stopping the regimen in
patients with sustained increase of CD4 count (>200) for 6 months or more (with proof by imaging
that the therapy succeeds).
o Preferred: trimethoprim-sulfamethoxazole
o Alternative: dapsone, dapsone + pyrimethamine + leucovorin +/- aerosolized pentamidine,
atovaquone
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Cryptosporidiosis
Epidemiology:
• Transmitted via the fecal-oral route (ingestion of oocysts from contaminated water) or person-to-
person transmission (oral-anal contact, from changing diapers of infants).
• Highest risk in patients with CD4 count of <100
• Low incidence in areas with access to effective ART
Clinical manifestations:
• Acute / subacute onset of watery diarrhea, nausea, vomiting or abdominal cramping. Fever occurs
in one third of the patients
• Complications: dehydration, malabsorption and malnutrition. Involvement of the biliary tree →
cholangitis or pancreatitis
Diagnosis:
• Microscopy of stool sample – search for oocysts (consider repeating the test on other samples)
under modified acid-fast or other stains.
• DFA or ELISA
• Biopsy of the small intestines
Treatment: ART with immune restoration results in complete remission
• Consider nitazoxanide or paromomycin (there is no consistent and effective treatment)
• Symptoms relief and supportive care: antidiarrheals, hydration, nutritional support, infusion of
electrolytes

Viruses
Cytomegalovirus (hCMV) Disease
Epidemiology:
• Usually caused by reactivation of a latent infection (in patients with advanced
immunosuppression – CD4 count < 50)
• Risk factors: patients without ART, previous opportunistic infections and high viral load (more
than 105 copies)
Clinical manifestations:
• Retinitis (most common)
o Usually unilateral (if remains untreated it can progress to the second eye)
o Hemorrhage and retinal exudates
o Visual field defects e.g. scotoma, eye floaters
• Colitis, cholangiopathy
o Mucosal hemorrhage which can deteriorate to perforation
o Fever, malaise, weight loss, anorexia, abdominal pain, severe diarrhea
• Esophagitis
o Fever, painful swallowing (odynophagia), mid-epigastric or retrosternal discomfort
• Pneumonia
o Dyspnea, non-productive cough, hypoxemia
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• Neurologic disease
o Dementia – lethargy, confusion, fever
o Ventriculo-encephalitis – cranial nerves palsy, nystagmus, rapid and aggressive progression
up to death
o Ascending polyradiculomyelopathy (similar to Guillian-Barré syndrome) – urinary retention,
progressive leg weakness → loss of nervous control of the bowel and bladder
Diagnosis:
• Blood culture
• PCR (viremia does not necessarily indicate an end-organ disease)
• Antigen assays
• Serology – see “TORCH infections”
• Fundoscopy (for retinitis)
• Endoscopy (for colitis/esophagitis) and sampling for biopsy
• BAL (for pneumonia)
• CSF investigation (in neurologic disease)
Treatment: note that late relapses occur often due to drug resistance
• Ganciclovir / valganciclovir – nucleotide analogs which inhibit viral DNA synthesis
• Foscarnet
• Cidofovir
• Fomivirsen
# ART – should be given to patients with CMV retinitis, GI disease or pneumonia (only after response
to the specific therapy, to avoid immune reconstitution syndrome).

Herpes Simplex Virus (HSV) Disease

Epidemiology:
• In general, HSV-1 is more prevalent than HSV-2
• 95% of HIV patients are seropositive for either HSV-1 or HSV-2
Clinical manifestations:
• HSV-1 (mostly): herpes labialis – local sensory syndrome (pain, itching) and then vesicles which
progress to ulcers. Lasts 7-10 days if remains untreated and can always reoccur.
• HSV-2 (mostly): herpes genitalis – begins with manifestations as in herpes labialis. Then –
o Mucosal disease – vaginal or urethral discharge, often with dysuria
o Perineal disease – inguinal lymphadenopathy
o In advanced immunosuppression (CD4 <100) there can be non-healing ulcers on the perineum
or the buttocks.
• HSV keratitis, HSV encephalitis, HSV retinitis, neonatal HSV, herpetic whitlow (lesion on the tip of
the thumb)
Diagnosis: clinical (according to the features) and laboratory analysis of a swab from a fresh lesion-
• Tzank smear
• Viral culture
• HSV antigen detection
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Treatment:
• Famciclovir – for orolabial/genital
• Acyclovir – for orolabial/genital/mucocutaneous/encephalitis
• Valacyclovir – for orolabial/genital
• Trifluridine -for keratitis
# In case of acyclovir resistance – Foscarnet, Cidofovir

Human Herpes Virus 8 (HHV8) Disease

Epidemiology:
• Higher prevalence among MSM (regardless of HIV presence)
• Common in some Mediterranean countries and parts of sub-Saharan Africa
• Usually seen in advanced immunosuppression
Clinical manifestations:
• Kaposi sarcoma (KS)
• Castleman disease (rare)
• Primary effusion lymphoma (rare)
Diagnosis: biopsy (from lesions sample)
Treatment: consult with a specialist
• Ganciclovir, foscarnet, cidofovir – non-specific against the virus, but were found to suppress KS
• ART for qualified patients – can also contribute to healing of the lesions

Progressive Multifocal Leukoencephalopathy (PML, JC Virus Disease)

Epidemiology: most people are infected early in life (70% of seropositivity in adults)
Clinical manifestations:
• Insidious onset, rapid progression over weeks/months
• Cognitive dysfunction, dementia, seizures, ataxia, aphasia, cranial nerve deficits,
hemiparesis/quadriparesis, coma
Diagnosis: combination of the clinical features and radiologic findings-
• CT scan – single/multiple hypodense non-enhancing cerebral white matter lesions (can be in the
cerebellum or the brain stem)
• MRI – more sensitive in detecting the lesions
• CSF evaluation – detection of JC virus by PCR (however, there can be false-negatives)
• Brain biopsy – definitive diagnosis (not mandatory)
Treatment: there is no specific therapy
• ART with increase in CD4 count can improve the neurologic function
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Human Papilloma Virus (HPV) Disease

Epidemiology:
• Transmitted by sexual contact
• Increased incidence of the infection among HIV patients, as well as the risk for genital warts,
cervical intraepithelial neoplasia (CIN) and anal intraepithelial neoplasia (AIN).
Clinical manifestations: cauliflower-like lesions (aka condyloma acuminate), flat keratotic
plaques/papules at the site of contact.
• Size: 2mm-2cm
• May occur in clusters at multiple sites
Diagnosis: usually clinical
• Biopsy – to establish the diagnosis or determine the presence of high-grade dysplasia/neoplasia
• Pap smear – also for screening, twice in the first year after HIV diagnosis (then annually)
• Colonoscopy
 92

Infections in Pregnancy (TORCH)

Infectious diseases comprise 7-10% of the causes of fetal abnormalities where most of them, at least in
some degree, are preventable. The infectious agents of these disorders are (abbreviated TORCH):

Toxoplasma gondii (Toxoplasmosis) (T)

• Viruses: • Bacteria: • Parasites:
Others o Parvovirus B19 (T) o T. Pallidum (Syphilis) (T) o T. cruzi (Chagas) (T)
o HBV (T,I), HBC, HEV o Listeria monocytogenes (T,I) o Plasmodium spp.
o Flavivirus: West Nile, o Group B Strep. (I) (malaria) (T)
Dengue, Zika o Salmonella typhi
o Influenza virus (H5N1 o Borrelia burgdorferi
aviary, H1N1 swine) o Chlamydia trachomatis (I)
o Ebola virus o Campylobacter fetus (T)
o HIV (T,I) o Mycobacterium tuberculosis (T)
o Enterovirus (I)
Rubella (T)
hCMV (T)
Herpes viruses (T,I) • HSV1, HSV2, VZV (only during labor)

I – Intrapartum infection, T – transplacental infection

The clinical problems clinicians face in cases of maternal infections:

1. Asymptomatic infection in the mother - prevalent in many infections
2. Difficulty in dating the infection (define when it was acquired)
3. Inadequate laboratory diagnosis
4. Inadequate prenatal diagnosis (US/amniocentesis)
5. Infections with no therapy
6. Inadequate information and counselling

Course of Infection
There are three courses of infections during pregnancy:
• No infection in the fetus and after birth (newborn)
• Congenital infections - infection in utero through the bloodstream, spread across the placenta.
• Perinatal infections – infection during labor by encountering the flora of the mother
The consequences of the last two can be:
• Embryonic death - resorption, abortion and still birth.
o Common during the first two weeks of embryonic development
• Intrauterine growth retardation or malformations
o In acute primary infection the defects are more severe.
• Premature infant
o Common during the third trimester (cytokines and prostaglandins release)
• Early onset infection
• Sequalae/complications
• Asymptomatic infection
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Pre-conceptional
infection

o If possible – delay
the pregnancy
o Low risk of
congenital
infection
o No prenatal
diagnosis

Weeks 1 and 2 Weeks 3-8 Week 9 until birth

• Formation of extra-embryonic • Formation of major structures • Several organs are being
structures (most critical period) developed – brain, spinal cord
o Any infectious agent will o High risk of congenital and the limbs
result in spontaneous infection - most infectious o These structures can be
abortion or embryonic death. agents can lead to major affected, and a functional
structural defects (e.g. heart disturbance can occur (e.g.
defects) mental deficiency)
Peri-conceptional / first trimester infection (1 month Second / third trimester infection:
before or after last menstruation):
• Can be asymptomatic
• Prenatal diagnosis is highly recommended (18th • Prenatal diagnosis is recommended less as the
week) pregnancy progresses (in the 3rd trimester not
• Monthly ultrasound recommended at all) – due to complications of
• Clinical and laboratory check-up of the newborn the examination (invasive procedures).
• Monthly ultrasound
• Newborn check up

Throughout the gestation period there is a shift in the immunological tolerance of the mother: from cell
mediated (Th1) to humoral (Th2) immunity. Therefore, before the pregnancy check the immune status of
the mother.
Suspected infection in pregnancy: Screening principles:
• Exclusion or diagnosis of acute infection (can result in − Is the infection frequent?
severe defects) − Is it serious?
• Infection dating − Is the diagnosis valid?
• Clinical serological monitoring of the infection − Is there a treatment?
• Possible prenatal diagnosis − Is the cost/benefits balance correct?
• Newborn follow up − Is the risk acceptable?
The most dangerous period of acquiring an infection is in the first trimester – where both the probability
of congenital infection and the severity of clinical signs are quite high.
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Prevention
1. Primary – prevention of maternal infections (before and during pregnancy)
• Vaccination (Rubella, VZV, HBV)
• Serological screening (Rubella, Syphilis, Toxoplasma)
• Information – increase the awareness
• Hygienic prophylactic means – education and avoidance eating dangerous food (Toxo, CMV)
o Cook meat to well-done (so the interior will have a temperature of 67˚C)
o Use deep frozen meat (directly from stores)
o Wash hands, utensils, vegetables and fruits (also peeling them) before preparing meals
o Avoid contact with cat feces
o Drink only potable water
2. Secondary – prevention of vertical transmission
• Early diagnosis in the mother
• Therapy of the mother (Toxoplasma, Syphilis, HIV)
• Therapy of the fetus (Toxoplasma, CMV)
• Prenatal diagnosis (Toxoplasma, PVB19)
3. Tertiary – reduction of sequalae in newborns
• Early diagnosis of congenital infections in newborns – clinically, serologically and by PCR
• Serological therapy (Toxoplasmosis, CMV, Syphilis)
• Clinical laboratory follow-up

Agents
Toxoplasma Gondii
Generalities
Features:
• Protozoa; obligate intracellular
• Capable of infecting all warm-blooded animals
(zoonotic) – highly transmissible
• 25% of human population is chronically infected
• Pseudocysts – in the CNS/skeletal muscles
(most common), also in the heart
Transmission: fecal-oral route
• Mussels can have cysts from polluted water
• Cysts can remain in soil and be infective for
years – depends on the environmental
conditions (temperature and humidity)
Epidemiology:
• The most common parasite in developed countries
• Distributed world-widely (yet seroprevalence has decreased in recent years)
• Low prevalence in Scandinavia and the UK – probably due to the cold climate
 95

Clinical manifestations:
• Acquired toxoplasmosis – (in adult, immunocompetent) subclinical, sometimes manifests as
chorioretinitis
• Congenital toxoplasmosis – ranges from subclinical infection to fetal loss. The classic triad of
severe infection (rare):
o Hydrocephalus
o Intracerebral calcifications
o Retinochoroiditis
• Toxoplasmosis in immunocompromised patients – a life-threatening condition (reactivation of a
latent infection can lead to death)
Diagnosis
Screening for toxoplasmosis is mandatory in only few
European countries, some only perform postnatal
screening.
− Seroconversion: when a specific antibody becomes
detectable in the serum.
− Avidity: the affinity of a specific antibody to its
antigen. In the process of affinity maturation, the
avidity increases as the infection progresses.
Therefore, high avidity marks that the infection
occurred long time ago and low-avidity antibodies
are found after a primary antigenic stimulation.
The algorithm for prenatal screening:

Negative test Serological screening Positive test

IgG-, IgM-
IgG+, IgM-
In the first trimester
IgG-, IgM+ IgG+, IgM+
or before pregnancy

