Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand
Prapas Patchanee,
Prawitchaya Tanamai,
Phacharaporn Tadee,
Matthew D. Hitchings,
Jessica K. Calland,
Samuel K. Sheppard,
Dethaloun Meunsene,
Ben Pascoe,
Pakpoom Tadee
Affiliations
Prapas Patchanee
Integrative Research Center for Veterinary Preventive Medicine, Department of Food and Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
Prawitchaya Tanamai
Integrative Research Center for Veterinary Preventive Medicine, Department of Food and Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
Phacharaporn Tadee
Faculty of Animal Science and Technology, Maejo University, Chiang Mai, Thailand
Matthew D. Hitchings
Swansea University Medical School, Swansea University, Swansea, UK
Jessica K. Calland
The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
Samuel K. Sheppard
The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
Dethaloun Meunsene
Department of Veterinary Medicine, Faculty of Agriculture, National University of Laos, Vientiane, Loas PDR
Ben Pascoe
The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
Pakpoom Tadee
Integrative Research Center for Veterinary Preventive Medicine, Department of Food and Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
Background Monophasic Salmonella Typhimurium or S. enterica 1,4,[5],12:i:- is among the top five serotypes reported in Thailand. In this study, nineteen monophasic S. Typhimurium from the pig production chain in Chiang Mai and Lamphun provinces during 2011–2014 were sequenced and compared to a globally disseminated clone. Isolates were probed in silico for the presence of antimicrobial resistance genes and Salmonella virulence factors, including Pathogenicity Islands. Results All isolates were from sequence type 34 (ST-34) and clustered similarly in core and pangenome genealogies. The two closest related isolates showed differences in only eighteen loci from whole-genome multilocus sequence typing analysis. All 19 isolates carried aminoglycoside and beta-lactam class resistance genes and genes for five or more different antibiotic classes. Seven out of 14 known SPIs were detected, including SPI-5, SPI-13 and SPI-14, which were detected in all isolates. Conclusions The multi-drug resistant clone, ST-34 was sampled at all stages of pork production. This clone has infiltrated global agricultural processes and poses a significant public health risk. Differences in the core and accessory genomes of the isolates we collected suggest that strains persist though the pork production process, with evidence of mutation within the core-genome and horizontal acquisition of genes, potentially via sharing of pathogenicity islands and plasmids. This highlights the importance of surveillance and targeted intervention measures to successfully control Salmonella contamination.
