Genomic Features of MCR-1 and Extended-Spectrum β-Lactamase-Producing Enterobacterales from Retail Raw Chicken in Egypt

Mustafa Sadek; José Manuel Ortiz de la Rosa; Mohamed Abdelfattah Maky; Mohamed Korashe Dandrawy; Patrice Nordmann; Laurent Poirel

doi:10.3390/microorganisms9010195

Genomic Features of MCR-1 and Extended-Spectrum β-Lactamase-Producing Enterobacterales from Retail Raw Chicken in Egypt

Microorganisms. 2021 Jan 19;9(1):195. doi: 10.3390/microorganisms9010195.

Authors

Mustafa Sadek^{1

2

3}, José Manuel Ortiz de la Rosa^{1

2}, Mohamed Abdelfattah Maky³, Mohamed Korashe Dandrawy³, Patrice Nordmann^{1

2

4

5}, Laurent Poirel^{1

2

4}

Affiliations

¹ Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland.
² INSERM European Unit (IAME, France), University of Fribourg, CH-1700 Fribourg, Switzerland.
³ Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83522, Egypt.
⁴ Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, CH-1700 Fribourg, Switzerland.
⁵ Institute for Microbiology, University of Lausanne and University Hospital Centre, CH-1011 Lausanne, Switzerland.

Abstract

Colistin is considered as a last resort agent for treatment of severe infections caused by carbapenem-resistant Enterobacterales (CRE). Recently, plasmid-mediated colistin resistance genes (mcr type) have been reported, mainly corresponding to mcr-1 producers. Those mcr-1-positive Enterobacterales have been identified not only from human isolates, but also from food samples, from animal specimens and from environmental samples in various parts of the world. Our study focused on the occurrence and characterization of mcr-1-positive Enterobacterales recovered from retail raw chicken in Egypt. From the 345 retail chicken carcasses collected, a total of 20 samples allowed to recover mcr-1-positive isolates (Escherichia coli, n = 19; Citrobacter freundii, n = 1). No mcr-2- to mcr-10-positive isolate was identified from those samples. The colistin resistance trait was confirmed for all those 20 isolates with a positivity of the Rapid Polymyxin NP (Nordmann-Poirel) test. Minimum inhibitory concentrations (MICs) of colistin for all MCR-1-producing isolates ranged between 4 and 16 μg/mL. Noticeably, 9 out of the 20 mcr-1-positive isolates produced an extended-spectrum β-lactamase (ESBL), respectively producing CTX-M-9 (n = 2), CTX-M-14 (n = 4), CTX-M-15 (n = 2), and SHV-12 (n = 1). Noteworthy, the fosA4 gene encoding resistance to fosfomycin was found in a single mcr-1-positive E. coli isolate, in which both genes were located on different conjugative plasmids. The pulsed-field gel electrophoresis (PFGE) patterns were identified, corresponding to 10 different sequence types (STs), highlighting the genetic diversity of those different E. coli. Whole-genome sequencing revealed three major types of mcr-1-bearing plasmids, corresponding to IncI2, IncX4, and IncHI2 scaffolds. The occurrence of MCR-1-producing multidrug-resistant Enterobacterales in retail raw chicken is of great concern, considering the possibility of transmission to humans through the food chain.

Keywords: ESBLs; MCR-1; fosA4; plasmid-mediated colistin resistance; poultry.