No seroconversion = no No seroconversion = no Seroconversion Previous immunity

immunity immunity Avidity test for IgG only • Confirmed by a second
• Hygienic prophylaxis (only if there is high level) example a month later
• Monthly follow-up up to • Do not repeat the test
one month after delivery Perform a second test in other laboratories
• Counselling for future • Keep the report for
pregnancies Avidity is low to intermediate further pregnancies
• Acute infection Avidity is High
• Begin therapy by Spiramycin (Italian
protocol)
• It is better to wait 6 weeks since the
infection to preform amniocentesis
• If the woman is before pregnancy –
postpone it for at least six months

Do not stop the follow-up before a negative serology, since in many cases the baby may seem healthy
(subclinical infection). Usually after one year the serology is completely negative.
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Problems in the interpretation of specific IgM:

• Specific IgMs may persist unchanged in serum for months following the natural infection.
• False positives may occur due to:
o Current viral infections (e.g. PVB19, EBV, CMV)
o Autoimmune diseases
o Incorrect laboratory methods
• IgM test cannot distinguish neither between primary infection and reinfection, nor the phase of
the infection (early/late)
Algorithm of serological diagnosis of congenital Toxoplasmosis:

Negative test At birth: Positive test

Amniotic fluid PCR (or not performed) sampling of both the mother and the Amniotic fluid PCR
IgM, IgA, IgG-IgM WB fetus sera, and the amniotic fluid IgM / IgA / IgG-IgM WB

Perform three monthly follow-ups Increased / not-decreased titers Infected newborn

IgM, IgA, IgG, IgG/IgM WB Start therapy
Decreased titers Clinical and serological follow-ups

Sero-negativity at the age

of 12 months

No infection

Methods of diagnosis: assess the cost-to-benefit ratio to decide which test to use.
• ELISA
• ISAGA – more sensitive, can show IgM for longer period
• LDBio Toxo II IgG – immunoblot, ready to use, rapid test
• PCR – highly sensitive, but does not assist in dating the infection
• New cellular immunity test based on IFNγ
• Saliva test (very expensive)
Treatment
In case of acute maternal infection:
1. Spiramycin (before 20 weeks) + US controls
2. Prenatal diagnosis (best at 18 weeks) – if amniocentesis positive, see “fetal contamination”.
3. At delivery: blood samples of both the mother and the newborn, immunological tests and clinical
examination
Recommended prevention of mother-to-fetus transmission:
1. Spiramycin 3g/day – give as soon as possible, might not be effective in late phase of maternal
infection
When fetal contamination is highly suspected or proven:
1. Pyrimethamine 25g/day + Sulfadiazine 50-100mg + leucovorin
2. Fansidar 2tab/week
3. Fansidar 2tab/10 days + leucovorin
 97

Post-natal treatment (of infected newborn):

1. Pyrimethamine + Sulfadiazine/Sulfadoxine
(Fandisar – less common) + Folinic acid
Treatment monitoring
2. Trimethoprim + Sulfamethoxazole (Bactrim)
3. Treatment 12 months after birth: • CBC every 15 days (at first), then every few
• Pyrimethamine 1mg/Kg once a day months
• Sulfadiazine 50mg/Kg/day (divided to - If neutrophils count is <750/mm3 →
two times) stop treatment
• Folinic acid 50mg every 7 days • Urinalysis – monthly test for proteinuria
4. Treatment 14 months after birth: (AE of sulfadiazine)
• Pyrimethamine 1.25mg/Kg every 10 days
• Sulfadiazine 25mg/Kg/day every 10 days
• Folinic acid 50mg every 7 days

Parvovirus B19
Generalities
Features:
• The only erythrovirus pathogenic to humans
• Very stable virions – they cannot be destroyed by chemical agents
• Parvo = small genome, ssDNA, not enveloped
• Has three genotypes (1-3)
• Has three proteins: two structural (VP, very similar in structure) and one non-structural (NS)
o VP1 – contains an additional segment (“unique region”) which can exist outside of the virion,
and confers the resistance against immune response
o VP2 – found on 95% of the capsid, it is the protein at which the antibody response is directed.
This protein can bind the P antigen on many types of cells (yielding the main pathogenicity of
the virus).
o NS1 – plays a role in replication, packaging, gene transcription and apoptosis (cytotoxicity)
Epidemiology:
• According to the genotype-
o 1: widely distributed
o 2: less frequent, incidentally found in heart biopsies
o 3: found in Western Africa, France and the Americas
• Higher prevalence around late winter to early spring (as well as higher incidence of seroconversion
= pay special attention during this time)
• Seroprevalence increases with age (in elderly – 85%)
• Susceptible pregnant women: 34-65%
• Highest infection rate is among: school teachers, daycare workers or women with nursery/school-
age children.
Transmission: due to the high stability of the virions, they can be transmitted by all blood products or
by aerosol transmission.
 98

Clinical Manifestations
Viral-load:
• Peak of viremia and the maximum risk of vertical transmission is at the 7 th day following the viral
entrance.
• Asymptomatic infection is very common (50% of the cases)
• In case of symptoms appear –10-14 days after viral entry
• The viral load is the only factor correlated with the vertical transmission rate (not the severity of
symptoms)
Pathogenesis: VP2 binds the P antigen found on the following cells (and few others), inducing their
destruction. The latter is expressed as the following manifestations:

Megakaryocytes If transmitted to the fetus,

Thrombocytopenia Erythroid progenitor cells all these processes lead to
Anemia (+decreased Cardiac myocytes the development of fetal
reticulocytes) hydrops.
• Increase of Heart failure Endothelium
extramedullary
erythropoiesis and Damage to vessels
hypoalbuminemia
• Hyperkinetic
circulation

Symptoms and signs:

• Erythema infectiosum (fifth disease24) – rash all over the body, due to the precipitation of immune
complexes (antigen-antibodies).
• Fever, myalgia, headache
• Arthropathy (in females)
• Thrombocytopenia
• Meningoencephalitis
• Hepatitis
• Myocarditis, vasculitis
• Aplastic crises (in immunocompromised patients)
Fetal risks:
• Risk of vertical transmission: 33-51%
• Risk of fetal death: highest before 11-12 weeks of gestation, since at that time RBC start to be
produced by the liver (beforehand – by cytotrophoblasts, which contain the P antigen and found
on the placenta → placental destruction leads to fetal death)
o 1st trimester: 19% | 2nd trimester: 15% | 3rd trimester: 6%
• Risk of complication in infected fetuses: 10%
o Hydrops: 7.1% in <20 weeks of gestation, 1% after 32 weeks
o Fetal anemia, hypoalbuminemia
o Hepatitis
o Myocarditis (rare)
o Placentitis

24 The fifth disease in the list of diseases which cause skin rash in infants.
 99

Diagnosis
Maternal serum: presence of IgM
(serology) and/or vDNA (PCR). Acute and remote infection with
clearance of the virus from the blood
• DNAemia – acute infection >105,
recent infection >104 and less
indicates a recent/distant infection
Life-long: Anti-VP1 IgG
• IgM/IgG – by EIA/IFA Viremia
• IgG avidity – by EIA/blot Anti-VP2 IgG
• NS1 IgG – by blot Anti-VP2 IgM

# Serology by itself cannot date the

infection, always check the viremia
to confirm active infection:
− IgM can persist in serum, despite
the presence of IgG Persistent infection, also in pregnancy

− IgM can be negative, but DNA is

present in blood (false negative)
− There can be false positives, if Anti-VP2 IgM Anti-VP1 IgG
Viremia
the woman synthesizes anti- Anti-VP2 IgG
biotin antibodies. Anti-NS1 IgG
# Parvovirus B19 cannot be cultured
by conventional methods, only by
synthesis of recombinant antigens
(VP and NS) by other cells.
Ultrasound: fetal findings
• Liquid accumulation – edema, pleural effusion, pericardial effusion, ascites, hydrops and placental
edema.
• Cardiomegaly
• Hepatic and intestinal calcification
Middle cerebral artery doppler: good diagnostic tool because it shows the fetal blood velocity which
reflects on the anemic status.
Invasive methods: performed only when there are signs of fetal infection achieved by non-invasive
methods. Samples are taken according to the anemic status:
• Amniotic fluid – abnormalities suggest fetal infection without anemia.
• Fetal blood and amniotic fluid – in case of fetal anemia
In theory, every prenatal diagnosis should be confirmed after birth (can be expensive). Note that IgG
in the first year of life can be maternal (due to breastfeeding)
Treatment
Intrauterine transfusion (IUT): indicated in fetuses with hydrops (the treatment reduces significantly
the probability of death).
Prophylaxis: hand-washing and general maintenance hygiene (there is neither specific antiviral drug
nor a vaccine against B19)
 100

Syphilis (Treponema pallidum)

Generalities
Features:
• A gram-negative (theoretically) bacterium from the spirochetes class
• The most common human infection is by the subspecies T. pallidum.
• Other species include T. pallidum pertenue (Yaws), endemicum (Bejel) and carateum (Pinta):
cause endemic infections (transmission by contact in early childhood)
• Cannot be cultured (only on rabbits)
• Can be seen only by dark-field microscopy
Epidemiology:
• Increase in number of infected individuals, especially among MSM
• Increase in number of reported cases throughout Europe
• Highest incidence in people aged 25-34 (sexually-active)
• In developing countries – 3-15% of women in child-bearing age have syphilis
Transmission:
• Sexual transmission – by direct contact with an ulcer (chancre). The transmission is more likely if
there is already an HCV and/or HIV infection.
• Vertical (transplacental) transmission – mainly during the second half of pregnancy, but another
common transmission is perinatal (in contact with the birth canal). It can occur at any stage of the
infection if it is not treated properly, but the risk increases when the infection is less than one
year before gestation (the maximal risk is at 6 weeks of gestation).
o Primary/early secondary syphilis – 60-80% chances of transmission
o Late syphilis – 8% chances of transmission.
• Direct contact
• Blood transfusion (rare)
Clinical Manifestations
Congenital syphilis:
• In 30% of the cases – stillbirth
• In other 30% - the newborn will have congenital syphilis (mortality rate is up to 50%):
o Liver – inflammation in the interstitial stroma and perivascular network
o Lung – pneumonia alba (white – due to fibrosis and presence of inflammatory cells)
o GI tract – mucosal and submucosal inflammation and mononuclear infiltration
o Pancreas – perivascular inflammatory infiltrate
o Kidneys – deposition of immune complexes
o Bones – osteochondritis, periostitis, osteomyelitis
o CNS – thickening of the basilar meninges, neuronal injury (depends on the extent of vessels
involvement).
Disease in adults: (untreated patients)
• Primary – ulceration, can last 2-6 weeks, resolves spontaneously
• Secondary – dissemination with skin rash, multi-organ involvement (6 weeks – 6 months)
• Latency – can last many years, the bacterium is detectable but without an overt disease
 101

• Tertiary – neurosyphilis: in 40% of the cases – hypercellularity, hyperproteinorrachia25. Other

manifestations are: cardiovascular syphilis, late benign syphilis.
Diagnosis
Treponema pallidum is not-detectable in all stages of disease and cannot be cultured.
Direct diagnosis: must be performed before the appearance of antibodies, take sample from the
ulcer/lesion (the location which has the best samples for diagnosis). Note that these methods are not
widely available.
• Dark field microscopy – do not test if treatment has already started. The flaw of this exam is its
low sensitivity (74-86% due to similar structure of other Treponemas), but the specificity is quite
high (depends on the lab personnel).
• Antigen detection (DFA-TP) – by fluorescent microscopy. Again, the sensitivity is not so high, but
the specificity is sufficient.
• Molecular biology – take samples also from the blood/placenta/amniotic fluid or umbilical cord,
useful in diagnosis of congenital syphilis. It has both high sensitivity and specificity.
Indirect: can be used both for screening and diagnosis, take samples of serum/whole blood/CSF26
• CSF in neurosyphilis – WBC count 10-400/mm3, mostly lymphocytes, ↑ protein (45-200mg/dL)
• Serology – is used to:
o Confirm the direct diagnosis of syphilis (essential mean)
o Diagnosis of latent syphilis
o Treatment follow-up
# There is no serological test that distinguishes between other treponemal infections – keep in
mind when performing serological studies in endemic areas.
Treponemal tests (TT): used as a confirmation of NTTs because they cannot distinguish between
active and past infections, and cannot show response to therapy
o Fluorescence (FTA-Abs) – detection by immunofluorescence, can be positive even after
treatment but it is possible to differentiate IgM from IgG. In fact, this is the best test that can
find IgM.
➢ Indications: congenital syphilis (IgM), confirmation of RPR or negative TPHA
o Agglutination (TPPA/TPHA)27 – specific anti-treponemal ab, quantitative tests with high
specificity but cannot differentiate between past (treated) and active infections.
➢ Best in the detection of neurosyphilis
o ELISA (CLIA- automatically) – qualitative test (not correlated with disease activity)
➢ Detects IgG and IgM (very sensitive in early/primary infections)
o Rapid tests – by immunochromatography. Rapid, useful in developing countries, do not
require professional assistance, require only a finger prick, has high sensitivity and specificity.
However, cannot distinguish past/current infection.
o Western blot – usually the test with the maximum sensitivity
➢ Indications: confirmation of IgG test, congenital syphilis (IgM)

25 Hyperproteinorrachia – increase in CSF proteins

26 Check CSF if the patient is during latent disease / shows neurologic signs / NTT titers show no response to therapy / the patient
develops an HIV infection in addition to syphilis
27 Prozone phenomenon – in case of high ab titer a flocculate is not observed. Dilute the sample to have more balanced ag:ab

ratio and a flocculate will appear.

