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Occurrence of the Colistin resistance gene mcr-1 and additional antibiotic resistance genes in ESBL/AmpC-producing Escherichia coli from poultry in Lebanon: A nationwide survey

Abstract : The objective of the present study was to determine genomic characteristics of expanded-spectrum cephalosporin (ESC)-resistant Escherichia coli spreading in healthy broilers in Lebanon in 2018. Rectal swabs (n = 280) from 56 farms were screened for the presence of ESC-resistant E. coli isolates. Antimicrobial susceptibility and extended-spectrum b-lactamase (ESBL)/AmpC production were determined by the disk diffusion method. Whole-genome sequencing (WGS) of 102 representative isolates of E. coli was performed to determine their phylogenetic diversity, serotypes, sequence types (ST), acquired resistance genes, and virulence-associated genes. Fifty-two out of 56 farms housed broilers carrying ESC-resistant E. coli isolates. These farms had large and recurrent antimicrobial practices, using, for some of them, critically important antibiotics for prophylactic and therapeutic purposes. Among the 102 sequenced multidrug-resistant (MDR) E. coli isolates, the proportion of ESBL, plasmid-mediated AmpC b-lactamase (pAmpC) producers, and ESBL/pAmpC coproducers was 60%, 27.6%, and 12.4%, respectively. The most prevalent ESBL/ pAmpC genes were bla CMY-2 , bla CTX-M-3 , bla CTX-M-15 , bla CTX-M-27 , and bla CTX-M-14b (n = 42, n = 31, n =15, n = 9, and n = 7, respectively). These ESBL/pAmpC producers were distributed in different STs, most being well-known avian-associated and sometimes pathogenic STs (ST-10, ST-48, ST-93, ST-115, ST-117, and ST-457). Phylogenetic single nucleotide polymorphism (SNP) analysis confirmed their genetic diversity and wide dispersion across the Lebanese territory. Most isolates were also resistant to ciprofloxacin (101/102 with 3 QRDR mutations), and 19/102 isolates from 11 unrelated STs also carried the mobile resistance gene mcr-1. This survey illustrates the alarming prevalence of MDR E. coli resistant to medically important antibiotics in broilers in Lebanon. This advocates the need for surveillance programs of antimicrobial resistance in Lebanon and the reduction of excessive use of antibiotics to limit the spread of MDR E. coli in food-producing animals.
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https://hal.inrae.fr/hal-03338913
Contributor : Benoit Doublet <>
Submitted on : Thursday, September 9, 2021 - 10:35:02 AM
Last modification on : Wednesday, September 15, 2021 - 2:15:41 PM

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Myriam Mikhayel, Sébastien Leclercq, Dolla Sarkis, Benoît Doublet. Occurrence of the Colistin resistance gene mcr-1 and additional antibiotic resistance genes in ESBL/AmpC-producing Escherichia coli from poultry in Lebanon: A nationwide survey. Microbiology Spectrum, American Society for Microbiology, 2021, 9 (2), 15 p. ⟨10.1128/spectrum.00025-21⟩. ⟨hal-03338913⟩

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