GROUP A WORK

Members
Name Reg No.
Josephine Kimeu BMLSUP/2022/54985
Kelvin Wauna BMLSUP/2022/56513
David Sayee BMLSUP/2022/52380
Festus Ngumo BMLSUP/2022/54223
Joseph Muriuki BMLSUP/2022/52336
Simon Mwololo BMLSUP/2022/56479
Deogratis Tangara BMLSUP/2022/53165

RESPIRATORY TRACT INFECTION

INTRODUCTION
Respiratory tract infection refers to any of the number of infectious diseases involving
respiratory tract. Infections of the respiratory tract are grouped according to their
symptomatology and anatomic involvement.
The respiratory tract infections is classified is classified into two types. They are:
 Upper Respiratory tract infection
 Lower Respiratory tract infection
Upper Respiratory infection:

Acute upper respiratory infections (URI) include the common cold, pharyngitis, epiglottitis, and
laryngotracheitis. These infections are usually benign, transitory and self-limited, although
epiglottitis and laryngotracheitis can be serious diseases in children and young infants. Etiologic
agents associated with URI include viruses, bacteria, mycoplasma and fungi. Most upper
respiratory infections are of viral etiology. Epiglottitis and laryngotracheitis are exceptions with
severe cases likely caused by Haemophilus influenzae type b. Bacterial pharyngitis is often
caused by Streptococcus pyogenes.
Pathogenesis:

Organisms gain entry to the respiratory tract by inhalation of droplets and invade the mucosa.
Epithelial destruction may ensue, along with redness, edema, hemorrhage and sometimes an
exudate.
Laboratory Diagnosis of Upper Respiratory Infections
The diagnosis of the upper respiratory infections is based on microbiological diagnosis and
symptomatic diagnosis. Common colds can usually be recognized clinically. Bacterial and viral
cultures of throat swab specimens are used for pharyngitis, epiglottitis and laryngotracheitis.
Blood cultures are also obtained in cases of epiglottitis.
Pharyngitis: The goal in the diagnosis of pharyngitis is to identify cases that are due to group a
beta-hemolytic streptococci, as well as the more unusual and potentially serious infections. The
various forms of pharyngitis cannot be distinguished on clinical grounds. Routine throat cultures
for bacteria are inoculated onto sheep blood and chocolate agar plates. Thayer-Martin medium
is used if N gonorrhoeae is suspected. Viral cultures are not routinely obtained for most cases
of pharyngitis. Serologic studies may be used to confirm the diagnosis of pharyngitis due to
viral, mycoplasmal or chlamydial pathogens. Rapid diagnostic tests with fluorescent antibody or
latex agglutination to identify group a streptococci from pharyngeal swabs are available. Gene
probe and polymerase chain reaction can be used to detect unusual organisms such as M
pneumoniae, chlamydia or viruses but these procedures are not routine diagnostic methods.
Sinusitis: For acute sinusitis, the diagnosis is made from clinical findings. A bacterial culture of
the nasal discharge can be taken but is not very helpful as the recovered organisms are
generally contaminated by the resident flora from the nasal passage. In chronic sinusitis, a
careful dental examination, with sinus x-rays may be required. An antral puncture to obtain
sinusal specimens for bacterial culture is needed to establish a specific microbiologic diagnosis.
Otitis: The diagnosis of both otitis externa and otitis media can be made from history, clinical
symptomatology and physical examinations. Inspection of the tympanic membrane is an
indispensable skill for physicians and health care workers. All discharge, ear wax and debris
must be removed and to perform an adequate otoscopy. In the majority of patients, routine
cultures are not necessary, as a number of good bacteriologic studies have shown consistently
the same microbial pathogens mentioned in the section of etiology. If the patient is
immunocompromised or is toxic and not responding to initial antimicrobial therapy
tympanocentesis (needle aspiration) to obtain middle ear effusion for microbiologic culture is
indicated.
Lower Respiratory tract Infection
Lower respiratory tract infections are any infections in the lungs or below the voice box. These
include pneumonia, bronchitis, and tuberculosis. These syndromes, especially pneumonia, can
be severe or fatal. Although viruses, mycoplasma, rickettsia and fungi can all cause lower
respiratory tract infections, bacteria are the dominant pathogens; accounting for a much higher
percentage of lower than of upper respiratory tract infections.
Pathogenesis and Clinical Manifestations
Infectious agents gain access to the lower respiratory tract by the inhalation of aerosolized
material, by aspiration of upper airway flora, or by hematogenous seeding. Pneumonia occurs
when lung defense mechanisms are diminished or overwhelmed. The major symptoms or
pneumonia are cough, chest pain, fever, shortness of breath and sputum production. Patients
are tachycardic. Headache, confusion, abdominal pain, nausea, vomiting and diarrhea may be
present, depending on the age of the patient and the organisms involved.
Causes of Lower Respiratory Infection

Infections in the lower respiratory tract are primarily the result of:
1. viruses, as with the flu
2. bacteria, such as Streptococcus or Staphylococcus aureus
3. fungal infections
4. mycoplasma, which are neither viruses or bacteria but are small organisms with
characteristics of both

Laboratory Diagnosis

Bacteriologic examination and culture of purulent respiratory secretions should always be

performed for cases of acute bronchitis not associated with a common cold. Patients with
chronic bronchitis should have their sputum cultured for bacteria initially and during
exacerbations. Aspirations of nasopharyngeal secretions or swabs are sufficient to obtain
specimens for viral culture in infants with bronchiolitis. Serologic tests demonstrating a rise in
antibody titer to specific viruses can also be performed. Rapid diagnostic tests for antibody or
viral antigens may be performed on nasopharyngeal secretions by using fluorescent-antibody
staining, ELISA or DNA probe procedures.

Pneumonia: Sputum should be examined for a predominant organism in any patient suspected
to have a bacterial pneumonia; blood and pleural fluid (if present) should be cultured. A sputum
specimen with fewer than 10 while cells per high-power field under a microscope is considered
to be contaminated with oral secretions and is unsatisfactory for diagnosis. Acid-fast stains and
cultures are used to identify Mycobacterium and Nocardia spp. Most fungal pneumonias are
diagnosed on the basis of culture of sputum or lung tissue. Viral infection may be diagnosed by
demonstration of antigen in secretions or cultures or by an antibody response. Serologic studies
can be used to identify viruses, M pneumoniae, C. burnetii, Chlamydia species, Legionella,
Francisella, and Yersinia. A rise in serum cold agglutinins may be associated with M
pneumoniae infection, but the test is positive in only about 60% of patients with this pathogen.
Some organisms that may colonize the respiratory tract are considered to be pathogens only
when they are shown to be invading the parenchyma. Diagnosis of pneumonia due to
cytomegalovirus, herpes simplex virus, Aspergillus spp. or Candida spp require specimens
obtained by transbronchial or open-lung biopsy. Pneumocystis carinii can be found by silver
stain of expectorated sputum. However, if the sputum is negative, deeper specimens from the
lower respiratory tract obtained by bronchoscopy or by lung biopsy are needed for
confirmatory diagnosis.
Rapid diagnostic tests, as described in previous sections, are available to identify respiratory
viruses: the fluorescent-antibody test is used for Legionella. A sputum quellung test can
specify S pneumoniae by serotype. Enzyme-linked immunoassay, DNA probe and polymerase
chain reaction methods are available for many agents causing respiratory infections.

General Diagnosing of respiratory infections

To determine if you have a lower respiratory infection, your physician will ask about your
symptoms and conduct a physical exam, listening for abnormal breath sounds. Tests may
include:
Sputum test: You may be asked to provide a sample of mucus to be checked for bacteria.

Tuberculin skin test: A small amount of tuberculosis antigen is injected under your skin. If a red
bump appears, it indicates that you have been exposed to TB.
Spirometry: This test measures the quantity and speed of air you exhale to estimate how much
your bronchial tubes are inflamed and narrowed.
Peak flow meter: This device measures how hard you can exhale. Peak flow meters can be used
at home to monitor your condition.
Arterial blood gas: This blood test checks the amount of oxygen and carbon dioxide in your blood
and measures your blood’s acidity.
Pulse oximetry: An oximeter measures the amount of oxygen in your blood with a sensor that’s
clipped onto your finger.
Chest X-ray: This test can identify the presence of pneumonia or other blockages in the airway.
Computed tomography (CT) scan: This test combines X-ray and computer technology to produce
detailed cross-sectional images of your chest cavity.
Bronchoscopy: An endoscope (a thin, flexible tube with a light and camera on the end) is inserted
into your airway to check for blockages or remove samples for testing.
Pleural fluid culture: A needle is inserted between your ribs to get a sample of the fluid between
your lungs and chest wall for testing.
Common Agents of Respiratory Infections