 102

Non-treponemal tests (NTT): to look for the activity
of the bacteria and the response to therapy.
o RPR – (rapid plasma reign) rapid diagnostic test
o VDRL – (venereal disease research laboratory
test)
o TRUST – (toluidine red unheated serum test)
Kinetics:
− Rapid and inexpensive
− Quantitative assay; reflects on activity
− Detect non-specific antibodies against
lipoidal (cardiolipin-lecithin-cholesterol)
antigen
− Non-specific for T. pallidum → false
positives

Algorithm of diagnosis (as recommended by the CDC):

Note that the reverse sequence is more accurate in the diagnosis.
Traditional approach Reverse sequence

Quantitative
RPR EIA/CLIA
(NTT) (TT)

PRP + PRP - EIA/CLIA + EIA/CLIA -

TPPA Quantitative RPR or confirmation

(TT) by another TT (TPPA)

TPPA + RPR +
TPPA - RPR -
Syphilis Syphilis
Syphilis ulnikely Syphilis ulnikely
(without dating) (without dating)

EIA/CLIA RPR TPPA

+ - + Primary / treated / latent
+ + - Primary / false-positive TPPA
+ + + Active infection / treated (RPR<32)

TPPA +
TPPA -
Syphilis
Syphilis unlikely
(without dating)
 103

Physical examination:
• Rhinitis
• Lesions on cutaneous and mucous membranes
• Condylomata lata
• Osteitis / periostitis / osteochondritis
• Ascites
• Hepatosplenomegaly
Treatment
In newborns:
• In proven/very likely congenital syphilis: 10-day drug regimen of either-
o Penicillin G – aqueous crystalline solution, IV of 10-15∙104 units/Kg/day
o Procaine penicillin G – IM administration 5∙104 units/Kg/day
• If congenital syphilis is less likely: follow-up and Benzathine penicillin G - IM administration 5∙104
units/Kg/day
• If RPR titers persist for 6-12 months: treat again (10-days) and check CSF

Rubella (RuV)
Generalities
Genome:
• +ssRNA, encapsulated, belongs to the Togaviridae family
• E1 and E2 genes – encode for glycoproteins found on the outer membrane
• Has two clades (1,2) each can be classified to several genotypes. 1a – the genotype that is targeted
by the vaccine
Epidemiology: world-wide distribution
Transmission: respiratory route or vertical transmission.
• Pre-conceptional rubella infection: no risk
• Infection in the first trimester: very high risk of transmission
• The risk is decremental is gestation proceeds
• Reinfection: (rare situation)
o Reinfection before 12 weeks of gestation: 8% risk of congenital infection
o Reinfection after 12 weeks of gestation: no risk
• Vaccination during pregnancy: no risk of transmission
Clinical Manifestations
The disease is often asymptomatic. Instead, if there are manifestations, they are non-specific e.g.:
• Fever (usually low-grade, less than 38.3˚C)
• Rash – similar pattern in many other conditions
• Adenopathy
• Arthralgia
 104

Manifestations of congenital rubella syndrome (CRS):

• Permanent:
o Cataract
o Retinopathy
o Sensorineural deafness
o Heart defects
o Microphthalmia
o Microcephaly
• Transient:
o Low birth-weight
o Hepatosplenomegaly
o Meningoencephalitis
o Thrombocytopenic purpura
o Bone lesions
Diagnosis
Since the symptoms are not specific for rubella alone, the diagnosis must be exclusively by laboratory
in two ways:
1. Direct – detection by PCR over a culture of the virus (expensive and takes time – therefore, this
method is more used in genotype studies)
2. Indirect – according
to serology i.e.
presence of rubella
antigens / anti-rubella
antibodies in the
serum.
The kinetics of
serology are depicted
in the graph.
Incubation period is
about two weeks.
IgM – not beneficial for diagnosis because there is no fixed pattern of IgM presence in the serum.
In most cases, it can persist for 2-3 months after the first contact with the virus. However, it can
be present for only one month or up to several years (IgM persistence).
IgG – presence of IgG usually marks life-long immunity after primary infection, but:
• IgG levels can be high also during:
o Vaccination
o Reinfection
o Non-specific stimulation of the immune system (cross-reactivity)
• The avidity index is not always reliable. This is because the avidity can be high a month
after the first contact (there are different patterns of avidity increase in infected and
vaccinated individuals).
 105

Prenatal Diagnosis
Indications: the guiding rule - correct interpretation of IgM assay results.
• Definite maternal infection until 18 weeks of gestation
• Reinfection during the first trimester
Timing: best to perform at 20-21 weeks of gestation, and 6-8 weeks after maternal infection (due to
the time which takes the virus to cross the placenta). Remember that suggesting amniocentesis
without a correct diagnosis is an unethical act.
Samples and techniques: take several samples (for confirmation) of:
• Amniotic fluid – check viral RNA (/viral isolation)
• Fetal blood – check IgM and RNA (/viral isolation)
Follow-up: continue the screening in the neonate in case of-
• Prenatal diagnosis
• Maternal rubella infection diagnosis
• IgM persistence
Take samples of biological fluids (mucus, sputum, urine or blood) – for PCR/virus isolation.
Neonatal Diagnosis
Indications:
• Suspected or confirmed maternal rubella during pregnancy
• Confirmation of prenatal diagnosis results
• Signs or symptoms at birth
Samples and techniques:
• Serology – IgM, IgG (Since IgG can cross the placenta, to confirm the presence of the virus in the
neonate check only after six months – to make sure they are synthesized by the neonate
exclusively)
• Virology – viral RNA/isolation (sample biological fluids – mucus, sputum, urine or blood)
Assessment of Immunity
Vaccination should be performed both in females and males (part of the MMR vaccine). When a
woman reaches a child-bearing age perform serological screening: before or after pregnancy – if the
woman is seronegative → recommend vaccination.
Prevention = Vaccination
The main mean against rubella virus is a live attenuated vaccine.
Adverse effects:
• Signs and symptoms: low-grade fever, lymphadenopathy, rash, acute transient arthritis
• Potential risks: not recommended during pregnancy (yet there is no recorded case of
transmission). Avoid pregnancy for one month after inoculation.
Efficacy:
• The vaccine provides life-long immunity in most cases (93%)
• Even though there are low titers of antibodies, people were found still resistant against infection.
 106

Human Cytomegalovirus (hCMV)

Generalities
Genome:
• dsDNA - belongs to the Herpesviridae family (aka HHV-5), genus: beta
• Received its name due to the cytopathic effect it causes – enlarges the cell (cyto-megalo)
• Has slow replication cycle
• Infection of:
o Epithelial cells, salivary glands, kidneys etc.
o In vitro – grows inside fibroblasts
• Latent in mononuclear cells (CD14+) and bone marrow cells (CD33+ and CD34+)
Transmission:
• Direct contact with body fluids – causes primary infection (there is very long virus shedding)
• Vertical transmission – it takes a long time until the virus can cross the placenta (6-8 weeks)
Note: seronegative pregnant women who already has a child is at high risk of acquiring a primary
infection (the child can get infected easily and transmit the disease to the mother, due to prolonged
viral shedding).
Epidemiology:
• Strictly host-specific (infects only humans)
• Seroprevalence of anti-hCMV antibodies depends on: age, ethnic origin, occupation, socio-
economic status.
o More prevalent in eastern countries / developing countries (>80% of the population)
o In Europe – the frequency is approximately 50%
Prevention: (in women)
• Avoid kiss babies on the mouth
• Avoid sharing utensils
• Preconceptional screening (better to know the risk before conceiving)

Clinical Manifestations
Type of infection: the probability of transmitting the virus to the fetus highly associated with the type
of the infection – primary/non-primary.
• Primary infection: exogenous infection to seronegative subjects. This is a very dangerous
situation because the transmission rate is higher than a non-primary infection, and the risk of
having a symptomatic congenital infection increases as pregnancy progresses:
o Pre-conceptional infections: transmission rate stands on approximately 5%. The infection is
usually asymptomatic.
o Infections in the 1st trimester: 20% chance of having congenital infection
o Infections in the 2nd trimester: 40-50% chance
o Infections in the 3rd trimester: 70% chance
 107

• Non-primary infection: has a transmission risk of ~2%, considered less critical because the risk of
defects is similar as in every other pregnancy. Non-primary infections usually result in an
asymptomatic congenital infection (yet, a study in Brazil proved that they can be equally
symptomatic). Maternal infections are classified to two cases-
o Reinfection: exogenous infection to seropositive subjects
o Reactivation: endogenous infection (latent) to seropositive subjects
Note that in countries with high prevalence of the virus, most infections are considered non-
primary.
Severe symptoms at birth: Moderate symptoms at birth:
• Hydrops • Intrauterine growth retardation: birth
• Respiratory distress (without another weight < 10° percentile
reasonable cause) • Petechia, purpura ,cutaneous hematome
• Microcephaly (PC < 10° percentile) • Hepatomegaly (clinical)
• Hypotonia • Splenomegaly (clinical)
• Hyperexcitability • Haemoglobin concentration <11g/dl (no
• Hyporeactivity (lethargia) other etiology)
• Persistent and significant poor sucking • ALT > 80 UI/L
• Seizures • Conjugated bilirubin > 10% of total
• Abnormal movements bilirubin
• Abnormal visual contact with absence of eye • Hearing loss demonstrated by the
pursuit absence of otoacustic emissions further
• Periventricular hyper echogenicity confirmed by abnormal auditory
• Ventricular dilatation > 12mm brainstem responses (ABRs)
• Chorioretinitis at fundoscopic exam
Diagnosis
Maternal Infections
The criteria for diagnosis are:
• IgG seroconversion – where a seronegative mother becomes seropositive. This is the most
important criterion, which best detected if the woman was tested beforehand for the presence
of hCMV (keep records of laboratory tests).
And/or
• Kinetics of hCMV-specific IgM and IgGs –
1st month of pregnancy 2nd month 3rd month until birth
IgM Usually positive in Depends on the time of infection, but in general there is decreased
primary infection, but can level, up to complete absence in late stages of pregnancy (can be
be negative in the very positive for a long period)
early phase
IgG Can be negative (in case Seroconversion occurs during pregnancy and immunity remains
of primary infection) forever.

Each result should be appropriately interpreted according to the gestational age – when in doubt,
refer the pregnant woman to a reference lab.
 108

Note: false positives of IgM-

o Non-specific reactivity: autoimmunity (rheumatoid factor, ANA) or cross-reactivity with
other viral infections.
o Recurrences
o Persistence
• Low IgG avidity index (AI) – the fraction of bound antibodies to an antigen, higher avidity means
better affinity maturation (enough time has passed since the beginning of the infection).
However, even though the infection can be dated as “old”, the avidity can be low/intermediate.
𝐼𝑔𝐺 + 𝑎𝑛𝑡𝑖𝑔𝑒𝑛 𝑎𝑓𝑡𝑒𝑟 𝑎𝑑𝑑𝑖𝑛𝑔 𝑑𝑖𝑠𝑠𝑜𝑐𝑖𝑎𝑡𝑖𝑜𝑛 𝑎𝑔𝑒𝑛𝑡
𝐴𝐼 = ∙ 100
𝐼𝑔𝐺 + 𝑎𝑛𝑡𝑖𝑔𝑒𝑛
• Neutralizing antibodies detection – antibodies which are different than IgM or IgG and have the
capacity of neutralizing the virus (not just bind its antigens) so it cannot replicate. The synthesis
is neutralizing antibodies is correlated with infection progression (seronegative test may mean
that the infection acquired recently).
• DNA detection in blood – qualitative and quantitative assessment by PCR. Note that high viral
load can occur also in asymptomatic patients, so performing this test alone might not be sensitive
enough.
• Physical examination / other laboratory tests – revealing clinical symptoms or biochemical
signs. Always look for patient complaints (fatigue, fever etc.), which have high occurrence but
usually are neglected.
o Lymphocytosis
o Increased levels of liver enzymes
A combination of all the above-mentioned criteria can help in dating the infection in 95% of the
cases – especially tell if this is a primary infection or not. This allows the physician to correctly inform
the pregnant woman if her fetus is at risk of acquiring an infection.
Congenital Infections
Indications for the diagnosis of a congenital infection:
• Maternal primary/non-primary infection – detected by laboratory tests
• Fetal morphological abnormalities – detected in US or MRI
• Clinical symptoms at birth
Fetal blood markers: the following parameters were found28 as the most sensitive prognostic
markers of a symptomatic congenital infection-
• Specific anti-hCMV IgMs
• DNAemia
• Platelets count
• β2 microglobulin
In case there is suspicion of congenital infection, it is best to perform amniocentesis at 20 weeks of
pregnancy because:

28ROC analysis of virologic, hematologic, immunologic and biochemical parameters found the most specific cutoff to distinguish
between a/symptomatic fetuses. 3 of the 4 parameters are highly suggestive of symptomatic congenital infection at birth
 109

