Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis

Abstract

Background: A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs.

Methods: A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity.

Results: A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72-4.81, p < 0.001, I² = 90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86-0.91, I² = 39.65%, p = 0.06), and the pooled specificity was 0.75 (95% CI: 0.51-0.90, I² = 88.64%, p < 0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86-0.92). The GRADE score indicated a low CoE.

Conclusion: The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis.

Keywords: Diagnostic performance; Meta-analysis; Metagenomic next-generation sequencing; Urinary tract infection.

Fig. 1

Flow chart of study retrieval

Fig. 2

Quality assessment of the included studies by the QUADAS-2 tool

Fig. 3

Comparison of pathogen detection positive rate between mNGS and culture in urine

Fig. 4

Forest plot of pooled sensitivity (A) and specificity (B) of mNGS in UTIs

Fig. 5

The sROC of mNGS diagnosis in UTIs

Fig. 6

Publication bias of diagnostic performance assessed by Deek’s funnel test