Clinical Illness Bacteria Viruses Fungi Other

Common cold Rare Rhinovirus, Rare Rare
(rhinitis) Corona virus,
Para- Influenza,
RSV, Influenza
virus
Pharyngitis Group A, beta- Adenovirus, Candida Rare
hemolytic coxsackiavirus A albicans
streptococci, Influenza,
Corynebacterium Rhinovirus,
, Neisseria Epstein Barr
gonorrhae virus,
Cytomegalovirus
Epiglottitis and Haemophilus Respiratory Rare Rare
Laryngotracheitis Influenza type B, Syncytia virus,
Corynebacter Para- Influenza,
diphtheria , Adenovirus,
Haamophilus herpes simplex
Influenza , Strep virus
Pneumoniae,
Mycoplasma
Pneumoniae
Pneumonic Strep Respiratory Histoplasma, Pneumocystis
Pneumoniae, Syncytia virus, apsulatum, carinii
Strep Pyogenes, Adenovirus, Blastomyces
Staph aureus, Para- Influenza, dermatitis,
Haemophilus Cytomegalovirus Candida
Influenza, , herpes simplex albican
Klebsiella virus, Varicella –
Pneumonia, E. zoster, Measles
coli virus
LABORATORY DIAGNOSIS OF GASTROINTESTINAL INFECTIONS

INTRODUCTION

The human gut literally teems with microorganisms from at least 1,000 different species that are
increasingly considered to be a valuable resource and their presence is necessary for the healthy
functioning of the gastrointestinal tract and, by default, the entire body. However, due to
continual contact with the environment, primarily via food, the gut is susceptible to infection
when a virus, parasite, or bacterium enters the area and disrupts normal gut microbiota (or flora
causing gastroenteritis, an inflammation of the gastrointestinal tract involving both the stomach
and the small intestine. Symptoms include diarrhea, vomiting, and abdominal pain.

The important causative agents of bacterial gastroenteritis and diarrhea

are Campylobacter, Salmonella,  Shigella, Plesiomonas, Vibrio, Yersinia
enterocolitica, Clostridioides difficile (formerly Clostridium difficile), and pathogenic strains
of Escherichia coli. Important causative agents of viral gastroenteritis are Adenovirus, Rotavirus,
Astrovirus, and Norovirus. Parasitic infections are caused by a variety of helminths, protozoa,
ciliates, and coccidian organisms. Acute gastrointestinal infections with diarrhea are mostly
caused by Giardia lamblia, Entamoeba histolytica, and Cryptosporidium species. Requests may
be made for chemical, bacteriological, viral, or parasitological analysis of stool specimens.
occasionally problem arises in the collection and transport of fecal specimens, so a rectal swab
must be used instead. Rectal swabs are preferred for isolation of the bacteria that invade the
mucus of the lower intestine e.g., Shigella.

Collection of fecal specimens

The fecal specimen should be collected in the early stages of the disease before the antibiotic
treatment is started when pathogens are likely to be present in the stool in high numbers. stool
should be collected in a sterile container with a tight-fitting leak-proof lid. The specimen should
be processed as soon as possible not more than 2 hours.

Small amount should be collected on a swab inserted in the stool and rotated and inoculated in a
suitable transport media like Cary-Blair transport medium for all enteric pathogens and alkaline
peptone water which is suitable for Vibrio spp.
collection of rectal swabs.

Sterile cotton swabs should be used to collect specimen which is moistened with sterile
bacteriostatic fluid or transport medium, inserted via the rectal sphincter, rotated then withdrawn.
it should be examined for fecal staining. The swab taken may be used for microscopic
examination for protozoa, but stool is preferred. if to be processed within 2 hours, it is placed in
a sterile tube with a screw cap but if longer, it should be inoculated in transport media.

Examination of specimens

Stool specimens were examined macroscopically for:

i) consistency
ii) color
iii) atypical components like mucus, parasites, or blood.

then examine microscopically for:

i) parasites e.g., ova or cysts

ii) leukocytes
iii) atypical components like blood.