➢ CMV crosses the placenta after 6-8 weeks since the beginning of infection
➢ Screening of fetal urine can be performed only after the development of the kidneys (start to
function in the 16th week of pregnancy).
Cordocentesis is performed in the next weeks (up to week 22) as a confirmation test. If both tests
are positive the woman can choose to undergo therapeutic abortion.
Diagnosis at Birth
Sampling of the following body fluids (within 7 days after birth):
• Urine and/or saliva – DNA quantification (real-time PCR)
• Blood – DNA quantification and presence of specific IgM
• Dried blood/saliva spots – DNA detection
Perform neonatal screening on symptomatic (severely/moderately) neonates – see “clinical
manifestations”, as well as on asymptomatic neonate, considering the following aspects:
− Parents acceptance
− Cost/benefit (if the mother is seronegative throughout gestation there is no need to screen the
neonate)
− Sensitivity/specificity
− Confirmation of screening results
− To aid the prognosis (controlling viral load)
− Prevent future diseases/sequalae
Note: salivary PCR must be confirmed with urinary PCR – there can be false-positives due to breast-
feeding (the antibodies are transferred to the neonate).
Therapy
Therapeutic abortion: performed in Italy up to 22 weeks because later in pregnancy induction of labor
results in giving birth to live newborn (beforehand it can result in still birth).
Drugs: administered only for severe symptomatic neonates (see list of severe symptoms in clinical
manifestations) – Gancyclovir/Valacyclovir for six months.
 110

Invasive Fungal Infections

Invasive infections are defined as infections which infiltrate areas of the body expected to be sterile (CSF,
blood, lungs). These infections are associated with high morbidity and mortality because the patients at
risk often have multiple comorbidities – especially defects in cellular immune response
(immunocompromised patients i.e. chemotherapy, AIDS patients, post-transplant).
Invasive fungal infections are very difficult to:
• Diagnose – diagnostic tests are slow, with low sensitivity and specificity, expensive
• Treat – due to limited therapies, toxicity, drug-drug interactions, expensive

Epidemiology
The most common fungal infections are due to Candida spp., Aspergillus spp. and Cryptococcus
neoformans. The latter is the most dangerous, causing most of the cases of mortality due to fungal
infections. Most of the fungal agents, classified according to their form (underlined fungi are
opportunistic pathogens):
Yeasts Molds Dimorphic Fungi
• Candida spp. • Aspergillus spp. • Histoplasma capsulatum
• Cryptococcus spp. • Fusarium spp. • Coccidioides immitis
• Scedosporium prolificans • Blastomyces dermatitidis
• Zygomycetes Mucor • Paracoccidioides spp.
• Zygomycetes Rhizopus • Sporothrix spp.
• Zygomycetes rhizomucor • Penicillum marneffeii
• Zygomycetes absidia

Fungi are widely distributed in soil, plant debris and organic substrates. 7% of all eukaryotic species on
earth are fungal, but there only 600 species which are pathogenic to humans.

Aspergillus
Generalities
Epidemiology:
• The most common species which infect humans are: A. fumigatus, A. flavus, A. terreus and A. niger
• Can grow on soil, decaying matter and air (even in temperatures of 40 to 50°C) – can grow in
different locations inside houses (basements, condiments, ventilation ducts etc.)
Morphology: unique hyphae and conidia (non-motile, asexual spores of fungi)
Pathogenesis:
•
Epidemiology of Candida spp. is shifting towards more non-albicans infections
Invasive staphylococcal infections in IVDU – cavitation due to septic emboli
 111

Parasitic Infections - Protozoa

Malaria
Malaria, a disease caused by the parasite Plasmodium is emerging as a common disease nowadays, seen
even in developed countries, due to the increase in worldwide traveling. Plasmodium is a
coccidian/sporozoan parasite which grows inside red blood cells. There are 5 species of Plasmodium
which infect humans: P. falciparum, P. vivax, P. ovale, P. malariae and P. knowlesi. The species are
distinguishable by epidemiology, morphology, differences in life cycle and clinical manifestations.

Generalities
Replication Cycle
Plasmodium requires two hosts:
• Mosquito (Anopheles) – in which sexual reproduction occurs
• Humans and other mammals – asexual reproduction
Vector Humans
(Anopheles mosquito)
Hypnozoites – dormant form in the liver of P.
Ovale and P. Vivax (do not reproduce)
Mosquito bite
Sporozoites Trophozoites

Sporogenic cycle Exo-erythrocytic cycle, in

the Liver (aka schizogony) Schizonts
Gametocytes Lasts 8-25 days
P. Vivax, P. Falciparum Mosquito bite Rupture of hepatocytes
P. Ovale Can activate sexual reproduction Merozoites
P. Malariae Rupture Entry to erythrocytes
Erythrocytic cycle
(in the blood)
Schizonts Trophozoites

Reactivation of the hypnozoites found in hepatocytes results in relapse29 of the infection, months to
years after the initial disease. Therefore, they should be treated with an additional specific drug
(Primaquine).
Trophozoites start as immature and have a ring form. They become mature trophozoites and then
schizonts. When the cell ruptures, they are called merozoites and can infect more cells with which they
come in contact.
Merozoites can transform into gametocytes and can only be activated within the mosquito. The
gametocytes start the sexual replication, which is crucial for the survival of the parasite.

Modes of Transmission
• Mosquito bite
• Blood transfusions – from an infected donor, mostly in countries that do not perform screening
• Drug injection – by PWID who share needles
• Congenital – a rare but possible mode of transmission

29 Relapse – activation of dormant forms | Recurrences – failure of treatment to clear all the parasites from erythrocytes
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Criteria for Severe Malaria

Severe cases of malaria can occur in infections of P. falciparum, P. knowlesi and P. vivax. The following
criteria were chosen by the WHO to define these particular cases.
Clinical: Laboratory:
• Impaired consciousness or coma • Metabolic acidosis
• Inability to walk/sit/feed • Hypoglycemia
• Multiple convolutions • Severe anemia
• Respiratory distress/acidotic breathing • Hemoglobinuria
• Circulatory shock • Increase in serum creatinine (renal
• Jaundice with another vital organ dysfunction impairment)
• Abnormal bleeding • Hyper-parasitemia
Plasmodium Falciparum
Epidemiology:
• Widespread in tropical areas
• Produces the most severe disease among the Plasmodium species (most likely to be fatal if remains
untreated)
Life-cycle features: can produce high parasitemia due to-
• Can infect all red blood cells (all ages), and multiple sporozoites can infect a single cell
• Can be sequestered in body tissues by cytoadherence, avoiding the clearance of RBCs by the spleen
• Incubation period of 7-10 days (shortest of all species)
Clinical manifestations:
• Malignant tertian fever (every 36-48h), chills
• Liver involvement – abdominal pain, severe nausea, vomiting (of bile) and diarrhea
• Anemia – due to massive destruction of erythrocytes (also non-infected cells) during the
erythrocyte-stage schizogony, and decreased production of erythrocytes. Since the mechanism is
hemolysis, it results in increased bilirubin levels in blood → jaundice.
• Cerebral malaria – the major load of parasites and cell debris in blood can cause occlusion of
cerebral capillaries (cytoadherence and aggregation of platelets, leukocytes and malarial pigment).
The condition can result in coma and death.
• Blackwater fever – renal damage due to the intravascular hemolysis which results in marked
hemoglobinuria. The latter can deteriorate to acute renal failure, tubular necrosis, nephrotic
syndrome and death.
Microscopy (of peripheral blood smear):
• Erythrocytes maintain their morphology (unlike in infections by
other species)
• Appliqué/accollé - multiple ring forms inside RBCs (species-specific)
located on the interior edge of the cell
• Crescentic gametocytes – also typical only for P. falciparum
• Maurer’s dots – reddish granules inside cells
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Plasmodium Vivax
Epidemiology:
• Widespread in tropics, subtropical and temperate areas (most geographically spread) except for
West Africa
• The infection is more tolerable, and most patients can survive without treatment for several years
Life-cycle features:
• Infections of reticulocytes only
• Incubation period of 10-17 days
Clinical manifestations:
• Influenza-like symptoms (headache, myalgia), photophobia,
anorexia, nausea and vomiting
• Benign tertian fever (every 48h) and chills (after erythrocytes
rupture)
• If the infection is untreated it can deteriorate to severe malaria
(see above)
Microscopy:
• Schüffner’s dots – pink granules in erythrocytes
• Trophozoites – have an ameboid ring appearance
• Gametocytes – round
• Schizonts have up to 24 merozoites

Plasmodium Ovale
Epidemiology: patchy in West Africa, and can be found in Southeast Pacific, Asia and South America
Life-cycle features:
• Infections of reticulocytes only
Clinical manifestations: similar to P. vivax, except for the severity of
the disease (milder form)
• Benign tertian fever
Microscopy:
• The infected cells enlarge and usually acquire an oval shape
• Schüffner’s dots – pink granules
• The cell border is distorted (ragged/fimbriated)
• Schizonts have up to 12 merozoites

Plasmodium Knowlesi
Epidemiology: Southeast Asia, zoonotic (macaque monkeys)
Life-cycle features: affects all erythrocytes but less intensely than P. falciparum
Clinical manifestations: can result in severe disease (see criteria above)
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Plasmodium Malariae
Epidemiology: patchy worldwide, but less prevalent than the
other strains
Life-cycle features:
• Infections of mature erythrocytes only (with relatively rigid
cell membrane)
• Do not have dormant forms in the liver
• Incubation period of 18-40 days (but can take months-years)
Clinical manifestations:
• Early symptoms: flu-like
• Quartan fever pattern
• Untreated infections can last up to 20 years
Microscopy:
• Since cells with rigid membrane are affected, the cells do not
change their morphology during the parasite replication.
• Schizont (1) composed of 6-12 merozoites, arranged in a
rosette
• Band/basket forms – (2) pigments in the cytoplasm that
appear long (band) or around a vacuole (basket)
• Ziemann’s dots – occasional finding, reddish granules inside
the cells

Diagnosis
Microscopy
Examination of blood smears under the microscope is a good way to confirm the diagnosis of malaria
and identify the species who caused the disease. The best time to take blood samples is between the
paroxysms of fever, where most of the microorganisms are found inside the erythrocytes.
• Take both thick and thin smears:
o In thick smear the microorganisms can be better detected
o In thin smear it is possible to best distinguish between the species
• Stain the samples by Giemza stain and observe them under the
microscope.
• Note that there might be co-infections of several species of
plasmodium in the same patient.
• Use microscopy also to check the effectiveness of the treatment

Immunological Techniques – Rapid Diagnostic Test (RDT)

Detection of plasmodial proteins by immunochromatography:
• For P. falciparum only – histidine-rich protein 2 (PfHRP2) and lactate dehydrogenase (PfLDH)
• For all others (shared) – plasmodium lactate dehydrogenase (pLDH) and aldolase
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Antibodies against these proteins are embedded in bands on a strip, and color in red if the test is
positive. The test takes only 25 minutes.
Disadvantages:
• The test does not quantify the parasitemia
• Test for PfHRP2 can remain positive for several weeks after the infection was controlled

Molecular Techniques – PCR

PCR is the most sensitive diagnostic tool for malaria, but it is a quite expensive exam and not available
in the field (where most cases are diagnosed). For these reasons, PCR is less used in the clinics and can
play a role as a second-line test (especially in cases where the suspected patient takes anti-malarial
prophylaxis).

Treatment
The therapy of malaria is based on the epidemiological and characteristics of the disease, so the
physician must assess correctly the patient history, microscopical evidence and the results of the RDT.
Chloroquine – used to be the main drug against malaria, but nowadays there are areas in which strains
of Plasmodium are resistant for this drug (P. falciparum and vivax).
Patients with chloroquine-resistant Plasmodium strains can be treated by:
• Atovaquone + proguanil (Malarone) – can be used also for prophylaxis
• Mefloquine /and artesunate – very efficient
• Pyrimethamine-sulfadoxine (Fandisar)
• Doxycycline
• Amodiaquine – a chloroquine analog. Highly toxic (not frequently used)
Primaquine – a drug against hypnozoites (dormant forms in the liver, present only in P. vivax and P.
ovale infections), contraindication: G6PD patients.
Mefloquine – a prophylactic drug. Contraindication: psychiatric patients.
Prophylaxis is usually administered as anti-malarial drugs in lower concentrations (for both hepatic and
erythrocytic cycles). It never confers a 100% coverage, but it is highly recommended especially in areas
endemic for P. falciparum.
Note: always advise pregnant women to avoid travelling to endemic areas, unless it is urgent matter.

Amebiasis
There are several species in the Entamoeba genus30, but the only one that can infect humans is
Entamoeba histolytica, and causes the disease amebiasis aka amebic dysentery. Other opportunistic
pathogens are Naegleria fowleri and Acantomoeba spp. (cause meningoencephalitis and keratitis).

30The non-pathogenic (commensal) members of the genus are: E. dispar, E. moshkovskii, E. hartmanni, E. gingivalis, E. nana and
Entamoeba coli
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Generalities
Epidemiology:
• It is estimated that 10% of the world’s population is infected by either E. histolytica or E. dispar.
• In tropical countries the frequency can be up to 50% (common in areas of poor sanitation)
• High prevalence observed in orphanages, prisons and mental hospitals (crowded places / population
more likely to get infected)
Transmission:
• Fecal-oral route (ingestion of contaminated water that contains cysts).
• Anal sexual intercourse
Life cycle: humans are the only hosts.

Contaminated water
Excretion in
feces
Cysts Trophozoites
Infectious when
ingested
Trophozoites Maturation followed
Released by stomach by ingestion
acidity, spreads and when
resides it causes
Prevalent in the colon/liver but can reach the
Abscess diaphragm -> lungs -> pericardium

Necrosis

• E. histolytica is a facultative pathogen – can “metastasize” to other organs from the colon.

