Salmonella enterica serotype 4,[5],12:i:- in swine in the United States Midwest: an emerging multidrug resistant clone

Abstract

Background

Salmonella 4,[5],12:i:-, a worldwide emerging pathogen that causes many foodborne outbreaks mostly attributed to pig and pig products, is expanding in the U.S.

Methods

Whole genome sequencing was applied to conduct multiple comparisons of 659 S. 4,[5],12:i:- and 325 S. Typhimurium from different sources and locations (i.e. U.S. and Europe) to assess their genetic heterogeneity, with a focus on strains recovered from swine in the U.S. Midwest. In addition, presence of resistance genes and other virulence factors was detected and the antimicrobial resistance phenotype of 50 and 22 isolates of livestock and human origin, respectively, was determined.

Results

The S. 4,5,12:i:- strains formed two main clades regardless of their source and geographical origin. Most (84%) of the U.S. isolates recovered in 2014–2016, including those (50/51) recovered from swine in the U.S. Midwest, were part of an emerging clade. In this clade, multiple genotypic resistance determinants were predominant, including resistance against ampicillin, streptomycin, sulphonamides and tetracyclines (ASSuT). Phenotypic resistance to enrofloxacin (11/50) and ceftiofur (9/50) was found in conjunction with the presence of plasmid-mediated resistance genes (qnrB19/qnrB2/qnrS1 and bla_CMY-2/bla_SHV-12, respectively). Also, higher similarity was found between S. 4,[5],12:i:- from the emerging clade and S. Typhimurium from Europe than with S. Typhimurium from the U.S.

Conclusions

Salmonella 4,[5],12:i:- currently circulating in swine in the U.S. Midwest are likely part of an emerging multidrug resistant clade first reported in Europe, and can carry plasmid-mediated resistance genes that may be transmitted horizontally to other bacteria and thus could represent a public-health concern.