Prevalence and characterization of Salmonella in pigs from conventional and organic farms and first report of S. serovar 1,4,[5],12:i:- from Korea

•MDR Salmonella incidence was significantly more in conventional than organic farms.•MLVA showed clonal dissemination of S. Typhimurium and S. 1,4,[5],12:i:- strains.•Spread of blaCTX-M-15 was due to both clonal spread and horizontal dissemination.•First report on the occurrence of Salmonella serotype 1,4,[5],12:i:- from Korea.•First report of CTX-M-15 in swine S. Virchow and qnrS1 in S. Rissen from animals. This study compared the prevalence of Salmonella spp. and their antimicrobial susceptibilities in pigs from conventional and organic farms during 2012–2013 in Korea and characterized them by molecular methods. Altogether, 100 nontyphoid Salmonella were isolated: 47 from 1324 pigs (3.5%) from conventional farms and 53 from 641 pigs (8.3%) from organic farms. The most frequent serovar was Typhimurium (49%) followed by Panama (24%), 1,4,[5],12:i:- (5%), and Virchow (5%). Overall, the isolates were most often resistant to tetracycline (75%) followed by ampicillin (66%), streptomycin (57%), and gentamicin (44%). The prevalence of antimicrobial resistance, multi-drug resistance phenotype, and resistance to tetracycline, ampicillin, and gentamicin were significantly higher in swine Salmonella from conventional farms than those from organic farms. The most common resistance pattern was ampicillin–gentamicin–tetracycline (n=16). All eight ceftiofur-resistant Salmonella identified produced CTX-M-15. Overall, decreased susceptibility to ciprofloxacin was observed in 39 isolates. Among them, a single isolate was positive for qnrS1 gene. An insertion sequence ISEcp1 was detected upstream of blaCTX-M gene in all isolates. The spread of blaCTX-M-15 gene was attributed to combination of clonal expansion and horizontal dissemination mediated by IncHI2 plasmid. Multilocus variable number of tandem repeats analysis demonstrated clonal dissemination of S. Typhimurium and S. 1,4,[5],12:i:- strains in pigs. To our knowledge, this is the first report of blaCTX-M-15 gene in S. Virchow from pigs and qnrS1 gene in S. Rissen from animals. This study also reports the first occurrence of Salmonella serovar 1,4,[5],12:i:- from Korea and CTX-M-15 producing Salmonella from pigs in Korea.