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

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