Longitudinal analysis of carbapenem-resistant Escherichia coli in a Southern Chinese hospital (2015–2021): Epidemiology, genetics, and resistance mechanisms

Abstract

This study conducted a retrospective genomic and epidemiological analysis of Escherichia coli (CREC) in a large general hospital in southern China. From 2015–2021, the characteristics of 183 CREC strainswere determined via minimum inhibitory concentration (MIC) determination and whole-genome sequencing (WGS). The carbapenem resistance mechanisms of carbapenemase-producing carbapenem-resistant E.coli (CP-CREC) and non-carbapenemase-producing carbapenem-resistant E. coli (non-CP-CREC) were investigated through a combination of porin genes (ompC/ompF) assessment and antimicrobial resistance gene detection/copy number quantification. We observed a diverse population structure of CREC, with a total of 60 different sequence types (STs) assigned. A total of 48.6% (89/183) of theisolates were extraintestinal pathogenic E. coli, including the first reported O16-ST131 strains carrying carbapenem resistance genes. Adhesion and invasion experiments revealed that the O16-ST131 CP-CREC strains had strong adhesion and invasion abilities. The majority of CREC strains (90.2%, 165/183) were predicted to have reduced expression of at least one outer membrane porin gene (ompC/ompF). Compared with CP-CREC, non-CP-CREC presented significantly higher copy numbers of extended-spectrum β-lactamase (ESBL) genes (median copy number variants = 3.635 × , P ＜0.001) and ampC genes (median copy number variants: 2.80 × , P = 0.022). High-risk clones (i.e., ST131, ST410, and ST167) persisted long term in the hospital through both CP-CREC and non-CP-CREC forms. Genetic environment analysis revealed that bla_NDM was located in a conserved genetic environment (dsbD - trpF - bla_NDM). This work provides a comprehensive description of CREC and offers new insights into CREC surveillance based on WGS in China.