Day 9 Mycology & Applied January 2021

MYCOLOGY
MYCOLOGY
• Characteristics of fungi
- They are eukaryotic organisms.
- They reproduce by means of spores both sexual (meiotic)
and asexual (mitotic) spores may be produced.
- Vegetative forms may be unicellular (yeasts) or composed
of hyphae.
- Cell walls are composed mostly of chitin.
- Fungal cell membrane contains ergosterol.
- They are heterotrophic, not autotrophic.
Classification of fungi
A- Morphological classification: 3 types:
1. Filamentous fungi (moulds): These grow as hyphae (septate or non-
septate). On artificial media, they form large filamentous colonies. They
reproduce by the production of various kinds of spores (conidia).
Examples include the zygomycetes (Rhizopus, Absidia, Mucor….),
Aspergillus, Penicillum and the dermatophytes (Trichophyton,
Microsporum and Epidermophyton)
2. Yeasts: These grow as single cells. On artificial media, they form
compact colonies. They reproduce by budding and may form
pseudohyphae. Examples include Cryptococcus neoformans,
Malassezia, Trichosporon and Candida albicans and other Candida
species.
3. Dimorphic: i.e., have 2 forms of growth:
- At 22°C on artificial media, they grow as hyphae.
- At 37°C (body temperature) on enriched media or in tissue, they
grow as yeasts.
• Examples include Histoplasma capsulatum, Blastomyces dermatidis and
Coccidioides immitis.
B- Clinical classification of fungi
1. Superficial mycoses: Affecting the horny layer of the skin, e.g.,

Pityriasis versicolor.
2. Cutaneous mycoses: Affecting the deep layers of the skin, e.g.,

candidia and dermatophytes.
3. Subcutaneous mycoses: In which fungi present in the soil are

implanted in the subcutaneous tissue by trauma, e.g., mycetoma,
blastomycosis and sporotrichosis.
4. Deep (systemic) mycoses: These are usually caused by fungi

that live free in nature, i.e., opportunistic. Most infections are
subclinical. However, some cases may develop severe and even
fatal infection, e.g., pneumocystis pneumonia, blastomycosis,
cryptococcosis, histoplasmosis & occasionally, candidiasis.
B- Clinical classification of fungi
5. Mycotoxicosis: It is produced by consumption of

food containing fungal toxins:
- Mushroom poisoning which causes damage to liver, kidney
and bone marrow.
- Aflatoxin of Aspergillus flavus may cause chronic liver
damage and cancer.
6. Allergic disorders: Spores of free-living fungi as

Aspergillus may be the allergen in some cases of atopy
(asthma, hay fever, urticaria, etc.).
Diagnosis of fungal infections
A) Specimens are collected according to the site of infection such as
skin scales, nail clippings, hairs, respiratory secretions, biopsies,
blood...etc.
B) Direct detection
1. Microscopical examination of unstained preparations to
demonstrate hyphae, spores or yeast cells. In case of superficial and
cutaneous mycoses, the specimen (skin scales, nail clippings or hairs)
is first mounted with 10-20% KOH to dissolve keratin.
2. Microscopical examination of stained preparations: Different
stains are used, e.g., Gram’s stain, India ink, Periodic Acid Schiff (PAS),
silver stains and lactophenol cotton blue stain.
3. Antigen detection (e.g., cryptococcosis & aspergillosis)
C) Cultivation
• Different culture media are recommended.

• The most commonly used are Sabouraud’s dextrose agar
(SDA).
• Growth of most fungi is better at 25-30°C.
• If deep mycotic infection is sustained (which is usually
caused by dimorphic fungi), enriched media are inoculated
and incubated at 37°C to allow growth of the yeasty phase of
the fungus.
D) Identification of culture growth by:
1. Colony morphology including the surface and reverse views of
the growth is the principal way for identifying fungi.
2. Microscopic examination of wet and stained smears to
distinguish the different types of hyphae and conidia (spores).
3. Biochemical tests.
E) Serodiagnosis: Detection of specific antibody may help in

diagnosis of systemic mycoses.
F) Skin testing (delayed type hypersensitivity).

Treatment of fungal infections
Antifungal Drugs:
• Because fungi are eukaryotes, the range of non-toxic

systemically active antifungal drugs is still limited.
• The most commonly used drugs are amphotericin B,

griseofulvin, flucytosine, terbinafine, fluconazole,
Ketoconazole, Itraconazole and mycostatin (nystatin).
PITYRIASIS VERSICOLOR
• It is a common fungus infection of the horny layer

of the skin. It affects the upper part of the trunk and
sides of the neck. It appears as scaly macules,
either hyperpigmented or hypopigmented. The
causative organism is Malassezia furfur.
DERMATOPHYTES
• Three Genera of dermatophytes infect man: Microsporum,

Trichophyton and Epidermophyton.
• They affect the keratinized tissue (hair, nail and skin).
Infection is transmitted by direct or indirect contact.
• The disease is characterized by being superficial, extends
radially and heals at the centre to form circular lesions called
ringworm.
• The sources of infection may be man (anthropophilic),
animals as dogs and cats (zoophilic) and soil (geophilic).
Clinical types of dermatophytes
Ringworm is usually referred to as tinea. According to the

site there are several types of ringworm infections:
1. Tinea capitis (ringworm of the scalp)

2. Tinea pedis (athlete's foot)
3. Tinea unguinum (ringworm of nails)
4. Tinea circinata (ringworm of non-hairy skin)
5. Tinea cruris (ringworm of the skin of the groin)
6. Tinea barbae (ringworm of the skin of beard)
Aspergillosis
• It is caused by Aspergillus fumigatus, rarely by Aspergillus niger

and A. flavus. The spores are found in air and are continuously
inhaled.
Clinical presentations:
1. Allergy, e.g., bronchial asthma (type I hypersensitivity).
2. Non-invasive infections, e.g., colonization of a preexisting lung cavity
and otitis.
3. Invasive infection occurs in severely immunocompromised patients
with leukaemia, organ transplant recipients & patients under steroid
therapy.
4. Mycotoxicosis: Aflatoxin of A. flavus is hepatotoxic and carcinogenic.
CANDIDIASIS
Candidiasis (moniliasis) is most frequently caused by Candida
albicans and rarely due to infection by other non-albicans
species, e.g., C. stellatoidea, C. krusei…etc. Candida albicans is
present as normal flora in the oral cavity, vagina and intestine.
Predisposing factors to candidiasis:

1. Diabetes
2. Broad-spectrum antibiotic treatment (superinfection)
3. Steroid therapy
4. Immunosuppression
5. Prolonged exposure to water, pregnancy and old age
Clinical features of CANDIDIASIS
• Superficial: Affecting skin and mucous membranes:
- Oral thrush
- Vulvovaginitis
- Paronychia (nail infection)
- Interdigital
- Intertrigo (between skin folds), e.g., diaper rash
- Chronic mucocutaneous candidiasis is usually associated with T-cell
deficiency.
• Systemic: Affecting the lung or kidney. It usually complicates an

underlying disease as TB, malignancy or immunosuppression.
Laboratory diagnosis of candidiasis
Specimens from skin, mouth, vagina, sputum…etc., are subjected to:
1. Microscopic examination of a Gram-stained smear for the presence of

Gram-positive oval, budding yeast cells and pseudohyphae.
2. Cultivation: C. albicans can grow on most culture media at 37°C. The
selective medium is Sabouraud’s dextrose agar (SDA) containing
chloramphenicol. After 1-2 days, yeast colonies appear creamy white,
pasty with yeasty odour. C. albicans is differentiated from other
Candida species by the followings:
- Formation of germ tubes in serum at 37°C within 1-2 hours
- Formation of chlamydospores on corn meal agar
- Biochemical reactions
Cryptococcosis
• It is caused by Cryptococcus neoformans.

• The organism is present in the soil contaminated with
excreta of birds particularly pigeons. Infection occurs by
inhalation.
• It may result in lung infection (cryptococcus pneumonia).
• Spread to the central nervous system leads to meningitis.
Laboratory diagnosis of cryptococcosis
1. Detection of the organism in sputum or CSF. A smear stained

with India ink will demonstrate Cryptococcus neoformans as
budding yeast cells surrounded by a large gelatinous capsule.
2. Culture: on SDA, the organism gives mucoid colonies. Growth is
identified by characteristic morphology, urease positive and
pathogenicity to mice.
3. Detection of capsular antigen in the CSF, by latex agglutination
test.
4. Detection of specific antibodies in the patient’s serum.
PNEUMOCYSTIS JIROVECI
• Pneumocystis jiroveci is an opportunistic fungus that lives in

the lungs of humans.
• Most people are infected with P. jiroveci by the age of four and
develop no symptoms, unless they are immunocompromised.
• It causes interstitial pneumonia in association with HIV
infection, primary immunodeficiency, prolonged steroid treatment,
organ transplantation and cancers.
• P. jiroveci pneumonia (PCP) is the most common opportunistic
infection in AIDS patients.
• The organism can be detected in clinical specimens by PCR or
after staining with silver stain.
MYCETOMA
(MADURA FOOT or MADUROMYCOSIS)
• Mycetoma is a clinical syndrome characterized by granuloma,

tumefaction, multiple abscesses, draining sinuses & pus with
granules.
• It is a localized infection that involves cutaneous and

subcutaneous tissue, fascia, and bone.
• It usually affects the foot and rarely the hands and buttocks.
• The organisms involved are present in the soil and are implanted,
by trauma, into the tissue, especially in bare footed people.
Therefore, lesions are localized at the site of the trauma.
Types of mycetoma
1. True fungi (Eumycotic mycetoma)
2. Actinomycetes (Actinomycotic mycetoma)
• It is important to know whether the mycetoma is caused by

fungi or actinomycetes because actinomycotic mycetoma
will respond to antibiotics while fungal infection will not. The
latter needs surgical treatment up to amputation.
Types of mycetoma
Actinomycotic mycetoma Eumycotic mycetoma
Causative agent Bacterial: e.g., Fungal: e.g., Madurella
Actinomadura madurae, mycetomatis, Madurella
Nocardia brasiliensis and grisea and Allescheria
Streptomyces somaliensis boydii
Colour of Mainly yellow (sulphur) Mainly black & white
granules
Microscopic Thin fragmented Thick hyphae & spores
exam filaments
Culture On blood agar, aerobic On SDA, incubated at 30°C
and anaerobic
Chemotherapy Effective - No or poor response
- Needs surgical
treatment and may be
amputation
Pyrexia of Unknown
Origin
(PUO)
Pyrexia of unknown origin (PUO)
• It’s defined as fever (as a

predominant clinical feature) for at
least 10 days without an obvious cause.
• Infective causes are responsible for

75% of cases of acute PUO.
Major causes of PUO
•Infections (75%)
• Neoplasms
• Autoimmune diseases (as SLE & rheumatic fever)
• Drug induced fever
• Granulomatous disease
Infective causes of PUO
A- Non-specific causes:
• Cryptic abscesses in liver, abdomen, pelvis
and retroperitoneal or mediastinal sites
• Infective endocarditis
• Urinary tract infections
• Ear, sinus or dental infections
B. Specific causes of PUO
• Bacterial diseases:
• Enteric fever
• Brucellosis • Typhus
• Tuberculosis • Leptospirosis
• Q fever • Relapsing fever
• Nocardiosis
D.D. of PUO
• Viral diseases:
• Hepatitis A or B
• AIDS
• Lassa fever
• Yellow fever
• CMV
• Infectious mononucleosis (EBV)
D.D. of PUO
Fungal diseases: • Protozoal diseases:

• Cryptococcosis • Malaria
• Candidiasis • Amoebiasis
• Pneumocystis • Toxoplasmosis
• Histoplasmosis • Trypanosomiasis
• Aspergillosis
Laboratory Diagnosis of PUO
• CBC count & microscopic examination
• Urine analysis
• Blood chemistry
• Cultures
• Serology
• Other tests
1. CBC count & microscopic examination:
• Anemia is an important finding & suggests a serious

underlying disease.
• Ensure that leukemias are not missed in a leukemic or pre-

leukemic cases.
• Suspect EBV infection if the patient has lymphocytosis

with atypical cells.
• Leucocytosis may suggest an occult bacterial infection.
• Diagnose malaria & spirochaetal diseases with the aid of

direct examination of the peripheral blood smear; however,
repeated examinations are often necessary.
2. Urine analysis:
• Exclude UTIs & malignant tumors of the urinary tract;
however, not all of them consistently are associated with
pathologic findings in the urine.
3. Blood chemistry:
• At least one liver function test is usually abnormal, with an
underlying disease originating in the liver or a disease that
causes non-specific alterations of the liver (e.g.,
granulomatous hepatitis).
• Most other chemistry tests rarely contribute to the

diagnosis, though they are frequently ordered.
4. Cultures:
• Blood cultures (both aerobically & anaerobically) are
essential in the evaluation; however, no more than 6 sets of
blood cultures are required.
• Routinely culture the patients' urine.
• Cultures of sputum & stool may be helpful in the presence

of signs or symptoms suggestive of pulmonary or GIT
disease, respectively.
• Perform cultures for bacteria, mycobacteria & fungi in all

normally sterile tissues & liquids that are sampled during
further workup. These tissues & fluids include bone
marrow or lymph node aspirates, CSF, pleural or peritoneal
fluid.
5. Serologies:
• Serologies are most helpful if paired samples show a

significant, usually 4-fold, increase of antibodies
specific to an infectious microorganism.
- Brucellosis, CMV, infectious mononucleosis, HIV,

amebiasis, toxoplasmosis & chlamydial diseases are
diagnosed by serology.
• These diagnostic tests are of limited value in most

patients with FUO, but they are appropriate for
evaluation of the above illnesses in the correct clinical
& epidemiological setting.
6. Other tests:
• Frequently check antinuclear antibody (ANA) titers,

rheumatoid factor, thyroxine level & ESR because they are
helpful in diagnosing some selected conditions (lupus,
rheumatoid arthritis, thyroiditis, hyperthyroidism). Their
diagnostic accuracy is limited in other autoimmune &
collagen vascular diseases.
• In patients in whom Giant Cell Arteritis (GCA) &

Polymyalgia Rheumatica (PMR) are suspected, checking
the ESR may be particularly useful because the ESR is
nearly always greater than 60 mm/h (& often is much
higher, especially in GCA).
SALMONELLA
Salmonella
• Widespread in nature.
• Found in intestinal tract of mammals, birds and reptiles.
• Poultry is one of the primary reservoirs of the organism.
Medically important Salmonella
Salmonella Enteritidis& Typhimurium (G.E.)
Salmonella Typhi & Paratyphi A,B,C (typhoid fever)
Salmonella Choleraesuis (septicemia)

Typhoid & Paratyphoid Fever
Antigenic Structure
1. The O (somatic) antigens, heat-stable polysaccharides

of the cell wall lipopolysaccharide (LPS).
2. The H (flagellar) antigens, heat-labile proteins

(flagellin) of the flagella.
3. The Vi antigen, a heat-labile capsular polysaccharide

antigen, overlying the O-antigen in few serovars, e.g.
S. Typhi.
A schematic diagram of a single Salmonella typhi cell showing the
locations of the H (flagellar), 0 (somatic) and Vi (K envelope)
antigens
Enteric fever
(Typhoid & Paratyphoid Fever)
• Typhoid fever is caused by Salmonella Typhi.
• A similar milder syndrome is caused by

“paratyphoidal” strains of Salmonella: Salmonella
Paratyphi A, Paratyphi B & Paratyphi C.
Enteric Fever
(TYPHOID & PARATYPHOID FEVERS)
• Enteric fever is defined as ‘a generalized infection of the

reticuloendothelial system & intestinal lymphoid tissue
accompanied by sustained fever & bacteraemia’.
• Globally, typhoid fever is more common than

paratyphoid fever.
Typhoid Fever Map
Modes of Transmission
• Oral transmission via food or drink handled by an
individual who chronically sheds the bacteria through
stool or, less commonly, urine.
• Hand-to-mouth transmission after using a

contaminated toilet & neglecting hand hygiene.
• Oral transmission via sewage-contaminated water or

shellfish or by flies & cockroaches.
Susceptibility & Immunity
• All seasons, usually in summer & autumn.
• Most cases in school-age children & young adults.
• Both sexes are equally susceptible.

Pathogenesis 1
• Humans are the only reservoir (either patients or
healthy carriers).
• The number of bacilli needed for infection is >105

bacteria.
• The organism adheres to the mucosa of the small

intestine then invades the submucosal layer.
Pathogenesis 2
• Invasion of macrophages in the lymphoid tissues occur
then Salmonellae are transported by lymphatics to
mesenteric lymph glands.
• It disseminates into the blood-stream (1st bacteraemia

during the 1st week of illness).
Pathogenesis 3
• At the same time, uptake of the organisms by spleen &
liver occurs where replication inside macrophages takes
place.
• 2nd bacteraemia occurs & the organism is then

transported to the gall bladder to be excreted with bile
into the small intestine.
Pathogenesis 4
• Re-invasion of small intestine & uptake in Peyer’s
patches take place.
• The organism is excreted with faeces (from the 2nd week

of the disease).
• In about 25% of cases, the organism is excreted in urine

(after the 2nd week of the disease).
Pathogenesis Summary
• Faeco-oral transmission.
• Multiplication in the Peyer’s patches of the intestine

Lymphatics
Blood stream
Liver bile stools

Or
Kidneys urine (25%)
S.Typhi. liver、spleen、gall、
BM ,ect
2nd bacteremia early stage&acme stage
(1-3W）
stomach
Bac. In gall
Bac. In
Lower feces
ileum mononuclear phagocytes
peyer's patches & S.Typhi eliminated

mesenteric lymph nodes convalvescence stage
(4-5w)
LN Proliferate,swell 1st bacteremia
necrosis
defervescence stage thoracic
(Incubation stage)
Enterorrhagia,i
（3-4w） duct 10-14d
ntestinal
perforation
CLINICAL FEATURES
• Incubation period: 10-14 days.
• Onset: slow, insidious & vague in the form of fever, headache

& malaise, diffuse abdominal pain & constipation.
• During the first week, the fever becomes steadily higher on a

stepwise pattern.
• During the second week, the fever may be steady or may

swing.
Special Manifestations
• In children: Often atypical

• Sudden onset with high fever.
• Respiratory symptoms & diarrhea.
• Convulsions common in < 3 years.
• Relative bradycardia rare.
• Splenomegaly, roseola (rose spots) & leucopenia less
common.
Special Manifestations
• In the aged:
• Temperature not high, weakness common
• More complications
• High mortality
Relapse
• Symptoms & signs reappear.
• The bacilli have not been completely removed.
• Some cases relapse more than once.

Complications
• Relapse
• Bowel perforation & intestinal haemorrhage (before
the era of antibiotics)
• Carrier state
• Toxic hepatitis: common, 1-3 weeks hepatomegaly,
ALT elevated, improve in 2~3 weeks.
• Toxic myocarditis: seen in 2-3 weeks, usually severe
toxemia.
• Bronchitis, bronchopneumonia: seen in early stage.
Other complications:
• Toxic encephalopathy
• Hemolytic uremic syndrome (HUS)
• Acute cholecystitis
• Meningitis
• Nephritis
Cases & Chronic Carriers
• Cases discharge Salmonella from

incubation, more in 2~4 weeks after
onset, a few (about 2~5%) last longer
than 3 months.
• May persist to become chronic

(intestinal or urinary) carrier.
• Chronic carrier: Typhoid Mary

Laboratory Diagnosis of Enteric Fever
Specimens
For Culture:
• Blood from the first day of illness (during 1st week).
• Faeces/Urine from the 2nd week onwards.
• Bone marrow is rarely indicated.
For Serology: Serum from the 2nd week onwards.

Direct detection
• Direct detection by microscopy is useless.

Cultivation
Blood or bone marrow culture
▪ Samples should be cultivated by blood culture

technique.
▪ Subcultures are plated on MacConkey agar &

incubated at 37oC.
Blood culture
• 80~90% positive during the first 2 weeks of illness &

50% in 3rd week.
• Not easy in 4th week.
• Re-positive when relapse.

• Bone marrow culture is the most sensitive test, specially
in patients pretreated with antibiotics.
• Urine & stool cultures increase the diagnostic yield but

are positive less frequently.
• Stool culture: better in 3~4 weeks (& may be done after

a cholagogue for the diagnosis of carriers).
• The duodenal string test: to culture bile, useful for the

diagnosis of carriers.
Stools Culture
▪ Faecal specimens should be inoculated directly on

both solid media & enrichment (tetrathionate or
selenite) broth.
▪ Subcultures from enrichment broth are done after

overnight incubation on solid media.
▪ Differential selective solid media such as MacConkey,

DCA, Salmonella-Shigella (SS), and Hektoen (HE) agar
are used.
▪ All cultures are incubated at 37ºC.

Identification 1
• After 24h incubation, colonies should be examined

for morphology, Gram stain & oxidase.
• Colony showing Gram-negative bacilli and is oxidase

negative is considered an Enterobacteriaceae.
SS/MacConkey Agar
Identification 2
• Salmonella is identified by:
• testing the colony for biochemical reactions.
• or by slide agglutination using O serogroup

antibodies.
Biochemical Reactions
(Sugar Fermentation/Citrate/Indole)
Biochemical Reactions
(Urease/TSI)
Georges-Fernand-Isidor Widal
(French physician)
•Widal in 1896, described

the Widal test that proved
a value in cases where
positive cultures have been
unobtainable.
Widal test a Popular test in the Diagnosis of Typhoid
Fever:
• Widal test is a presumptive serological test for enteric

fever.
• In case of Salmonella infections, it demonstrates the

presence of agglutinating antibodies against the O-
somatic & H-flagellar antigens in the serum.
Widal test – A standard tube
agglutination test
• Test technique also permits the detection of antibody

titre.
• A constant amount of the antigen is added to a series of

tubes containing serum dilutions.
• The Antibody titre is the highest dilution of serum

showing visible agglutination.
Widal Test
1. Serial dilution of the patient’s serum
1/20 1/40 1/80 1/160 1/320 1/640
2. Constant amount of known antigen added
1/20 1/40 1/80 1/160 1/320

Widal Test
Ab titre: highest dilution (lowest concentration) of

patient’s serum showing a positive agglutination reaction
Widal Test
Widal test
Five types of antigens
• 1 Somatic (O) antigen, 4 flagellar (H) antigens (1 for each
of S. typhi, S. paratyphi A, B, C).
• Antibodies start to appear AFTER the 1st week of illness.
• 70% positive in 3~4 weeks & can prolong up to several
months.
• In some cases, antibodies appear slowly, or remain at a
low level & some (10~30%) don’t appear at all.
Widal Test
• Antibodies can be detected at the beginning of the

second week onwards. At least 2 serum samples
should be obtained at intervals of 7-10 days to detect
rising of antibody titre.
• In the antibody response of enteric fever, O antibody

signifies active infection (because it disappears faster
than H antibody).
• On the other hand, H antibody signifies the type of

infecting organism.
Interpretation of Widal test
• Test results need to be interpreted

carefully in the light of:
• Past history of enteric fever
• Typhoid vaccination
• Antibody level in the populations

in endemic areas of the world
• "O" agglutinin antibody titer ≥1:80 and "H" ≥1:160 or 4
fold rise in “H" supports a diagnosis of typhoid fever.
• "O" rises alone, not "H", early in disease .
• Only "H" positive, "O" negative, often non-specifically

elevated by immunization or previous infections (Vaccinated
people have both O & H antibodies if recently immunized & H antibody alone in
cases of past-vaccination).
• False positive in some autoimmune diseases or in infection
with related members of Enterobacteriaceae due to cross
reactive antibodies.
• In endemic areas, healthy people have antibody titre due to

subclinical infection (Titres up to 1:40 are considered normal).
• Some positive in blood culture, but negative in Widal test.

