Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden

Abstract

The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.

Virulence Determinants and Genetic Diversity of Yersinia Species Isolated from Retail Meat

“…ST18 was isolated from clinical cases in Sweden, Germany, New Zealand, France, the United Kingdom and Brazil [26,53,56,63]. ST18 was identified in pigs, dogs and bovine sources [53]. In general, the present study confirmed that Y. enterocolitica STs 12 and 18 were associated with pathogenic Y. enterocolitica 4/O:3 and 2/O:9 bioserovars.…”

“…Additionally, resistance to neomycin, streptomycin, tetracycline, chloramphenicol, cephalosporins and carbapenems was reported, which indicates the potential for the development of antimicrobial resistance in Y. enterocolitica. The occurrence of antimicrobial resistance in Y. enterocolitica in meats may be attributed to applications in animals; thus, the antimicrobial resistance in Y. enterocolitica should be monitored [49,52,53].…”

“…Plasmid and chromosomal virulence genes are important for the full pathogenicity of Y. enterocolitica. yadA and virF are present in pathogenic strains and located at the virulence plasmid, and are crucial for adherence, the transcriptional activity of yop and yadA and invasion into the host cell [20,53]. Strains of pathogenic bioserotype 1B/O:8 from pork were reported to be ail, ystA and virulence plasmid negative due to the apparent loss of pYV [55,56].…”

“…Out of the STs associated with pathogenic Y. enterocolitica, ST18 was reported to correspond to 4/O:3 and ST12 to biotype 2-3/O:9 [62]. ST18 was isolated from clinical cases in Sweden, Germany, New Zealand, France, the United Kingdom and Brazil [26,53,56,63]. ST18 was identified in pigs, dogs and bovine sources [53].…”

Prudent Antimicrobial Use Is Essential to Prevent the Emergence of Antimicrobial Resistance in Yersinia enterocolitica 4/O:3 Strains in Pigs

“…This pattern appears to be common in Y. enterocolitica strains in several European countries ( Baumgartner et al, 2007 ; Sihvonen et al, 2011 ; Bonardi et al, 2014 , 2016 ). Karlsson et al (2021) reported a chromosomally encoded multi-drug resistance cassette containing resistance genes to these three types of antimicrobials and mercury.…”