Clinical Manifestations
The non-invasive disease:
• Can be asymptomatic
• Diarrhea, abdominal pain, cramps
The amoebic cells have the ability of adherence, cytolytic and proteolytic activity. The pathogenesis of
the parasite is dependent on these abilities and the host immune response (if it can block the
proliferation of the parasite). Therefore, the non-invasive infection can persist and become invasive –
the trophozoites can penetrate the intestinal mucosa and obliterate epithelial cells.
Invasive disease:
• Button hole ulcer – in the intestines (aka amebic colitis), invasion is
underneath the raised margins (which remain intact). In the center of the
ulcer there is high degree of necrosis, while the amebae infiltrate under
the mucosa (progress laterally or downwards). If several ulcers are
present, they can merge – which can result in perforation.
• Ameboma – a type of granuloma, thickening of the surroundings of the
ulcer (can be confused with a tumor.
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Complications:
• Amebic colitis -bloody diarrhea (due to ulcers)
• Perforation of an ulcer → localized abscesses (main complication) or peritonitis
• Dissemination – entry of the pathogen to the blood circulation. The most common affected site is
the liver (the amebae come from the portal system) – amoebic liver abscesses (ALA) begin as small
foci, then enlarge while obliterating the hepatocytes.
↓
The center of the abscess contains a necrotic material which seems (and often called) “anchovy
paste” – yellow/red/brown turbid liquid of dead hepatocytes and erythrocytes, bile and fat. The
liquid should not be referred as pus (only in superinfection by bacteria, which is not very common).
• The parasite can further spread to the brain, pleura/lungs (if there is a localization on a bronchus,
the patient can cough fomites with the parasite) or the pericardium.
Common signs and symptoms:
• Fever
• RUQ pain
• Hypertension
• Single lesion – in most cases (60%), the most common location is the right lobe

Diagnosis
• ELISA – of anti-amoeba antibodies (found in most cases)
• Stool culture / aspiration of the necrotic material – not so sensitive (poor detection of trophozoites
– 15% and 30% positive respectively)
• In physical examination - elevated right hemidiaphragm
• Very high WBC count (which is unusual because the condition is typical in hematological disorders)
• US – (mainly in the liver) detection of abscesses (irregular walls) or cysts (clear-cut walls)
Consider amebiasis in the differential diagnosis of focal brain lesions (ask if the patient traveled to
endemic areas)

Treatment
• Metronidazole / Ornidazole 750mg TID for 10 days (successful treatment in most cases)
• Emetine/dehydrometine – sometimes co-administered with metronidazole (in more severe cases,
due to their toxicity)
• Paromomycin – a luminal agent, to eradicate colonization
+ Fluid and electrolytes transfusion (restore the loss due to diarrhea)
Abscess drainage or removal of the cysts by surgery are controversial, since they can release units of
the parasite to the environment. Incorrect therapy can result in relapses due to the dissemination of
the parasite by blood.
Indications for drainage by needle:
• Risk of rupture
• No response for chemotherapy
• Pregnancy
• Size: diameter 4-10cm
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Indications for surgery:

• Rupture
• Complications – lesion in left lobe / multiple lesions in the abdomen
• Lack of improvement, even after drainage

Leishmaniasis
The leishmania spp. is family of zoonotic parasites, transmitted by the female phlebotomine sand-fly,
which can only fly close to the ground. In the hosts, the parasite proliferates intracellularly.

Generalities
Epidemiology:
• Cutaneous leishmaniasis (1-1.5 million cases worldwide every year)
o Mediterranean, South West Asia, Morocco, Ethiopia – L. tropica and aethiopica
o Northern Africa, Middle East and some parts of central Africa – L. major
o Central and south America – L. panamensis
o Texas – L. mexicana
• Mucosal leishmaniasis - South America (Brazil, Peru and Bolivia) by L. braziliens
• Visceral leishmaniasis (0.5 million cases worldwide every year)
o Middle East – L. infantum,
o India – L. donovani
o Latin America – L. chagasi
o Brazil – L. amazonesis
# Changes in the ecological systems by humans increase the exposure to the sand-fly.
Life cycle: Sand-fly Humans
(Vector) Bite (Host)

Promastigotes Promastigotes
Phagocytosis by
In the digestive tract macrophages
Amastigotes Amastigotes
Within the macrophage
Bite
Proliferation -> several weeks until
symptoms appear
• The amastigote is resistant against the lysozyme activity, in fact, it depends on the low pH to
proliferate. The proliferation of amastigotes inside macrophages induces an inflammatory
response.
• After the reproduction fills the cell, it is lysed releasing the amastigotes in the surroundings to infect
other cells.

Clinical Manifestations
Onset of symptoms depends on the type of the syndrome, but usually takes several weeks to months
following the bite, since it takes time for the amastigotes to proliferate. The onset of symptoms can be
gradual or sudden. Moreover, the inflammatory response makes the infection to be always
accompanied by fever.
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A single species can cause more than one syndrome (under “epidemiology” there are the most common
species causing the syndrome).

Cutaneous Leishmaniasis
The manifestations are the result of the granulomatous inflammatory response usually at the site of
the bite: deep skin lesions (ulcerations) which can be dry and crusted/moist and filled by exudate.
• Symptoms begin two weeks - several months after the bite and can be resolved spontaneously
• Ulcerations have sharp and raised edges
• The ulcerations can lead to infections by opportunistic bacteria (on the skin – Staph. or Sterp.)
• Diffused cutaneous leishmaniasis – disseminated lesions that appear at several site on the skin.
They are associated with faulty immune system, thus more difficult to treat and subjected to
relapses.

Mucosal Leishmaniasis
The result of the inflammatory response by mononuclear cell on a mucosal surface in the head – nose
(mostly), mouth and trachea, as well as the genital mucosa. In severe cases it can complicate into
collapse of the nose (2-3% of the cases). This syndrome cannot be resolved spontaneously.
• Less common syndrome
• Ulcerations have sharp and raised edges
• Symptoms include: nasal stuffiness, discharge, pain or nose bleed (epistaxis)

Visceral Leishmaniasis (Kala Azar)

Kala Azar, aka black fever, is the most severe form of leishmaniasis, which can be 100% fatal if remains
untreated. The disease affects internal organs, commonly the liver and the spleen.
• Incubation period can take months to years (usually 3-8 months) until sign and symptoms appear
• Small papule at the place of the sand-fly bite
• Signs and symptoms: irregular fever pattern (mimics malaria), weight loss, hepatosplenomegaly
and anemia
o Acute disease – paroxysm (rapid progression), dry skin
o Subacute disease – slow and progressive, weakness and loss of weight
# When bone marrow is affected → pancytopenia
• Even after the patient has cured, cutaneous leishmaniasis can still be developed

Diagnosis
Physical Examination
Acute disease findings:
• Spleno/hepatomegaly – hard and non-tender
o In HIV patients there might not be splenomegaly
• Dry skin (in people with lighter skin – the skin becomes greyish)
Subacute disease findings:
• Progressive weight loss
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Laboratory Tests
Indirect diagnosis:
• CBC and serology – during the acute phase. Search for anemia, leucopenia and
hypergammaglobulinemia / pancytopenia in visceral Leishmaniasis
• ELISA – detects anti-Leishmania antibodies. Note that there can be cross-reactivity (especially in
the acute phase – IgM) and that HIV patients do not develop antibodies
• In HIV patients – samples include BAL and pleural effusion aspirate.
Direct diagnosis:
• Microscopy – Giemza stain / Wright stain of lymph node, bone marrow
biopsy or skin lesions (in the cutaneous form). Search for amastigotes
inside mononuclear cells (rod-shaped kinetoplast)
• Molecular techniques – PCR. More sensitive than microscopy but it is
more expensive
Differential Diagnosis:
• Lymphoma
• Infectious mononucleosis
• Brucellosis
• Chronic malaria
• Hepatosplenic schistosomiasis

Treatment
Visceral Leishmaniasis
• Liposomal Amphotericin B
o Immunocompetent patients – 3mg/Kg of body weight (at days 1-5, 14 and 21)
o The course can be repeated if the infection persists
o Immunocompromised patients – 4mg/Kg of body weight (at days 1-5, 10, 17, 24, 31 and 38)
• Miltefosine – against visceral (Indian) Leishmaniasis. Interferes with the parasite’s signaling
pathways and membrane synthesis
Cutaneous Leishmaniasis
The therapy depends on the site of infection on the body.
• Stibogluconate – against cutaneous Leishmaniasis
• 15% Puromycin and 12% methylbenzethonium chloride
• Thermotherapy – heating the lesion by radiofrequency waves to 50˚C
• Antimony
• Fluconazole (500mg, twice a day for 6 weeks)
• Following cutaneous Leishmaniasis → immunity against the stain (except for Middle-Eastern or
Brazilian species
Mucosal Leishmaniasis
• Mucosal leishmaniasis requires a reconstructive surgery as part of the treatment
• Stibogluconate and Amphotericin B (combined)
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Chagas Disease (Trypanosomiasis)

Chagas disease is caused by the parasite Trypanosoma cruzi. The disease is also known as American
trypanosomiasis, where African trypanosomiasis is caused by another strain – T. brucei.

Generalities
Epidemiology: T. cruzi is a zoonotic parasite, found in tropical areas in central and south America
(especially Brazil, but also in Mexico and some cases were recorded in south Texas).
Transmission:
• By the vector – Triatoma infestans (triatomine), a bug found in endemic areas
• Blood transfusions / organ transplantations
• Vertical transmission
• Fecal-oral route – rare, mostly by contaminated water
Life cycle: Humans
(Host)
Defecates on the skin
Triatoma Metacyclic trypomastigotes
(Scratching of the affected
area enhances the infection) + Flagella
Amastigotes

Taken by
Multiplication
another bite
inside cells
Cell lysis and release
Travel by blood of the parasites
(Chronic phase)
Lymph nodes
CNS
Skin GI Tract
Heart

• The parasites reside mostly in smooth or cardiac muscles, affecting their innervation
• The parasites multiply by binary fission

Clinical Manifestations
Natural history of the infection: 95% are After 4 to 12 Reactivation, can
asymptomatic, weeks (9 weeks occur years later (only
Acute Phase The rest develop on average) in 20-30% of the cases)
fever with/out
myocarditis
The acute phase is accompanied by non-specific Chagas heart disease
signs such as: Digestive
megasyndromes
• Chagoma - rash and swelling of the bite area Acute infection
Subclinical, long-
term infection
• Swollen lymph nodes
• Fever, fatigue, nausea, vomiting and diarrhea Meningoencephalitis
• Hepato- and/or splenomegaly
• Romaña sign – if the bug bit the eye – painless
swollen eyelid
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Intermediate Phase
The parasite burrows into the cardiac walls, resulting in myocarditis:
• Conduction abnormalities → arrhythmias
• Formation of thrombi → thromboembolism
• Dilation (aneurism) at the apex → heart failure or sudden cardiac death
Chronic phase
• In the CNS – meningoencephalitis (or separately)
• Dermatologic – skin ulcerations, erythematous papules (nodules)
• Gastrointestinal – mega-esophagus, mega-colon (constipation), mega-gallbladder, achalasia-like
syndrome, salivary gland hypertrophy.
o All these manifestations of the parasite affect the innervation of smooth muscles – apart of
the abnormal appearance, the parasite also causes reduced motility expressed by delayed
gastric emptying or constipation.

Diagnosis
History and Physical Examination
Consider the geographic prevalence of the parasite – if the patient has travelled to endemic areas.
Imaging
X-ray image shows enlarged cardiac silhouette, but this is a very non-specific sign: can be either
effusion or dilation. Therefore, US is the first diagnostic tool the physician should use if there is a
suspicion of a cardiac disorder – can immediately visualize if there is effusion or not.
Laboratory Examination
1. Serology – IgM (acute phase) or IgG (chronic phase).
• Check by ELISA / Immunofluorescence / Indirect heme-agglutination (IHA) test
• 2/3 tests are enough for the diagnosis
2. Blood culture – during the acute phase (6-10 weeks following the bite the parasite is almost
undetectable in the blood)
3. Microscopy – of thick coat / buffy coat smear
4. PCR – positive tests are used only for confirmation of congenital infections or for evaluation of
therapy.
• Note that genetic material can persist in blood even if the patient is cured, or there can still
be an active disease even if the PCR test is negative.

Treatment
• Anti-parasitic: Benzidazole / nifurtimox – for patients younger than 50 years, in less severe
infections
• Therapy of the parasitic manifestations:
o Amiodarone – drug against arrhythmias
o ACE inhibitors – against LV deterioration
o Anticoagulants – to prevent thromboembolism
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Parasitic Infections - Helminths - Trematodes (Flukes)

Schistosomiasis
Generalities
Features
Schistosomiasis is an infection caused by several species of the helminth Schistosoma.
Species Epidemiology Structure of eggs Target tissues
Africa, Cyprus, Portugal Oval with large Urinary bladder, prostate or
Schistosoma Haematobium
terminal spine uterine venous system
Africa (incl. Madagascar), Oval with large Liver (mostly)
Schistosoma Mansoni
Saudi Arabia side spine
Japan, China, Philippines Round, smaller Superior mesenteric vein -> can
Schistosoma Japonicum
eggs lead to the most severe disorders
Schistosoma Mekongi Southeast Asia Liver
Schistosoma Intercalatum Rare

Epidemiology
Acute infections are common in international travelers, whereas chronic infections are more common
in habitants of endemic areas. Humans
Lose tails
Cercariae (Host)
Life cycle
Proliferation
Water Bloodstream
Snails (Rivers/lakes)
(Intermediate host)
Target tissues
Hatching, releasing miracidia Eggs Excretion in Proliferation and
urine/feces maturation

• The infection can be transmitted only in fresh water (rivers, lakes), since the parasite resides in
specific snail species.
• The parasites penetrate the body through the skin and reach by the bloodstream to the target
tissue (see “features”)
• Eggs are shed in feces/urine into fresh water
• The life cycle can help in ruling out other clinical conditions
• Disruption of ecological systems by building dams/urbanization enhances transmission.