• 'Vi" antibodies often useful for carrier (1:40). This is a
surface antigen easily lost during cultivation (Vi titres
seem to correlate better with the carrier state than do O
or H titres).
• Antibody level may be lower when using antibiotics early.

Causes of False-Positive Widal Test
• Previous immunization with Salmonella antigen
• Cross-reaction with non – typhoidal Salmonella
• Variability & poorly standardized commercial antigen

preparation
• Infection with malaria
• Other Enterobacteriaceae sharing the same antigens

Causes of False-Negative Widal Test
• The carrier state
• An inadequate inoculum of bacterial antigen in the host

to induce antibody production
• Previous antibiotic treatment
• Variability in the preparation of commercial antigens
• Technical difficulty or errors in the performance of the

test
Widal test is century old,
Is it loosing importance ?
• These reactions were the earliest (in 1896) to be adapted

to diagnostic laboratory for the diagnosis of typhoid fever.
• This test is now supplemented by more sophisticated

procedures.
Declining importance of Widal test
• The value of the salmonella agglutination tests has

declined as the incidence of typhoid fever has decreased,
at least in the developed world.
• The general use of vaccines has increased.
• The ever increasing-numbers of antigenically- related

serotypes of Salmonella have been recognised.
Serology - Importance of Repeated Tests
Criteria for diagnosing Primary Infection
• 4 fold or more increase in titre of IgG or total antibody
between acute & convalescent sera.
• Presence of IgM.
• Seroconversion.
(A single high titre of IgG (or total antibody) - very unreliable)
Criteria for diagnosing Reinfection

• Four fold or more increase in IgG titre between acute &
convalescent sera.
• Absence or slight increase in IgM.
Typical Serological Profile After Acute Infection
Note that during Reinfections, IgM may be absent or present at a low level transiently
Other Diagnostic Tests 1
• Slide agglutination test: In many places, instead of

the standard Widal test, a quantitative slide
agglutination test is used.
• Haemagglutination (HA) test: a useful alternative to

Widal test for the serological diagnosis of typhoid
fever in endemic areas.
• Countercurrent immunoelectophoresis
Other Diagnostic Tests 2
• Dot blot test: to detect IgG & IgM against the flagellar
antigen from Salmonella enterica serovar Typhi.
• Antigen detection tests: by co-agglutination test or

ELISA.
• DNA detection tests: by PCR.

Prognosis:
• Case fatality 0.5～1%, but high in old ages, infants &

serious complications.
• About 3% of patients become fecal carriers.

Prevention
(A) Hygienic measures
• Avoid contamination of food & water by rodents or

other animals that excrete salmonellae.
• Proper sewage disposal & chlorinated water supply.
• Pasteurization of milk & proper cooking of poultry,

meat & eggs.
Prevention
(A) Hygienic measures
• Hand wash prior to food handling.
• Food handlers are examined periodically to diagnose

carriers, who should be treated or excluded from
handling food.
Prevention
(B) Immunological measures
• TAB vaccine: A heat killed vaccine. The suspension contains

Salmonella Typhi, S. Paratyphi A and S. Paratyphi B. The
vaccine is given as 2 S.C. doses with one month interval, to be
followed by a booster dose some months later.
• Acetone-killed bacterial suspension of Salmonella Typhi: It is
given as 2 S.C. doses followed by a booster dose some months
later.
• Oral typhoid vaccine: A live avirulent mutant strain of S. Typhi.
• The Vi capsular polysaccharide of S. Typhi: given IM.
Antimicrobial susceptibilities
• Multidrug-resistance in S. Typhi strains has become a

problem.
• Because of the emergence of drug resistance to

chloramphenicol, now the drug of choice for enteric
fever & septicaemia is either ceftriaxone or
ciprofloxacin.
• Ampicillin or ciprofloxacin should be used in chronic

carriers of S. Typhi.
Treatment of Chronic Carriers
• Ofloxacin 0.2 bid or ciprofloxacin 0.5 bid, 4～6 weeks.
• Ampicillin 3～6g/day tid plus probenecid 1～1.5g/day. 4～

6 weeks.
• TMP+SMZ
2 tabs. Bid. 1～3 months.
• Cholecystitis may require cholecystectomy.

SHIGELLA
• Shigella causes bacillary dysentery in man; the severest
form of the disease is caused by S. dysenteriae type 1.
• Man is the natural reservoir for shigellosis.

Antigenic Structure
• Shigellae are non-motile (no H antigens).
• Classification (serological typing) of shigellae is

based upon biochemical reactions & structure
of the O antigens.
• There are four serogroups that are considered

species.
Serogroups, Species & Serotypes
(Serovars) of Shigella
O Species No of Useful Sugar
Sero- O Fermentations
groups Serotypes Glucose Lactose Mannite
A S. 13 + _ _
dysenteriae
B S. flexneri 8 + _ +
C S. boydii 18 + _ +
D S. sonnei 1 + Late +
Pathogenesis of Bacillary Dysentery 1
• Bacillary dysentery is a specifically human

disease.
• It is associated with heavy inflammation of the

colonic mucosa & pseudo-membrane
formation.
• Characterized by tenesmus & diarrhoea in

which the stools contain blood, pus & mucus.
Pathogenesis of Bacillary Dysentery 2
• Ingestion of few organisms (100-200

organisms) is able to cause disease, so
person-to-person transmission can occur.
• Transmission: Faeco-orally.
Virulence Factors 1
1. Invasiveness
The essential pathogenic

process of bacillary
dysentery is invasion of
mucosal epithelium of the
terminal ileum & large
intestine.
The organism does not

invade into the blood.
Virulence Factors 2
2. Shiga Toxin
• Shiga toxin is an exotoxin produced by S. dysenteriae
type 1.
• The toxin can act as an enterotoxin & neurotoxin that

may cause meningismus & coma.
• In shigellosis, the toxin may damage blood vessels

that could contribute to mucosal damage & may
cause renal failure seen in haemolytic uraemic
syndrome (HUS).
Clinical Picture
Laboratory Diagnosis of Bacillary Dysentery 1
• Specimens: Fresh stools.
• Direct detection: Direct microscopy can not identify

Shigella but is done to differentiate bacillary from
amoebic dysentery:
In bacillary dysentery, large number of PMNLs &

some RBCs are seen.
Cultivation (at 37°C/24 hours)
• Faecal specimens should be initially inoculated onto:

• MacConkey & DCA.
• Enrichment broth (selenite or tetrathionate broth)

subcultures from enrichment broth are done.
Identification
• Colonies are examined for morphology, motility, Gram
stain & oxidase.
• Any colony showing non-motile Gram-negative bacilli

& oxidase negative is considered an
Enterobacteriaceae.
Laboratory Diagnosis of Bacillary
Dysentery 4
• Shigella produces colourless (lactose non-

fermenting) colonies on MacConkey agar.
• Shigella is identified by:

• Biochemical reactions
• or by slide agglutination using O serogroup
antibodies.
Prevention & Control
• Shigella carriers (rare).
• Public health measures:

• Environmental sanitation
• Health education
• Safe water supply
• Proper sewage disposal
• Electrolyte & fluid replacement is an essential part of

treatment.
Antimicrobial Susceptibilities
• Susceptibility testing should be done because of the

widespread antimicrobial resistance among Shigella
strains.
• Recommended antibiotics:
• Ampicillin
• Fluoroquinolones (e.g., ciprofloxacin)
• Nalidixic acid
• Trimethoprim/ sulfamethoxazole
Brucella
• Brucella organisms are normal flora of the genital
& urinary tracts of many animals.
• Brucellosis is a zoonotic disease.
• The organisms are facultative intracellular

pathogens & cause brucellosis in man & animals.
Species or biovars are named after their host
or the disease they produce:
1. B. abortus infects cattle; the placenta is infected,

causing abortion in the animal.
2. B. melitensis infects sheep & goats.
3. B. suis infects pigs.
4. B. canis infects dogs.

BRUCELLOSIS
(Undulant fever or Malta fever)

The Many Names of Brucellosis
Human Disease
• Malta Fever
• Undulant Fever
Animal Disease
• Mediterranean Fever
• Bang’s Disease
• Rock Fever of Gibraltar
• Enzootic Abortion
• Gastric Fever
• Epizootic Abortion
• Slinking of Calves
• Ram Epididymitis
• Contagious Abortion
Transmission to Humans
• Conjunctiva or broken skin contacting infected tissues

(e.g., Blood, urine, vaginal discharges, aborted fetuses
or placentas).
• Ingestion
• Raw milk & unpasteurized dairy products
• Rarely through undercooked meat
Transmission to Humans
• Inhalation of infectious aerosols:

• Stables, slaughter houses, handling of Brucella cultures in the
laboratories.
• Inoculation with vaccines:

• B. abortus strain 19, RB-51
• B. melitensis Rev-1
• Conjunctival splashes, injection
• Person-to-person transmission is very rare.
• Incubation varies: 7-21 days to several months.

Transmission in Animals
• Ingestion of infected tissues or body fluids
• Contact with infected tissues or body fluids

• Mucous membranes, injections
• Venereal
• Swine, sheep, goats or dogs
Who is at Risk?
• Occupational Disease
• Cattle ranchers/ dairy farmers
• Butchers
• Veterinarians
• Meat inspectors
• Lab workers
• Hunters
• Travelers
• Raw dairy consumption

Virulence Factors
1. S-LPS: relatively poor inducer of IFN-Ɣ & TNF-
α.
2. Production of inhibitors of phagolysosome fusion

(e.g., adenine & guanine monophosphate).
3. OMP 25: downregulates TNF-α impaired

activation & cytotoxic function of NK cells.
N.B.: Elimination of Brucella depends on macrophage activation by Th1

cell-mediated immune response.
Clinical manifestations
Incubation period: usually 1 week – 3 months

(even 10 months IP has been reported).
Infective dose: very low (particularly B. melitensis)

10 organisms.
Brucellosis usually presents as acute (˂2 months)

or subacute (2-12 months) febrile illness which
may persist and progress to chronic disease (˃1
year) with severe complications.
Systemic symptoms include fever, which is usually
prolonged & intermittent (undulant: temperature
remains normal during the early part of the day &
rises during the evening), chills, weakness, malaise,
body aches, sweating & headache.
Brucellosis may also involve the liver, heart

(endocarditis) & CNS (meningitis).
In its subacute form, it may resemble tuberculosis.

Human Disease
• Can affect any organ or system.
• All patients have a cyclical fever.
• Variability in clinical signs

• Headache, weakness,
arthralgia, depression,
weight loss, fatigue,
liver dysfunction.
Complications
• Osteoarticular complications in 20-60% of cases:
Arthritis, spondylitis, osteomyelitis.
• Hepatomegaly may occur.
• Gastrointestinal complications in 2-20% of cases.
• Genitourinary involvement: Orchitis & epididymitis

are most common.
Complications
• Neurological
• Depression, mental fatigue.
• Cardiovascular
• Endocarditis.
N.B.: Blood donations of infected persons should not be accepted.

