Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic species complex.
Johanna Dabernig-Heinz, Gabriel E Wagner, Karola Prior, Michaela Lipp, Sabine Kienesberger, Werner Ruppitsch, Torunn G R��nning, Dag Harmsen, Ivo Steinmetz, Eva Leitner
Author Information
Johanna Dabernig-Heinz: Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria. ORCID
Gabriel E Wagner: Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria. ORCID
Karola Prior: Department of Periodontology and Operative Dentistry, University Hospital M��nster, M��nster, Germany.
Michaela Lipp: Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
Sabine Kienesberger: Institute of Molecular Biosciences, University of Graz, Graz, Austria. ORCID
Werner Ruppitsch: Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria. ORCID
Torunn G R��nning: Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.
Dag Harmsen: Department of Periodontology and Operative Dentistry, University Hospital M��nster, M��nster, Germany.
Ivo Steinmetz: Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria. ORCID
Eva Leitner: Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
The environmental bacterium displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.