Clinical Manifestations
The pathophysiological basis of the infection is the inflammation and granulomatous reactions formed
around and against the eggs, which reside inside vital organs.
Cercarial dermatitis – minutes to hours after swimming in fresh water (with snails carrying the parasite)
Other symptoms and signs appear 3-6 weeks after exposure (following proliferation of the parasite).

Acute Schistosomiasis
Katayama fever – sudden onset of: fever, malaise, fatigue, myalgia, abdominal pain and headache
which last for 2-10 weeks. Other manifestations: hepatosplenomegaly and lymphadenopathy.
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Chronic Schistosomiasis
Chronic and Specific Manifestations
Most of the symptoms are due to the chronic exposure to the parasite and/or chronic inflammatory
response against the eggs that are lodged in the liver/colon/bladder (see histological samples). There
will be upper abdominal discomfort/pain, palpable lymphadenopathy and hepatomegaly (often with
splenomegaly.
Periportal (hepatic) fibrosis (Symmer’s pipe-stem
fibrosis) – eggs reach the liver via the mesenteric
veins and lodge in the lobules. Fibrotic
complications of the inflammation usually take 5-15
years to develop. They can lead to portal
hypertension → ascites (rare) and the use of
collaterals → esophageal varices (increase the risk
of death).
Notes:
1. Can occur also in young children (emerging
need of screening in endemic countries).
2. Despite the fibrosis, the hepatic function is
maintained i.e. only an architectural disorder,
liver function tests will be normal (differential
from other post-viral chronic liver diseases)
Intestinal Schistosomiasis – over time, the immune
reaction against the eggs is dampened, thus leading
to the intestinal form of the disease (in S. mekongi,
mansoni and japonicum). The frequency of the
symptoms is correlated with the intensity of the
disease. The clinical presentation:
• Non-specific intermittent abdominal pain
• Bloody stool – due to rectal bleeding (e.g. from
ulcers)
• Diarrhea
• Histologically – segments of mucosal
hyperplasia, pseudo-polyposis or polyposis
In some patients the response against the eggs is
very low and consequently, extensive fibrosis
develops, with the risk of complication to periportal
fibrosis.
Urinary system – manifestations by S. haematobium. Eggs and parasites lodging in the bladder lead
to inflammation (bladder ulcerations) that results in:
• Disruption and friability of the mucosa i.e. “sandy patches” → hematuria, urinary frequency and
burning micturition
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• Progression to chronic fibrosis of the urinary tract: can become obstructive (wall thickening) →
hydroureter/hydronephrosis, bacterial superinfection and renal failure.
• The chronic inflammation can complicate to polyps, calcification, squamous cell carcinoma (SCC)
of the bladder (multifocal, appear in younger age than usual).
Genital system – (by S. haematobium)
In females, eggs can be deposited in the vesical plexus In males, urogenital Schistosomiasis
and result in inflammatory lesions in all the organs of manifests as:
the system (ovaries, fallopian tubes, cervix, vagina and
vulva). The resulting manifestations of the infection:
• Stress incontinence • Hematospermia and oligospermia
• Infertility • Hydrocele, testicular masses (pseudo-
• Increase transmission of HIV - higher probability tumor)
of acquiring the infection in unprotected sexual • Epididymitis, Orchitis, prostatitis
intercourse • Dyspareunia (painful sexual
• Increased risk of cancer intercourse)
Chronic, Non-specific Manifestations
Anemia, malnutrition and childhood development impairment – the chronic inflammation results in
anemia of inflammation, and the effect is seen on nutrient absorption, normal growth, iron
metabolism, physical strength and cognitive function (all decrease).
CNS – (S. japonicum) eggs deposition causes spinal compression/increased ICP. Both are associated
with the presentation of meningoencephalitis, which manifests as:
• Fever (pyrexia), headache, vomiting
• Altered sensorium, blurred vision, speech impairment
• Seizures (Jacksonian epilepsy)
• Acute transverse myelitis / subacute myeloradiculopathy – spinal cord compression, more
common in acute Schistosomiasis. Can result in lumbar/leg pain, muscle weakness, sensory loss
and in worse cases – paralysis or bladder incontinence.
Lungs – respiratory nodules cause dyspnea and cough
The most dangerous manifestations of Schistosomiasis, which increase the risk of morbidity, are:
• Periportal fibrosis
• Hydronephrosis
• Complications of anemia (immune-mediated) – most common cases of morbidity

Diagnosis
Acute Schistosomiasis
• CBC - eosinophilia
• Hepatosplenomegaly (in physical examination / US)
• Specific antibodies / circulating antigens – can be positive/negative (antigen detection is better to
perform in early phases of the infection, where antibodies are more common in chronic patients).
• Examination of urine, stool or tissue biopsies for eggs – can be negative, since eggs are not
constantly shed.
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Chronic Schistosomiasis
• Stool O&P (ova and parasites) – can be negative, since eggs are not constantly shed in the stool.
Take samples three times.
• Serology – detection of Schistosoma antigens or anti-Schistosoma antibodies
• Rectal/colon/bladder imaging (endoscopy) and biopsies – examine the histology (if eggs are visible)
• US –
o Intestines – wall thickening, pseudo-kidney appearance (symptoms are similar to IBD)
o Liver (and spleen) - hepatosplenomegaly and perihilar (liver) lymphadenopathy. Fibrosis is
graded and categorized into several patterns:
Pattern A Normal findings

Pattern B Non-specific thickening of the portal branches, hyperechoic

dots scattered in the parenchyma.

Pattern C Pipe-stems Can appear in

mixed pattern (DC)

Pattern D Echogenic material (fibrosis) around

the portal stem

Pattern E Includes pattern D and extension of the

echogenic patches.

On the right – mixed pattern of E+C

Pattern F Streaks and bands from the portal hilum to the capsule

Pattern G Divided into –

Gn – fibrosis appears as narrow
meshes (left)
Gw – fibrosis appears as wide meshes

Treatment
Praziquantel – prescribed to all species. Note that it has mild side-effects such as fever/abdominal
discomfort.
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Clonorchiasis/Opistorchiasis
Both Clonorchis spp. and Opisthorchis spp., aka Asian river flukes, cause infections of the biliary tree.
These species include:
• Opisthorchis/Clonorchis sinesis – found in China and Vietnam
• Opisthorchis viverrini – found in Southeast Asia (Thailand, Malasia)
• Opisthorchis felineus – found in Northwest Asia and some parts of Eastern Europe

Generalities
Transmission: fecal-oral route, found especially in raw fish
Structure: 8-15mm in length. The eggs differ in morphology-
• Clonorchis sinesis – oval-shaped with “shoulders” on the narrower end of the egg
Life cycle: Transform Metacercariae In humans - ingestion
In fish
Duodenum
Cercariae
In snails
Larvae Bile ducts
Hatching releases miracidia
Reside and proliferate
Eggs
(can stay even 50 years)

• Definitive hosts include: humans, dogs, pigs, cats, badgers, minks, weasels and rats.
• The eggs are transferred from the feces to water, where they are ingested by snails
• In severe infections the flukes can penetrate the gallbladder and pancreatic ducts.

Clinical Manifestations
Pathogenesis: the adult flukes obstruct the biliary tree in several mechanisms-
• Mechanical obstruction – due to high reproduction and proliferation
• Destruction and desquamation of the ductal mucosa – due to sucking of the blood from the layers
below.
• Inflammation – due to metabolites of the parasite, irritation and increased likelihood of
superinfections. Can complicate to adenomatous hyperplasia and goblet cell metaplasia.
• Cholelithiasis – due to stagnation of bile. These are pigment stones (made of bilirubin carbonate)
The disease is limited to the biliary tree (liver parenchyma is rarely affected), but the flukes can
penetrate the pancreas through the pancreatic duct (proximity to the biliary tree; Can complicate to
pancreatitis).
Symptoms: in early stages/mild infections the patients can be asymptomatic
• Abdominal pain
• Fever
• Jaundice
• Nausea
• Hepatomegaly
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Complications:
• Intrahepatic cholelithiasis
• Portal hypertension
• Pancreatitis
• Liver abscess
• Cholangiocarcinoma (poor prognosis)

Diagnosis
The definitive diagnosis is by demonstrating the presence of percolated (infiltrated) eggs in the stool,
duodenal aspirate or adult flukes by surgery.
1. Stool test (O&P) – there are three techniques:
• Direct smear
• Kato-Katz method
• Formalin-ether
2. Blood test – in acute infections search for eosinophilia / ↑ALP
3. ELISA – not a major diagnostic tool, used commonly as an additional tool for the stool test.

Treatment
Praziquantel – 25mg/Kg of body weight, three times in a single day. For severe infections – proceed the
treatment for an additional day.

Fascioliasis
Fascioliasis is an infection caused by the helminth Fasciola hepatica (sheep liver fluke)/gigantica. It is
common especially among people who handle cattle or sheep.

Generalities
Epidemiology: spread world-wide, especially in the Middle East (Egypt, Iran), India, China and Latin
America (Peru, Bolivia, Chile, Cuba). Humans are accidental hosts. A particular snail is the intermediate
host.
Transmission: fecal-oral route, via contaminated water or ingestion of fresh-water plants
Life cycle:

Duodenum

Peritoneal cavity -> Liver -> bile ducts

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Clinical Manifestations
Some infections can be asymptomatic. The manifestations of the parasite include a spectrum of
disorders focused in the liver and the bile ducts: liver abscess, hepatitis, cholangitis or cholecystitis.
Acute fascioliasis: occurs 2-4 weeks after the ingestion.
• Fever
• RUQ pain
• Hepatosplenomegaly – elevated transaminases without jaundice
• Eosinophilia
Chronic fascioliasis:
• Biliary colic
• Anorexia and weight loss
• Pruritus
• Eosinophilia
• Increase in γGT, ALP
• Stool sedimentation – ova and antibodies are present

Diagnosis
Samples of: bile, stool or blood. Be aware of the disease and its symptoms – with incorrect DDx the
disease can be interpreted as cholelithiasis or liver malignancy.
Laboratory tests:
• CBC – leukocytosis (eosinophilia) anemia
• Inflammatory markers – elevated ESR
• Liver function tests – increase in liver enzymes
• Stool O&P – eggs will appear only in chronic infections
• Bile microscopy – look for eggs
Imaging:
• Ultrasound – fleeting hypo-echogenic liver foci in acute fascioliasis, gallstones
• CT – several hypoechoic foci

Treatment
Triclabendazole 10mg/Kg of body weight – single dose. It is effective but not available in many countries.
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Parasitic Infections - Helminths - Nematodes

Strongyloidiasis
Generalities
Epidemiology:
• Can be found in tropical regions
• Zoonotic – examples for animal reservoirs: domesticated animals, pets, bears and swine
Transmission:
• Penetration of the skin – direct contact with feces or soil, when the human is present in the habitat
of the helminth.
• Sexual intercourse
Life-cycle: In humans

Filariform larvae Circulatory system Lungs

Rhabditiform larvae Cross the alveolar net
Trachea
Maturation and Ascending
reproduction Upper GI tract Pharynx
On warm and Excretion of larvae
moist soil Stool
Clinical Manifestations
Most patients are asymptomatic in the early stages of the infection, so symptoms start when there is a
large colonization of the helminth.
• Papular erythematous rash – at the site of penetration
• Loffler’s Pneumonitis (Syndrome) – pneumonia caused by migration of the parasite into the lungs.
Since it is of parasitic origin, the main differential for the diagnosis is that the pneumonia is
eosinophilic.
o Present with cough and/or wheezing
o Severe forms: fever, dyspnea, hemoptysis (rare)
• Intestines – burning abdominal pain, diarrhea (may be bloody), malabsorption, nausea and vomiting
• Hyperinfection syndrome – mostly in immunocompromised patients: meningitis, sepsis, severe
abdominal pain, peritonitis or endocarditis.
o Presentation: hemoptysis, periumbilical purpura, skin rash, angioedema.
 Due to re-infection – the presence of the helminths can persist for up to 35-40 years.

