Microevolution of monophasic variant of epidemic Salmonella Typhimurium (S. 4,[5],12:i:-)

Salmonella Typhimurium is a major cause of food-borne gastroenteritis. In 2005 a monophasic variant of S. Typhimurium (S. 4,[5],12;i:-) sequence type ST34 and ASSuT antimicrobial resistance profile (AMR) emerged as a worldwide epidemic. Pigs are the main reservoir of this pathogen, pork and pork products represent the predominant vehicles of S. 4,[5],12;i:-. In this study, whole-genome sequencing was used to investigate the population structure and the persistence of S. Typhimurium and S. 4,[5],12;i:- ST34 on Irish pig farms. Additionally, the ability of the isolates to produce biofilms was assessed as this represents an important strategy for environmental survival and persistence. Farm-specific clones persisting between production cycles were identified. No unequivocal association between biofilm formation and persistence was observed; however, epidemic clones formed more biofilms than non-epidemic genotypes suggesting the advantage conferred by this trait. During persistence on farm, microevolution enhancing biofilm formation, but also AMR and heavy metal resistance was observed following the acquisition of IncHI2 plasmids. The phage-encoded virulence factor SopE was sporadically described in S. Typhimurium but was associated with epidemic types. sopE was acquired by S. 4,[5],12;i:- ST34 following lysogenic conversion by the novel prophage mTmV. The findings that the acquisition of sopE occurred multiple, independent times in S. 4,[5],12;i:- ST34 and was concomitant with the emergence of this pathogen in pigs suggested that the acquisition of sopE was positively selected and may have contributed to the success of S. 4,[5],12:i:- ST34. mTmV was virtually absent in S. Typhimurium serovar types despite its ability to infect a variety of S. Typhimurium genotypes, but disseminated to diverse S. enterica serovars, potentially contributing to the emergence of novel pathovariants. Variants of mTmV and novel bacteriophages carrying sopE, which were identified in association with sopE copy number variation, likely promote the dissemination of sopE