Urine

Urinary tract infections (UTI) are one of the most commonly encountered acute infectious diseases. Urine specimens for culture are collected when the following syndromes are suspected:

  • cystitis (bladder infection)
  • pyelonephritis (Kidney infection)
  • asymptomatic bacteriuria (most commonly important during pregnancy)
  • acute prostatitis (Prostate infection)

See Urine Culturing from Medical Student course notes.

“Sterile” vs “Non-sterile” urine samples

Urine in the normal bladder is free of microorganisms, i.e. it is sterile. However, the area around the urethra especially in women may have large numbers of microorganisms present. Because voided urine must pass through the urethra there is a large possibility of it being “contaminated”.

When a catheter is left in the bladder (an “indwelling” catheter) the urine frequently becomes contaminated with microorganisms. Sometimes a permanent artificial opening is constructed (usually following bladder removal for cancer) called an “ileal conduit”. A piece of small bowel is used to attach the ureters to the skin of the abdominal wall. Sampling through an ileal conduit almost always results in contamination making interpretation of cultures very difficult.

The only urine samples that are treated as “sterile body fluids” are collected surgically through the skin. The most common sample is a suprapubic tap (mostly from neonates). A surgically placed nephrostomy tube (almost always done in radiology) done to drain an obstructed ureter is also treated as a “sterile body fluid”.

“Non-sterile” Urine Samples

  • Midstream urine (MSU)
  • Neonatal bagged urine
  • Indwelling catheter (Foley catheter) urine
  • Ileal conduit urine
  • Suprapubic catheter urine

“Intermediate Sterility” Urine Samples

  • In and out catheter / catheter insertion urine
  • Bladder/cystoscopy urine

“Sterile” Urine Samples See Sterile body fluid culture

  • Nephrostomy urine when the nephrostomy tube is first inserted (almost always done in radiology).
  • Suprapubic bladder aspirate (Tap)

Setup

Direct Examination

Not routinely performed. If specifically requested and approved by charge technologist or microbiologist, perform Gram stain directly on unspun specimen.

Culture

Automated
Place specimen on the WASP instrument. See WASP manual.

Manual
Mix the urine specimen and dip a sterile calibrated 1 µL loop vertically into the sample. Streak the loop down the centre of the plate and then cross-streaked at a 90° angle to the inoculum (colony count streak pattern).

Media Incubation
Blood Agar (BA) O2, 35°C x 24 hours
MacConkey Agar (MAC) O2, 35°C x 24 hours

Interpretation

Cultures with no growth

Discard no growth routine cultures after 18-24 hrs incubation except:

  • Suprapubic urine – re-incubate for another 24hrs.
  • When yeast or non-specified fungus is requested – re-incubate for another 24 hrs at room temperature.
  • If colonies are too small – re-incubate for another 24hrs.

Cultures with growth

1 colony = 1 x 106 CFU/L.

  • Workup cultures according to the criteria in Tables 1 and 2 below.
  • Save Group B streptococcus isolates for 7 days at room temperature in case further susceptibility testing is required.
  • Save positive yeast cultures for 7 days at room temperature in case further work-up is required.

Potential Uropathogens

  • Enterobacteriaceae
  • Pseudomonas aeruginosa
  • Other gram negative bacilli
  • Enterococcus spp.
  • beta-haemolytic streptococci
  • Staphylococcus aureus
  • Staphylococcus saprophyticus
  • Streptococcus pneumoniae
  • Yeast
  • Corynebacterium urealyticum
  • Aerococcus urinae – only considered a pathogen when predominant (in amounts greater than 10 times non-pathogens)
  • Other CNS – only considered a pathogen when predominant (in amounts greater than 10 times non-pathogens)

Non-uropathogens (normal skin/urogenital flora)

  • Lactobacillus spp.
  • diphtheroids (not C. urealyticum)
  • viridans Streptococci (not A. urinae)
  • Bacillus spp.

