Urine Cultures

One of the most common test done in the microbiology lab is the urine culture.

“Uncomplicated” urinary tract infections (UTI’s) are more common among females and involve infections of the lower urinary tract. “Complicated” UTI’s occur equally among men and women and are often associated with an underlying anatomical or physiological disorder. UTIs result in more than seven million doctor visits annually, according to the American Urological Association Foundation. The elderly, diabetics, pregnant women, patients with bladder and kidney dysfunctions, and patients with urinary catheters are among those most at risk for acquiring a complicated UTI. 1.

For most people, the prevalent UTI condition is the uncomplicated bacteriuria where significant numbers of bacteria have colonized the urinary tract, sometimes with an absence of notable signs and/or symptoms of an infection. 2.

Studies have shown that more women than men under 60 years of age are prone to develop uncomplicated UTIs, but over the age of 60, more men are likely to develop complicated UTIs than women. 1, 2.

The majority of urinary tract infections are caused by gram negative organisms. At Microculture Inc., more than 90 percent of our positive urine cultures are caused by E. Coli. The following table shows the differences between causative agents of uncomplicated and complicated UTIs. 3.

PathogenGram StainUncomplicated UTIComplicated UTI
E. ColiNeg70-90%40-55%
Proteus MirabilisNeg
Alkaline urine
Pseudomonas AeruginosaNeg0-1%2-10%
Enterococcus faecalisPos12-15%15-20%

Urine cultures remain the gold standard for confirming UTI diagnosis, and, when coupled with antimicrobial susceptibility testing, allow the physician to know which antimicrobial will be effective. When colony counts are performed using a calibrated inoculation loop to streak the plates, an approximate quantification of uropathogenic organisms is also available. Quantification, or determining how many organisms per milliliter of urine are present in the patient sample, not only gives the physician a clue as to the severity of infection, but also helps detect false positives or contamination. Commonly, false positives result when the urine is not collected properly and bacteria in the urethra or perineal area are inadvertently introduced into the specimen, or if samples are left unrefrigerated.

There are three main clues that lead the microbiologist to believe the urine is contaminated:

1. Low colony count. (very few organisms per mL urine)
2. More than one species or mixed types of organisms.
3. The presence of certain non pathogenic species of bacteria which are known to be common urethral contaminants. These include coagulate negative staph in low numbers, diptheroids, alpha strep, and other non enteroccocal strep.

An exception is when there are low numbers of pathogenic organisms such as E. coli and it is a pure culture (the only organism present). Studies have shown that these cultures are significant and susceptibility testing is warranted.4,5 At Microculture Inc., we perform susceptibility testing on counts as low as 10,000 /ml in this circumstance. Counts of 40,000/ml to more than 100,000/ml are typical with specimens from patients with UTIs. With catheterized specimens, susceptibility testing is routinely performed on lower colony counts, since there is less chance that the specimen is contaminated.

Urinalysis testing is often used to try to determine if a culture is necessary. Dipstick tests commonly include tests for nitrites, which are formed when gram negative bacteria such as E.coli reduce nitrates, and tests for presence of wbcs such as a positive result of the neutrophil enzyme, leukocyte esterase. Bacteria may be present in a contaminated sample, and conversely, may not be present in specimens at various stages of a UTI. 6. Caution is advised when relying on dipstick results only. If clinical picture indicates, most physicians will request that a culture be performed.


  1. Foxman B. The epidemiology of urinary tract infection. Nat. Rev. Urol. P 2010, 653-660.
  2. Hoota TM and Stamm WE. Diagnosis and treatment of uncomplicated urinary tract infection. InfectDis. Clin. North Am. 1997 11: 551-581.
  3. Stamm, WE, Hootan TM. Management of urinary tract infection in adults. N Engl J. Med. 1993, 329-1 328-34.
  4. Colodner R, Eliasberg T, Chazan B, Raz R. Clinical significance of bacteriuria with low colony counts of Enterococcus species. Eur J Clin Microbiol Infect Dis. 2006 Apr;25(4):238-41.
  5. Walsh CA, Moore KH. Overactive bladder in women: does low-count bacteriuria matter? A review. Neurourol Urodyn. 2011 Jan;30 (1):32-7. doi: 10.1002/nau.20927.
  6. European Urinalysis Guidelines (pg.27) Scan J. Cling Lab Invest 2000.