Immunity
• Brucella is able to survive intracellularly in
phagocytic cells. Therefore, the host defense
depends on cellular immunity.
• Delayed hypersensitivity reactions are

responsible for the granuloma & abscess formation
in bones or any organ.
• Antibody response to brucella includes

production of IgM, IgG & IgA.
Laboratory Diagnosis
A) Specimens:
▪ Blood or bone marrow aspirate (during the acute illness)
▪ Joint fluid (of patients with arthritis)
▪ Pus (from abscesses)
▪ CSF
B) Direct detection in clinical materials:

• PCR
• Gram stain is useless.
Laboratory Diagnosis (cont.)
C) Cultivation:
1. Blood culture: a large sample of blood is taken (10-30 ml) &
is added to 50-100 ml broth (heart infusion or brucella broth).
Subcultures are done on enriched media (e.g., serum dextrose
agar or blood agar) every 48 hours & growing organisms are
identified.
Since the organism is difficult to isolate on initial cultivation,
blood cultures should not be regarded negative except after
prolonged incubation for 6-7 weeks in presence of 10% CO2.
2. Direct inoculation of other specimens onto serum dextrose

agar, blood agar & chocolate agar to be incubated under 10%
CO2.
Culture
Brucella colonies appear

small, translucent &
convex.
B. abortus requires 10%

CO2 for primary growth.
D) Identification:
Colonies are examined by Gram stain:
Members of the genus Brucella are very small Gram-negative

bacilli (coccobacilli) appearing like “fine sand“.
Non motile
Non capsulated
Non spore-forming
D) Identification:
Identification of Brucella is carried out on 2 levels genus &
species:
1. The growth is identified as a Brucella genus if:

• It is catalase positive, oxidase positive & urease positive.
• Reduces nitrates.
• B. abortus & B. suis produce H2S.
• Agglutinates with Brucella monoclonal antibodies to A & M
antigens.
B.R.
D) Identification:
2. Species can then be identified according to:
➢ CO2 requirements
➢ H2S production
➢ Dye sensitivities (basic fuchsin & theonine)
➢ B. abortus phage sensitivity.
E) Serologic tests:
Two serum samples should be collected:
One at the onset of illness & the second after 14-21 days.
1. Standard tube agglutination test (STAT) for total antibody
(IgG + IgM):
It is the commonest test used for diagnosis of brucellosis.
It detects antibodies to the 3 major Brucella spp. pathogenic
for humans: B. abortus, B. melitensis & B. suis.
A single titre of ≥160 or a fourfold rise in titre or greater is
considered significant.
E) Serologic tests: (cont.)

False-negative results may be obtained.
Therefore, the following procedures should be implemented during
performance of the test:
a- Wide range of serum dilutions (start with 1:20 up to

1:5120) in order to eliminate the prozone effect that is
commonly encountered in cases of brucellosis.
b- ‘Anti-Brucella Coomb’s test’ (or mixed agglutination

reaction; MAR) should be done for negative results to
eliminate the effect of incomplete or blocking antibodies
(IgA).
2. Immunocapture agglutination test

3. Latex agglutination test
4. Complement fixation test
5. ELISA for IgG or IgM
F) Brucellin test:
It is a skin test similar to tuberculin test and is based on DTH.
It is of diagnostic help in certain situations.
Prevention
1. Pasteurization of milk & its products.
2. Control of infections in animals.
3. Live attenuated vaccine for cattle.
Treatment
• Treatment of brucellosis requires combination of
antibiotic therapy for a prolonged period due to the
intracellular residence of the organisms.
• Tetracyclines, aminoglycosides, rifampin & trimethoprim-
sulfamethoxazole have been all used with success.
Treatment of Choice
• Combination therapy has the best efficacy

• Doxycycline for six weeks in combination with
streptomycin for 2-3 weeks or rifampin for 6 weeks.
• CNS cases treat 6-9 months.

Prognosis
• May last days, months or years.
• Recovery is common.
• About 5% of treated cases relapse

• Failure to complete the treatment regimen.
• Sequestered infection requiring surgical drainage.
• Case-fatality rate: <2% (untreated)

BRUCELLA ENDOCARDITIS
• Brucella endocarditis varies from less than 1 to 4% of all
cases of bacterial endocarditis depending on the
geographic area.
• Most patients with B. melitensis endocarditis follow a

subacute course over a period of 2 to 10 weeks.
• Fever, generalized aches, cardiac murmur & enlargement

of the liver & spleen are the most prominent clinical
findings.
BRUCELLA ENDOCARDITIS
• On rare occasions, Brucella endocarditis follows an

afebrile course, complicated by disseminated
intravascular coagulation (DIC).
• In patients with prosthetic valves, relapsing bacteremia

after appropriate treatment for acute brucellosis is an
important clue to the diagnosis of endocarditis.
Pathology & ECG
• Brucella endocarditis is a destructive process predominantly involving the

aortic valve & perivascular tissues.
• Evidence of underlying valvular disease, including prosthetic valves, is noted

in two-thirds of patients.
Fatality
• The valvular lesions have been described as bulky & ulcerative
with microabscesses within the cusps, destruction of the
commissures & calcification.
• Myocardial abscesses have been found in 43% of patients; aortic

root abscess seems to be a common complication when the
aortic valve is involved. Ring abscesses leading to valve
detachment occur in most instances of prosthetic valve
endocarditis.
• These observations help to explain the high fatality rate for

Brucella endocarditis.
Diagnosis
• Depends on the isolation of Brucella spp. from blood cultures or

cardiac tissue.
• Isolation of Brucella is hazardous & the physician should inform

the microbiologist of such a suspected diagnosis.
• Blood cultures are positive for Brucella in more than 80% of cases
if the incubation time is prolonged to 4-6 weeks. Culture of
vegetations commonly yields Brucella, even after prolonged
antimicrobial chemotherapy.
Treatment
• Although antimicrobial agent treatment can result in

sterilization of valve vegetations, only a few patients
have been cured by antibiotics alone & before the
introduction of open-heart surgery, the mortality of
Brucella endocarditis was greater than 80%.
• The current recommendation is combined medical &

surgical treatment, especially with infected prosthetic
valves.
Treatment
• Quinolones are very efficient in vitro but have been very

disappointing in clinical trials, with failure rates of 16 to
66% in acute brucellosis; therefore, they should not be
used.
• Most authors recommended treatment of Brucella
endocarditis with a combination of doxycycline & either
rifampin or streptomycin for several months. It is
advisable to extend therapy for a minimum of 6 to
8 weeks, postoperatively.
• A progressive drop in antibody titer is evidence that the
patient is cured. Patients with a relapse or a failure have
high levels of IgG remaining.
STREPTOCOCCi
Main Species of Streptococci
1. S. pyogenes
2. S. pneumoniae: causing pneumonia, meningitis, otitis

media, sinusitis, etc.
3. Viridans streptococci: causing dental caries & SBE

S. pyogenes Cell Wall Antigens
S. pyogenes Virulence Factors
1. M protein
2. Fibronectin-binding protein (Protein F) & lipoteichoic acids (LTA)
3. C5a peptidase
4. Hyaluronic acid capsule
5. Invasins:
• Streptokinase (SK, fibrinolysin, streptococcal spreading factor)
• Hyaluronidase
• Nucleases (streptodornases A-D)
• Streptolysins (SLO, SLS)
6. Pyrogenic exotoxins (SPE A, B & C)
M protein
• Cell surface protein
• MOST important virulence factor:

• Allows bacteria to colonize skin
• Inhibits phagocytosis
• Immunogenic:
• 80 M serotypes
S. pyogenes Diseases
1. Pharyngitis, sore throat, tonsillitis

2. Scarlet fever (due to erythrogenic toxin)
3. Skin & soft tissue infections
4. Invasive streptococcal infections:
- Puerperal fever
- Acute endocarditis
- Necrotizing fasciitis
- Toxic shock syndrome
Viruses are common
S. pyogenes Infections causes of sore throat
Puerperal Acute
fever endocarditis
Scarlet fever
Necrotizing fasciitis
Cellulitis
Erysipelas
Impetigo
Post-Streptococcal
Sequelae
Post-Streptococcal Sequelae
• Non-suppurative sequelae:
• Acute rheumatic fever (ARF).
• Acute glomerulonephritis (AGN).
• Begin 1-4 weeks after an acute streptococcal illness.
• Pathogenesis: autoimmune mechanism.

• ARF follows only infections of the pharynx.

• Examples of rheumatogenic strains:
• M types 1,3,5,6 & 18.
• AGN can follow infections of the pharynx or the skin.

• Predominant nephritogenic strains:
• M types 4 & 25 ------------Throat infections.
• M types 2 & 60 ------------Pyoderma / Skin infections.
Acute Rheumatic Fever
Antibodies to M Inflammatory
protein cross-react response
with epitopes on
( Complement
heart myosin &
sarcolemmal activation)
membrane proteins
Damage of heart valves

In Acute rheumatic fever:
• Recurrence of streptococcal pharyngeal infections is common.
• Usually associated with an increased probability of rheumatic

fever.
• Repeated recurrences of rheumatic fever may cause valvular

damage.
• Thus, following a single attack, life-long antibiotic (penicillin)

prophylaxis is recommended.
Diagnosis of ARF:
NO single test is Pathognomonic.
Modified Jones criteria:

❑ Evidence of recent S. pyogenes infection + either:
➢ Two major criteria
➢One major & two minor criteria
Diagnosis of ARF
Major Criteria:
1. Carditis
2. Migratory polyarthritis Minor Criteria:
3. Erythema annulare 1. Arthralgia
4. SC nodules
5. Chorea
2. Prolonged PR
interval in ECG
3. Fever
4. Prior history of RF
Subcutaneous nodules
Erythema annulare
Diagnosis of ARF
Suggestive Criteria:
• + ASO
• +ve CRP
• ↑ ESR
• ↑ WBC
Diagnosis of ARF:
I. Evidence of recent streptococcal infection:
• History of acute tonsillitis / scarlet fever

/ +ve throat swab culture for S. pyogenes.
• Elevation of ASO titre (> 200 units)

Diagnosis of ARF:
Elevation of ASO titre:
• By latex agglutination
test.
• Titres up to 200 units are

considered normal.
• Most cases of ARF

demonstrate elevated
ASO > 200 units (usually
> 500).
Diagnosis of ARF:
Additional Ab tests, to confirm recent S. pyogenes

infection, include:
• Antistreptokinase (ASK) (titre > 80 units).
• Anti-DNase B (titre > 80 units).
• Anti-hyaluronidase (AHT) (titre > 128 units).

