Molecular epidemiology of carbapenem-resistant Escherichia coli in a tertiary hospital located in the Dabie Mountains region, China

TL;DR

This study investigates carbapenem-resistant Escherichia coli in a rural Chinese hospital, revealing high resistance and specific genetic markers.

Contribution

First systematic investigation of CREc epidemiology in the Dabie Mountains region of China.

Findings

CREc isolates predominantly carried blaNDM-5 and co-occurred with fosA3 and virulence genes.

Genomic analysis identified 24 distinct sequence types, with ST410 and ST692 being most prevalent.

High prevalence of resistance genes and virulence factors was observed in elderly patients with comorbidities.

Abstract

The emergence of carbapenem-resistant Escherichia coli (CREc) strains poses a growing threat to global public health, presenting significant clinical and therapeutic challenges. Although extensive studies have been conducted in urban areas and high-incidence countries, data on the prevalence and molecular characteristics of CREc in rural regions remain limited, particularly in areas like the Dabie Mountains in China. This knowledge gap is critical because regional variations in resistance mechanisms may differ substantially. This study aims to address this gap by investigating the molecular epidemiology, genetic diversity, and resistance mechanisms of CREc in a tertiary hospital located in this under-researched region, providing crucial data for regional surveillance and informed public health interventions.

Between 2018 and 2022, 33 CREc isolates were obtained from 33 patients at a tertiary hospital in the Dabie Mountains region of China. We performed a retrospective clinical analysis of the patients, followed by next-generation sequencing (NGS) and comprehensive bioinformatics analysis of all 33 CREc isolates. Additionally, phenotypic tests for carbapenemase and AmpC-type β-lactamase production were carried out.

This study analyzed 33 CREc clinical isolates from a mountainous region hospital in China. The isolates predominantly originated from elderly patients (66.7% aged ≥ 60 years) with comorbidities (75.8%). Phenotypic analysis showed that 97.0% of isolates produced carbapenemases (n = 32), with the gene encoding New Delhi Metallo-β-lactamase (blaNDM) variants (n = 30) dominated by blaNDM-5 (n = 24) and a notable proportion of blaNDM-13 (n = 4). In addition to carbapenemase genes, the most prevalent resistance genes were those conferring resistance to sulfonamides (97.0%, 32/33) and aminoglycosides (93.9%, 31/33). Notably, 36.4% (n = 12) of isolates exhibited fosA3-mediated fosfomycin resistance, with universal co-carriage of extended-spectrum-β-lactamase (ESBL) genes. Genomic analysis identified 24 distinct sequence types (STs), with ST410 and ST692 being most prevalent. Molecular investigation localized blaNDM within diversified Tn125 derivatives and the gene encoding Klebsiella pneumoniae Carbapenemase (blaKPC-2) with truncated Tn6296 elements. Virulence factor screening detected 71 virulence genes, including highly prevalent adhesins (fimH, 84.8%) and hemolysins (hlyE, 97.0%). Plasmid profiling showed predominant IncFII (81.8%) and IncX (63.6%) replicon types.

This represents the first systematic investigation of CREc epidemiology in this understudied region. Our results demonstrate a high prevalence of carbapenem resistance mediated primarily by blaNDM-5, with co-occurrence of other resistance genes (fosA3) and virulence factors (fimH/hlyE/csgA).

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