Characteristics and comparative genome analysis of Yersinia enterocolitica and related species associated with human infections in Switzerland 2019-2023.

ABSTRACT

PURPOSE: We aimed to characterise Yersinia enterocolitica from human clinical specimens in Switzerland using epidemiological, microbiological and whole-genome sequencing (WGS) data. METHODS: Isolates (n = 149) were collected between January 2019 and December 2023. Epidemiological data was noted and strains were characterized by biochemical and serological typing, antimicrobial susceptibility testing (AST), and WGS-based analysis. RESULTS: Most of the isolates (86%) were from stool specimens and 52% were from male patients. The patients' median age was 28 years (range < 1-94 years). Typing assigned the isolates to bioserotype 4/O3 (44%), biotype 1A (34%), bioserotype 2/O9 (21%), and bioserotype 3/O3 (1%). WGS identified Y. enterocolitica (n = 147), Y. alsatica (n = 1) and Y. proxima (n = 1). Seven isolates were multidrug resistant (MDR) and harboured plasmid pAB829 carrying aph(3″)-Ib, aph(6)-Id, and tet(Y) (n = 1), pAC120 carrying aph(6)-Id and tet(A) (n = 2), or a 12.6 kb Tn2670-like transposon containing catA1, aadA12, sul1, and qacEΔ1 (n = 4). Virulence factors (VFs) included ail (n = 99), invB, (n = 145), ystA (n = 99), ystB (n = 48) and pYV-associated VFs (n = 93). MLST and cgMLST analysis showed that BT 1A strains consisted of several STs and were highly diverse, whereas BT 2/O9 strains were all ST12 and clustered closely, and BT 4/O3 strains mostly belonged to ST18 but were more diverse. SNP analysis revealed two highly clonal BT 4/O3 subpopulations with wide spatio-temporal distribution. CONCLUSIONS: Y. enterocolitica BT 1A, BT 2/O9 and BT 4/O3 are frequently associated with human yersiniosis in Switzerland. WGS-based subtyping of Y. enterocolitica is a powerful tool to explore the genetic diversity and the pathogenic potential of human isolates.