Medizinische Universität Graz - Research portal
Selected Publication:
SHR Neuro Cancer Cardio Lipid Metab Microb
Dabernig-Heinz, J; Wagner, GE; Prior, K; Lipp, M; Kienesberger, S; Ruppitsch, W; Rønning, TG; Harmsen, D; Steinmetz, I; Leitner, E.
Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex.
J Clin Microbiol. 2024; 62(6):e0172523
Doi: 10.1128/jcm.01725-23
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- Leading authors Med Uni Graz
- Dabernig-Heinz Johanna
- Wagner-Lichtenegger Gabriel
- Co-authors Med Uni Graz
- Kienesberger-Feist Sabine
- Leitner-Meyer Eva
- Lipp Michaela
- Steinmetz Ivo
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- Abstract:
- The environmental bacterium Klebsiella oxytoca 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, K. oxytoca 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 til 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.
- Find related publications in this database (using NLM MeSH Indexing)
- Multilocus Sequence Typing - methods
- Klebsiella oxytoca - genetics, classification, isolation & purification
- Humans - administration & dosage
- Genome, Bacterial - genetics
- Phylogeny - administration & dosage
- Klebsiella Infections - microbiology
- Whole Genome Sequencing - administration & dosage
- Bacterial Typing Techniques - methods
- Genes, Essential - genetics
- Reproducibility of Results - administration & dosage
- Find related publications in this database (Keywords)
- cgMLST
- Klebsiella oxytoca
- nosocomial infections
- species complex
- resistance markers
- virulence markers
- molecular surveillance