Clinical and Chemical Pathology

Clinical Microbiology

Lectures: 1- Diagnosis of infectious diseases

2- Interpretation of microbiology Lab. Reports

Prof. Dr Maha Gaafar

Prof. Dalia Kadry
Assistant prof. Doaa Ghaith
Assistant Prof. Noha Salah
Assistant Prof. Amira Farouk
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Clinical Microbiology

Laboratory Diagnosis of infectious diseases

Intended learning Objectives:

1-List of causes of infectious diseases
2- Define the role of the microbiology laboratory
3-Identify laboratory tests required to diagnose infection
4- Outline microbiology sampling and Handling of Specimen

According to symptoms
• Urinary tract symptoms
• GIT symptoms
• CNS symptoms …etc
The tests needed for diagnosis are requested
• urine C/S
• stool C/S or Widal or H. pylori ag or ab --etc
• CSF examination and C/S …. etc
Role of the lab
- Instructions for proper sampling.
- Processing of the samples using:
o Cultural methods or
o Non cultural methods

Causes of infectious diseases

• Bacteria
• Viruses
• Fungus
• Parasites

I General approach to the diagnosis of bacterial infection

For most known bacteria we do culture and sensitivity as gold standard

method of diagnosis.
First step:
• Direct film from the sample ( Gram stain )
• Culture on appropriate media ---→nutrient, selective, differential---
etc
• Incubation for at least 24 hours
• The sample is placed on a sterile plate that contains specific
nutrients to encourage growth of microorganisms.
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• Selective media contain inhibitory substances that permit the
isolation of specific types of microorganisms.
• Many microorganisms, can easily be grown in a
• culture.
• Some bacteria, e.g spirochetes, cannot be cultured at all.

• Other bacteria, mycobacteria , can be cultured on special media

and take weeks to grow.
• After the microorganisms are cultured, tests to identify them and
to determine susceptibility and sensitivity to antimicrobial drugs
are done.

Second step:
Using the appropriate tests for identification of pathogenic bacteria
such as:
• Catalase
• Coagulase
• Oxidase
• Biochemical Reactions ----etc

Third step:
Performing antibiotic susceptibility test for the isolated pathogenic
bacteria

How to diagnose a bacterial infection when the culture is negative or

difficult to be done?
We can use different serological techniques for antigen and antibody
detection or nucleic acid detection using different molecular methods.

- Antibody detection in patient’s serum

• IgM-------> Indicates a current infection
• IgG--------> Always difficult to differentiate a current infection
from a previous infection eg.:
Slide agglutination as for Typhoid fever, brucella ….. etc
Serological tests for Syphilis
-
- Antigen detection
• Fluorescent antibody test for wide variety of bacteria
• Latex agglutination test as for H. influenzae etc
• Enzyme-Linked immunosorbent Assay for wide variety of
bacteria…..etc
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- Nucleic acids detection using polymerase chain reaction (PCR) or
DNA probes to detect the DNA or RNA of the organism …. etc

II General approach to the diagnosis of Viral diseases

Cell culture (viruses replicate only in living cells) with presumptive

identification by the characteristic cytopathic effect( CPE) and definitive
identification by using known monoclonal antibody.

Serologic procedures for viral antigen and antibody detection

- Antibody detection in patient’s serum
• Ig M (recent infection)
• Ig G (rise of antibody titer by 4-fold rise a sign of recent infection)
e.g. If the titer in acute phase is ¼ and after 10-14 days (convalescent
phase) the titer is 1/16 this means recent infection
Viral antigen detection in patient’s blood or body fluids by various tests
but most often by ELISA eg. Surface antigen of HBV, rapid antigen test
for SARS-COV-2
Nucleic acids detection using polymerase chain reaction (PCR) or
DNA probes to detect the DNA or RNA of the virus…etc

III General approach to the diagnosis of fungal diseases

• Direct microscopic examination either by treating the specimen

with 10%KOH or staining it with special stain.
• Culture of the fungi frequently on Sabouraud’s agar which
facilitates the appearance of the slow growing fungi by inhibiting
the growth of bacteria in the specimen.
• Serologic tests which are useful in systemic mycosis.
• Nucleic acids detection using polymerase chain reaction (PCR)
or DNA probes

