Culture – Urine

Background

Urinary tract infections (UTIs) have been around for as long as humans have had urinary tracts. Hippocrates believed that symptoms were caused by an imbalance of four humors. Ancient treatment regimens in the pre-antibiotic era ranged from bed rest to narcotics, and also included various herbs, enemas, and, in the heroic era of medical treatments, “judicious bleeding.”

While medicine has advanced a great deal since then, the diagnosis and management of UTIs remain nuanced, challenging, and fraught with complications. The overuse of antibiotics has changed medicine’s relationship with UTIs and disease altogether, though humanity now finds itself facing epic levels of antimicrobial resistance, teetering on the brink of a post-antibiotic civilization. Excessive antibiotic use is also driving a national epidemic of Clostridioides difficile infection, with alarming rates of morbidity and mortality. It is, therefore, incumbent upon clinicians to understand when to use and when not to use antibiotics. Incorrectly interpreted urinalysis and urine cultures are too frequently the cause of inappropriate antibiotic prescription.

What follows is a guide to understanding the urine culture: a remarkably helpful test to guide antibiotic use, when appropriate. This chapter focuses on bacterial UTIs and largely side-steps fungal and viral UTIs. It concludes with a basic overview of the antibiotics used to treat UTIs, as outlined by the Infectious Diseases Society of America (IDSA), as well as some practical pearls regarding treatment of UTIs.

How to Use It

Urine culture does not indicate the presence of a UTI.

• Urine culture does indicate:

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    If there are any microbes living in the urine at the time of collection

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      Humans have natural flora in the genitourinary system just as in the gastrointestinal system.

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      Therefore, it is important to consider the clinical status of the patient.

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        It is the presence of symptoms (think irritation of the bladder wall; i.e., dysuria, frequency, some women report vaginal irritation, bladder spasm, pelvic pain, back pain, and of course systemic signs like fevers, etc.) that determines if a UTI is present.

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      Pyuria, the presence of white cells in the urine, does not establish the presence of infection. Its absence, however, renders a UTI very unlikely.

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      It is also possible to have a contaminated and thus “false-positive” urine culture (more likely with epithelial cells in the urinalysis) or “false-negative” leukocyte esterase in the urinalysis. See Chapter 58: Urinalysis for details about this test.

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    The identity of any bacteria living there (e.g., Escherichia coli )

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    The quantity of bacteria expressed in colony-forming units (CFUs)

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      100,000 CFU is not sensitive or specific for a UTI.

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        Patients must be symptomatic to warrant treatment, otherwise this is probably colonization.

Susceptibility is derived by exposing organisms to antibiotics and seeing which ones inhibit their growth most effectively. Susceptibility is either reported as raw data using the minimum inhibitory concentration (MIC) or is interpreted using Clinical and Laboratory Standards Institute (CLSI) criteria.

The CLSI interpretations provide a clinical assessment for whether certain bacteria are “susceptible,” “resistant,” or “intermediate” to a certain antibiotic. These interpretations are derived from both the MIC and pharmacokinetic knowledge of the antibiotic in question; therefore, the significance of MIC depends on which bacteria and antibiotic duo are being tested. This is why MIC numbers cannot be meaningfully compared among antibiotics when looking at a sensitivity report.

A final word of caution—the results of antimicrobial susceptibility testing assume that in vitro antibiotic activity parallels in vivo reality. This is not always the case. Multiple host, bacterial, and drug-dependent factors may complicate the picture (e.g., absorption, biofilms). These are not accounted for by in vitro analysis. As such, susceptibility data is meant to inform, not dictate, clinical decision making.