Emergence of multidrug-resistant Escherichia coli producing CTX-M-, MCR-1-, and FosA in retail food from Egypt

Authors: RAMADAN, HAZEM - Mansoura University; SOLIMAN, AHMED - Kafrelsheikh University; Hiott, Lari; Woodley, Tiffanie; CHATTAWAY, MARIE - Public Health England (PHE); JENKINS, CLAIRE - Public Health England (PHE); Frye, Jonathan; Jackson, Charlene

Submitted to: Frontiers in Cellular and Infection Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2021
Publication Date: 7/13/2021
Citation: Ramadan, H., Soliman, A.M., Hiott, L.M., Woodley, T.A., Chattaway, M.A., Jenkins, C., Frye, J.G., Jackson, C.R. 2021. Emergence of multidrug-resistant Escherichia coli producing CTX-M-, MCR-1-, and FosA in retail food from Egypt. Frontiers in Cellular and Infection Microbiology. 11: Article e681588. https://doi.org/10.3389/fcimb.2021.681588.
DOI: https://doi.org/10.3389/fcimb.2021.681588

Interpretive Summary: Multidrug resistant (MDR) bacteria from retail food poses a major public health threat. In this study, MDR Escherichia coli isolates from ground beef, chicken carcasses, and humans were analyzed using whole genome sequencing (WGS). WGS analysis revealed the existence of multiple resistance genes in the E. coli isolates including those conferring resistance to beta-lactams, colistin, and fosfomycin. The genetic structure of the colistin resistance gene in a chicken isolate analyzed in this study has been previously identified in human and food E. coli isolates from Egypt. A colistin and fosfomycin resistant chicken isolate was also closely related to a chicken E. coli isolate from China. As E. coli co-harboring colistin and fosfomycin resistance genes have only been recently reported, this study shows rapid spread of this genotype that shares similar genetic structures with regional and international E. coli lineages originating from both humans and food animals. Adopting a WGS-based surveillance system is warranted to facilitate monitoring the international spread of MDR pathogens. This data is important to scientists studying dissemination of antimicrobial resistance in order to devise better detection methods.

Technical Abstract: Multidrug resistant (MDR) bacteria from retail food poses a major public health threat. In this study, MDR Escherichia coli isolates from retail food (n=11, six isolates from ground beef and five from chicken carcasses) and humans (n=2) that displayed overlapping Multilocus Sequence Types (MLST), were analyzed using whole genome sequencing (WGS). In silico WGS analysis revealed the existence of multiple resistance genes among the examined E. coli isolates. Of the six CTX-M-producing isolates from retail food, blaCTX-M-14 was the prevalent variant identified (83.3%, 5/6). Two plasmid-mediated fosfomycin resistance genes, fosA3, and fosA4, were detected from retail food isolates (one each from chicken and beef), where fosA4 was identified in the chicken isolate 82CH that also carried the colistin resistance gene mcr-1. The blaCTX-M-14 and fosA genes in retail food isolates were located adjacent to insertion sequences ISEcp1 and IS26, respectively. The mcr-1 genetic structure (nikA- nikB- mcr-1- pap2- top) in chicken isolate 82CH has been previously identified in human and food E. coli isolates from Egypt. Hierarchical clustering (HierCC) of core genome MLST revealed clustering of chicken isolate 82CH, co-harboring mcr-1 and fosA genes, with a chicken E. coli isolate from China at the HC200 level (= 200 core genome allelic differences). As E. coli co-harboring mcr-1 and fosA genes has only been recently reported, this study shows rapid spread of this genotype that shares similar genetic structures with regional and international E. coli lineages originating from both humans and food animals. Adopting WGS-based surveillance system is warranted to facilitate monitoring the international spread of MDR pathogens.