Metagenomic Characterization of Nitrite-Negative Urinary Tract Infections and Identification of an optrA-fexA Co-Localization in a Primary Healthcare Setting in China.

INTRODUCTION

Urinary tract infections (UTIs) showing negative nitrite results create a diagnostic blind spot for Gram-positive pathogens. The plasmid-mediated resistance genes optrA (linezolid) and tet(X) (tigecycline) pose severe therapeutic challenges, but their genomic context in primary healthcare settings remains poorly characterized.

METHODS

Deep metagenomic sequencing was performed on urine samples from 20 patients with complex nitrite-negative UTIs and pyuria in China. Antibiotic resistance genes (ARGs) were profiled using a read-mapping threshold (>50 reads for tet(X)) and de novo assembly.

RESULTS

optrA was ubiquitously detected via read mapping. Based on our pre-established cutoff, tet(X) reads were identified in 55% (11/20) of samples. Crucially, genomic assembly captured the physical co-localization of optrA and the phenicol exporter fexA on a single contig in one sample (JX-NY001). Virulence factor profiles varied across samples.

DISCUSSION: This study provides genomic evidence of high-risk resistance determinants in community nitrite-negative UTIs. However, results are limited by the DNA-level metagenomic approach without culture confirmation. Molecular surveillance is needed to monitor these cryptic multidrug-resistance clusters.