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

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