Renal

microbiology
SYLLABUS
UTI: (P. 349)
Types, Organisms, laboratory diagnosis (P. 350)
Renal tuberculosis: (P. 351)
Pathogenesis, laboratory diagnosis (P. 352)
Post-streptococcal Glomerulonephritis: (P. 353)
Pathogenesis, laboratory diagnosis
Schistosomiasis: (P. 354)
Pathogenesis, laboratory diagnosis

VI

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MICROBIOLOGY

URINARY TRACT INFECTION (UTI) ii. Lower UTI (bladder and urethra) Cystitis,
urethritis.
Past Questions:
- On the basis of complication: Uncomplicated
1. Methods of specimens collection for the
or complicated.
diagnosis of urinary tract infection. (5) [05 June]
- On the basis of source of infection:
2. Name the three common agents causing UTI.
Community acquired or nosocomial.
Among them name one, which is most common
Causative agents: [04]
and explain why? (1.5+3.5 = 5) [04 Dec]
- Most common agent for UTI is E.coli because it
3. Short notes on:
is the normal commensal of rectum and anal
a. Urinary tract infection. (UTI) [3] [07 June]
canal which can easily spread to the urinary
b. Lab diagnosis of urinary tract infection (UTI) tract which is close proximity to anus.
[3] [07 Dec(3), 05 Dec] i. Bacteria: E.coli (60–90%), Klebsiella
c. Significant bacteriuria [3] [02 Dec] pneumonae, Proteus, Pseudomonas,
d. Isolation of urinary pathogens. [3] [09 July] Staphylococcus saprophyticus.
e. Urine collection for culture. [3] [08 July] ii. Virus: Herpes simplex virus, Adenovirus
f. PSGN [3] [02 Dec, 01 July] iii. Fungi: Candida albicans.
4. Discuss laboratory diagnosis of cystitis. [2](013) iv. Parasites: Trichomonas vaginalis, Schistosoma
 Presence of multiplying organism in urinary tract. hematobium.
Significant bacteriuria: [02] Normal bacterial flora found in urethra VI
5 - Coagulase negative staphylococcus
- Kass proposed that the presence of 10 bacteria
per ml in a clean-catch midstream urine (excluding S.saprophyticus)
specimen indicated urinary tract infection. - Mycobacterium smegmatis
-  10 bacteria/ml : Significant growth; perform
5
- Viridans streptococcus
antibiotic sensitivity test. Indicates UTI. - Non haemolytic streptococci
- 103–104 bacteria/ml: Doubtful; repeat the culture.
- Diphtheroids
- ≤103 bacteria/ml: Not significant; indicates
- Anaerobic cocci
contaminants. Indicates absence of UTI.
Types of UTI: - Mycoplasma species
- On the basis of duration: Acute (short Predisposing factors:
duration) or chronic (long duration). - Female gender (since they have short urethra)
- On the basis of route of infection: Ascending - Diabetics
i.e.retrograde via the urinary tract (the most - Urinary catheterization
common route) or descending i.e. via - Vesicoureteric reflux
hematogenous. - Sexual intercourse
- On the basis of presence of symptoms: - Pregnancy
Asymptomatic or symptomatic.
Route of infection:
- On the basis of site involved:
- Ascending route
i. Upper UTI (kidney and ureter):
- Haematogenous route
Pyelonephritis, ureteritis
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 Microbiology

Clinical features: iii. Culture:

a. Lower UTI:  MacConkey’s Agar: Differential media to
- Urethritis differentiate lactose fermenters (E. coli &
- Dysuria (painful or difficult urination) Klebsiella) produce pink colored colonies.
- Frequency and urgency [MCQ 2013]
- In case of acute urethral syndrome bacterial  CLED (Cysteine Lactose Electrolye Deficient)
count may be found to be less than 105
media. Selective media for E. coli (produces
b. Upper urinary tract symptoms pink colonies)
- Fever
 Blood agar: Non-selective media.
- Lower back pain
 Semiquantitative culture techniques include:
- And lower urinary tract symptoms
Laboratory Diagnosis: [05,07,013] a. Calibrated loop method
Specimen collection: b. Dip slide method
Urine collection c. Filter paper/filter strip method
1. Non –invasive method  Interpretation of results: Kass criteria
2. Invasive method
a.  105bacteria/ml: Significant growth;
1. Non-invasive method
perform antibiotic sensitivity test.
a. Collection of morning midstream urine:
b. 103 – 104 bacteria/ml: Doubtful; repeat
 Early morning mid stream urine: Two
the culture.
samples for women & one for males.
b. Urinary catheterization c. ≤103 bacteria/ml: Not significant;
indicates contaminants.
VI 2. Invasive method
i. Suprapubic bladder aspiration Filter paper method:
 Suprapubic aspiration of urine: For Gram +ve organisms
uncooperative patients & children.
No. of colonies /ml No. of organisms/ ml
 Specimen is collected in sterilized bottle
with tight fitting lid. > 30 > 105
Transport: 30 105
- At 4C within 2 hours. If delay, boric acid(10%)
is used as preservative. 10–29 104 - 105
Processing: 0-9 < 104
i. Macroscopy: Colour  turbid due to presence
Gram -ve organisms
of pus cells.
ii. Direct light microscopy by Gram’s stain shows No. of colonies /ml No. of organisms/ ml
presence of pus cells:
> 25 > 105
 ≤ 10 pus cells per high power field  mild
infection. 25 105
 11–40 pus cells per high power field 
moderate infection. 5–25 104 - 105
 > 40 pus cells per high power field  heavy 0-4 < 104
infection.

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iv. Biochemical reactions: Definition [06]

 E.coli & Klebsiella are catalase +ve &  Chronic granulomatous lesion of kidney caused by
oxidase –ve. species of Mycobacteria (M. tuberculosis, M. bovis
Klebsiella & Atypical mycobacteria).
E. coli
pneumonae  Sites effected in renal tuberculosis are
Indole + - - Ureter
- Bladder
MR + -
- Kidney
VP - + - Genito-urinary tract-epididymis
Citrate - + - Seminal vesicles & prostate

@ I am (M) E.coli.]  20 – 40 % cases coexist with HIV.

 Proteus produces urease & most of its  Most common extra-pulmonary site for TB – 20%
species are indole +ve except P. of all extra-pulmonary TB
mirabilis.  It is generally a disease of young adults ( 20-40y)
v. Griess nitrite test:  Common in developing countries
 Detection of nitrite produced by bacteria  More common in males (other UTIs are more
from nitrate which is present in urine. common in females)
vi. PCR: Detection of genome by amplification  Usually unilateral, more common in right kidney
process.
Causative agents:
Rapid screening test for significant bacteriuria VI
- M. tuberculosis
1. Gram stain
- M. bovis
2. Pyuria
Mode of transmission:
3. Nitrate reductase test
- Usually hematogenous i.e. secondary to
4. Catalase test pulmonary TB
- Direct spread from adjacent infected pelvic
organs.
RENAL TUBERCULOSIS Predisposing factors:
Past Questions: - Pre-existing abnormalities of renal tract
1. Define renal tuberculosis. How do you collect - Always secondary to primary focus elsewhere
urine sample for lab diagnosis of renal - Silent bacillemia accompanying pulmonary TB
tuberculosis ? (1+4 = 5) [06 Dec] - Bacteremia
2. Write short notes on - Reactivating after a period of dormancy
a. Renal tuberculosis. [3] [10 Jan] - Reactivation of latent infection
b. Lab diagnosis of renal tuberculosis. - Dialysis, corticosteroid therapy, HIV infection.
[3] [03 June 01 Dec]

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Pathogenesis: cultures but shows numerous pus cells &

RBCs). Thus, renal TB must be considered in
Mycobacterium reaches to kidney through various cases of pyuria w/o bacteriuria
routes as mentioned above - 5 evidence of pulmonary TB or lymphatic TB
may be present
Ulcerocaseous TB
i. Evening rise of temperature
Initially multiple granuloma forms in cortex & ii. Weight loss
adjacent to granuloma (may remain inactive for iii. Night sweats
decades) iv. Malaise
v. Anorexia – loss of appetite & renal lump
Tubercular Cortex capillary rupture may be felt = associated enlargement of
perinephric prostate, epididymis & seminal vesicles
abscess Bacilli reaches to medulla Laboratory diagnosis: [01,03,06]
(proximal tubules)
Specimen:
Sinus in loin
Granuloma formation on calyces - Early morning whole urine: 3 samples
Fistula & strictures of tubules collected in sterilized bottle with tightly fitting
lid. [MCQ 2013]
- Renal biopsy.
Fibrosis & scarring of Bacilli in renal pelvis
kidney with chronic - Other less frequent: Prostatic massage fluid,
abscess formation Tuberculous pyelitis Sperm, Endometrium, Cervical swabs, Cervical
Upper UTI byopsy.
Non-functioning
kidney/tubercular Note: MSU- is not useful since excretion of TB bacilli
VI pyonephritis/caseous Ureteric stricture from kidney is intermittent
kidney/ putty
kidney/cement kidney Golf hole appearance Concentration:
in bladder - By Petroff’s method:
A bag of pus/store house
Decontamination:
of mycobacterium
i. By mixing equal volume of urine + 4% NaOH
Tubercular hydronephrosis and left for 15-30 min.
ii. Centrifugation at 3000 rpm for 30 mins &
Renal tuberculosis
sediment is used for culture.
Clinical features:
iii. The deposit is neutralized with N/10 or 8%
- Disease is oligosymptomatic usually – relapsing
HCl in the presence of an indicator (eg:
urinary complaints are rather characteristic
phenol red) and the decontaminated
findings
deposit is examined
1. Urinary frequency- earliest symptom & dull
Processing:
pain in the loin
2. Dysuria –painful urination – because of acid 1. Microscopy:
urea may be present  Direct Gram stain - Pus cells in urine (pyuria).
3. Haematuria – due to TB ulcer on papilla  AFB stain(ZN stain) of centrifuged
4. Abacterial sterile acid pyuria- urine is urine/biopsy: Pink beaded acid fast bacilli
opalescent, pale or yellow, acidic in reaction & in blue background.
(no organisms/bacteria are grown on repeated
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2. Culture on: POST STREPTOCOCCAL

 Lowenstein Jensen's media (egg based) for GLOMERULONEPHRITIS
6-8 weeks/ BACTEC system for rapid
Past Questions:
culture: reports taken after 2 weeks, M.
1. Explain in brief the pathogenesis and laboratory
tuberculosis produces irregular, rough,
diagnosis of post-streptococcal
tough & buff colonies
glomerulonephritis. [2+3=5] [10 July]
 7H Middle Brook (Agar based) 2. Write short notes on PSGN [3][02 Dec, 01 July]
3. Biochemical tests:  Immune related inflammatory disease of kidney
especially involving the glomerulus occurring few
M. weeks after β-hemolytic streptococcal group A
M. bovis
tuberculosis infection (sore throat) infections of the pharynx or
the skin.
Niacin test + -
 Poststreptococcal glomerulonephritis occurs most
Catalase & oxidase test + + frequently in children 6 to 10 years of age, but
adults of any age can also be affected.
Nitrate reduction test + - Pathogenesis: [10]
Aryl sulphatase test - - - Basically two mechanisms:
i. Cross reaction of antibodies directed against
Note: M-protein of streptococci with glomerular
basement membrane (GBM) proteins.
- Isoniazid resistant tubercle bacilli are catalase &
ii. Deposition of antigen-antibody complexes
oxidase negative. in (GBM).
- Neutral red test is +ve only for virulent strains of - These two pathways lead to complement
tubercle bacilli. activation & damage to the glomerular basement
membrane (GBM) & structures of kidney. VI
4. Immunofluoroscence test: Auramine- Laboratory diagnosis: [10]
Rhodamine staining. - Based on retrospective diagnosis of
5. Guinea-pig inoculation: +ve in 90% cases streptococcal infection by demonstration of
high level of antibody to streptococcal toxins.
6. Antibiotic sensitivity test.
i. ASO(anti-streptolysin O) titre: Indicates
7. Tuberculin skin test-Mantoux test: strongly prior streptococcal infection & titres of
+ve >200 are significant.
8. Modern methods: ii. Anti-DNAse B estimation: Done when ASO
titre is not significant & titres >300 are
 Rapid test: Bactec(radioactiveC14 is significant.
inoculated to culture media and C14O2 is iii. Streptozyme test: A passive slide
detected since bacillus is microaerophilic) haemagglutination test using erythrocytes
sensitized with crude preparation of
 Gas liquid chromatography to detect
extracellular antigen of streptococci. It is
tuberculostearic acid. used as sensitive and specific screening test
 Molecular methods: PCR which is +ve for nearly all type of
streptococcal infection.
 - interferon assay (for latent renal TB).
iv. Fluorescent antibody technique: Rapid
 Cystoscopy identification.
 Renal USG v. Anti-hyaluronidase test.

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SCHISTOSOMA HEMATOBIUM Lifecycle:

(BLOOD FLUKE) Eggs (non operculated with terminal spines) are
 Schistosoma japonicum inhabits in the portal hatched (i.e. Oviposition occurs) in small venules of
venous system vesical venous plexus around urinary bladder (UB)
(where eggs are arranged in chain held by the spines)
 Acquired by: Skin contact with water
contaminated by cercaria 
 The basic pathologic lesion is the egg granuloma in Eggs escapes via vessels and  leading to UB
pierces mucosa of Urinary carcinoma and
the liver and colon painless terminal
Bladder hematuria
Etiology :
- 3 major species of human Schistosoma – Blood 
flukes: Eggs reaches UB cavity and passes along with urine
a. S. mansoni: Is mainly found in Africa and 
Madagascar. Passed in water where eggs are hatched to give
miracidia (free swimming forms)
b. S. japonicum: Is found in China , Philippines

* S.mansonia and S.japonicum cause disease of
Each of them enters soft tissue of snail (Bulinus) and
the bowel and liver. casts off cilia and gives rise to 1st generation
c. S. haematobium: Causes urinary sporocyst.
schisotosomiasis, scattered throughout 
Africa, parts of Arabia, the near East, Multiplies to give rise to 2nd generation
Madagascar and Mauritius. sporocyst(tubular sporocyst).
Morphology 
Mature worms: Each then give rise to fork tailed cercaria (infective)
VI - 1-2 cm long and released in water

- Dioecious
Enters human skin via abraded area  Dermatitis
Female : long and thin.

Male: short and thick, resembles a rolled leaf
Larva (schistosomule)reaches peripheral venules,
having a groove on his ventral part in which the
right side of heart, lungs and left side heart
longer, more slender female is held in copulo

- Paired male and female adult worms.
Enters systemic circulation and reaches mesenteric
- The female schistosomilum is the darker, artery, capillary bed of intestine
curled worm within the male's gynacophoric 
canal. Enters portal circulation and Toxic metabolite from
Eggs: intrahepatic portion schistosomule causing
anaphylactic reaction
- Miracidia in it

- Schistosoma mansoni eggs – Oval,89 x 67µ Larva grows to adult and gets sexually differentiated
with lateral spine.

- Eggs leaves host when host excretes
Moves against blood stream to vesical plexus
Cercariae:

- Fork-tailed cercariae (200-500 µm long)
Then undergoes copulation and eggs are hatched
- Visible to the naked eye.(Infective Form)
which are passed in urine and cycle repeats

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Note: Late stage: Chronic

a. Egg is non operculated with terminal spine, redia • Enlarged liver and spleen
(one of the larval stages) is absent although it is • Weight loss, severe liver disease
trematode. • Anemia, jaundice, ascites
b. Female remains in gynaecophoric canal of male. • Fibrosis of the intestine
Life span = 20-30 years but female is longer than Terminal stage of schistosomiasis
male. i. Is characterized by portal vein hypertension
syndrome,
c. Adult lives in copula in venous plexus.
ii. Ascites, emaciation, varicosity, splenomegaly
Lifecycle: & anemia are commonly found.
1. Site of inhabitation: the portal vein system, iii. Liver fibrosis / cirrhosis
mainly in the inferior mesenteric vein. iv. The patients die of secondary infection,
2. Infective stage: Cercaria upper digestive tract bleeding, hepatic coma.
3. Infective route: By skin Complications:
4. Intermediate hosts: Bulinus snail • Heart Failure
• Epilepsy
5. Reservoir hosts: mammals such as buffalo, cattle,
wild rodents, goat, monkey, pig, fox - a zoonotic Lab diagnosis:
disease i. Direct demonstration of egg:
6. Eggs are main pathogenic factor: (They are in laid - In urine or stool or rectal biopsy specimen
in the liver and intestinal wall. Some of them are under microscopy  reveals characteristic
discharged in feces to complete its life cycle). terminal spines in the egg.
7. The development in human body requires 25-30 ii. Serological test: VI
days. Cercaria can live 1-3 days. Life span of the - Ab detection by:
adults is about 20-30 years.  Indirect Immunofluorescence (IIF): Titre of
Clinical features: 1:16 is diagnostic.
Acute (Katayama fever)  ELISA: Titre of 1:32 is diagnostic.
- Occur 4 to 8 weeks after initial infection 3. History of hematuria and detection
• Itchiness of the skin - By using Dip stick method.
• Bloody, mucoid stools 4. X-rays
• Fever & cough - Shows calcified eggs in urinary bladder wall .
• Diarrhea, abdominal pain, dysenteric attacks 5. Blood count:
• Lymph node enlargement
- Eosinophilia.
• Hepatosplenomegaly

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SPECIAL POINTS FOR MCQs

1. UTI due to Staphylococcus saprophyticus is common in sexually active women.
2. Differential media for urinary pathogens are CLED & MacConkey's media.
3. Significant bacteriuria means ≥10^5 bacteria per ml of urine.
4. Most common pathogen for UTI is E. coli.
5. Pseudomonas, Klebsiella and Staphylococcus are common pathogens causing nosocomial UTI.
6. Early morning midstream urine is best specimen for diagnosis of UTI.
7. P-pilli of E.coli is main virulence factor responsible for UTI.
8. All enterobacteriaceae are catalase+ve & oxidsase -ve except Shigella dysentriae type I which is
catalase -ve.
9. Preservative for urine sample is Boric acid.
10. Renal tuberculosis is usually secondary to pulmonary TB.
11. Tissue destruction in tuberculosis is due to type IV hypersensitivity reaction.
12. Renal TB is very frequently associated with HIV. Here classical symptoms of TB are masked due to
immunosupression.
13. Renal TB presents with painless hematuria.
14. Best sample for diagnosis of renal TB is early morning whole urine.
15. Abacterial pyuria is a feature of renal TB i.e. pus cells are present but cultures are -ve for bacteria.
16. Cross reaction of antibodies directed against the M protein of streptococci with the glomerular
basement membrane is the primary pathogenetic mechanism in the development of post
streptococcal glomerulonephritis.
17. Anti-streptolysin O titres of >200 are diagnostic for the diagnosis of PSGN.
VI
18. Egg of blood fluke is non operculated with terminal spine.
19. Redia is absent in blood fluke although it is trematode.
20. Female blood fluke lives in gynaecophoric canal of male but female is longer than male.
21. Adult blood fluke lives in copula in vesical venous plexus of human.
22. Tests to find out significant bacteriuria are standard loop techniques and dip slide culture method.
23. In UTI, colony count of 105/ml is considered significant while count between (104–105)/ml is
doubtful but count less than 104 is considered significant if:
a. Prior antibiotic therapy b. Urinary tract obstruction
c. Presence of fungal infection d. Presence of pyelonephritis
e. If specimen has been collected by suprapubic aspiration.
24. Eiken test is precipitation test done for E.coli.
25. Symptomatic bacteriuria is usually associated with pyuria but pyuria may be absent in
asymptomatic bacteriuria.
26. For ZN staining of urine sample acid alcohol mixture is used as decolourizer to exclude the
urinary commensal Mycobacterium smegmatis.
27. Most common nosocomial infection is UTI.
28. Post streptococcal glomerulonephritis is manifested as oliguria, hematuria, hypertension and edema.
29. Granulomatous lesion of renal tuberculosis is located on cortical glomeruli.
30. Bactec is a modern method for diagnosis of renal tuberculosis which uses C14.
31. Schistosoma hematobium may lead to carcinoma of urinary bladder and painless hematuria.

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