Related Experiment Video
Updated: Aug 26, 2026

Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization
Published on: October 18, 2019
Metagenomic Characterization of Nitrite-Negative Urinary Tract Infections and Identification of an optrA-fexA
Jie Chen1,2, Yuhan Guan1,2, Wenqin Li2
1General Department, Jiashan County Huimin Street Community Health Service Center, Jiaxing, Zhejiang, People's Republic of 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.
Related Concept Videos
Urinary Tract Infection III: Diagnostic Studies and Interprofessional Care
Microbiota of the Urogenital Tract
Urine Studies II: Urine Culture and Sensitivity Test
Urinary Tract Infection I: Introduction