Diagnosis

This can be confirmed through laboratory tests used for culture or antigen detection from stool
specimens. Stool culture is the method of choice for diagnosing bacterial intestinal infections;
however, infections caused by Clostridium difficile can be diagnosed by the detection of toxins
A and B in stools. The screening of C. difficile colonization is performed by antigen-based
immunoassays, e.g., toxin A and B detection using chromatographic/lateral flow membrane
cartridge devices or enzyme immunoassay (EIA)., and infections caused by diarrheagenic
Escherichia coli by PCR detection of specific virulence factor genes harbored by several E. coli
pathotypes. The techniques used to diagnose viral gastrointestinal infections include the
detection of viral antigens and nucleic acids.
The specimen should also be cultured for enteric pathogen identification and then the specimen
should be inoculated soonest after a reception in the laboratory for probable identification of
shigella and campylobacter spp. if there is a delay, should be stored at 40C.

suitable media of varying selectivity for primary plating which allow certain enteric pathogenic
bacteria to grow while inhibiting the growth of gram-positive bacteria and some gram-negative
bacteria. inoculation can be done directly from recall or fecal swabs.

Gastrointestinal infections caused by parasites can be diagnosed by testing for trophozoites and
cysts of protozoa, or larvae and eggs of helminths in stool by direct microscopic examination,
with concentration techniques or by specific stains.

Inoculation of agar plates

Selectable media is used for culturing. for the microbiological culture of Shigella species,
salmonella species, Yersinia, Enterocolitica, and E. coli, general purpose media of low
selectivity e.g., McConkey, and another media of moderate or high selectivity e.g., DCA or XLD
should be used.

for culturing Campylobacter species, specially designed selective media is used e.g., Mueller
Hinton agar with 5% sheep blood.

many Vibrio strains grow on McConkey agar, but selective e, media like TCBS, sucrose agar,
alkaline bile salt agar (BSA), and tellurite taurocholate gelatin (TTG) are preferable.

antibiotic susceptibility testing

This is used to determine microbial resistance to antibiotic therapy, this can be done by the Disk
Diffusion method and in line with CLSI standards.
 BLOOD STREAM INFECTIONS.
INTRODUCTION
Blood stream infections (BSI) refers to the presence of organisms in blood which are threat to
every organ in the body.
It causes shock, multiple organ failure and DIC (Disseminated Intravascular Coagulation).
The presence of bacteria in blood is called Bacteremia while bacteria circulate and actively
multiply in the blood stream is called Septicemia.
Viremia- The presence of virus in blood.
Parasitemia- The presence of parasite in blood
The presence of fungi in blood is called Fungemia.

ETIOLOGICAL AGENTS
1. Bacteria – S. aureus, S. pneumoniae, E. coli
2. Fungi – C. albicans, H. capsulatum
3. Parasites – T. gondii, P. malaria
4. Virus – Epstein Barr Virus, Cytomegalovirus, SARS, SARS CoV
2(Novel corona virus), HSV, HIV. Hepatitis etc.

TYPES OF BACTEREMIA
1. Transient Bacteremia
It is the sudden destruction of the tissue.
It occurs during brushing teeth, chewing food, manipulation of infected tissues, devices inserted
through contaminated mucosal surface, surgery in non- sterile sites.
2. Continuous Bacteremia- the organism released into the bloodstream at fairly constant rate.
It occurs in the early stages of certain infections such as typhoid fever, brucellosis &
leptospirosis.
TYPES OF BACTEREMIA
3. Intermittent bacteremia- organism released into the blood stream at various time intervals.
It is found in patients with undrained abscess. occurs in the early stages of meningitis,
pneumoniae,
pyrogenic arthritis and osteomyelitis.
They are 2 types: Intravascular and extravascular.
The factors that contribute bloodstream infections are
1) Use of immunosuppressive agents’
2) Widespread use of broadspectrum antibiotics.
3) Invasive surgical procedures.
4) Prolonged survival of prolonged ill patients.
INTRAVASCULAR INFECTION
Originates within cardiovascular system which include
1. Infective endocarditis
2. Mycotic aneurysm
3. Suppurative thrombophlebitis
4. Intravascular catheter associated bacteremia
1. INFECTIVE ENDOCARDITIS
It is the infection of the endocardium.
It is characterised by the presence of vegetation which is composed of platelets, fibrin,
inflammatory cells and entrapped organism.
It is mainly caused by viridans streptococci.
It is a normal inhabitant of oral cavity which enters into the bloodstream through gingivitis,
predontitis or dental manipulation.
2. MYCOTIC ANEURYSM
It is the inflammation of arterial wall and characterized by the bulging of arterial wall and its
rupture.
The etiological agent is similar to that of endocarditis.
3. SUPPURATIVE THROMBOPHLEBITIS
It is the inflammation of vein wall and characterized by alteration in the vein endothelial lining
followed by clot formation.
It is found in hospitalized patients using IV catheters.
4. INTRAVENOUS CATHETER ASSOCIATED BACTEREMIA
 Central venous catheter is a triple lumen used to provide fluid, blood products, medications,
antibiotics and nutrition.
Bacteremia occurs in two routes:
1. Movement of organism from patient skin to catheter.
2. Movement of organism from catheter to catheter tip within the blood stream.
It is mainly caused by Staphylococcus aureus and it causes biofilm formation on catheter surface.

