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) Escherichia coli isolates from retail food and humans assigned into similar Multilocus Sequence Types (MLST) were analyzed using whole genome sequencing (WGS). In silico analysis of assembled sequences 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. Sequence analysis of the reconstructed mcr-1 plasmid (p82CH) showed 96–97% identity to mcr-1-carrying IncI2 plasmids previously identified in human and food E. coli isolates from Egypt. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of chicken isolate 82CH, co-harboring mcr-1 and fosA4 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 fosA4 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.

Virulence Determinants and Plasmid-Mediated Colistin Resistance mcr Genes in Gram-Negative Bacteria Isolated From Bovine Milk

“…Colistin-resistant E. coli isolates exhibited resistance to cephalothin, cefazolin, ceftazidime, ampicillin, amoxicillinclavulanic acid, cefoxitin, cefotaxime, piperacillin-tazobactam, and fosfomycin. Concurrently, nearly similar patterns were obtained recently for E. coli against several antibiotics in India, Croatia, and Egypt (Zdolec et al, 2016;Singh et al, 2018;Ramadan et al, 2021;Soliman et al, 2021). For K. pneumoniae isolates, the antibiotic resistance pattern was closely like the pattern of Brazilian MDR K. pneumoniae isolates (Ferreira et al, 2019).…”

“…A previous study has identified mcr-1 gene in one E. coli isolate from a cow suffering from subclinical mastitis in Egypt (Khalifa et al, 2016). Although the mcr-1 gene was detected frequently from different samples (Khalifa et al, 2016;Lima Barbieri et al, 2017;Ramadan et al, 2021), it is foremost found here in the raw milk samples. Marvelously, one E. coli isolate carrying mcr-1 gene obtained from hard cheese made from raw milk was reported in Egypt very lately (Ombarak et al, 2021), which in turn lightens the importance of raw milk quality control checks in Egypt, focusing on farm workers as well as the animal itself.…”

Associations between antimicrobial resistance in fecal Escherichia coli isolates and antimicrobial use in Canadian turkey flocks

“…In our previous analysis, the odds of being a high user of antimicrobials in turkeys were significantly higher for those that used any antimicrobial via water and those that used folate pathway inhibitors, bacitracin, and tetracyclines. These findings highlight the potential role of co-selection for resistance or selection for fitness of specific AMR strains and could be explained by the co-location and transmission of antimicrobial resistance genes on mobile genetic elements (e.g., plasmids or integrons) (Johnson et al, 2012;Sheikh et al, 2012;Ahmed et al, 2013;Cazer et al, 2019;Ramadan et al, 2021). Another potential explanation is that the long-term use of antimicrobials (e.g., bacitracin for prevention of necrotic enteritis) may alter the population of antimicrobial-resistant strains in the gut flora (Agunos et al, 2020) interfering with the succession of the microbial population from resistant toward a more susceptible population.…”

Chromosomal studies on drug resistance genes in extended spectrum β-lactamases producing-Klebsiella pneumoniae isolated from equine

“…Moreover, the five lineages typed as OXY-5 in the current study were related to lineages recovered from isolates of K. oxytoca with human origin. The discrimination of the sources of these lineages indicated the widespread of such resistance gene across continents, in different species of either bacteria and/or animals and human being, this's attributed to the global trading of different types of food animals either as frozen meat or as processed food products [47], in addition to, the close contact between human and animals without commitment to perfect infection control rules, permitting the transmission of the carrier bacteria from and to human and the exchange of the resistance genes inbetween different bacterial species.…”