Next-generation sequencing: A reliable tool for the diagnosis and treatment of complicated and recurrent urinary tract infections

This article was sponsored by MicroGenDX.

URINARY TRACT INFECTIONS (UTIs) are a common outpatient infection, especially in women aged over 65 years. At least 1 in 2 women will have a UTI in her lifetime. In all, 20% to 40% of these women will have 1 recurrence, and, of those, up to 50% will go on to have multiple recurrences.1,2 The gold-standard diagnostic tool for UTI is urine culture, a technology that relies upon the ability of the causative organism(s) to grow in artificial conditions. The problem with culture is that many organisms that cause symptomatic urinary tract infections will not grow on standard culture medium, or will grow “mixed urogenital flora,” making identification of a causative pathogen difficult or impossible.

Empiric treatment with 5 days of nitrofurantoin or 3 days of sulfamethoxazole-trimethoprim is effective in managing the majority of uncomplicated acute UTIs, yet many patients coming to the urology practice for specialist evaluation are beyond this simple fix. A common line is, “I had a UTI, my primary care provider gave me [empiric antibiotic therapy]. My symptoms never went away, and now, after multiple antibiotics, my cultures are negative, but I still have symptoms.”

What is the next step? Using standard culture only, patients often are left with a diagnosis of chronic interstitial cystitis or chronic bladder pain, and they remain in a cycle of UTI-type flares. At this stage, patients often receive many rounds of empiric antibiotic therapy or other medications and procedures unnecessarily. This should not be the next step; better diagnostic testing must be used to find the pathogen(s).

The good news is that there are better ways to diagnose a UTI and formulate a plan for directed antibiotic therapy!

Advanced microbial analysis exists in 2 primary categories, polymerase chain reaction (PCR) testing and next-generation sequencing (NGS). PCR involves DNA amplification and matching of that DNA to a small set of known organisms. There are many PCR companies in the urology space that offer a test menu of about 18 to 40 organisms and regional antibiotic resistance data. With up to a 91% sensitivity, PCR testing provides a much better chance at getting a positive result than culture does, if the patient harbors 1 of the 40, or fewer, organisms in that test panel.3 However, PCR alone is not enough.

NGS offers the most comprehensive evaluation of the urinary microbiome. In comparison to the 40 organisms detectable by PCR, NGS analyzes all microbial DNA within a sample (eg, urine, semen, or vaginal or rectal specimen) and compares it to a database of species. One company, MicroGenDX, has a database of over 50,000 bacterial and fungal organisms. MicroGenDX’s approach combines quantitative PCR (qPCR) testing with NGS and allows clinicians to receive rapid PCR results in 24 to 48 hours and the full sample microbiome in 3 to 5 days from receipt of the sample with 99% accuracy and a proven noninferiority to culture.4-6 The company has identified approximately 5,800 species in urine from over 157,000 samples processed. Even more astonishing, a recent study of their database found that Escherichia coli was the predominant species in 29.6% of samples, calling for further analysis of the belief that E. coli is the most common cause of UTI.


An 80-year-old male with known overactive bladder presented to the urology clinic for intermittent dysuria with frequency and urgency of urination, but he had no gross hematuria, fever, or flank pain. His urinalysis showed trace protein levels, but was negative for leukocyte esterase, red blood cells (RBCs), and nitrite. A urine PCR-only test was ordered, which detected no pathogenic organisms; however, a methicillin resistance gene was detected. At his 3-week follow-up, he reported no change in his symptoms. Subsequent urinalysis was negative for leukocyte esterase, RBCs, and nitrite. A qPCR + NGS urine test from MicroGenDX was sent, and results showed a medium (105-107) bacterial load with E. coli (53%), Klebsiella aerogenes (26%), and Enterococcus faecalis (17%). Neither companies’ PCR test detected the E. coli, likely due to mutations in the organism. Genetic resistance was detected to β-lactam and methicillin. Based on these results, the patient was given amoxicillin-clavulanate. He reported improvement in frequency, urgency, and dysuria at his next visit.

Molecular UTI diagnostics are an alternative to culture that provide more sensitive, specific, and timely results. NGS through MicroGenDX eliminates the common equivocal result of “mixed urogenital flora” or “greater than 2 organisms predominate” encountered with standard urine culture. While superior to culture, PCR testing alone lacks the ability to detect many atypical pathogens and mutated organisms. NGS allows clinicians to assess the complete microbiome for pathogens and treat the patient accordingly, using genetic resistance gene information and regional resistance patterns to increase antibiotic stewardship and improve patient outcomes.


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  2. Anger J, Lee U, Ackerman L, et al. Recurrent uncomplicated urinary tract infections in women: AUA/CUA/SUFU guideline. J Urol. 2019;202(2):282-289. doi:10.1097/JU.0000000000000296
  3. Wojno KJ, Baunoch D, Luke N, et al. Multiplex PCR based urinary tract infection (UTI) analysis compared to traditional urine culture in identifying significant pathogens in symptomatic patients. Urology. 2020;136:119-126. doi:10.1016/j.urology.2019.10.018
  4. Coba G, George Coba, Koo T, et al. MP71-03: Comparison of novel DNA-based tools for bacterial detection in patients with chronic urinary tract infection (CUTI). J Urol. 2019;201(suppl 4):e1046-e1047. doi:10.1097/01.JU.0000557115.69479.1b
  5. Mouraviev V, McDonald M. An implementation of next generation sequencing for prevention and diagnosis of urinary tract infection in urology. MicroGen Diagnostics. Published December 5, 2019. Accessed January 15, 2021.
  6. Coba G, Koo T, Zaman S, et al. MP47-07: Comparative value of chronic urinary tract infection (UTI) diagnosis between standard culture sensitivity and next generation sequence (NGS) in urine samples. J Urology. 2019;201(suppl 4):e689-e690. doi:10.1097/01.ju.0000556319.92548.c7