Background: The emergence and spread of carbapenem-resistant Escherichia coli (E. coli ) pose a serious threat to human health worldwide. This study aimed to investigate the molecular mechanisms underlying carbapenem resistance and their prevalence among E. coli  in China.
Methods: A collection of 5796 E. coli  clinical isolates were collected from the First Affiliated Hospital of Wenzhou Medical University from 2002 to 2017. Sensitivity to antibiotics was determined using the agar dilution method. The detection of carbapenemases production and the prevalence of resistance-associated genes were investigated through modified carbapenem inactivation method (mCIM), PCR and sequencing. The mutations in outer membrane porins genes (ompC  and ompF ) were also analyzed by PCR and sequencing assays. The effect of efflux pump mechanism on carbapenem resistance was also tested. E. coli  were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).
Results: A total of 58 strains (1.0%) of carbapenem-resistant E. coli  were identified. The strains carrying bla _KPC-2 and bla _NDM accounted for 22.4% (13/58) and 51.7% (30/58), respectively. Among bla _NDM- positive strains, 27 bla _NDM genes were assigned to bla _NDM-5, while the remaining three strains were bla _NDM-1, whereas bla _VIM, bla _IMP, bla _OXA-48, and bla _SHV were not found. The CTX-M-type β-lactamase genes accounted for 96.6% (56/58). In addition, bla _TEM-1 genes were identified in 58.6% of tested strains. In carbapenem-resistant isolates, mutations in OmpC (the majority of mutated sites were D192G and Q104_F141del, accounting for 54.5%) and OmpF (large deletions S75_V127del, W83_D135del and Q88_D135del) were detected. Of note, the antibiotic resistance was not associated with overexpression of efflux pump. Moreover, MLST categorized the 58 carbapenem-resistant isolates into 19 different sequence types. PFGE analysis revealed that homology among the carbapenem-resistant isolates was low and sporadic.
Conclusion: The bla _NDM was the principal resistance mechanism of carbapenem-resistant E. coli  in the hospital. bla _NDM-5 is becoming a new threat to public health and the alteration of outer membrane porins might help further increase the MIC of carbapenem.
Keywords: Escherichia coli , carbapenem-resistant, carbapenemase, outer membrane porin, epidemiology