Acute glomerulonephritis
• AGN results from deposition of Ag-Ab complexes
on the basement membrane of kidney
glomeruli, where they provoke an inflammatory
response that damages the kidney.
• Recurrences are uncommon & antibiotic

prophylaxis following an initial attack is
unnecessary.
Diagnosis of AGN:
There are elevated antibody titres for:
• Anti-Dnase
• Antihyaluronidase
• ASO titres are generally low

(rarely may be high after throat infection).
Respiratory Tract Infections
Eyes & Nose are the portals of entry to the respiratory

system:
• Primarily spread by inhalation (droplets or airborne)
• Contact (direct or indirect)
• Aspiration of endogenous flora of the oropharynx
• Animal exposure (e.g., anthrax, pneumonic plague)

Diseases of the Upper Respiratory Tract
•Pharyngitis, tonsillitis & sore throat

•Pharyngitis is seen most frequently in children
from 2 years of age through adolescence.
Pharyngitis, Tonsillitis & Sore Throat
Viral infections Bacterial infections Fungal
commonest infections
1. Adenovirus (the most 1. Streptococcus pyogenes Candidiasis

common) (the most common bacterial (Oral thrush)
2. Rhinoviruses cause)
3. Coronaviruses 2. Vincent's angina
4. Parainfluenza viruses 3. Mycoplasma pneumoniae
5. Influenza viruses 4. C. diphtheriae (very rare
6. Enterovirus groups: due to vaccination)
Coxsackie viruses A
7. Herpesviruses (rare):
VZV, EBV, CMV &
HSV-1
Acute Otitis Media
Most common causes are:
• Streptococcus pneumoniae
• Haemophilus influenzae
• Moraxella catarrhalis
• Streptococcus pyogenes
• Staphylococcus aureus
• Some viruses, e.g., respiratory syncytial virus
External otitis
• Common problem in swimmers; especially in

warm-weather months.
• Staphylococcus aureus & Pseudomonas aeruginosa

are the most common agents of this condition.
Diseases of the lower respiratory tract (LRI)
• Tracheitis, bronchitis, bronchiolitis
• Pneumonitis:
•inflammation of the alveoli.
• Pneumonia:
•when alveoli are filled with pus & fluid and
pleurisy is present
Pneumonia
Typical Atypical
fever, pleuritic chest

sputum is scanty or
pain, productive cough
absent
with sputum
• Classification into typical or atypical is not
much helpful in diagnosis.
• Sputum may be mucoid & profuse with

atypical pneumonia.
Pneumonia
Community- Hospital-
acquired acquired
Community-acquired pneumonia
• Bacterial pneumonia:
1. Streptococcus pneumoniae (the most common bacterial cause)
2. Enterobacteriaceae: K. pneumoniae (especially important in alcoholics)
3. H. influenzae
4. Mycoplasma pneumoniae (school-age students → young adulthood)
5. Legionella pneumophila
6. Chlamydophila pneumoniae & Chlamydophila psittaci. Chlamydia
trachomatis (neonates)
7. S. aureus
8. P. aeruginosa (primary cause of pneumonia in cystic fibrosis patients)
9. Coxiella burnetti
10. Moraxella catarrhalis
11. S. agalactiae (neonates)
12. Mycobacterium tuberculosis
Community-acquired pneumonia
• Viral pneumonia
• Influenza A virus
• Respiratory syncytial virus: in infants and young children
N.B., Viral infections may set the stage for secondary bacterial infections.
• Fungal pneumonia
1. Pneumocystis jiroveci: causes disease among
immunocompromised, especially AIDS patients.
2. Dimorphic fungi: Histoplasma capsulatum, Blastomyces
dermatidis and Coccidioides immitis
3. Filamentous fungi (moulds): Aspergillus, Rhizopus and Mucor
Atypical pneumonia
• This condition is characterized by scanty or absent
sputum, associated with low grade fever and influenza-
like illness.
Causes:
• Bacterial agents:
• Mycoplasma pneumoniae, Chlamydia trachomatis,
Chlamydophila pneumoniae, Chlamydophila psittaci, Legionella
pneumophila, Coxiella burneti
• Fungal agents:
• Pneumocystis jiroveci
• Viral agents:
• Measles, influenza virus parainfluenza viruses, RSV, adenoviruses
Nosocomial pneumonia
• Early onset pneumonia occurs during the first 4 days of
hospitalization.
1. Moraxella catarrhalis
2. Haemophilus influenzae
3. Streptococcus pneumoniae
4. Viruses (e.g., influenza A, B viruses or respiratory syncytial virus)
• Late onset pneumonia is the commonest form & is caused by:

1. Enterobacteriaceae (40%): K. pneumoniae, Serratia marcesens...etc.
2. Staphylococcus aureus (25%) including methicillin-resistant S. aureus.
3. Gram-negative bacilli: e.g., P. aeruginosa (15%), Acinetobacter species,
Legionella pneumophila
4. Viruses (e.g., influenza A and B or respiratory syncytial virus)
5. Pneumocystis jiroveci
6. Filamentous fungi (moulds): Aspergillus
7. Yeasts (e.g., Cryptococcus neoformans)
8. Anaerobic bacteria
Patients with underlying lung disease
• Patients with chronic obstructive lung disease (COPD):

• S. pneumoniae, H. influenzae, M. catarrhalis & P. aeruginosa are
common pathogens.
• Patients with cystic fibrosis: S. aureus & P. aeruginosa
• Patients with cavitary lung disease: frequently due to TB are

at high risk to develop aspergilloma (growth of the aspergillus in
the form of a fungal ball), which is difficult to distinguish between
it and actual tissue invasion.
Pneumonia in immunocompromised patients
• Immunocompromized patients are at high risk for all
recognized respiratory tract pathogens.
• It is important to distinguish the type of
immunosuppression: (because different types of immunosuppression
predispose to infection with different pathogens)
• AIDS patients are susceptible to Pneumocystis jiroveci, S.

pneumoniae & multidrug resistant M. tuberculosis.
• Solid organ transplant recipients are at risk for pneumonia with CMV,
HSV, Legionella spp.
• Patients with neutropenia are at risk of infection with different

bacteria but also have a high risk of invasive aspergillosis & other
invasive fungal infections.
Laboratory diagnosis
• Specimens
• Sputum, nasopharyngeal or endotracheal aspirate, BAL or blood
• Sputum
• obtained by deep cough, induction, aspiration, or bronchoalveolar lavage (BAL).
• Rarely, lung biopsy is required for diagnosis.
• Sputum smears must be 1st examined to determine that it is a true sputum & not saliva.
• Purulent sputum is defined as secretions from the lungs, bronchi, or trachea that
contain ≥25 WBCs and ≤10 squamous epithelial cells per low power field.
• Acceptable specimens are then subjected to the different methods of diagnosis to
determine the aetiology of pneumonia.
• Positive blood cultures are very helpful in diagnosis because

30% of cases of bacterial pneumonia have bacteraemia.
Laboratory diagnosis
• Examination for TB
• Examination for fungal infections

MICROBIAL DISEASES OF THE GIT
Bacterial Diseases of GIT
• Infections
• Pathogens enters GIT &
multiply.
• Bacteria may penetrate the
intestinal mucosa or may pass
to other systemic organs.
• Delay in appearance of
symptoms while pathogen
increases in number or • Intoxications
invades tissue. • Ingestion of a preformed
• Usually, fever is present. toxin.
• Sudden onset of symptoms
(within few hours).
• Fever not always present.
Bacterial Diseases
• Acute or chronic gastritis, peptic ulcer,

duodenal ulcer, GERD, gastric cancer
• Helicobacter pylori
Bacterial Diseases
• Non-invasive bacterial gastroenteritis (non-inflammatory diarrhea):

• Acute watery diarrhoea without fever.
• Affect the small intestine
• Enterotoxin production
• No mucosal destruction
Caused by:
• Clostridium perfringens: food poisoning
• Enterotoxigenic E. coli
• Bacillus cereus: diarrhoeal form of food poisoning
• Clostridium difficile: antibiotic associated diarrhoea
• Vibrio cholerae serogroups O1 and O139: cholera
Bacterial Diseases
• Invasive bacterial gastroenteritis (inflammatory diarrhoea):
• mucosal invasion with resulting inflammation
• Affect the large intestine
• may be associated with fever, abdominal pain and dysentery
• Stools may be bloody and contain many leukocytes
• Caused by:
• Salmonella Enteritidis & Salmonella Typhimurium (Salmonella food
poisoning)
• Shigella species (bacillary dysentery)
• Campylobacter (90% are C. jejuni): (Campylobacter enteritis)
• Enteroinvasive E. coli
• Enterohemorrhagic E. coli (E. coli O157:H7)
• Listeria monocytogenes: (food poisoning)
• Vibrio parahaemolyticus: (food poisoning)
• Yersinia enterocolitica: (enterocolitis)
• Aeromonas spp.: (diarrhoea)
Bacterial Diseases
(Ingestion of preformed bacterial toxins)
• GIT symptoms with

vomiting as a primary
symptom; diarrhoea may
also be present, e.g.,
food poisoning
• Neurological
• Bacillus cereus food manifestations:
poisoning (emetic form) • Botulism food
poisoning (Clostridium
botulinum toxin).
Bacterial Diseases
• Intestinal infection presenting with systemic illness:
• Salmonella Typhi or Salmonella Paratyphi A, B and C:

(enteric fever)
• Campylobacter jejuni: (Guillain Barré syndrome)
• Listeria monocytogenes: (septicaemia or meningitis)
• Vibrio vulnificus: (septicaemia)

Viral Diseases
• Viral gastroenteritis:
1. Rotavirus is the leading cause of infantile gastroenteritis.
2. Norwalk virus is the leading cause of epidemic viral
gastroenteritis in school children & adults.
3. Astroviruses cause sporadic gastroenteritis in infants, children,
elderly and the immunocompromised patients.
4. Enteric Adenoviruses 40 & 41 represent the second most
common cause of viral gastrointestinal disease in children.
5. Parvoviruses
• Viral infection of salivary glands & pancreas:

1. Mumps virus
2. Human herpes virus 7 (HHV7)
Fungal Diseases
• Ergot poisoning
• Mushroom poisoning
• Aflatoxin poisoning (Aspergillus flavus mycotoxin)
• Candidiasis
Food-Borne Illnesses
&
Food Poisoning
• Patients with food-borne illnesses typically present with
GIT symptoms (vomiting, diarrhoea, abdominal pain).
• Food-borne illness may occur in the form of an

outbreak.
• An outbreak is defined as an incident in which two or more
individuals experience a similar illness resulting from the
ingestion of the same food.
Common Types of Food Poisoning
1. Staphylococcus aureus
2. Salmonella typhimurium & S. enteritidis
3. Clostridium perfringens
4. Clostridium botulinum
5. Bacillus cereus
6. Listeria monocytogenes
7. Vibrio parahaemolyticus
Type of Food
Staphylococcus aureus - Carbohydrate rich food (e.g., cake, pasta and koskosi)
- Protein rich food like milk and its products (e.g., ice
cream)
S. Enteritidis & Raw or undercooked eggs, contaminated poultry

S. Typhimurium
Clostridium perfringens Cooked meat stored at the inappropriate temperature

Clostridium botulinum Canned food, sausage & salted fish
Bacillus cereus
a. Emetic form Improperly refrigerated cooked or fried rice
b. Diarrhoeal form Meat
Listeria monocytogenes - Fresh soft cheese

- Ready-to-eat meat
Vibrio parahaemolyticus Undercooked or raw seafood (e.g., fish, shellfish)

Pathogenesis
Staphylococcus aureus Preformed enterotoxin (Commonest type of bacterial food
poisoning)
S. Enteritidis & Invade and replicate in the epithelial cells of intestines (No
S. Typhimurium toxin)
Clostridium perfringens Multiplication & release of enterotoxin in gut
Clostridium botulinum Preformed neurotoxin
Bacillus cereus
a. Emetic form Preformed heat-stable enterotoxin
b. Diarrhoeal form Heat-labile enterotoxin
Listeria monocytogenes Multiplication & invasion of intestinal epithelium
Vibrio parahaemolyticus Thermostable haemolysin

Onset of Symptoms
Staphylococcus aureus very short, 1- 6 hrs
S. Enteritidis & 8-48 hrs

S. Typhimurium
Clostridium perfringens 8-24 hrs
Clostridium botulinum 12-72 hrs
Bacillus cereus
a. Emetic form short incubation, 1-6 hrs
b. Diarrhoeal form longer incubation, 6-24 hrs
Listeria monocytogenes 9–48 hrs
Vibrio parahaemolyticus 2–48 hrs

Clinical Picture
Staphylococcus aureus Severe vomiting and diarrhoea, but no fever
S. Enteritidis & Severe diarrhoea, fever and abdominal cramps

S. Typhimurium
Clostridium perfringens Diarrhoea and abdominal cramps
Clostridium botulinum Diplopia, blurred vision, bulbar weakness;

paralysis
Bacillus cereus
a. Emetic form Vomiting and abdominal cramps
b. Diarrhoeal form Diarrhoea and abdominal cramps
Listeria monocytogenes Diarrhoea, abdominal cramps, fever
Vibrio parahaemolyticus Watery diarrhoea, abdominal cramps, vomiting

Diagnosis
Staphylococcus aureus Stools, vomitus and food remnants can be tested for
enterotoxin and cultured for S. aureus
S. Enteritidis & Stools culture

S. Typhimurium
Clostridium perfringens - Quantitative culture from the stools.
- Demonstration of enterotoxin in the stools
Clostridium botulinum Detection of botulinal toxin in serum, stools, gastric
contents, or implicated food
Bacillus cereus
a. Emetic form Stools and food specimens for culture and toxin
identification
b. Diarrhoeal form
Listeria monocytogenes Detection of antibody to listeriolysin O.
Vibrio parahaemolyticus Isolation of V. parahaemolyticus from stools or food

URINARY TRACT INFECTIONS
Urinary tract infections (UTI) are
common & cause significant
morbidity & mortality.
Bladder urine is normally sterile.

