Campos-Madueno, Edgar I.; Moser, Aline I.; Jost, Géraldine; Maffioli, Carola; Bodmer, Thomas; Perreten, Vincent; Endimiani, Andrea (2022). Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: Human and non-human settings may share high-risk clones. Journal of global antimicrobial resistance, 28, pp. 206-215. Elsevier 10.1016/j.jgar.2022.01.016
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Background: The spread of carbapenemase-producing K. pneumoniae (CP-Kp) strains belonging to high-risk sequence types (STs) is a concern. For Switzerland, national data about the molecular features (especially the STs) of the CP-Kp of human origin is not available, while in veterinary clinics ST11 and ST307 blaOXA-48-possessing Kp strains have been recently reported.
Methods: We analyzed a collection of 285 Kp genomes (170 were CP-Kp) isolated in Switzerland from human and non-human sources during 2006-2020. Whole-genome sequencing, core genome phylogenies and public databases were implemented to present a detailed overview regarding their carbapenemases, STs, and plasmids.
Results: The top 5 STs were (main carbapenemase gene): ST512 (blaKPC-3), ST258 (blaKPC-2) and ST101 (blaOXA-48) consisting of strains of human origin only, ST11 (blaOXA-48) and ST307 (blaOXA-48) strains isolated from human, animal, and environmental sources. However, during 2016-2020, the main STs for CP-Kp were ST11 (17.6%), ST307 and ST101 (both 14.7%), while ST258 (5.9%) and ST512 (4.4%) significantly declined. Most of the carbapenemase genes were carried on plasmids already described. Core genome analysis revealed that ST11 Kp of animal and human origins were closely-related, while those of ST307 were distant.
Conclusions: We described, for the first time, the features of the CP-Kp circulating in Switzerland among human and non-human settings. Our genomic analysis revealed that the emerging high-risk ST11 and ST307 lineages were often isolated from non-human settings. This study provided a baseline for further WGS-based One-Health surveillance of CP-Kp and emphasized the need of metadata to track dissemination routes between the different settings.
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