IV Diagnosis of most common pathogenic protozoa

• Intestinal infections:
Diagnosis is made by microscopic examination of fresh stool specimen
for Entamoeba and giardia or by using modified acid-fast stain in
Cryptosporidia.
• Urogenital infections: (Trichomonas vaginalis)
Diagnosis is made by detection of motile trophozoites in vaginal or
urethral secretions or rarely by culture.
• Blood and tissue infections:
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Diagnosis is made by microscopic examination for certain types such as
malaria or by antibody detection as in case of toxoplasma or by both
methods in case of Trypanosoma

Microbiology Sampling and Handling of Specimens

ILOs
By the end of the presentation you will be able
To:
• Know the key to accurate laboratory diagnosis
• Recognize guidelines for specimen selection,
collection and storage.
• Recognize rejection criteria of microbiology samples
• Underline general rules for safety in specimen
management
• Recognize most of the pre-analytical errors in
microbiology.

I General guidelines for specimen selection and collection

a) Aseptic precautions to minimize the chances of contamination

particularly by normal flora.
b) Correct type of specimen from the correct anatomic site.
c) Optimal time of specimen collection.
d) Adequate volume of the sample.
e) Clear labeling of the specimen with patient's name, ID number,
specific site, date, time of collection and initials of the collector.
f) Adequate information should be provided in the request forms such
as specific site from which the sample is collected, any antibiotic
therapy administered to the patient before or during the collection
of the sample, any suggestions as regards specific pathogens in a
particular sample and if a suspicion of infections caused by
pathogens that are likely to be hazardous to laboratory personnel.
It is also good to mention any underlying diseases like diabetes,
steroid therapy or if patient is on chemotherapy.
Importance: These informations give the laboratory staff an
opportunity to examine the samples in totality.
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II Transport and storage of the collected material:

a) All specimens should be transported to the laboratory as soon as

possible preferably within 2 hours.
b) If there is any delay, the lab. should be contacted for suitable
transport media or information about correct storage of the sample.
c) Samples that should be refrigerated if there is any delay:
- Urine
- Sputum
- All catheter tips
- Feces
- All genitourinary tract samples for Chlamydia
- All nasopharyngeal samples for culture

d) Samples that should not be refrigerated

- Blood
- Body fluids for culture
- Any sample suspected to contain Neisseria
- Any sample suspected to contain Hemophilus
- All pus samples and wound swabs for culture

Criteria for rejection of samples

- Unlabeled samples or improperly labeled samples

- Samples received in wrong, leaking, cracked or broken
containers
- Samples with obvious contamination
- Unpreserved samples the are received more than two hours
after the collection
- Samples not appropriate for a particular test

III Safety:

Care should be taken during transport of infectious materials from the

patient to the lab. and between the labs.
General rules for safety in specimen management:
- Using personnel protective equipments such as (gloves, gowns
masks, goggles) when collecting specimens and during
laboratory processing.
- Using leak-proof specimen containers and transport the
containers within a sealable, leak-proof plastic bag.
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Selection And Collection Of Common Clinical Specimens

For Bacterial Culture

Blood culture:
Points to be remember ed :
– The number of viable organisms circulating in the blood is
very small. At least 4-5ml of blood should be drawn for
aerobic and anaerobic cultures and about 8-10ml should be
drawn for fungal and mycobacterial blood cultures. For
infants it is not advisable for volumes of less than 1 ml to be
collected. (according to manufacturer instructions)
– Blood should not be allowed to clot to prevent trapping of
bacteria.
– No blood for culture should be drawn from a vascular line. If
not possible blood should be drawn below an existing line.
– The blood should be collected before starting the therapy.