UTI is the presence of microorganisms in the urinary tract.
Most patients with UTI have “significant bacteriuria“

(i.e., a bacterial count > 105 bacteria/ml) in a suitably
collected & well transported mid-stream sample of urine.
Pathogenesis
& Clinical presentation
• Ascending infection: Organisms from the faecal flora

usually enter the urinary tract by ascending from the
perineum & peri-urethral sites.
• Haematogenous route: Rarely, the kidneys may be

infected via blood, particularly after a S. aureus
bacteraemia.
Predisposing Factors
1. Short female urethra
2. Sexual intercourse
3. Senile prostatic hypertrophy
4. Structural & neurological abnormalities of the urinary tract
5. Instrumentation, e.g., urinary catheters
6. Other host factors, e.g., Diabetes mellitus & immuno-

suppression
Causative organisms
• E. coli is the commonest cause.

• 80% of cases in general practice
• 50% of cases in hospital practice.
•Enterococcus faecalis
• S. saprophyticus (particularly in young sexually active women)
•Proteus mirabilis, K. pneumoniae & other Enterobacteriaceae
• Pseudomonas aeruginosa
• CoNS other than S. saprophyticus
• Streptococcus agalactiae (in neonates)
• Mycobacterium tuberculosis
• Anaerobic bacteria (Bacteroides fragilis)
• Adenoviruses (acute haemorrhagic cystitis in children)
• Candida species (Candida albicans & non-albicans Candida)
Laboratory Diagnosis
I. Sample collection:
• After adequate cleaning of the external genitalia with

tap water & drying, a mid-stream specimen of urine is
obtained in a sterile container.
• In infants, adhesive sterile bags may be used.
• Suprapubic aspiration is occasionally necessary in

infants & in pregnancy.
• Catheter sample should be avoided unless the patient is

already catheterized.
II. Transport to the laboratory:
within 2 hours of collection, maximally.
If not possible, the sample should be kept at 4°C.
III. Microscopic examination:

for the presence of pus cells, RBCs, bilharzial ova, casts,
crystals, … etc.
IV. Viable bacterial count:

A measured volume of uncentrifuged urine is spread on the
surface of a solid medium & incubated. Colonies are counted
then the result is expressed as CFU/ml.
Laboratory diagnosis (cont.)
V. Culture:
Urine deposit is cultured on nutrient agar, blood agar &
MacConkey’s medium.
After incubation at 37oC for 24 hours, the growing colonies
are identified.
VI. Antibiotic sensitivity test is done for the

isolated bacteria.
VII. When T.B. is suspected, 5 successive morning

samples are subjected to Z-N staining & culture on L.J.
medium.
Sterile pyuria
There is no growth on ordinary culture media despite the
presence of pus cells in urine (more than 10/HPF).
This may be due to:
1. Renal tuberculosis.
2. Female genital tract infections.
3. Non-gonococcal urethritis (in male patients such as
Chlamydia trachomatis)
4. Infection by anaerobic bacteria, genital Mycoplasma or
L-forms of bacteria
5. Recent antimicrobial chemotherapy
6. Prostatitis
7. Non-infectious conditions: Neoplasia of the renal tract,
renal calculi, catheterization & fever in children
independent of the cause.
PROSTATITIS
Prostatitis must always be considered in the
differential diagnosis of UTI.
The male urethra courses through the centre of the

prostate on its way to the bladder. This relationship allows
for invasion of UT pathogens into the prostate, causing
acute bacterial prostatitis.
Patients with prostatitis will present with symptoms of UTI

& a large tender prostate.
The enlarged prostate may also cause symptoms of bladder

obstruction by physically blocking urine flow.
Causative agents:
Gram-negative bacteria that cause UTI as well as
Chlamydia, Mycoplasma & Ureaplasma species.
Diagnosis:
Prostatic secretion or urine may be collected, after massage
of the prostate via the rectum. This method releases any
sequestered bacteria or inflammatory cells from the prostate.
URETHRITIS
Urethritis is an inflammatory condition that can be
infectious or post-traumatic.
Urethritis is predominantly a disease of adult men.
Infectious causes of urethritis are typically sexually-

transmitted.
Categories of urethritis
1. Gonococcal urethritis:
due to Neisseria gonorrhoeae
2. Non-gonococcal urethritis (NGU)

Categories of urethritis (cont.)
2. Non-gonococcal urethritis due to:
❑ Chlamydia trachomatis (serotypes D-K).
❑ Ureaplasma urealyticum
❑ Mycoplasma hominis
❑ Trichomonas vaginalis
➢ Pyogenic bacteria as E. coli, staphylococci & streptococci.
They usually occur in the presence of urethral stricture or post-
traumatic following catheterization, instrumentation or foreign
body insertion.
➢ Intrameatal warts by human papilloma virus

➢ Intrameatal ulcer by Herpes simplex virus
➢ Intrameatal chancre
➢ Adenovirus
CNS Infections
CNS Infections
• Meningitis
• Encephalitis
• Brain abscess
• CNS intoxication
Encephalitis
• Caused primarily by viruses:
• Herpes viruses (the commonest)
• Arthropod-borne viruses:
• West Nile virus
• Eastern & Western equine encephalitis viruses
• St. Louis encephalitis virus
• Rabies virus
Brain Abscess
• They occur through:
• Direct extension from a contagious site (e.g., infected

paranasal sinus)
• Following trauma
• Haematogenous spread from another infected site

(usually endocarditis or a lung abscess)
Brain Abscess
• Causative organisms:
• S. aureus & Gram-negative rods (following trauma)

• Viridans streptococci
• Actinomyces Spp.
• Anaerobic bacteria
• Aspergillus Spp.
• Nocardia Spp.
• Zygomycetes
CNS Intoxication
• Caused by:
• Tetanus toxins (causing spastic paralysis)
• Botulinum toxins (causing flaccid paralysis)

MENINGITIS
• Meningitis is infection & inflammation of the

membranes surrounding the brain and spinal cord.
• There are two major forms of meningitis:

• Septic meningitis
• Aseptic meningitis:
• viruses, fungi, M. tuberculosis or spirochaetes
Types of Meningitis
• Viral meningitis
• generally, less severe
• resolves without specific treatment
• Bacterial meningitis
• can be severe
• may result in brain damage, hearing loss, or
learning disability.
Therefore, bacterial meningitis is considered a
medical emergency (needs immediate treatment &
chemoprophylaxis).
Bacterial Meningitis
A) Common causes
• Neisseria meningitidis: commonest cause
worldwide
• Haemophilus influenzae type b (Hib)
• Streptococcus pneumoniae
• Mycobacterium tuberculosis
B) Less common causes
• Listeria monocytogenes
• Staphylococcus species
• Streptococcus species
• Gram-negative enteric bacilli
• Pseudomonas aeruginosa
• Spirochetes:
• Leptospira interrogans (Weil’s disease),
• Treponema pallidum (syphilitic meningitis in secondary syphilis
& neurosyphilis in tertiary syphilis)
• Borrelia burgdorferi (Lyme disease)
C) Neonatal meningitis
• Streptococcus agalactiae
• Escherichia coli (usually having K1 antigen)
• Listeria monocytogenes
• Klebsiella pneumoniae
• Citrobacter spp.
Viral Meningitis
A. Enteroviruses:
• Echovirus
• Coxsackie A and B viruses
• Poliovirus
• Enterovirus type 71
B. Paramyxovirus:
• Mumps
C. Herpes viruses:
• Herpes simplex
• Varicella-zoster
D. Arboviruses
E. Lymphocytic choriomeningitis virus
F. Adenoviruses
G. HIV
Fungal Meningitis
• Cryptococcus neoformans
• Coccidioides immitis
Laboratory Diagnosis of Meningitis 1
A- Specimens
• CSF
• by lumbar puncture,
• before initiation of antibiotic therapy
• under strict aseptic precautions
• Blood: for blood culture

B- Physical & Chemical Analysis of CSF

• In bacterial meningitis: cloudy CSF, neutrophils
predominate, low glucose, high protein
• In aseptic meningitis: lymphocytes predominate.
In viral causes: normal glucose, high protein
Serum CRP: can differentiate bacterial from viral

meningitis (positive in bacterial & negative in viral
meningitis).
C- Direct detection
• Gram-stained smears (of CSF sediment):

• N. meningitidis (Gram-negative diplococci,
intracellular, in some PMNLs)
• Hib (Gram-negative coccobacilli)
• S. pneumoniae (Gram-positive diplococci)
• Ziehl-Neelsen stain: to detect AFB.
• Dark ground microscopy: for fresh unstained smear

may reveal motile leptospira.
C- Direct detection
• India ink stain: in cryptococcosis
• Direct antigen detection: of N. meningitidis, Hib

and S. pneumoniae by latex agglutination or
fluorescent antibody test in CSF or blood
• Molecular techniques: PCR on CSF or blood allows

the rapid diagnosis of some viral agents.
D. Cultivation
• CSF deposit: plated onto chocolate & blood agar in a
humid atmosphere with 5-10% CO2 at 37°C.
• Blood samples: blood culture technique.

Subcultures are plated on chocolate and blood agar
and incubated as above.
• Blood culture is usually positive as bacterial meningitis is
often associated with bacteraermia.
D. Cultivation
• Lowenstein-Jensen medium: in suspected tuberculous

meningitis
• Fletcher’s medium: in suspected leptospiral meningitis
• Sabouraud’s dextrose agar: in suspected fungal meningitis
• Inoculation of CSF onto cell cultures: in suspected viral

meningitis
E- Identification of cultures is carried out in a

systematic way according to suspected organism.
F- Serology: It is useless for early diagnosis of

bacterial meningitis. However, in viral causes,
demonstrating IgM antibody or four-fold
increase in paired sera (IgG) is useful.
DISEASES TRANSMITTED FROM MOTHER TO FOETUS
• Pre-natal (congenital) infections:

(transmitted to the foetus by transplacental route)
I. Viruses: 1. Rubella
2. Cytomegalovirus
3. Herpes simplex virus
4. HIV
5. Varicella zoster virus
6. B19 virus
II. Bacteria:
1. Treponema pallidum
2. Listeria monocytogenes
III. Protozoa: Toxoplasma gondii

DISEASES TRANSMITTED FROM MOTHER TO FOETUS
• Peri-natal infections: (transmitted during birth)

I. Bacteria
1. Neisseria gonorrhoeae (Ophthalmia neonatorum)
2. Chlamydia trachomatis (neonatal conjunctivitis,
pneumonia)
3. Streptococcus agalactiae (neonatal sepsis)
4. Listeria monocytogenes (listeriosis; septicaemia,
meningitis)
II. Viruses
1. Hepatitis B virus
2. HIV
3. Herpes simplex
4. Cytomegalovirus
• Diagnosis
• Serologic tests for both mother and child =

