Prevalence and genomic characterization of pathogenic blaNDM-positive Escherichia coli from retail meats: The first large-scale study in 22 cities of China.

Retail meat is a suspected reservoir of blaNDM-positive carbapenem-resistant Escherichia coli (CREC), resulting in foodborne illnesses in humans. Abuse of antibiotics in swine and chicken farming is common in China, however, large-scale studies about blaNDM-positive CREC from retail meats and their pathogenicity in China are rare. In the present study, we sampled 817 pork and chicken meats, from 152 markets in 22 cities of China, during the period of 2017-2020, and analyzed the prevalence of and genomic characteristics of pathogenic blaNDM-positive CREC. A total of 203 CREC carrying 7 blaNDM variants were obtained in the 185 CREC-positive meat samples. Notably, 37.2 % of the blaNDM-positive isolates co-harbored mcr-1, conferring resistance to nearly all currently available antibiotics. We firstly revealed high prevalence rates of blaNDM-positive ExPEC (extraintestinal pathogenic E. coli, 19.1 %), APEC (avian pathogenic E. coli, 29.0 %) and UPEC (uropathogenic E. coli, 32.2 %) in retail meats in China, and found that chicken meat had a higher detection rate of pathogenic CREC than pork. The most common blaNDM subtype in pathogenic strains was blaNDM-5, followed by blaNDM-9. The blaNDM-13 subtype was firstly found in isolates from meat. Whole-genome sequencing showed these pathogenic strains had high genetic diversity, with ST457, ST156 and ST6751 being the main sequence types. The genetic relationship among CREC of different origins based on phylogenomic analysis indicated the wide spread of these isolates, which was confirmed by the high similarities of the blaNDM/mcr-1-bearing plasmids from meats and from animals and humans in different geographical areas. The horizontal transmission of these multidrug-resistant pathogens was mainly mediated by transferable blaNDM-5-bearing IncFIB, IncFIC and IncX3 plasmids, blaNDM-9-bearing IncB/O plasmids and mcr-1-bearing IncI2 and IncX4 plasmids. This study highlighted retail meat could act as an important vehicle for spreading pathogenic blaNDM-positive CREC between animals and humans.