Methodology of drawing blood for culture

• Choose the vein
• The area of the skin over the venipuncture site should be cleaned in
a circle of 5cms diameter starting from the center. Apply 2% iodine
then allow it to dry, this should be repeated at least twice then
cleaned with 70% alcohol. The sterile area should not be handled
by unsterile hand.
• Sterile gloves should be worn when the disinfected site is palpated.
• Withdraw blood the needle should be changed before the blood is
injected into the culture bottle.
• After removing the needle, the area should be cleaned with a 70%
alcohol.
Urine samples:
Urinary tract is usually sterile except for the urethra which may harbor
certain commensals.
• Precautions
• Samples should be collected in sterile wide-mouthed containers.
• Women should be instructed to clean the area around the urethral
meatus.
• No antiseptic solution should be used.
• Mid-stream urine specimen is ideal to carry all bacteria from
bladder.
• The first early morning sample of urine represents the most
concentrated samples.
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• Regarding catheter sample collection, no sample should be
collected from the urosac bag by emptying the bag into sterile
container.
•
Respiratory tract specimens
• Lower respiratory secretions:
– Sputum
– Endotracheal secretions (by passing a long catheter into the
tracheobronchial tree and sucking out the secretions with a
syringe)
– Bronchoalveolar lavage (BAL) by bronchial washing.

Sputum
• It is the most common sample sent to the lab. for culture
• It is frequently contaminated with oropharyngeal flora and the
upper respiratory tract secretions.
• The sample should be collected before the administration of
antibiotics.
• An early morning deep cough sample is necessary.
The patient is instructed to rinse the mouth before giving the sample to
collect as far as possible the highly purulent secretion without any
contamination with saliva.

• A direct smear is used to screen for excessive squamous epithelial

cells which indicates saliva. Sputum will be rejected if 10 or more
squamous epithelial cells are seen per low power field on gram
stain. The nursing station will be called, and a
new sputum specimen will be requested.

• Upper respiratory secretions:

– Throat swab
– Nasopharyngeal aspirates (usually obtained when it is not
possible to obtain sputum in children with
bronchopneumonia by a sterile catheter passing through one
nostril as far as the nasopharynx and the secretion is
aspirated by a syringe).
– Nasal swabs ( A cotton swab moistened with sterile saline is
rubbed against the inner side of the nasal mucosa used to
detect carrier of MRSA )
– Nasopharyngeal swab
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Throat swab

The fauces are visualized by pressing the tongue down. The tonsil, uvula
and the posterior pharyngeal wall are completely visualized.
• Any patches or plaques could be seen in the throat at this stage.
• - At least two swabs should be collected, one for culture and the
other for direct smear.

Pus / Wounds / Burns culture

Special care should be taken to avoid contamination of the sample

with commensal organisms from the skin.
• All wound swabs should be collected before applying an antiseptic
dressing to the wound.
• Closed lesions may be drained using a syringe and a needle.
• No pus sample should be refrigerated.
• A swab is never preferred to liquid pus samples for aerobic or
anaerobic cultures.
• The swab should always be collected from the central necrotic area
of the wound taking care not to touch the sides of the wound.
• If the lesion is known to contain anaerobes, pus should be collected
by a close syringe technique and sent within 10 minutes to the lab. ,
if there will be any delay transport media should be used.

Stool Specimen

• All samples should be collected in a clean, dry, disinfectant free

container which is wide and free of urine and water.
• The container needs not to be sterile.
• Rectal swab is useful when it is not possible to obtain a stool
Sample

Body fluids
– Pleural fluid
– Peritoneal fluid
– Pericardial fluid
– Synovial fluid
– Cerebrospinal fluid
– Other fluids like cyst aspiration fluid
• The techniques for collection, transport and processing of all
fluids is almost the same.
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• The fluid should be collected in at least two sterile tubes and
should be carried out by a physician under complete aseptic
precautions.

Catheter (Venous or arterial )

Collect in Screw-capped sterile tube

Disinfect the entry site with 70% alcohol, aseptically remove the catheter
and send it immediately to the lab.

Eye
Bedside inoculation of the culture plates is better, seal and
transport to the lab immediately
For infections on the surface of the eye, specimens are collected
with a swab or by corneal scrapings, for deep-seated infections,
aspiration of aqueous or vitreous fluid is performed,

Genitals (Swab immersed in transport medium)

The area of inflammation or exudates should be sampled, avoid

collection of normal flora because they may inhibit or overgrow
the pathogens

Ear (Swab or capped needless syringe)

A throat swab may be helpful in acute otitis media without
tympanic membrane rupture
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Fever of Unknown Origin (FUO)

Intended learning Objectives:

1- Define fever of unknown origin
2- Identify causative agents and laboratory tests required for
diagnosis.