Diagnosis
• Stool O&P –
o Note that eggs are often absent in the stool due to eggs hatching
o Diagnosis requires demonstration of the Rhabditiform larvae in the stool/duodenal fluid
• ELISA – not so sensitive in this case because the test can be negative or cannot distinguish between
current and past infections.
• CBC – increase in peripheral eosinophils count
• Baermann funnel gauze method – live larvae are concentrated out of a feces specimen, which allows
detecting them by microscopy better.
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Treatment
Because of the potential danger of severe infection, even asymptomatic patients are treated. Patients
with hyperinfection syndrome should be treated for at least a week.
• Ivermectin – administered two days
• Albendazole / Mebendazole

Parasitic Infections - Cestodes

Cysticercosis
Cysticercosis is a chronic parasitic disease caused by the parasite Taenia solium, a cestode. Due to the
increase in international traveling, as well as the disease chronicity, the disease is nowadays more likely
to occur in non-endemic countries. The parasite can appear in two forms, both can be hosted by humans:
• Adult form – the intestinal tape worm
• Larval form – metacestode/cysticercus

Generalities
Epidemiology:
• Common in: central/south America, sub-Saharan Africa, India, China and southeast Asia
• The number-one cause of seizures in endemic countries
Transmission: fecal-oral route (by contaminated water or eating undercooked pork meat)
Life cycle: requires two obligate hosts, where each one has a different form of the parasite.
Pigs Humans
Muscles GI tract

Hatch and release Eggs

Oncospheres Spherical, armed with
oncospheres
develop 3 pairs of hooks
Hatch and release
oncospheres

Excretion in feces
Blood stream

Muscles Liver Lungs

Brain and eyes
Develop into cysticercus

The scolex, or the “head” of the parasite, has a diameter of about 1mm and is the part which attaches
to the host gastrointestinal epithelium. To do so, it contains four suckers and two rows of hooks.
Another reason for having this structure is because the worm cannot synthesize lipids, so it “sucks”
them from the host cells.
After the adherence to the host wall, the worm starts to reproduce from the neck region. The new
segments are called proglottids, and the more they become further from the neck they are more mature
and larger (sacs of eggs). A chain of proglottids can reach to a length of 2-8m.
Excretion of the parasite is not constant – therefore, some O&P tests can come out negative.
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Clinical Presentation
The clinical manifestations of the parasite are considered a spectrum of diseases, since they depend on:
• The location and number of parasites in the body – usually manifest in the brain, but can be in
muscles, liver or the lungs (can cause inflammation and tissue destruction).
• The host immune response against the parasites – e.g. when an antigen leaks out of the calcification,
it triggers the host immune response (which results in edema).
Note: non-inflamed cysticerci cause less symptoms, even if they are numerous.

Neurocysticercosis (NCC)
Classification:
• Location: (can be a mixed form in high parasite load)
o Parenchymal – involves the brain tissues
o Extra-parenchymal – involves the subarachnoid space, the ventricles, the spinal cord or the
eyes (the most dangerous location in which the cysts can reside is the fourth ventricle).
• Activity:
o Inactive disease – there is no evidence of a viable infection (or only degenerating parasite). The
hallmark of an inactive infection is the appearance of calcifications, which are well-defined and
solid (2-10mm in diameter). They are the consequence of a fibrotic reaction against the
parasite.
o Active disease – contains both viable cysticerci and degenerating parasites.
Active parenchymal infection is the most common form of NCC.
Symptoms:
• Parenchymal NCC – seizures (associated with active parenchymal cysts), headache
• Extra-parenchymal NCC – increased ICP → hydrocephaly (obstruction of the sinuses by the
cysticerci), headache, nausea/vomiting, dizziness, altered mental status and ocular disturbances.
o The onset can be abrupt / intermittent / gradual.
o Bruns syndrome – abrupt changes in head position that cause intermittent hydrocephalus,
headache, vomiting and dizziness.
• Cysticercal encephalitis – diffuse cerebral edema, increased ICP, seizures and altered mental status
(more common in children and females).

Diagnosis
• Imaging – (expensive, not applicable in many endemic countries)
o US – detects cysticerci in superficial muscles (with linear probe), or detection of cysts in the
eyes.
o CT – calcification detection (more sensitive than MRI) Cysticerci found in the CSF have the same
density as the latter: in MRI they have a different intensity which makes it easier to detect them.
o MRI –detection of cysticerci in the ventricles: there is contrast enhancement of inflammation
sites in active infection (but not in all cases). Also capable of detecting the scolex.
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(1) CT, calcification (hyperdense)

(2) CT, focal accumulation of fluids
– due to an inflammatory
response.
(3) MRI of multiple cysts (ring
enhancement in T2)
(4) MRI of cysts in the lateral
ventricle
(5) US of a cyst in the internal
oblique muscle

Parenchymal cysticerci are typically 4-20mm in diameter. Extra-parenchymal cysts can be up to

10cm in diameter. The cyst wall is thin, so it is usually invisible. The scolex, if visible, is 1-3mm long
and attached to the border of the cyst.
The calcifications have a diameter of 2-10mm, appear very dense and supra-tentorial.
• Histology of the brain/spinal cord biopsy
• Fundoscopy – white disc (cyst) on the retina
• Western blot (WB) – has the best specificity among immune assays, but it is not widely available
and quite expensive.
# Serology or ELISA of CSF - not for neurocysticercosis, due to the poor sensitivity and specificity (high
rates of false positives/negatives).
Del Brutto criteria – a • Histologic findings of the parasite in a brain/spinal cord biopsy of
scoring system that includes Absolute a lesion
several epidemiological, criteria • Cystic lesions where scolexes are visible in CT/MRI
• Finding the parasite in a fundoscopy examination (white disc)
clinical and laboratory
• Lesions are suggestive of NCC according to imaging studies
criteria. Diagnosis is made Major • Positive serum immunoblots of anti-cysticercal antibodies
when an absolute criterion / criteria • Good response to therapy by albendazole/praziquantel
two major and two minor • Spontaneous resolution of small lesions
• Lesions are compatible with NCC in imaging studies
criteria are present.
• Positive CSF ELISA of anti-cysticercal antibodies or cysticercal
Probable diagnosis is when antibodies
Minor
one major criterion and • Clinical manifestations are suggestive of NCC
criteria • Cysticercosis outside the CNS
three minor criteria are
• Epidemiologic compatibility – living/traveling to endemic areas
present. • Evidence of household contact with Taenia solium
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Differential Diagnosis
Infectious: Non-infectious:
• Bacterial or fungal abscess • Neoplasm
• Neuro-toxoplasmosis • Vascular malformations
• Cerebral toxocariasis • Scars
• Cryptococcosis
• Tuberculosis
• Strongyloidosis

Treatment
There are no guidelines in NCC therapy – the treatment is adjusted to each individual patient (according
to the symptoms he/she experiences). Contact an expert if there is uncertainty.
• Praziquantel / Albendazole - anti-parasitic drugs. The use is controversial since they make the cysts
more fragile and can result in complications or poor surgical outcomes.
• Anti-epileptic drugs – to treat the seizures
• Anti-inflammatory drugs
Extra-parenchymal NCC often requires surgery and note that post-operative chemotherapy is
controversial: many centers that operate on NCC patients noted that if chemotherapy is not
administered post-op there are no recurrences. However, these observations were made with methods
which are less sensitive than the available methods today.
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Principles and Stewardship of Antibiotic Therapy

The History of Antibiotics
Antibiotics were discovered by Alexander Fleming in 1928 by accident – he noticed molds that grow on
bacterial culture and inhibit the growth of the latter. These molds are of the fungi Penicillium notatum,
and the active component, penicillin, was extracted from the culture and was tested for use in humans
against bacterial infections.
Penicillin was first used in 1940, and ever since many other antibiotic classes have been developed.
Unfortunately, due to incorrect use of some antibiotics, drug resistance has emerged. The process is
inevitable, but to delay further resistance physicians must use the antibiotics correctly.

Features of Antibiotics
Mechanisms of action:
• Cell wall synthesis inhibition – β Lactams, Glycopeptides, Phosphomycin
• Inhibition of protein synthesis – Aminoglycosides, Macrolides, Oxazolidinones, Tetracyclines,
Glycylcyclines
• Inhibition of nucleic acid synthesis –Nitrofurantoin, (Fluoro-)quinolones
• Inhibition of folate synthesis – Sulfonamides (+Trimethoprim)
• Disruption of the cell membrane – Lipopeptides
Mechanisms of resistance:
• Production of enzymes – e.g. beta-lactamase
• Alterations in outer membrane permeability
• Alterations of target sites
• Efflux pumps
• Alterations of metabolic pathways
How to choose the correct antibiotic: consider all the following factors-
• Host factors – investigate different conditions that the patient has:
o Medical history – comorbidities i.e. coexistent illnesses
o Allergies – prevent anaphylactic shock
o Sepsis – consider the use of “stronger” antibiotic
o Renal / hepatic function – e.g. do not prescribe a drug which is metabolized by the liver to a
patient with cirrhosis.
o Pregnancy – a contraindication of many antibiotics
o Age / compliance – consider the ability of the patient of taking many pills each day
• Organism factors – identify the causative agent (after drawing several blood samples) or start
therapy against known/likely organisms. Cover the greatest range of agents possible. Examples:
o UTI / sepsis emerged from UTI → gram-negative bacteria are the most common agents
o Skin infections → gram-positive bacteria or fungi in immunocompromised patients
After the agent has been identified, always check the susceptibility of the bacteria to different
antibiotics, to avoid resistance.
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• Drug factors
Pharmacokinetics
Absorption (bioavailability)
Distribution – some drugs cannot reach
particular organs
Metabolism (inducer/inhibitor of CYP3A4)
Excretion (Kidney/liver/GI tract)
Pharmacodynamics
Distinguish between bacteriostatic/bactericidal drugs
MIC – minimal drug concentration that inhibits growth of isolated
bacteria31
Synergism/antagonism – drug-drug interactions
Concentration-dependent/time-dependent killing –
aminoglycosides and β-lactams/glycopeptides, respectively
Post-antibiotic effect

o As well as: side effects, drug-drug interactions, previous therapy

• Dose: severity of the infection, liver/renal function
• Route of administration
• Duration of treatment

What Is an Antimicrobial Stewardship Program?

Antimicrobial stewardship involves interventions and reasoning, designed to improve the appropriate
use of antimicrobials: promoting the consideration of the following factors, to make the therapy optimal
in every patient-
• Drug regimen – combination of drugs etc.
• Dose – use of low dosage increases probability of resistance, high dosage may lead to adverse
effects
• Duration of therapy
• Route of administration
With the emergence of many drug-resistant strains, the entire world must change the way it prescribes
and uses antibiotics. Behavioral changes among the population must include prevention of infection
transmission by vaccination, hand-washing, safe sexual intercourse and good food hygiene. An
egregious example is that antibiotics can be also consumed in food – many of the meat products found
in supermarkets are treated by antibiotics.
Antibiotic resistance:
• Can affect anyone – at any age and in every country
• Makes more infections harder to treat (treatment becomes less effective)
• Leads to higher medical costs
• Prolonged hospital stays
• Increases the mortality
The goals of antimicrobial stewardship are:
• Achieve optimal clinical outcomes related to antimicrobial use
• Minimize toxicity and other adverse effects
• Reduce the costs of health care for infection
• Limit the natural selection of antimicrobial-resistant strains

31 Breakpoint – a
dynamic clinical marker, the MIC value assessed by a drug agency according to the epidemiology of the infection
and the prevalence of sensitivity/resistance in the geographic area.
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Pitfalls in Antibiotic Use

The following sections describe situations of incorrect administration of antibiotics. Each one of the
points below is the solution to these problems.
1. Use of antibiotics when not needed (especially when confusing bacterial and viral infections)
• Influenza – treat with antibiotics only immunocompromised and elderly patients.
2. Inappropriate dosage
• Administer the antibiotic according to the guided number of days (any deviation from the
guidelines is incorrect use of the drug)
3. Prolonged antimicrobial prophylaxis than really needed.
• Prophylaxis is considered as the administration of an antimicrobial agent for less than 24h,
commonly before surgeries (3-day drug-regimen is defined as therapy, thus cannot be called
prophylaxis). Try to time the peak in drug concentration during the procedure, but do not
continue with drug administration after the surgery.
4. Unnecessary use of broad-spectrum antibiotics
• Use antibiogram to check the susceptibility of different strains to different antibiotics.
5. The perceived urge to “cover all pathogens”
• Pathogen prevalence – important factor of empirical therapy
6. Choosing the wrong antibiotic for the likely infection (confusing gram-positive and gram-negative
bacteria as the etiological agents)
• Pathogen prevalence – important factor of empirical therapy
• Use antibiogram to check the susceptibility of different strains to different antibiotics.
7. Choosing an antibiotic against a strain which is likely already resistant
8. Choosing an antibiotic which does not penetrate the site of infection
• Fluoroquinolones are beneficial due to high absorption in soft tissues, but they may lead to
many side effects (PO administration AEs are similar to IV’s)
• Daptomycin – inappropriate in lung infections
Cell wall inhibitors:

β-Lactams
The family of beta-lactams consists of three sub-classes of antibiotics: penicillins, cephalosporins and
carbapenems.

Penicillins
Structure: β-lactam + thiazolidine rings + side chain (determines the various drug entities)
Mechanism:
• Inhibition of cell wall synthesis by binding to PBPs, thus blocking transpeptidation
• Bactericidal
Resistance mechanism: β-lactamases (enzymes breaking the ring) or modified PBPs
Adverse effects: allergic reactions (<10% of patients), anaphylaxis (rare, 0.004-0.4%), might affect the
GI tract, blood or CNS.
Excretion: by renal tubular cells
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Natural Penicillins (1st generation)

Directed against (agents) Directed against (diseases)
Penicillin G (IV) Group A, B streptococci • Secondary and tertiary syphilis (CNS involvement)
Penicillin V (PO) Neisseria meningitidis • Prophylaxis of rheumatic fever recurrences
• Prophylaxis of Streptococcal / H. influenzae infection
in splenectomized patients
Benzathine penicillin (IM) • Primary syphilis (syphiloma)

Methicillin Derivatives (2nd generation)

Directed against (agents) Directed against (diseases)
Oxacillin (IV) Staphylococci (methicillin • MSSA/MSSE infections
Flucloxacillin (PO) sensitive) – most are beta-
Methicillin (in-vitro) lactamase producers
Aminopenicillins (3rd generation)
Directed against (agents) Directed against (diseases)
Ampicillin (IV) Wider spectrum which includes • Endocarditis (+/- gentamycin)
some gram-negative bacteria • Meningitis – by Listeria monocytogenes
Amoxicillin (PO/IV) (Salmonella spp., E. coli) • UTI (+clavulanic acid)
• URTI
• H. pylori infection

Acylaminopenicillins (4th generation)

Directed against (agents) Directed against (diseases)
Piperacillin (IV) Wide-spectrum: Gram-positive • MSSA/MSSE
+ tazobactam and negative, but neither on
Ticarcillin ESBL nor MRSA

Tazobactam – a β-lactamase inhibitor. Piperacillin-tazobactam is an empiric treatment of severe

infections (gram-positive and negative).

