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

• Published in: Infection, genetics and evolution genetics and evolution, 2024-09, Vol.123, p.105652, Article 105652
• Main Authors: Stevens, Marc J.A., Horlbog, Jule Anna, Diethelm, Andrea, Stephan, Roger, Nüesch-Inderbinen, Magdalena
• Format: Article
• Language: English
• Subjects: Phylogeny; Resistance; Virulence; Whole-genome sequencing; Yersinia enterocolitica; Yersiniosis
• ISSN: 1567-1348; 1567-7257; 1567-7257
• DOI: 10.1016/j.meegid.2024.105652

We aimed to characterise Yersinia enterocolitica from human clinical specimens in Switzerland using epidemiological, microbiological and whole-genome sequencing (WGS) data. 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. 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/O:3 (44%), biotype 1A (34%), bioserotype 2/O:9 (21%), and bioserotype 3/O:3 (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/O:9 strains were all ST12 and clustered closely, and BT 4/O:3 strains mostly belonged to ST18 but were more diverse. SNP analysis revealed two highly clonal BT 4/O:3 subpopulations with wide spatio-temporal distribution. Y. enterocolitica BT 1A, BT 2/O:9 and BT 4/O:3 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. •Whole genome sequencing proved a powerful tool to subtype Yersinia enterocolitica.•Y. enterocolitica BT 1A strains were genetically highly diverse.•Y. enterocolitica BT 2/O:3 strains were all ST12 and clustered closely.•Y. enterocolitica BT 4/O:3 strains mostly belonged to ST18 but were more diverse.•Two highly clonal BT 4/O:3 subpopulations had wide spatio-temporal distribution.