Colistin resistance genes in Escherichia coli and Salmonella spp. in pets, wild and food-producing animals in Portugal
Creators: name: Pista, Angela
name: Ribeiro, Sofia
name: Fontes, Mariana
name: Lopes, Iuri
name: Silveira, Leonor
Publisher: name: Zenodo
Year: 2022

description: <strong>Background.</strong> Antimicrobial resistance (AMR) is one of the main threats to global health. The dissemination of mobile colistin resistance genes (<em>mcr</em>) is a major concern affecting humans, animals and environment. Food-producing animals are considered the main reservoir of <em>mcr</em> genes. However, the role of wild animals and pets is less studied. Here, we investigate the <em>mcr</em> occurrence among wild animals, wild birds, food-producing animals and pets. <strong>Methods.</strong> Between 2019 and 2021, a total of 613 faecal samples were obtained from wild animals (boars, n=51; deer, n=62; other, n=19), wild birds (n=109), food-producing animals (cattle, n=40; pigs, n=133), and pets (cats and dogs, n=199). Isolation was performed in selective and non-selective medium, followed by identification of virulence genes of E. coli by PCR, and Salmonella serotyping. The <em>mcr</em> 1-5 genes were screened by PCR in all E. coli and Salmonella isolates. Whole-genome sequencing was used to investigate the presence of AMR genes, sequence types and phylogeny of all pathogenic and <em>mcr</em>-carrying isolates. Genomic analyses were performed through bioinformatics tools available at the CGE web server. <strong>Results.</strong> The overall occurrence rate of <em>E.coli</em> and <em>Salmonella</em> was 81.7% (501/613) and 2.4% (15/613), respectively. The <em>mcr</em>-1 gene was detected in 3.2% (16/501) of the <em>E. coli</em> isolates, all of them recovered from pigs (16.6%; 16/128), more specifically from piglets (25.4%; 16/63). All the <em>mcr</em>-1-positive isolates were associated to pathogenic <em>E. coli</em>: ExPEC (n=11), EPEC (n=4) and ETEC/EPEC (n=1). Phenotypically, all the <em>mcr</em>-1-positive isolates showed resistance to colistin and sulfamethoxazole, and high rates of resistance to tetracycline, ampicillin and trimethoprim; 12 were multidrug-resistant and 7 showed resistance to fluoroquinolones. Genomic analysis confirmed the presence of the <em>mcr</em>-1.1 gene variant. One isolate was an extended-spectrum β-lactamase (ESBL)-producer (<em>bla</em>CTX-M-32). The acquired <em>qnrB19</em> gene was detected in 1 isolate and the <em>qnrS1</em> gene in 3 other isolates. The most frequently found plasmid replicons were IncHI2/IncHI2A, IncFIB, IncFII and IncX4. None <em>Salmonella</em> isolates harboured the <em>mcr</em> genes. <strong>Conclusions.</strong> The only <em>mcr</em> gene detected in this study was <em>mcr</em>-1.1. Besides the general low prevalence of the resistance to colistin mediated by <em>mcr</em> genes, all cases were identified in <em>E. coli</em> recovered from faeces of food-producing animals, namely in piglets. All <em>mcr</em>-1.1-positive isolates presented several virulence genes, reflecting the pathogenic potential of these isolates. Our results highlight the importance of a continuous surveillance of antimicrobial resistance in a One Health approach. <strong>Funding.</strong> This work has received funding from the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 773830) – OHEJP DiSCoVeR project.