Metagenomics in the diagnosis and treatment of urinary tract infections: A systematic review and meta-analysis

BACKGROUND: Urinary tract infections (UTIs) are common causes of hospital admissions and contribute to anti-microbial resistance. Urine cultures have long laboratory turnaround times leading to empirical antibiotic prescribing and can miss polymicrobial infections. Metagenomic next-generation sequencing (mNGS) increases pathogen identification, but it is unclear whether this leads to improved patient care.

METHODS: This systematic review was conducted in accordance with PRISMA guidelines. Studies focusing on hospitalised UTIs, which compared mNGS to standard cultures were included. Literature searches included MEDLINE, EMBASE, Scopus and the Cochrane Central Register of Controlled Trials (CENTRAL). The Quality Assessment of Diagnostic Accuracy Studies -2 tool was used to assess study quality. Clinical outcomes included laboratory turnaround times and antibiotic prescriptions. A meta-analysis for pathogen positivity rates and subgroup analysis for pre-determined subgroups were completed.

RESULTS: Studies were small and often of low quality. Whilst mNGS pathogen positivity rate (PPR) was numerically higher across all studies, in the meta-analysis, this difference failed to reach statistical significance (OR = 2.72, 95 % CI [0.78-9.52], p = 0.147) and study heterogeneity was high (I² = 83 %, p < 0.01). mNGS achieved higher polymicrobial identification in samples (410/839 (48.87 %) vs. 94/762 (12.34 %), and laboratory turnaround times appeared faster compared to standard culture.

CONCLUSION: mNGS is a promising technology for UTIs, particularly in reducing laboratory turnaround times and for polymicrobial infections. More studies are needed to understand the potential clinical benefits of deploying these systems.