Definition
Fever more than 38 ◦C, lasting more than 3 weeks with no diagnosis
despite 1 week of inpatient investigations or 3 weeks as an outpatient

The initial evaluation of (fever of unknown origin) FUO typically

involves:
History taking
Physical examination
Routine blood chemical tests
Blood counts
Cultures of urine and blood
Abdominal CT
Further testing is generally more invasive and depends on the patient‘s
condition.

Causes of FUO:
Infections (30-40%), neoplasms (20-30%), collagen vascular diseases
(10-20%), numerous miscellaneous diseases (15-20%) and Remain
unknown or spontaneous resolution (5 and 15%)
•In children, infections are the most common cause
•Neoplasms and connective-tissue disorders are more common in elderly
persons
•If it persists for more than one year are less likely to be caused by
infections and neoplasms and much more likely to be due to
granulomatous diseases.
Some infections will be discussed in details like Brucellosis and typhoid
fever.

Brucellosis
Brucellosis is a zoonotic infection caused by the bacterial genus Brucella.
It is an infectious disease that spreads from animals to people it is more
common in some geographical areas e.g. The Mediterranean Basin and
south and Central America.
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Transmission
• Eating undercooked meat or consuming unpasteurized/raw dairy
products
• Breathing in the bacteria that cause brucellosis (inhalation)
• This risk is generally greater for people in laboratories that work
with the bacteria

How is brucellosis diagnosed?

Making the diagnosis of brucellosis can sometimes be difficult because of
the similar symptoms and signs shared with other febrile illnesses. An
accurate history obtained by a health-care provider (including travel
history, occupation, animal exposure, etc.) may be very helpful in raising
the suspicion of brucellosis as a possible diagnosis .

Diagnostic Laboratory Tests

Specimens
• 1-Blood sample
• 2- Biopsy material culture (lymph nodes, bone, etc)
• 3- Any fluid (eg, synovial fluid, pleural fluid, or cerebrospinal fluid
(CSF), but the yield is usually low.
• 4-Serum for serologic tests.
Additional blood tests may demonstrate anemia, low platelets, a low
white blood cell count, and elevated liver function tests

A-Culture
Any potential Brucella specimens should be handled under a biohazard
hood. Diagnosis of brucellosis is definitive when Brucella organisms are
recovered from blood, bone marrow, or other tissue. The laboratory
should be alerted to keep the cultures for 3-4 weeks.
*Blood culture:
Isolation rates are much higher in acute cases presenting with
symptomatic disease of less than 2 weeks and the recovery rate can be
improved through blood samples taken in the pyrexial phase. in chronic
cases bacteriologic confirmation is less successful.
*Bone marrow cultures:
Increases the recovery rate at any stage of disease.
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B-Serology
The tube agglutination test, serum agglutination test (SAT), Rose Bengal
test (RBT), Coombs‘ test (CT) and ELISA:
Serologic testing is the most commonly used method of diagnosing
brucellosis. Repeated serologic testing is recommended if the initial titer
is low.

Interpretation
-Titers higher than 1:80 define active infection. A high IgG antibody titer
or a titer that is higher after treatment suggests persistent infection or
relapse.
-Titers higher than 1:160 in conjunction with a compatible clinical
presentation are considered highly suggestive of infection.
-Titers higher than 1:320 are considered to be more specific, especially in
endemic areas. Seroconversion and evolution of the titers can also be
used for diagnosis.
-SAT suffers from high false-negative rates in complicated and chronic
cases.
-A fourfold or higher rise in Brucella agglutination titer between acute-
and convalescent-phase serum specimens obtained at least 2 weeks apart
may prove the infection.

C- Polymerase chain reaction (PCR) has been developed for the

detection and rapid diagnosis of Brucella species in human blood
specimens.

Differential diagnosis:
Fever of unknown origin
- Infections: Infectious Mononucleosis (EBV & CMV)
,Tuberculosis,Typhoid fever, Bacterial meningitis, Endocarditis ,HIV
infection ,Urinary tract infection, Malaria, Intra-abdominal and
Retroperitoneal Abscesses, Rickettsial diseases
-Collagen vascular disease
-Neoplasms
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TYPHOID FEVER

Typhoid fever caused mainly by salmonella typhi .It is occasionally

caused also by salmonella paratyphi A or B, or salmonella cholerasuis.
Transmission is by the fecal-oral route through contaminated water or
food.
The incubation period is highly variable (1-6) weeks.

