Genomic characterization of blaNDM-5- and mcr-1-positive Escherichia coli from retail chicken meat reveals distinct plasmid organizations

Abstract

Carbapenems and polymyxins are critically important antimicrobial agents for treating severe infections caused by multidrug-resistant Gram-negative bacteria. The global dissemination of the carbapenem resistance gene blaNDM and colistin resistance gene mcr-1 threatens the effectiveness of these last-line antibiotics. From a One Health perspective, food-producing animals and retail meat products may serve as reservoirs and vehicles for antimicrobial resistance determinants. This study investigated the occurrence and genomic characteristics of blaNDM-5- and mcr-1-coharboring Escherichia coli recovered from retail chicken meat to characterize their potential for dissemination through the food chain. Among 67 retail meat samples collected in Xuancheng, China, two meropenem-resistant E. coli isolates carrying both blaNDM-5 and mcr-1 were recovered exclusively from chicken meat. Antimicrobial susceptibility testing and hybrid whole-genome sequencing revealed that the isolates belonged to ST155 and ST165 and exhibited multidrug resistance. Phylogenetic analysis showed that both isolates were genetically distinct from global genomes of the same ST carrying blaNDM and/or mcr-1, suggesting that the two isolates were not derived from recent clonal dissemination represented in the analyzed dataset. Complete genome analysis identified two distinct plasmid organizations of blaNDM-5- and mcr-1: one isolate carried blaNDM-5 and mcr-1 on separate plasmids, whereas the other harbored both genes on a single conjugative IncHI2 plasmid. Comparative genomic analyses demonstrated high similarity between these plasmids and plasmids reported from humans, animals, and food sources. These findings highlight that poultry-associated E. coli may serve as carriers of important resistance determinants with potential for plasmid-mediated dissemination, emphasizing the need for integrated One Health genomic surveillance.