ToRCH profile.
• ToRCH profile refers to Toxoplasmosis, Rubella,

Cytomegalovirus and Herpes
• Demonstration of specific IgM antibodies or a

4-fold rise of specific IgG antibodies indicates
recent infection.
MICROORGANISMS TRANSMITTED BY
BLOOD TRANSFUSION
1. Hepatitis viruses B, C, D
2. HIV types 1 & 2
3. Cytomegalovirus (CMV)
4. Epstein-Barr virus (EBV)
5. Human T-cell leukaemia virus (HTLV-1)
6. Human parvovirus B19
7. Brucella
9. Malaria parasite
10. Blood free from infectious agent may be contaminated by
bacteria during withdrawal from the donor or from the
environment.
MICROORGANISMS TRANSMITTED BY BLOOD
TRANSFUSION
• CMV, EBV, HTLV and malaria are

present in the cellular components of
blood, thus, are not transmitted by
plasma.
• Treponema pallidum & malaria die

when stored at 4°C within 3-5 days,
so are not transmitted by stored
blood.
Sexually Transmitted Diseases
(STDs)
Sexually Transmitted Infections
• Bacteria
1. Neisseria gonorrhoeae
2. Chlamydia trachomatis (serotypes D –K and serotypes L1, 2, 3)
4. Haemophilus ducryei (causing chancroid)
5. Klebsiella granulomatis (causing granuloma inguinale)
6. Mycoplasma & Ureaplasma
• Viruses • Parasites
1. Herpes simplex virus type II • Trichomonas vaginalis
2. Hepatitis B, C virus (infrequent)
3. HIV
4. Human papillomaviruses
5. Molluscum contagiosum virus
Sexually transmitted diseases are often mild infections that
can be cleared up with simple medical treatment. If left
untreated, however, serious complications can result.
• Birth defects
• Blindness
• Bone deformities
• Cancer
• Heart disease
• Infertility
• Mental retardation
• Death
ZOONOTIC
DISEASES
Zoonotic diseases are
transmitted to humans from
lower animal reservoirs.
Vectors may also be reservoirs

in some types of zoonotic
disease transmission.
Some occupations have a

higher incidence of reservoir
contact such as veterinarians,
slaughterhouse & carpet mill
workers, farmers & butchers.
Transmission
1. Direct contact with infected tissues or infectious

fomites
2. Ingestion of infectious tissue (or milk)
3. Inhalation of infectious aerosols
4. Inoculation by the bite of an infected reservoir

or vector animal
Zoonotic infections
1) Bacterial:
− Brucellosis (Brucella species)

− Tuberculosis (M. bovis)
− Yersinosis (Y. enterocolitica)
− Listeriosis (L. monocytogenes)
− Anthrax (B. anthracis)
− Leptospirosis (L. interrogans)
Zoonotic infections (cont.)
1) Bacterial:
− Q fever (Coxiella burnetii)

− Bubonic plague (Y. pestis)
− Lyme disease (Borrelia burgdorferi)
− Endemic relapsing fever (Borrelia duttoni)
− Rocky Mountain spotted fever (Rickettsia rickettsii)
− Endemic typhus (Rickettsia typhi)
Zoonotic infections (cont.)
2) Viral:
❖ Rabies
❖ Yellow fever
❖ Dengue fever
❖ Haemorrhagic fever viruses
PATHOGENS TRANSMITTED
BY MILK & MILK PRODUCTS
• The following pathogens come from diseased animals &

are excreted in milk.
• They can be eradicated by pasteurization.
1. M. bovis
2. Brucella abortus & melitensis
3. Coxiella burnetii
PATHOGENS TRANSMITTED
BY MILK & MILK PRODUCTS
Pathogens contaminating milk:
a- Bacteria:
• Salmonella Typhi and S. Paratyphi
• Shigella species
• Campylobacter species
• Staph. aureus
• Strept. pyogenes
• Verotoxin producing E. coli
• Vibrio cholerae
b- Viruses:
• Poliomyelitis & enteroviruses
• Hepatitis A & E
• Rotavirus
c- Aflatoxin produced by Aspergillus flavus
BIOLOGICAL WARFARE & BIOTERRORISM
• The use of biological agents to inflict disease and/or

death on humans, animals or plants.
• The biological agent used include microorganisms as

well as microbial toxins, plants and animals.
Category (A): easily disseminated & cause high mortality

1. Anthrax
2. Smallpox
3. Botulism
4. Hemorrhagic fever viruses
5. Plague
Category (B): less easily disseminated & cause moderate

morbidity & low mortality
1. Brucellosis
2. Q Fever
3. Staphylococcus toxin
Category (C): Pathogens that could be engineered for mass

dissemination in the future because of availability.
1. Drug-resistant TB
2. Hantavirus (mice)
3. Yellow fever (mosquito)
Pyogenic Infections
• The term refers to an infection characterized by severe

local inflammation, usually with pus formation, generally
caused by one of the pyogenic bacteria,
• i.e., It's any infection that can produce the accumulation

of dead leukocytes & infectious agents, forming pus.
Common Disease Processes caused by Pyogenic
Infections
• Local skin & soft tissue infections, e.g.,

• Folliculitis
• Impetigo
• Styes
• Carbuncles
• Furuncles
• Cellulitis
• Erysipelas
• Necrotizing fasciitis
• Surgical site & other wound infections
Common Disease Processes caused by Pyogenic
Infections
• Deep-seated bone & joint infections, e.g.,
• Osteomyelitis
• Septic arthritis
Organisms Incriminated in Pyogenic Infections
• Streptococcus pyogenes
• Pneumococci
• Neisseria gonorrhoeae
• Neisseria meningitidis
• Some members of the genus Bacillus
• Some members of the genus Clostridium
• Pseudomonas spp.
• Klebsiella spp.
• Actinomycetes
Diagnosis of Pyogenic Infections
• Specimens:
• Pus from wounds or collections, either aspirated from
an abscess cavity, or swabbed from a wound
discharge.
• Drained abscess cavity material
• CSF (in case of meningitis)
• Urethral discharge (in case of gonorrhoea)
• Direct examination:
• Demonstrates pus cells & organisms extra- or

intracellularly.
• Direct antigen detection using latex agglutination in

case of capsulated meningococci, pneumococci, or
Klebsiella.
• PCR is resorted to in case of serious or life-threatening

infections.
• Culture & isolation:
• Media for culture is selected according to settings and

suspected organisms. Routinely, blood and chocolate
agar as well as a selective indicator medium, such as
MacConkey’s agar, are inoculated.
• Anaerobic culture is also done in case of deep seated
or foul-smelling abscesses.
• Grown colonies are examined microscopically &
biochemical reactions are performed to identify
isolated strains.
Skin & Soft Tissue Infections
1. Localized infections of the skin
A. Localized infections of the skin
A. Bacterial
Infection Organism
Folliculitis, furuncles, carbuncles or abscess S. aureus

Cellulitis, erysipelas, impetigo (pyoderma),
S. pyogenes
necrotizing fasciitis
Primary syphilis (chancre) Treponema pallidum
Malignant pustule Bacillus anthracis
Burn & wound infection Pseudomonas aeruginosa
Actinomycotic mycetoma Actinomycetes
B. Localized infections of the skin
B. Fungal
Superficial mycoses: Pityriasis

Yeasts: Malassezia furfur
versicolor
Cutaneous candidiasis Yeasts: Candida species
Cutaneous mycoses Dermatophytes
Madurella & Allescheria

Eumycotic mycetoma
Spp.
C. Localized infections of the skin
C. Viral
Skin warts Human papillomaviruses
Herpes simplex HSV 1 or 2
Zoster (shingles) Varicella-zoster virus
Roseola infantum Human herpes viruses 6
Erythema infectiosum Human parvovirus B19
Molluscum contagiosum
Molluscum contagiosum
virus (MCV)
2. Systemic diseases with skin rash
Disease Organism
Bacterial
Meningococcaemia Neisseria meningitides
S. aureus,
Toxic shock syndrome
S. pyogenes
Scarlet fever S. pyogenes
Rocky Mountain Spotted Fever Rickettsia rickettsii
Secondary syphilis Treponema pallidum
Lyme disease Borrelia burgdorferi
Staphylococcal scalded skin
S. aureus
syndrome
2. Systemic diseases with skin rash
Disease Organism
Viral
Chickenpox Varicella-zoster virus (VZV)
Measles Rubeola virus
German measles Rubella virus
Febrile illness Echoviruses
AIDS HIV
Smallpox Variola virus
INFECTIVE
ENDOCARDITIS
Infective Endocarditis (IE) is usually
suspected in a patient with fever & a new or
changing cardiac murmur.
Diagnosis is based on the presence of vegetation

on echocardiography & positive blood cultures.
The common bacteria involved are:
1. Viridans streptococci (infective endocarditis)
2. CoNS (particularly with prosthetic valve)
3. Streptococcus pyogenes
4. Staphylococcus aureus
5. Enterococcus species
6. Haemophilus species
7. Coxiella burnetii (Q fever)

BLOOD CULTURE
In most bacterial infections of the blood (bacteraemia), the
organisms are not numerous & so, direct plating of a drop of
the patient’s blood will usually give false-negative result.
For diagnosis of such infections:

❑ 5 - 10 ml of venous blood should be obtained for each
culture & is added to 50-100 ml broth.
❑ The culture should be incubated anaerobically &

aerobically at 37oC.
❑ Subcultures are done on suitable solid media every 48

hours & the growing organisms are identified.
Blood culture can better be performed by automated

machines for obtaining rapid results.
For better results, repeated blood samples should be
collected from different sites, preferably before the start of
antibiotic therapy.
Therefore, cultures of 3 sets of blood, drawn within a 24 -

48 hours period, are sufficient to establish a diagnosis of
bacteraemia.
Culture-negative is best defined when negative blood

cultures (at least 3 venous blood cultures) are obtained
repetitively.
Advantages of the large volume of broth:
1. It reduces the concentration of natural antimicrobial

constituents in the blood to a sub-inhibitory level.
2. It allows the growth of few organisms.
3. In patients under antibiotic therapy, neutralization or

diminution of the presence of antibiotics in blood may be
accomplished by:
- Incorporating sodium polyanetholsulfonate (SPS), which inactivates
aminoglycosides in the broth.
- Processing the blood in the presence of resins which remove

antibiotics, as well as some bacterial inhibitors, present in the blood).
Infectious diseases that can be diagnosed by
blood culture include:
1. Enteric Fever
2. Brucellosis
3. Endocarditis
4. Meningitis
5. Puerperal sepsis
6. Relapsing fever
7. Necrotizing fasciitis
8. Toxic shock syndrome
Hospital-acquired Infections
(Healthcare-associated Infections/
Nosocomial Infections)
Hospital-acquired infections (HAIs)
• An infection acquired by a patient in a hospital (or

other healthcare facility e.g., nursing home or
rehabilitation center) which was not present or
incubating at admission.
• Infections occurring more than 48 hours after
admission are usually considered nosocomial.
• HAIs are a serious problem in the hospital. Therefore,

each hospital should have an infection control (IC)
program designed to prevent acquisition of infections.
Factors favouring healthcare-associated infections
• Host factors
• Microbial factors
Factors favouring healthcare-associated infections – 1
• Host factors
✓Extreme of age (neonates & elderly)
✓Lowered resistance
✓Instrumentation e.g., using urinary catheters,
ventilators, endoscopes, venous and arterial
catheters
Factors favouring healthcare-associated infections – 2
• Microbial factors
✓The hospital environment harbours highly virulent organisms

e.g., S. aureus, E. coli, Klebsiella and Pseudomonas.
✓ However, opportunistic pathogens may cause infection in
immunosuppressed patients.
✓The wide use of antibiotics in the hospital favours the

development of microbial drug resistance e.g., MRSA, VRSA
and VRE.
Sources of infections
1. Endogenous, where the organism is
acquired from the patient’s own normal
flora
2. Exogenous
• People: whether other infected
patients or medical personnel
• Hospital environment: e.g.,

instruments, ventilators, bedpans and
air condition system
• Blood & blood products

