KoSC isolates for cgMLST establishment

The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic resistant strains, that recently caused 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 is of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least 6 closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify clusters within these species whole genome sequencing is necessary. The resolution is achievable with core genome MLST extending typing of a few housekeeping genes to thousands of core genome genes. Opposed to SNP calling approaches cgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange. We established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks.