Q5 LONG ANSWER 10M ★ High-yield

Describe the laboratory diagnosis of urinary tract infection and infective diarrhoea.

Microbiology · 2nd Professional — Para-Clinical

Urine — Collection

Method	Technique and use
Midstream clean-catch (MSU)	The routine specimen. An early-morning sample after cleaning the perineum with water (not antiseptic, which inhibits growth); the first portion is discarded to flush the distal urethra, and the midstream is collected. Early-morning urine has been in the bladder for hours, allowing bacterial multiplication and giving a valid count
Catheter specimen	Aspirated aseptically from the sampling port, never from the drainage bag and never by disconnecting the closed system
Suprapubic aspiration	The reference standard, bypassing the urethra entirely, so any growth is significant. Used in neonates and infants and where contamination cannot otherwise be excluded
Urine bag (paediatric)	Highly prone to contamination; a positive result must be confirmed by catheter or suprapubic specimen, though a negative result is useful
Terminal midday urine	For Schistosoma haematobium eggs
Three early-morning specimens	For genitourinary tuberculosis — the whole volume is concentrated, since bacilli are shed intermittently and in small numbers

Transport within 2 hours, or refrigerate at 4°C for up to 24 hours, or use a boric acid container. Urine is an excellent culture medium, so a specimen left at room temperature allows a few contaminants to multiply into a "significant" count — producing a false diagnosis of infection

Urine — Examination and Interpretation

Macroscopic — turbidity, blood, and the classical characteristics; dipstick for nitrite (produced by Enterobacterales reducing dietary nitrate, and specific but insensitive — requiring several hours in the bladder, and negative with Enterococcus and Pseudomonas, which do not reduce nitrate) and leucocyte esterase (sensitive, less specific)
Microscopy of uncentrifuged urine — pyuria (more than 10 leucocytes per mm3, or more than 5 per high-power field of centrifuged deposit); red cells; white cell casts, which localise infection to the kidney; bacteria; and squamous epithelial cells, whose presence indicates contamination
Semi-quantitative culture by the calibrated loop method, using a loop delivering a known volume onto blood agar and MacConkey or CLED medium

Count and setting	Interpretation
≥105 CFU/mL of a single organism in a clean-catch MSU	Significant bacteriuria (KASS criterion). In an asymptomatic person, two consecutive specimens are needed
104–105	Doubtful — repeat
≥102–103 in a symptomatic young woman	Significant — the "acute urethral syndrome"; applying the 105 threshold here misses genuine infection, which is the commonest interpretive error in urine microbiology
Any growth from suprapubic aspiration	Significant — the bladder is normally sterile
≥103 in a symptomatic catheterised patient	Significant — but symptoms are required, and asymptomatic bacteriuria is not treated
Three or more organisms	Contamination — repeat with proper technique
Pyuria with a sterile culture	"sterile pyuria" — consider prior antibiotics, tuberculosis, Chlamydia or gonococcal urethritis, fastidious organisms, stones, tumour, interstitial nephritis or analgesic nephropathy

CLINICAL PEARL

The Kass threshold of 105 was derived from asymptomatic pregnant women, and applying it to a symptomatic young woman misses real infection. A woman with dysuria and frequency may have only 102 organisms per mL, because rapid diuresis and frequent voiding prevent the count from building. Reporting such a specimen as "no significant growth" and withholding treatment is a common error — the threshold depends on the clinical question, not on the laboratory.

Stool — Collection and Examination

Collect early in the illness and before antibiotics, into a clean dry wide-mouthed container free of urine, water and disinfectant; select portions with blood, mucus or pus. A rectal swab is acceptable where stool is unavailable, particularly in children and in cholera
Transport within 2 hours or use CARY-BLAIR medium; alkaline peptone water or VR medium for cholera. Examine within 30 minutes for trophozoites
Macroscopic — consistency (rice-watery in cholera; blood and mucus in dysentery), and worms or proglottids
Microscopy — saline and iodine wet mounts for ova, cysts and trophozoites; pus cells and red cells, whose presence indicates an invasive (inflammatory) diarrhoea and whose absence points to a toxin-mediated or viral cause. Hanging-drop preparation shows the darting motility of Vibrio cholerae, abolished by specific antiserum
Culture media — MacConkey and XLD or DCA for Salmonella and Shigella, with selenite F broth as enrichment; TCBS for Vibrio; Campylobacter selective agar at 42°C in microaerophilic conditions; and sorbitol-MacConkey for E. Coli O157
Non-culture tests — modified acid-fast stain for the coccidia (which must be requested specifically); antigen tests for rotavirus, Giardia, Cryptosporidium and Entamoeba histolytica; C. Difficile GDH and toxin testing; and multiplex PCR panels
Three specimens on alternate days for parasites, because excretion is intermittent

Distinguishing Inflammatory from Non-inflammatory Diarrhoea

Feature	Inflammatory (invasive)	Non-inflammatory (secretory)
Site	Colon	Small intestine
Stool	Small volume with blood and mucus; tenesmus	Large volume, watery, no blood or pus
Fever	Usually present	Usually absent
Stool microscopy	Pus cells and red cells present	Few or NO pus cells
Mechanism	Mucosal invasion and ulceration	Enterotoxin or reduced absorptive surface
Organisms	Shigella, Salmonella, Campylobacter, enteroinvasive and enterohaemorrhagic E. Coli, Entamoeba histolytica, C. Difficile	V. Cholerae, enterotoxigenic E. Coli, rotavirus, norovirus, Giardia, Cryptosporidium, preformed toxin of S. Aureus and B. Cereus
Approach	Culture is worthwhile; antibiotics may be indicated	ORS and zinc; culture rarely needed; antibiotics usually not indicated

The presence of pus cells in the stool is a cheap and immediate triage, distinguishing the group in whom culture and antibiotics may help from the much larger group who need only rehydration

Applied Aspects

Do not apply the 105 threshold to a symptomatic patient; treat a young woman with typical symptoms and a lower count, and record why
Do not treat asymptomatic bacteriuria except in pregnancy and before urological instrumentation; treating it in the catheterised and the elderly selects resistance and confers no benefit
Refrigerate or use boric acid if the urine cannot reach the laboratory within 2 hours; a warm specimen left for hours converts contamination into a diagnosis
Most acute diarrhoea needs no stool culture — it is self-limiting and the result arrives after recovery. Culture is indicated for bloody diarrhoea, severe or persistent illness, fever with systemic features, the immunosuppressed, recent antibiotics, outbreaks and food handlers
Ask for a modified acid-fast stain in HIV with chronic diarrhoea; the coccidia are invisible on routine microscopy
ORS and zinc, not antibiotics, are the treatment for most childhood diarrhoea; the laboratory's role is chiefly to identify the minority who need something more
Look for pus cells in the stool before deciding whether to culture; their presence identifies invasive disease and their absence identifies the majority who need only fluids
Send a hanging-drop preparation in suspected cholera; the darting motility abolished by antiserum gives a presumptive diagnosis within minutes, which matters in an outbreak
Sterile pyuria should prompt a search for tuberculosis and for chlamydial or gonococcal urethritis, and three early-morning urine specimens are the appropriate next step in India
White cell casts localise infection to the kidney, which distinguishes pyelonephritis from cystitis on a simple microscopic examination
Nitrite is specific but insensitive — negative with Enterococcus and Pseudomonas, and in frequent voiding — so a negative dipstick does not exclude infection
Culture stool in bloody diarrhoea, not in every diarrhoea; the result of a routine culture in self-limiting watery illness arrives after the patient has recovered
Three or more organisms in a urine culture means contamination, and the right response is a repeat specimen with proper technique rather than an antibiotic
Screen and treat asymptomatic bacteriuria in pregnancy, where it progresses to pyelonephritis and preterm birth — one of the few settings in which treating it is clearly right
Suprapubic aspiration settles a doubtful result in an infant, since any growth from a normally sterile bladder is significant and bag specimens are unreliable

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