Molecular Characterization of Multidrug-Resistant From Foodborne Outbreaks in Sweden.

The foodborne pathogen 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 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 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 (), streptomycin (), sulfonamides (), and a mercury resistance module. This chromosomally encoded Tn transposon has previously been reported associated with IncFII plasmids in : a clinical isolate from Japan in 1950s, a outbreak from Australia in 1997, and serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with B (encoding an ABC transporter), , and its own ORI and ORIt sites, sharing high homology with small B- plasmids from . This is the first time that Tn and plasmids have been reported in . Taken together, our study showed that the Swedish 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.