EXTRAVASCULAR INFECTION
It is the infection of lymphatic system and It includes liver, spleen and bone marrow.
Portal of entry: genitourinary tract (25%), respiratory tract (20%), abscess (10%), surgical wound
infections (5%), miscellaneous sites (10%).
Clinical manifestations
1. Septecemia / Sepsis
This is the presence of bacteria and its toxic products in blood.
Symptoms include fever, hyperventillation, respiratory alkalosis, diarrhoea.
2. Septic shock
It occurs due to the production of cytokines from tumor necrosis factor and interleukins.
Symptoms include fever, renal failure, change in mental status.
3. DIC (Disseminated Intravascular Coagulation)
It is characterized by
I. Formation of blood clots within blood vessels.
ii. Bleeding due to the depletion of coagulation factors.

LABORATORY DIAGNOSIS.
1. Specimen collection
The blood should be collected before antimicrobial therapy.
The skin is wiped with 70% isopropyl alcohol.
Using sterile disposable syringe, the blood is collected aseptically by venipuncture.
The blood volume is around 10-20 ml for adults and 1-5 ml for infants.
The collected blood transported to the laboratory in anticoagulant containing tube. Heparin,
EDTA are not used, because it inhibits the growth of organisms.
Hence, Sodium polyanethol sulphonate (SPS) is acoagulant for blood culture.

2. Blood culture media

It consists of nutrient broth and anticoagulant.
It includes Trypticase soy broth, Brainheart infusion broth,Columbia or Brucella broth.
Biphasic medium is used as a conventional culture medium.

3. Instrument based system

I. BACTEC System
BACTEC is a fully automated machine which consists of incubator, shaker and incubator.
It consists of a glass permeable flourescene to measure Co2 produced by microorganisms.
ii. BacT Alert
It is based on the colorimetric detection of Co2.
iii. Versa TREK System
It is unique agitation system during blood culture
inoculation

4. Identification
The isolated organism is identified by colony morphology,
gram staining, biochemical reactions and serological tests.
HACEK refers to group of fastidiuos slow growing bacteria.
It is a gram negative bacilli.
It is found in mouth.
It includes Hemophilus species, Cardiobacterium hominis etc.
Blood cultures from HACEK patients take 7-30 days to become positive.
Antibiotic sensitivity test is essential for effective therapy.
n/b The drug resistance is very common.

Commonly Used Techniques.

1. Dilution Methods: Broth Dilution and Agar Dilution
This a Conventional technology which still in widespread use.
2. Antimicrobial Gradient Method.
The gradient strip test is a combination of disk-diffusion and dilution method of AST,
having advantageous properties of both methods. It allows the MIC to be determined while
keeping it simple and easy to use. The method is based on the diffusion of an antibiotic
through agar with a continuous gradient.
3. Disk Diffusion Test
The most widely used routine AST in clinical microbiological laboratories. It has been
standardized to test the susceptibility of the most common and clinically relevant bacteria that
cause human diseases.
4. Automated and Semi-Automated Devices Based on Microdilution Susceptibility
Testing
Automated and semi-automated devices for bacterial ID and AST are worthy of the task and
have significantly improved laboratory efficiency.
5. Molecular-Based Techniques for Resistance Detection.
Molecular AST directly detects specific resistance genes, as well as mutations in and
expression of these genes. These molecular methods have been developed and tested as an
alternative for or complementary to conventional AST and are generally faster than classic
culture-based assays, with the test results available within one to a few hours.
6. Polymerase Chain Reaction.
The most widely used nucleic acid amplification-based method for the detection of
specific resistance genes are polymerase chain reaction (PCR). Both real-time and conventional
PCR rely on the amplification of nucleic acid sequences that encode resistance to an antibiotic.