TABLE 1: Criteria for identification and susceptibility testing of organisms isolated from “Non-sterile” Urine Samples

  • Midstream urine (MSU)
  • Neonatal bagged urine
  • Indwelling catheter (Foley catheter) urine
  • Ileal conduit urine
  • Indwelling suprapubic catheter urine
Types of Organisms # of each type Colony count x 106/L Work up / Report
1 <10 No count No work up / No significant growth
1 >10 Count ID + Sens
2 Both >100 >100 ID + Sens on both
>2 One >100 >100 ID + Sens
Other(s) <100 No count No work-up Do not report
>2 Two >100 >100 ID + Sens on both
Other(s) <100 No count No work-up Do not report
>2 All <100 No count No work up / No significant growth
Any # All <10 No count No work up / No significant growth
>2 All >100 >100 No work-up / Mixed growth comment

TABLE 2: Criteria for identification and susceptibility testing of organisms isolated from “Intermediate Sterility” urines – In and Out Catheter/Catheter Insertion, bladder/cystoscopy urines.

Types of Organisms # or each type Colony count x 106/L Work up / report
1 >10 Count ID + Sens
2 or 3 All >10 Count for each ID +Sens for each
Any # All <10 No count No work up / No significant growth
>3 Any number No count No work up / Mixed growth comment

Notes

  • When counting the number of different types of organisms, do not include <10 colonies of non-uropathogens.
  • Do not workup or report any number of colonies of non-uropathogens.
  • Consider coagulase-negative staphylococcus as uropathogens only when present in amounts >10- fold more that other non-uropathogens and a single strain. If more than one strain of CNS is evident do not consider as uropathogens.
  • For females 12-55 years, workup any amount of beta-haemolytic streptococcus to rule out Group B streptococcus.

Reporting

Gram Stain (if requested)

“(No) WBCs seen. (No) Bacteria seen” (without quantitation)

Culture

No growth report: “No growth”

Growth without work-up: “No significant growth”

Growth of >3 types of organisms without workup: Report “Several different types of bacteria were identified in this specimen. Further ID and susceptibility testing is generally not helpful in this circumstance and has not been performed. Please contact the laboratory if you feel the management of this particular situation would be helped by further testing.”

Growth with work-up

Preliminary report: Morphologic description of organism with corresponding colony count/L for each organism.

Final report: Organism name with corresponding colony count/L for each organism and susceptibility testing results.

If routine fungus is requested and no yeast isolated: “No yeast isolated.”

Growth of Group B streptococci from child-bearing age females (12-55years)

In significant amount: Report as Isolate with corresponding colony count/L and add: “Any women with GBS bacteriuria in any concentration during her pregnancy should received intrapartum chemoprophylaxis.”

In insignificant amount: Report the other isolate(s) if applicable or “no significant growth” and add comment “Group B streptococci isolated in small amount. Any women with GBS bacteriuria in any concentration during her pregnancy should received intrapartum chemoprophylaxis.”

Positive bagged urine reports add “The finding of bacteria in a bagged urine sample may reflect perineal colonization and is poorly predictive of true urinary tract infection. If UTI is a continuing concern please submit a sample for urinalysis and culture obtained by clean-catch, in-out catheter or suprapubic tap.”

References Murray P.R., Baron E.J., Pfaller M.A., Yolken R.H.. 2003. Manual of Clinical Microbiology, 8th ed. ASM Press, Washington, D.C.

Izenberg H.D.. 2003. Urine Cultures, 3.12.1 in Clinical Microbiology Procedures Handbook, 2nd ed. Vol.1 ASM Press, Washington, D.C.

Clarridge J.E., Johnson J.R., Pezzlo M.T. 1998. Cumitech 2B, Laboratory Diagnosis of Urinary Tract Infections, Coordinating ed., A.S. Weissfield. ASM, Washington, D.C.