Colistin Resistance Genes in Escherichia coli and Salmonella spp. Isolates from Pets, Wild and Food-producing Animals in Portugal, 2019-2021

Background: Antimicrobial resistance (AMR) is one of the main threats to global health. The dissemination of mobile colistin resistance genes (mcr) is a major concern affecting humans, animals and environment. Food-producing animals are considered the main reservoir of mcr genes, however the role of wild animals and pets is less studied. Here, we investigate the mcr occurrence among wild animals, wild birds, food-producing animals and pets. Material & Methods: Between 2019-2021, faecal samples obtained from wild animals (boars, N=39; deer, N=62; other, N=6), wild birds (N=98), food-producing animals (cattle, N=40; pigs, N=56) 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 mcr 1-5 genes were screened by PCR in all E. coli and Salmonella isolates recovered. Whole-genome sequencing was used to investigate the presence of AMR genes, multilocus sequence type and phylogeny of all pathogenic isolates, as well as mcr-carrying isolates. Results: The overall occurrence rate of E.coli and Salmonella was 77.8% (389/500) and 2.8% (14/500), respectively. Pathogenic E.coli was detected in 46.7% (50/107) of wild animals, 2.0% (2/98) of wild birds, 11.4% (11/96) of food-producing animals and 19.1% (38/199) of pets, while Salmonella was identified in 2.8% of wild animals (3/107), 3.1% (3/98) of wild birds, and 7.3% (7/96) of food-producing animals. The mcr-1 gene was detected in 1.8% (7/389) of the E. coli positive samples, all of them in isolates recovered from pigs (13.7%; 7/51). All this mcr-1-positive showed additional resistance phenotypes, including MDR, and several virulence genes. No cases of mcr genes were identified in Salmonella isolates. Conclusions: Pathogenic E. coli was significantly more frequent than Salmonella spp in the studied animals. Besides the general low prevalence of the resistance to colistin mediated by mcr genes, the only cases were identified in E. coli food-producing isolates, namely in pigs. Our results highlight the importance of a continuous surveillance of antimicrobial resistance in an OneHealth approach. Funding: This work has received funding from the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 773830) OHEJP Discover.