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Updated: Apr 28, 2026

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
Published on: December 23, 2022
Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe
Xu-Guang Chen1, Lei Zhou1, Kai Duan2
1Emergency Department of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
Background:
Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.
Methods:
In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.
Results:
mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly β-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.
Conclusion:
mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.
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