Cephalosporins
Structure: β-lactam + thiazolidine rings + side chain (determines the various drug entities)
Mechanism:
• Inhibition of cell wall synthesis by binding to PBPs, thus blocking transpeptidation
• Bactericidal
• The newer is the generation – better efficacy against gram-negative and poorer efficacy against
gram-positive bacteria.
Resistance mechanism: β-lactamases (enzymes breaking the ring) or modified PBPs
Adverse effects: allergic reactions (<1-3% of patients), anaphylaxis (usually lower incidence than
penicillin, 0.01%), might affect the GI tract, blood or CNS.
Excretion:
• By renal tubular cells – change the dosage if the patient has renal failure
• Exception: ceftriaxone (Rocephin TM, excreted by the liver so there is no need to change the dose)
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1st Generation
Directed against (agents) Directed against (diseases)
Cefazolin Staphylococci, Streptococci • Skin/soft tissue infections
Cefalotin • Surgical prophylaxis – of oxacillin-sensitive strains

In surgery prophylaxis - if there is a risk of oxacillin-resistance, use vancomycin.

2nd Generation
Directed against (agents) Directed against (diseases)
Cefuroxime Variable efficacy against gram+ • Used by gynecologists against inflammatory pelvic
Cefamandole Better efficacy against gram- disease (IPD)
Cefotetan • Used in skin/soft tissue infections (SSTI)
Cefoxitin

Adverse effect – low value of blood prothrombin (alteration of coagulation), and consequently
increased risk of bleeding.
3rd Generation
Directed against (agents)
Cefotaxime Active against wide-spectrum
Ceftriaxone of gram-negative bacteria:
• H. influenzae
• N. meningitidis
• M. catarrhalis
• S. Pneumoniae
Ceftazidime Best against P. aeruginosa
Cefepime
Directed against (diseases)
• Meningitis – add ampicillin if the agent is L.
monocytogenes
• Pneumonia – when the patient is treated in the
hospital
• Sepsis
• UTI (commonly caused by gram-negative bacteria)
• URTI

• Do not use on ESBL-producing strains due to fear of resistance.

• Ceftriaxone – not for pseudomonas infection
4th Generation
Directed against (agents) Directed against (diseases)
Ceftaroline Active against wide-spectrum • Skin and soft tissue infections
of gram-positive and gram- • Community-acquired pneumonia
Ceftobiprole negative bacteria:
• Including MRSA
• Not for pseudomonas

Less used in clinical practice due to the high costs.

Carbapenems
Structure: β-lactam derived from thienamycin (synthesized by Streptomyces cattleya)
Mechanism: (broadest antibacterial spectrum)
• Inhibition of cell wall synthesis by binding to PBPs, thus blocking transpeptidation
• Bactericidal
Resistance mechanism: modified PBPs or carbapenemases (enzymes breaking the molecules)
Adverse effects: allergic reactions or seizures (more common in imipenem therapy)
Excretion: by the kidneys
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Directed against (agents) Directed against (diseases)

Imipenem More effective against gram- • Bacteremia
negative • Pneumonia
Meropenem More active against gram- • UTI
positive (not MRSA) • Skin and soft tissue infections
• Intra-abdominal infections
• Meningitis (Meropenem)
Ertapenem Poor activity against
Pseudomonas, Enterococcus
and Acinetobacter (do not use
in cephalosporin-resistant
infections)
Good activity against anaerobes (E. coli, Streptococci, Staphylococci, Salmonella, Listeria etc.)

Glycopeptides
Structure: a modified tricyclic peptide
Mechanism:
• Inhibition of cell wall synthesis by binding to UDP-NAM pentapeptide (high affinity to the double D-
alanine terminus).
• Bactericidal
Resistance mechanism: VanA (of Enterococci, VRSA), thickened cell wall (of VISA – vancomycin
intermediate Staph. aureus)
Adverse effects: nephrotoxicity, “red man syndrome” – rash on the face, neck and torso.
Excretion: by the kidneys
Directed against (agents) Directed against (diseases)
Vancomycin Active against gram-positive bacteria, • MRSA infections
Teicoplanin including MRSA • Febrile neutropenia
Monitor: renal function (change the dosage if necessary), serum concentration (therapeutic drug
monitoring, TDM).

Lipopeptides
Structure: an analog of phospholipid
Mechanism:
• Integrates in the bacterial cell membrane, disrupting the membrane potential
• Bactericidal
Resistance mechanism: currently only in vitro
Adverse effects: GI or muscle toxicity
Excretion: by the kidneys
Directed against (agents) Directed against (diseases)
Daptomycin Active against gram-positive • Complicated skin and soft tissue infections (especially by ORSA)
bacteria, including • Right-sided endocarditis (use in left-sided endocarditis is only
glycopeptide-resistant strains authorized in the US)
• Not for lung infections (due to penetration)
Monitor: creatine-kinase (to avoid muscle toxicity)
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Protein synthesis inhibitors:

Oxazolidinones
Mechanism:
• Binds the 50S subunit of the ribosome, specifically the peptidyl-transferase center, inhibiting
protein synthesis
• Bactericidal
Resistance mechanism: currently only in vitro
Adverse effects: myelosuppression, serotonin syndrome (SS)32, optic neuropathy, lactic acidosis
Excretion: metabolism by the liver and excretion by the kidneys
Directed against (agents) Directed against (diseases)
Linezolid Active against gram-positive • Complicated skin and soft tissue infections
bacteria including MRSA, VRE • Pneumonia in the ICU (which occurs due to artificial
and mycobacteria ventilation)
• Multi-drug resistant gram-positive bacterial
infections
• Severe meningitis (best concentrated in CSF)

Macrolides
Mechanism:
• Bind the 50S subunit of the ribosome (inhibiting protein synthesis)
• Bacteriostatic
Resistance mechanism: efflux pumps, altered 23SrRNA
Adverse effects: GI symptoms, QT prolongation
Excretion: in urine and bile
Directed against (agents) Directed against (diseases)
Erythromycin Active against gram-positive • Pneumonia
Clarithromycin bacteria (Streptococci), M. • Legionnaire’s disease
Azithromycin pneumoniae, C. pneumoniae, L.
pneumophila In cases of allergy to penicillins (due to similar antibiotic
spectrum)

Lincosamides
Mechanism: bind the 50S subunit of the ribosome (inhibiting protein synthesis)
Resistance mechanism: altered 23SrRNA, inactivation by enzymes
Adverse effects: Clostridium difficile colitis (pseudomembranous)
Excretion: by bile and urine
Directed against (agents)
Clindamycin Active against Streptococci (including S. pneumoniae), MSSA, anaerobes, T. gondii, P.
falciparum

32 A group of symptoms due to serotonergic drugs - high body temperature, agitation, increased reflexes, tremor, sweating,
dilated pupils, and diarrhea.
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Aminoglycosides
Mechanism:
• Bind the 30S subunit of the ribosome (inhibiting protein synthesis)
• Bactericidal
Resistance mechanism: enzymatic modification, efflux pumps
Adverse effects: nephrotoxicity (5-25% of the cases) or ototoxicity. Do not administer for more than
two weeks.
Excretion: by the kidneys
Directed against (agents) Directed against (diseases)
Gentamycin Active on some gram-positive • Severe gram-negative infections – usually combined
Amikacin and mainly on gram-negative with a beta-lactam/vancomycin/anti-anaerobe
bacteria, including P. • Endocarditis – with ampicillin/vancomycin
aeruginosa.

Anaerobes are intrinsically

resistant.

Monitor: renal function (change the dosage if necessary), serum concentration (therapeutic drug
monitoring, TDM).

Tetracyclines
Mechanism:
• Inhibition of protein synthesis (bind to S30 subunit of the ribosome)
• Bacteriostatic
Resistance mechanism: efflux pumps, ribosomal protection proteins, enzyme inactivation
Adverse effects: photosensitivity, deposition in bones and teeth (contraindicated in children under 12
years), fatty liver
Excretion: doxycycline is excreted by the GI tract
Generation Name/s Indications Additional info.
1st Tetracycline
• Chlamydial infections, Rickettsia • Metabolized in the liver
Doxycycline, infections, Brucellosis (add rifampin)
2nd minocycline • Exacerbations of COPD, acne and pelvic
inflammatory disease (PID)
• Broad spectrum of gram-positive bacteria
Tigecycline (including MRSA, VRE) and gram-negative
3rd (Glycylcycline) (except for Pseudomonas and Proteus)
• Complicated SSTI, abdominal infections
Nucleic-acid inhibitors:

Rifamycins
Mechanism: inhibit DNA-dependent RNA-polymerase
Resistance mechanism: mutation in the rpoB gene (better to use in combination with another drug to
avoid resistance).
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Adverse effects: drug interactions (rifampin is a potent inducer of CYP450)

Directed against (agents) Directed against (diseases)
Rifampin Active against Streptococci • Strep/Staph infections
(including S. pneumoniae), • Mycobacterial infections
Rifabutin Staphylococci (including • Mycobacterial infections
MRSA), N. gonorrhea /
meningitidis, M. tuberculosis,
Brucella

Quinolones
Mechanism: inhibition of nucleic acid synthesis (by binding to DNA-gyrase and topoisomerase IV)
Resistance mechanism: mutations that cause altered target enzymes, altered cell permeability
Adverse effects: GI disorders (3-17% of the cases), seizures, arthropathy and tendon rupture
(contraindicated in children), QT prolongation.
Excretion: by the kidneys
Generation Name/s Indications Additional info.
st • Effective against gram-negative bacteria • Pediatric use
1 Nalidixic acid
(DNA gyrase)
• Increased activity (including P. aeruginosa) • Exists also in PO administration
Ciprofloxacin,
2nd Ofloxacin
• UTI, gonorrhea, prophylaxis of N.
meningitidis, Anthrax
• Effective against both gram-negative and
positive (topoisomerase IV) bacteria.
• Used against respiratory infections
3rd Levofloxacin
(pneumococci = S. pneumoniae) –
pneumonia, COPD
• UTI, SSTI
• pneumonia, COPD • Hepatic metabolism (caution in
4th Moxifloxacin • UTI, SSTI liver failure)

Folate inhibitors:

Sulfonamides
Mechanism:
• Inhibition of folate synthesis (used together with trimethoprim)
• Bacteriostatic
Resistance mechanism: production of competitor molecules, enzymes that disactivate the drug,
reduced membrane permeability
Adverse effects: GI disorders, hypersensitivity, blood disorders
Excretion: by the kidneys (metabolized by the liver)
Directed against (agents)
Co-triamoxazole • Active against broad spectrum of gram-positive (including MRSA) and gram-
(trimethoprim and sulfamethoxazole) negative bacteria, protozoa and fungi (P. jirovecii)
• Used in UTI, SSTI, P. jirovecii pneumonia
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Infection Control
Infection control is the first principle of infection prevention. Many infections are associated with
healthcare, and about 35-50% of them are due to only five practices:
• Use and care of urinary catheters
• Use and care of vascular access lines
• Therapy and support for pulmonary functions
• Surveillance of surgical procedures
• Hand hygiene and standard precautions
How to prevent spreading of infections:
• UTI due to catheterization (CA-UTI)
o Avoid using catheter irrigation
o Do not use systemic antimicrobials routinely as prophylaxis
o Do not change catheters routinely – replace (do not clean), if there is symptomatic bacteriuria
o Empty the collecting bag regularly, using a separate collecting container for each patient, and
avoid allowing the draining spigot to touch the collecting container
o Always keep the collecting bag below the level of the bladder
o Do not routinely use silver-coated or other antibacterial catheters
o Do not screen for asymptomatic bacteriuria in catheterized patients
o Do not treat asymptomatic bacteriuria in catheterized patients except before invasive urologic
procedures
• Catheter-associated bloodstream infections
o Hand hygiene
o Maximal sterile barrier precaution at insertion
o Skin antisepsis with alcohol-based chlorhexidine-containing products
o Subclavian access as the preferred insertion site for central line (femoral approach is less
recommended)
o Daily review of line necessity (infection appears with reddish border, feels hot in palpation)
o Standardized catheter care using a non-touch technique
o Respecting the recommendations for dressing change – do not clean if there is suspicion for an
infection
o Use appropriate container for the needles or contaminated waste
• Ventilator-associated pneumonia (VAP)
o Hand hygiene
o Isolation precautions
o Avoid intubation/reintubation – prefer non-invasive ventilation
o Disinfect the machinery
• Surgical site infections
o Try using less-invasive approaches, give prophylaxis (less than 24h), keep the surroundings as
hygienic as possible
• Good work practice –
o Hand-washing (and sanitizing), using gloves, protective clothes, keep the working clothes clean
and washed
o Behavior – do not work while being sick, cough or sneeze to the elbow