Diagnostic Laboratory Tests

A. Isolation of salmonella
1. Blood culture:
–It is the gold standard test.
–Best done within 5 days from the onset of fever
–Positive in the first week of illness in 80% of patients who have not
taken antimicrobials
–The rate of blood culture positivity declines thereafter, but one- forth
or more of patients still have positive blood cultures in the third week.
–Bone marrow cultures are often positive.
2. Stool cultures are often positive from the second week on.
3. Urine cultures may be positive after the second week.
4. Positive culture of duodenal drainage establishes the presence
of
Salmonellae in the biliary tract in carries.

B. Widal test:
Agglutinins rise sharply during the 2nd and 3rd week of infection.
• Best done 10-14 days after the onset of fever.
• Paired serum specimens, 7-10 days apart are needed to prove a
rising titre:
• High or rising titre of O (≥1:160)→ active infection.
• High titre of H ((≥1:160)→ past immunization or past infection.
• High titre of Vi (in some carries.)
• Possible cross reactive antibodies limits the use of the test,
especially in endemic areas.

C. PCR
–Gives rapid results
–Valuable in patients with suspected clinical findings but with
negative cultures.
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Differential diagnosis
The differential diagnosis depends on infections that are endemic in the
area where an individual contracted the infection.
• Fever of unknown origin
• Other gastrointestinal illnesses
• Other infections that have few localizing findings.
• Examples include tuberculosis, infective endocarditis, brucellosis,
lymphoma, and Q fever.
• Viral hepatitis, malaria, or amebiasis may be in the differential
diagnosis as well.

Summary
First week: blood culture gives the best results, stool and urine are
negative
Second week: blood and stool cultures are often positive, urine negative,
Widal test best done between 10-14 days.
Third week: blood and stool still are often positive, urine may be
positive.
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MENINGITIS

Intended learning Objectives:

1- Recognize the causative agents of meningitis
2- Identify laboratory tests required to diagnose cases of
meningitis

Meningitis is an inflammation of the protective membranes covering the

brain and spinal cord, known collectively as the meninges.
The inflammation may be caused by infection with viruses, bacteria, or
other microorganisms, and less commonly by certain drugs. Meningitis
can be life-threatening because of the inflammation's proximity to the
brain and spinal cord; therefore, the condition is classified as a medical
emergency.
A lumbar puncture diagnoses or excludes meningitis. A needle is inserted
into the spinal canal to extract a sample of cerebrospinal fluid (CSF), that
envelops the brain and spinal cord. The CSF is examined in a medical
laboratory.

Causes
Bacterial
The types of bacteria that cause bacterial meningitis vary according to the
infected individual's age group.
•In premature babies and newborns up to three months old,
common causes are group B streptococci (subtypes III which
normally inhabit the vagina and are mainly a cause during the first
week of life) and bacteria that normally inhabit the digestive tract
such as Escherichia coli (carrying the K1 antigen). Listeria
monocytogenes (serotype IVb) may affect the newborn and occurs
in epidemics.
•Older children are more commonly affected by Neisseria
meningitides )meningococcus) and Streptococcus pneumoniae
(serotypes 6, 9, 14, 18 and 23) and those under five by
Haemophilus influenzae type B (in countries that do not offer
vaccination(
•In adults, Neisseria meningitidis and Streptococcus pneumoniae
together cause 80% of bacterial meningitis cases. Risk of infection
with Listeria monocytogenes is increased in persons over 50 years
old. The introduction of pneumococcal vaccine has lowered rates
of pneumococcal meningitis in both children and adults.
Recent skull trauma potentially allows nasal cavity bacteria to enter the
meningeal space. Similarly, devices in the brain and meninges, such as
cerebral shunts, extraventricular drains or Ommaya reservoirs, carry an
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increased risk of meningitis. In these cases, the persons are more likely to
be infected with Staphylococci, Pseudomonas, and other Gram-negative
bacteria. These pathogens are also associated with meningitis in people
with an impaired immune system. An infection in the head and neck area,
such as otitis media or mastoiditis, can lead to meningitis in a small
proportion of people. Recipients of cochlear implants for hearing loss risk
more a pneumococcal meningitis.
Tuberculous meningitis, which is meningitis caused by Mycobacterium
tuberculosis, is more common in people from countries where
tuberculosis is endemic, but is also encountered in persons with immune
problems, such as AIDS.

