Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food From Egypt

Abstract

In this study, multidrug-resistant (MDR) <i>Escherichia coli</i> isolates from retail food and humans assigned into similar Multilocus Sequence Types (MLST) were analyzed using whole genome sequencing (WGS). <i>In silico</i> analysis of assembled sequences revealed the existence of multiple resistance genes among the examined <i>E. coli</i> isolates. Of the six CTX-M-producing isolates from retail food, <i>bla</i>_CTX-M-14 was the prevalent variant identified (83.3%, 5/6). Two plasmid-mediated fosfomycin resistance genes, <i>fos</i>A3, and <i>fos</i>A4, were detected from retail food isolates (one each from chicken and beef), where <i>fos</i>A4 was identified in the chicken isolate 82CH that also carried the colistin resistance gene <i>mcr</i>-1. The <i>bla</i>_CTX-M-14 and <i>fos</i>A genes in retail food isolates were located adjacent to insertion sequences IS<i>Ecp1</i> and IS<i>26</i>, respectively. Sequence analysis of the reconstructed <i>mcr-1</i> plasmid (p82CH) showed 96-97% identity to <i>mcr-1</i>-carrying IncI2 plasmids previously identified in human and food <i>E. coli</i> isolates from Egypt. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of chicken isolate 82CH, co-harboring <i>mcr-1</i> and <i>fos</i>A4 genes, with a chicken <i>E. coli</i> isolate from China at the HC200 level (≤200 core genome allelic differences). As <i>E. coli</i> co-harboring <i>mcr-1</i> and <i>fos</i>A4 genes has only been recently reported, this study shows rapid spread of this genotype that shares similar genetic structures with regional and international <i>E. coli</i> lineages originating from both humans and food animals. Adopting WGS-based surveillance system is warranted to facilitate monitoring the international spread of MDR pathogens.