Re-updating the taxonomy of Kluyvera genus for a better understanding of CTX-M ß-lactamase origin.

ABSTRACT

The taxonomic definitions within the Kluyvera genus are still unclear, as several deposits might belong to misidentified species or genus or genome assemblies comprehend large indeterminate nucleotide zones. In this study, we performed a comparative phylogenomic analysis of Kluyvera chromosomes and other selected Enterobacterales. We also included the genomic analysis of chromosomal blaCTX-M/KLU from Kluyvera isolates and assigned the plasmid-encoded blaCTX/M genes. The study allowed us to propose a new Kluyvera genomospecies and to better define Kluyvera genomosp. 5. Two new CTX-M sub-groups could also be suggested. Even if no chromosomal blaCTX-M/KLU gene can be found in K. intermedia and Kluyvera genomosp. 6, accurate identification can be achieved by using these gene sequences in the remaining strains.IMPORTANCEThe use of whole-genome sequencing (WGS) accelerated the identification of new Kluyvera species proposals, but a rigorous analysis of these sequences is needed for a better definition, including preexisting, and even established species. Kluyvera genomosp. 5 could be more clearly defined, and, among isolates that do not produce a chromosome-encoded CTX-M enzyme, true K. intermedia should be kept within the genus as well as a new genomospecies (Kluyvera genomosp. 6) different from K. intermedia. We could clean up true Kluyvera from those that deserved transfer to other genera, and some deposits as K. ascorbata, K. cryocrescens, K. georgiana, and several Kluyvera sp. to the real species. Two new sub-groups of CTX-M enzymes could be proposed. The accurate identification of the chromosome-encoded blaCTX-M/KLU gene in Kluyvera isolates could be a useful taxonomic tool to guide the species classification.