Viral
Viruses that cause meningitis include enteroviruses, herpes simplex virus
type 2 (and less commonly type 1), varicella zoster virus (known for
causing chickenpox and shingles),mumps virus, HIV, and LCMV.

Fungal
Most common fungal meningitis is cryptococcal meningitis due to
Cryptococcus neoformans. In Africa, cryptococcal meningitis is
estimated to be the most common cause of meningitis [21] and it accounts
for 20–25% of AIDS-related deaths in Africa.Other common fungal
agents include Histoplasma capsulatum, Coccidioides immitis,
Blastomyces dermatitidis, and Candida species.

Parasitic
A parasitic cause is often assumed when there is a predominance of
eosinophils (a type of white blood cell) in the CSF. The most common
parasites implicated areAngiostrongylus cantonensis, Gnathostoma
spinigerum, Schistosoma, as well as the conditions cysticercosis,
toxocariasis, baylisascariasis, paragonimiasis, and a number of rarer
infections and noninfective conditions.

Non-infectious
Meningitis may occur as the result of several non-infectious causes:
spread of cancer to the meninges (malignant or neoplastic meningitis) and
certain drugs (mainly non-steroidal anti-inflammatory drugs, antibiotics
and intravenous immunoglobulins). It may also be caused by several
inflammatory conditions, such as sarcoidosis (which is then called
neurosarcoidosis), connective tissue disorders such as systemic lupus
erythematosus, and certain forms of vasculitis (inflammatory conditions
of the blood vessel wall), such as Behçet's disease. Epidermoid cysts and
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dermoid cysts may cause meningitis by releasing irritant matter into the
subarachnoid ….etc

Diagnosis
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Urinary tract infections

Intended learning Objectives:

1- List causative organisms of urinary tract infections.
2- Recognize pathogenicity and predisposing factors
3- Define sterile pyuria
4- Interpret urine culture

UTIs represent a wide variety of syndromes including urethritis, cystitis,

prostatitis, and pyelonephritis.
One of the most commonly occurring infections that lead patients to seek
medical care. Approximately 10% of humans will have a UTI at some
time during their lives.
Young women are particularly susceptible, 40% of all women will suffer
at least one UTI at some point.
Infection in men occurs less frequently until the age of 50, when
incidence in men and women is similar.

Definition:
It is the presence of microorganisms in the urinary tract that cannot be
accounted for by contamination.
Classification:
According to anatomic site of involvement:
• Lower tract infection: cystitis, urethritis, prostatitis
• Upper tract infection: pyelonephritis, involving the kidneys
According to Degree
• Uncomplicated
- Occur in individuals who lack structural or functional
abnormalities in the UT that interfere with the normal flow of
urine.
- Mostly in healthy females of childbearing age
• Complicated
- Predisposing lesion of the UT such as congenital abnormality or
distortion of the UT, a stone a catheter, prostatic hypertrophy,
obstruction, or neurological deficit.
- All can interfere with the normal flow of urine and urinary tract
defenses, predisposes the patient to persistent infection,recurrent
infection, or treatment failure.

Asymptomatic bacteriuria: is bacteriuria > 105 bacteria/ml of urine

without symptoms, common among the elderly.
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Etiology:
The microorganisms that cause UTI usually originate from the bowel
flora of the host.
The majority of UTIs are caused by a single organism, except in patients
with stones, indwelling catheter, or chronic renal abscesses multiple
organisms may be isolated
Although this may be due to contamination and a repeat evaluation
should be done.
Uncomplicated UTI:
1. E.coli accounts for 85%
2. S.saprophyticus 5-15%
3. K.pneumoniae, proteus spp., Pseudomonas, and Enterococcus 5-
10%
4. S.epidermidis if isolated should be considered a contamination
Complicated UTIs
1. E.coli represents 50% of the cases, followed by K.pneumoniae,
a. protues sp, Pseudomonas, Enterococcus, Enterobactor spp.
2. Enterococcus fecalis 2nd most frequently isolated organism in
a. Hospitalized patients.
3. S.aureus infection is more commonly a result of bacteremia
producing metastatic abscesses in the kidney.
4. Candida spp. is common cause of UTI in critically ill and
chronically catheterized patients

Pathogenicity:
1. By ascending route following colonization or periurethral area by
enteric organisms.
2. Rarely hematogenous.

Predisposing factors:
Abnormalities in the UT that interfere with natural defenses
1. Obstruction can inhibit urine flow, disrupting the natural flushing
and voiding effect in removing bacteria from the bladder and
resulting in incomplete emptying
2. Conditions that result in residual urine volumes e.g., prostatic
hypertrophy, urethral stricture, calculi, tumors, and drug such as
anticholinergic agents, neurological malfunctions associated with
stroke, diabetes, and spinal cord injuries.
3. Other risk factors include: Shortness of female urethra, urinary
catheter,mechanical instrumentation, pregnancy, sexual intercourse
(honeymooncystitis) and the use of Contraceptive devices.
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Laboratory diagnosis:
Symptoms alone are unreliable for diagnosis, examination of the urine is
the cornerstone of diagnosis
The aim of microbiology laboratory in the management of urinary tract
infection (UTI) is to reduce morbidity and mortality through accurate and
timely diagnosis with appropriate antimicrobial sensitivity testing.
Collection of urine:
1. Midstream clean catch method and early morning sample are
preferred (instructions to the patients).
2. Catheterization for patient who are uncooperative or unable to
void,but introduction of bacteria in the bladder occurs at 1-2%.
3. Suprapubic aspiration, bypasses the contaminating organism in the
urethra, safe and painless.
4. Differential specimen from two ureters

Rejection criteria:
1. Specimen >2hrs, with no evidence of refrigeration (early transport
to the lab) .
2. Collection time and method have not been provided by the lab.
3. 24-h urine collection.
4. Specimens that arrive in leaky container
5. Foley catheter tips are unacceptable for culture, as they are
unsuitable for the diagnosis of urinary tract infections
(contaminated with urethral flora)
6. Urine from the bag of the catheterized patients
7. .Except for suprapubic bladder aspirates, anaerobic culture request
is rejected
.

Microscopic examination
1. Pyuria signifies the presence of infections. Sterile pyuria could be
due to false antibiotic intake, associated with urinary tuberculosis,
chlamydial, and fungal infections.
2. Hematuria, non-specific, may indicate disorders such as calculi or
tumor.
3. Proteinuria is found in the presence of infection
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Biochemical tests
1. Dipstick test for nitrite: bacteria in the urine can reduce nitrate→
nitrite false–negative: gm+ve or pseudomonas that do not reduce
nitrate, low urinary PH, frequent voiding and dilute urine.
2. Leukocyte esterase dipstick test
LE is found in neutrophils. Specific for detecting more than 10
WBC/mm3

Urine culture:
Indications:
1. UTI (symptomatic or asymptomatic patients)
2. Urinary tract obstruction
3. Bacteremia of unknown source.
4. Follow –up patients with indwelling catheter
5. Follow –up patients after removal of indwelling catheter
6. Follow –up of antibiotic therapy

Concept of Significant Bacteriuria: 105/ml and above considered to be

Significant
Significant low colony counts: New borne, children - Antibiotic
therapy - Excess use of water, dilution of urine (low PH) - Random
urine samples - Obstructive uropathy

Criteria for defining significant bacteriuria:

1. Symptomatic men: ≥10³ CFU bacteria/ml
2. Symptomatic women: ≥10² CFU coliform/ml, ≥10⁵ noncoliform
3. Asymptomatic individuals: ≥10⁵ bacteria/ml
4. Catheterized patients: ≥10³ bacteria/ml
5. Any growth on supra-pubic aspirate or intraoperative obtained
samples

Recurrent UTIs:
Up to 27% of young women with acute cystitis develop recurrent UTIs.
Reinfection: caused by a different organism than originally isolated and
account for the majority of recurrent UTIs.
Relapse: repeated infections with the same initial organism and usually
indicate a persistent infectious source.