Molecular characterization of extended-spectrum ß-lactamase producers, carbapenemase producers, polymyxin-resistant, and fosfomycin-resistant Enterobacterales among pigs from Egypt

Mustafa Sadek; José Manuel Ortiz de la Rosa; Mustafa Ramadan; Patrice Nordmann; Laurent Poirel

doi:10.1016/j.jgar.2022.05.022

Molecular characterization of extended-spectrum ß-lactamase producers, carbapenemase producers, polymyxin-resistant, and fosfomycin-resistant Enterobacterales among pigs from Egypt

J Glob Antimicrob Resist. 2022 Sep:30:81-87. doi: 10.1016/j.jgar.2022.05.022. Epub 2022 Jun 3.

Authors

Mustafa Sadek¹, José Manuel Ortiz de la Rosa², Mustafa Ramadan³, Patrice Nordmann⁴, Laurent Poirel⁵

Affiliations

¹ Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt; INSERM European Unit (IAME), University of Fribourg, Fribourg, Switzerland.
² Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME), University of Fribourg, Fribourg, Switzerland.
³ Al-Basatin Slaughterhouse, Cairo, Egypt.
⁴ Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME), University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland; Institute for Microbiology, University of Lausanne and University Hospital Centre, Lausanne, Switzerland.
⁵ Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME), University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland. Electronic address: laurent.poirel@unifr.ch.

PMID: 35667645
DOI: 10.1016/j.jgar.2022.05.022

Abstract

Objectives: To perform the first prospective surveillance evaluating the occurrence of genes encoding colistin resistance, fosfomycin resistance, carbapenemase, or extended-spectrum ß-lactamases (ESBLs) among Enterobacterial isolates recovered from the gut flora of pigs from Egypt.

Methods: Between February and April 2020, 81 rectal swabs were collected from pigs in a slaughterhouse, Cairo, Egypt. Samples were screened for different resistance mechanisms using SuperPolymyxin, ChromID ESBL, SuperFOS, and SuperCarba selective agar plates. Antimicrobial susceptibility testing was performed for all isolates using disk diffusion and broth microdilution techniques. PCR screening was performed for ESBLs, carbapenemases, mcr, and fosA genes. Mating-out assays, multilocus sequence typing analysis, and plasmid typing were also performed.

Results: A high prevalence of ESBLs, carbapenemases, fosfomycin, and colistin resistance genes was evidenced among those isolates. The predominant ESBL identified was bla_CTX-M-15, followed by bla_CTX-M-9. We also identified bla_NDM-5 and bla_OXA-244. fosA3, fosA4, and fosA6 were identified in E. coli isolates. In addition, 11 MCR-1 producers were recovered. Notably, co-occurrence of ESBL genes and mcr or fosA genes was observed. MLST analysis revealed a high clonal diversity, ruling out the dissemination of one major clone. IncFIB-type was predominantly present among ESBL and FosA producers. The bla_NDM-5 gene was carried on an IncX4-type, although the bla_OXA-244 gene was chromosomally located. The mcr-1 gene was carried on a diversity of plasmids (IncI2, IncX4, and IncHI2).

Conclusion: These results raise serious public health concerns as Egyptian pig meat could serve as a reservoir for antimicrobial resistance genes (ARGs), leading to worldwide dissemination.

Keywords: Carbapenemases; ESBL; Enterobacterales; Fosfomycin; Pigs; mcr.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bacterial Proteins* / genetics
Colistin* / pharmacology
Drug Resistance, Bacterial* / genetics
Egypt
Escherichia coli Proteins* / genetics
Escherichia coli* / drug effects
Escherichia coli* / genetics
Escherichia coli* / isolation & purification
Fosfomycin* / pharmacology
Klebsiella pneumoniae* / drug effects
Klebsiella pneumoniae* / genetics
Klebsiella pneumoniae* / isolation & purification
Meat / microbiology
Microbial Sensitivity Tests
Multilocus Sequence Typing
Polymyxins* / pharmacology
Prospective Studies
Swine* / microbiology
beta-Lactamases* / genetics

Substances

Bacterial Proteins
Escherichia coli Proteins
MCR-1 protein, E coli
Polymyxins
Fosfomycin
beta-Lactamases
carbapenemase
Colistin