Data from: Development and validation of a core genome multilocus sequence typing (cgMLST) scheme for Klebsiella oxytoca

The dataset hereby shared contains the genomes used to create and validate a newly proposed schema for Klebsiella oxytoca. As reference dataset, all publicly available K. oxytoca draft and complete genomes (199) were downloaded from RefSeq in NCBI database in September 2021. All assemblies were filtered by quality and identification methods in order to remove highly fragmented genomes (more than 200 contigs) and genomes that did not correspond to K. oxytoca sensu stricto. A series of assemblies, including complete and draft genomes, were removed because they (i) did not correspond to K. oxytoca species based on MLST or rMLST, and because they (ii) produced ANI values lower than 96% against K. oxytoca. Apart from some genomes that had no correspondence to K. oxytoca, several others were discarded because they did not correspond to K. oxytoca species sensu stricto, but other closely related species included in the K. oxytoca species complex, such as K. michiganensis or K. grimontii. Additional identification of blaOXY gene variants supported this observation. Finally, genomes that had not been assigned an assigned ST were also removed, since they would not contribute to the schema validation. Therefore, the final dataset consisted in 16 high-quality complete genomes of K. oxytoca sensu stricto.