Urine may be one of the most common specimens submitted to clinical microbiology laboratories, but the procedures for processing and evaluating these samples have remained largely unchanged for decades. Thanks to emerging findings and technologies, however, a new era in clinical microbiology is dawning.

For example, molecular analysis of urine specimens from healthy women has uncovered the existence of unique bacterial communities that make up the urinary microbiota, which is a surprising finding given that many of us have been taught that urine is sterile. While the significance of these communities is not well understood, the urinary microbiota may play a role in protecting individuals from or making them susceptible to urinary tract infection (UTI), similar to gastrointestinal microbial communities associated with protecting against invading pathogens.

 UTIs are among the most common bacterial infections worldwide, and in the U.S. alone annually result in more than 10 million visits to ambulatory care physicians. UTIs also account for a substantial number of prescriptions for antibiotics. While the proper use of antibiotics typically clears these infections, when used inappropriately they may contribute to the emergence of multi-drug resistant organisms and other sequelae such as recurring UTIs, renal damage, or Clostridium (Clostridioides) difficile infection. Given these realities, diagnostic stewardship for UTI facilitates targeted therapy and judicious use of antibiotics.

When the Gold Standard Isn’t Enough

Urine culture is the gold standard for diagnosing UTI. Standard urine culture techniques aim to detect a defined set of uropathogens, such as Escherichia coli, that commonly cause UTI. However, a substantial number of urine cultures from symptomatic patients yield negative results.

Culture-independent techniques have demonstrated that significant numbers of fastidious and anaerobic bacteria inhabit urine specimens. Several emerging uropathogens have recently been characterized that contribute to UTI pathogenesis, including Aerococcus species, Corynebacterium urealyticum, Actinotignum (formerly Actinobaculum) schaalii, and Haemophilus influenzae. These organisms often have fastidious growth requirements that sometimes conflict with standard culture methods.

For example, they may require a microaerophilic or anaerobic environment, yet standard incubation protocols for urine cultures call for ambient air. Some also need at least 48 hours for growth—twice the standard incubation interval for routine urine cultures—or enriched media. Many emerging anaerobic bacteria have likely gone underreported because culture techniques don’t adequately isolate them.

Several recent studies have demonstrated the utility of enhanced urine culture techniques in isolating fastidious emerging uropathogens. These enhanced techniques, which involve plating increased volumes of urine to media and incubating the media in a CO2-enriched environment, sometimes have yielded quite remarkable outcomes in comparison to standard culture. For instance, one study showed that standard urine culture was positive in only 33% of symptomatic women, whereas 84% of specimens cultured using enhanced methods isolated significant uropathogens. Isolating an organism from a specimen that would normally be classified as culture-negative facilitates targeted therapy and promotes antimicrobial stewardship.

Despite the success of enhanced urine culture methods, they should be used strategically and judiciously to prevent isolating and reporting of organisms that are colonizers of the urinary tract. To do otherwise could have the undesired effect of treating contaminated specimens or asymptomatic bacteriuria, which is unnecessary for most patient populations. This means that clinical laboratory professionals should reserve enhanced culture methods to isolate uropathogens when standard urine culture techniques have failed previously in patients with recurrent UTI.

On the Scene With Total Laboratory Automation

The good news is that total laboratory automation (TLA) in clinical microbiology laboratories has enabled labs to isolate fastidious and emerging uropathogens more often, even without using enhanced urine culture.

The decision to automate urine culture in laboratories with TLA is easy thanks to standardized urine collection devices and the fact that urine culture is such a high-volume test. Not surprisingly, TLA has vastly changed the workflow for urine cultures. As an example, plates no longer sit out on the bench for hours waiting to be read. Instead, they are read continuously and remain in the incubator unless further workup is required. This has resulted in growth of many bacteria at an accelerated rate. Thus, laboratories are noticing increased isolation of fastidious organisms that typically grow too slowly to be seen within 24 hours using traditional methods.

Novel methods such as enhanced urine culture and TLA have paved the way for increased recognition of emerging uropathogens. While further studies are needed to fully assess the clinical significance of many organisms previously missed by standard techniques, clinical laboratory professionals need to be aware that organisms such as Aerococcus species, Actinotignum schaalii, and Corynebacterium urealyticum are significant contributors to the pathogenesis of UTI and should not be ignored as contaminants. This knowledge will facilitate timely diagnosis and proper treatment of UTI.

Melanie L. Yarbrough, PhD, is an instructor in the Division of Laboratory and Genomic Medicine and Department of Pathology and Immunology at Washington University School of Medicine in St. Louis. +Email: myarbro@wustl.edu