Modes of transmission
1. Contact
2. Droplet
3. Airborne
4. Blood or needle prick
5. Common vehicle
6. Vector
1. Contact
✓Direct contact by hands of healthcare

personnel
✓Indirect contact by contaminated objects

e.g., thermometers
2. Droplet
• Droplets containing microorganisms are generated from
infected individuals during coughing, sneezing and talking.
• Droplets are large (> 5μm)→ travel short distance (within one
metre) and settle down rapidly
• Transmission requires close contact
2. Droplet (cont.)
• Diseases spread by droplets include;

• Covid 19
• Influenza,
• Rubella,
• Mumps,
• Pertussis,
• Pneumococcal pneumonia,
• Meningococcal meningitis
3. Airborne
• Droplet nuclei containing microorganisms are generated from evaporated
droplets.
• Droplet nuclei are small (< 5μm)→ remain suspended in air for long
periods and can be carried by air currents for long distances
• Transmission does not require close contact
3. Airborne (cont.)
• Diseases spread by droplets include;

• Tuberculosis,
• Measles,
• Chickenpox,
• Anthrax
4. Blood or needle prick
5. Common vehicle
• Transmission may occur by contaminated
items such as food, water, medication and
instruments.
6. Vector
• The infectious agents may be transmitted
through insects e.g., mosquitoes
Common types of HAIs
• Urinary tract infections (UTIs) e.g., by E. coli, Klebsiella,

Pseudomonas and Proteus
• Surgical site infections (SSIs) e.g., by staphylococci,

Gram negative bacilli and enterococci
• Lower respiratory tract infections (LRTIs) e.g., by S.

aureus and Gram- negative bacilli
• Blood stream infections (BSIs) e.g., by staphylococci,

Gram-negative bacilli and enterococci
Isolation precautions
• Special safety measures and practices used to prevent

transmission of the infectious organisms among patients and
healthcare workers.
• Based on the concept of isolating the organism and not the

patient.
• Categories of isolation precautions include:
❑ Standard precautions
❑ Transmission-based precautions
Standard precautions
• These are a set of infection control practices designed

particularly to prevent the transmission of the blood-
borne pathogens (HBV, HCV, HIV), in addition to other
organisms among patients and healthcare workers.
• The standard precautions assume that every patient is

potentially infected; therefore, they should be applied
to all patients all the time regardless of their infection
status.
Standard precautions
Type of Type of Important precaution

precaution patient/infection practices employed
Standard All patients 1. Hand hygiene

2. PPE such as gloves, masks, gowns
and goggles
3. Respiratory hygiene & cough
etiquette
4. Safe injection practices
5. Proper disposal of needles &
scalpels
6. Proper disposal of the infectious
hospital waste
7. Cleaning, disinfection &
sterilization of equipment
Transmission-based precautions:
• A set of infection control practices applied in

addition to the standard precautions when a
patient has a diagnosed infection.
• They are designed according to the mode of

transmission of this infection.
• They include:
➢ Contact precautions
➢ Droplet precautions
➢ Airborne precautions

Contact - Diarrhoea 1. Single room
- Wound and skin 2. Wearing gloves and gowns
infection
- Infection by
multidrug
resistant (MDR)
organisms

Droplet - COVID 19 1. Single room
- Influenza 2. Wearing standard mask
- Mumps
- Pertussis
- Meningococcal
meningitis
- Many others

Airborne - Tuberculosis 1. Single room with negative
- Measles pressure
- Chickenpox 2. Wearing N95 mask
Outbreak
• A sudden increase in occurrences of a disease in a

particular time and place; e.g., surgical wound
infection and MRSA outbreaks in ICUs.
Investigations of outbreaks in hospitals
• Microbiological sampling from patients, health

care workers and suspected sources
• Isolated organisms are identified to species level

followed by typing, either by non-molecular
methods (e.g., phage typing) or molecular
methods (e.g., plasmid profile analysis).
Recommended vaccinations of HCWs (CDC)
Vaccine Recommendation
Hepatitis B If no serologic evidence of immunity or prior vaccination, then HCW should get
a 3-dose series of Recombivax HB or Engerix-B (at 0, 1, 6 months) or a 2-dose
series of Heplisav-B, with the doses separated by at least 4 weeks. Get an anti-
HBs serologic test 1-2 months after the final dose.
Flu (Influenza) Get 1 dose of influenza vaccine annually.
MMR If no serologic evidence of immunity or prior vaccination, HCW should get 2
doses of MMR (1 dose now and the 2nd dose at least 28 days later). A third
dose of Mumps Virus–Containing Vaccine is recommended for persons at
increased risk for acquiring mumps during an outbreak.
Varicella If you have not had chickenpox (varicella) or if no prior vaccination or serologic
(Chiken pox) evidence of immunity, HCW should get 2 doses of varicella vaccine, 4 weeks
apart.
Tdap Get a one-time dose of Tdap as soon as possible if you have not received Tdap
previously (regardless of when previous dose of Td was received). Get either a
Td or Tdap booster shot every 10 years thereafter. Pregnant HCWs need to get
a dose of Tdap during each pregnancy.
Meningococcal Microbiologists who are routinely exposed to Neisseria meningitidis should get
meningococcal conjugate vaccine and serogroup B meningococcal vaccine.
Occupational Exposure of HCWs to Blood-Borne Pathogens
(HBV, HCV, HIV)
• Treatment of an Exposure Site:
• Wounds and skin sites that have been in contact with blood or
body fluids should be washed with soap and water; mucous
membranes should be flushed with water.
• No evidence exists that using antiseptics for wound care or

expressing fluid by squeezing the wound further reduces the
risk of blood-borne pathogen transmission; however, the use of
antiseptics is not contraindicated.
Occupational HBV Exposures
Risk of Occupational Transmission of HBV
• The risk of HBV infection is primarily related to the

degree of contact with blood & also to the HBeAg
status of the source person:
• If the blood was both HBsAg & HBeAg-positive, the

risk of developing clinical hepatitis is 22%-31%.
• The risk of developing clinical hepatitis from a

needle contaminated with HBsAg-positive & HBeAg-
negative blood is 1%-6%.
• Blood contains the highest HBV titers of all body fluids & is the most
important vehicle of transmission in the health-care setting.
• The concentration of HBsAg in body fluids can be 100-1000 fold

higher than the concentration of infectious HBV particles.
• Therefore, most body fluids are not efficient vehicles of
transmission because they contain low quantities of infectious
HBV, despite the presence of HBsAg.
Management of Occupational Exposure to HBV
Vaccination & antibody status Source is HBsAg positive/

of exposed person unknown
Unvaccinated HBIG x 1 and initiate hepatitis B

vaccine series
Previously vaccinated
• Known responder • No action taken
• Non-responder after two • HBIG x 2 (one month apart)

complete series
• Antibody response unknown • HBIG x 1 and re-vaccinate

Occupational HCV Exposures
Occupational Transmission of HCV
• The risk for HCV transmission from exposure to HCV infected

blood range from 0-7 %.
• The risk for transmission from exposure to fluids or tissues other

than HCV-infected blood is expected to be low.
• Environmental contamination with blood containing HCV has been

shown to represent a significant risk for transmission in
hemodialysis units where poor infection-control practices have
been implicated.
Recommendations for follow-up of Occupational HCV
Exposures - 1
• For the source, perform testing for anti-HCV:
• If HCV-positive source, test exposed person for anti-HCV & ALT

activity
• If source not infected, baseline testing not necessary.

Confirm all anti-HCV results reported positive by enzyme immunoassay
using supplemental anti-HCV testing (e.g., recombinant immunoblot assay;
RIBA)
Recommendations for follow-up of Occupational HCV
Exposures – 2
• For HCV, there is NO recommended post-exposure prophylaxis.
• Perform follow-up testing for the person exposed to an HCV-

positive source:
• At 4-6 months for anti-HCV and ALT activity

• If earlier diagnosis of HCV infection is desired, testing for HCV
RNA may be performed at 4-6 weeks
Occupational HIV Exposures
Risk of Occupational Transmission of HIV
• The average risk of HIV transmission to HCWs after exposure to

HIV-infected blood ranges from 0.1-0.3%.
• HIV transmission after non-intact skin exposure is estimated to be

less than the risk for mucous membrane exposures.
• The risk for transmission after exposure to body fluids or tissues

other than HIV-infected blood is probably considerably lower than
for blood exposures.
Management of Occupational Exposure to HIV
It is recommended to use antiretroviral drug PEP

regimens as soon as possible after an exposure for 4
weeks.

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MYCOLOGY

1. Superficial mycoses: Affecting the horny layer of the skin, e.g.,

2. Cutaneous mycoses: Affecting the deep layers of the skin, e.g.,

3. Subcutaneous mycoses: In which fungi present in the soil are

4. Deep (systemic) mycoses: These are usually caused by fungi

5. Mycotoxicosis: It is produced by consumption of

6. Allergic disorders: Spores of free-living fungi as

• Different culture media are recommended.

E) Serodiagnosis: Detection of specific antibody may help in

F) Skin testing (delayed type hypersensitivity).

• Because fungi are eukaryotes, the range of non-toxic

• The most commonly used drugs are amphotericin B,

• It is a common fungus infection of the horny layer

• Three Genera of dermatophytes infect man: Microsporum,

Ringworm is usually referred to as tinea. According to the

1. Tinea capitis (ringworm of the scalp)

• It is caused by Aspergillus fumigatus, rarely by Aspergillus niger

Predisposing factors to candidiasis:

• Systemic: Affecting the lung or kidney. It usually complicates an

Specimens from skin, mouth, vagina, sputum…etc., are subjected to:

1. Microscopic examination of a Gram-stained smear for the presence of

• It is caused by Cryptococcus neoformans.

1. Detection of the organism in sputum or CSF. A smear stained

• Pneumocystis jiroveci is an opportunistic fungus that lives in

• Mycetoma is a clinical syndrome characterized by granuloma,

• It is a localized infection that involves cutaneous and

1. True fungi (Eumycotic mycetoma)

2. Actinomycetes (Actinomycotic mycetoma)

• It is important to know whether the mycetoma is caused by

• It’s defined as fever (as a

• Infective causes are responsible for

Fungal diseases: • Protozoal diseases:

• Anemia is an important finding & suggests a serious

• Ensure that leukemias are not missed in a leukemic or pre-

• Suspect EBV infection if the patient has lymphocytosis

• Leucocytosis may suggest an occult bacterial infection.

• Diagnose malaria & spirochaetal diseases with the aid of

• Most other chemistry tests rarely contribute to the

• Routinely culture the patients' urine.

• Cultures of sputum & stool may be helpful in the presence

• Perform cultures for bacteria, mycobacteria & fungi in all

• Serologies are most helpful if paired samples show a

- Brucellosis, CMV, infectious mononucleosis, HIV,

• These diagnostic tests are of limited value in most

• Frequently check antinuclear antibody (ANA) titers,

• In patients in whom Giant Cell Arteritis (GCA) &

Salmonella Enteritidis& Typhimurium (G.E.)

Salmonella Typhi & Paratyphi A,B,C (typhoid fever)

Salmonella Choleraesuis (septicemia)

1. The O (somatic) antigens, heat-stable polysaccharides

2. The H (flagellar) antigens, heat-labile proteins

3. The Vi antigen, a heat-labile capsular polysaccharide

• Typhoid fever is caused by Salmonella Typhi.

• A similar milder syndrome is caused by

• Enteric fever is defined as ‘a generalized infection of the

• Globally, typhoid fever is more common than

• Hand-to-mouth transmission after using a

• Oral transmission via sewage-contaminated water or

• All seasons, usually in summer & autumn.

• Most cases in school-age children & young adults.

• Both sexes are equally susceptible.

• The number of bacilli needed for infection is >105

• The organism adheres to the mucosa of the small

• It disseminates into the blood-stream (1st bacteraemia

Day 9 Mycology & Applied January 2021

Day 9 Mycology & Applied January 2021