Molecular epidemiology and mechanisms of Escherichia coli resistance to ertapenem but not other carbapenems in China

Abstract

To investigate the molecular epidemiology and resistance mechanisms of carbapenem-resistant Enterobacteriaceae (CRE) with a specific phenotype resistant to ertapenem, but susceptible to meropenem and imipenem. Escherichia coli isolates ( n  = 424) were collected across the country; 54 isolates were CRE, of which 14 isolates were resistant to ertapenem but susceptible to meropenem and imipenem. Antimicrobial susceptibility testing were conducted using 17 drugs on the 14 isolates. Whole-genome sequencing (WGS) was used to analyze the isolates’ drug resistance genes carried, plasmid types, virulence genes, and drug resistance homology. Furthermore, efflux pumps and outer membrane proteins were analyzed. Only 25.9% of the CRE isolates were resistant to ertapenem, and no carbapenemase genes were detected in any isolate. All 14 isolates carried the genes encoding extended-spectrum β-lactamase (ESBLs), and 8 bla CTX-M subtypes were identified. Among these, bla CTX-M-15 (5 isolates) and bla CTX-M-14 (3 isolates) were the most prevalent. IncF plasmids (IncFIB, IncFIA, and IncFII) were the predominant plasmid types. Ten isolates simultaneously carried the highly virulent genes iucC and iutA . Efflux pump inhibition experiments with 14 isolates yielded negative results. Outer membrane protein analysis revealed that five of the isolates lacked OmpC. After genetic complementation with the outer membrane protein ompC gene, the minimum inhibitory concentration of ertapenem decreased 16–533 fold. Nine isolates with detectable OmpC expression also presented ertapenem monoresistance. Porin-coding gene disruption, ramA/marA gain-of-function mutations and efflux overexpression were excluded. Although these isolates harbored ESBL-encoding genes, ESBL alone could not confer ertapenem resistance. Potential mechanisms may include post-transcriptional porin repression, chromosomal ompC up-regulation or other permeability-altering chromosomal variants, and their precise mechanisms remain to be elucidated. These results suggest that the loss of outer membrane protein OmpC may be a key factor contributing to ertapenem resistance in carbapenemase-negative E. coli strains, and efflux pumps do not appear to mediate this resistance phenotype.