Comparison of polymerase chain reaction and next-generation sequencing with conventional urine culture for the diagnosis of urinary tract infections: A meta-analysis

Abstract

The limitations of conventional urine culture methods can be avoided by using culture-independent approaches like polymerase chain reaction (PCR) and next-generation sequencing (NGS). However, the efficacy of these approaches in this setting is still subject to contention. PRISMA-compliant searches were performed on MEDLINE/PubMed, EMBASE, Web of Sciences, and the Cochrane Database until March 2023. The included articles compared PCR or NGS to conventional urine culture for the detection of urinary tract infections (UTIs). RevMan performed meta-analysis, and the Cochrane Risk of Bias Assessment Tool assessed study quality. A total of 10 selected studies that involved 1,291 individuals were included in this meta-analysis. The study found that PCR has a 99% sensitivity and a 94% specificity for diagnosing UTIs. Furthermore, NGS was shown to have a sensitivity of 90% for identifying UTIs and a specificity of 86%. The odds ratio (OR) for PCR to detect Gram-positive bacteria is 0.50 (95% confidence interval [CI] 0.41–0.61), while the OR for NGS to detect Gram-negative bacteria is 0.23 [95% CI 0.09–0.59]. UTIs are typically caused by Gram-negative bacteria like Escherichia coli and Gram-positive bacteria like Staphylococci and Streptococci. PCR and NGS are reliable, culture-free molecular diagnostic methods that, despite being expensive, are essential for UTI diagnosis and prevention due to their high sensitivity and specificity.

Comparison of Polymerase Chain Reaction and Urine Culture in the Evaluation of Patients with Complex Urinary Tract Infections

“…Indeed, the number of organisms identified by next-generation sequencing may be bewildering to the clinician-one analysis revealed a median 41 bacterial genera, 2 eukarya species, and 3 viral sequences per sample [21]. A recent meta-analysis comparing results of PCR and NGS found that PCR had a 99% sensitivity and a 94% specificity for diagnosing UTIs, while NGS was shown to have a 90% and 86% sensitivity and specificity, respectively, for identifying UTIs [22]. Future studies comparing PCR and NGS are needed to better define the role of these tests, but at present, there is limited need for whole-genome sequencing of clinical isolates for pathogen identification on a large scale given the availability of alternative technologies that offer a faster turnaround time, greater cost efficiency, and lower complexity.…”