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

The taxonomic definitions within the 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 chromosomes and other selected . We also included the genomic analysis of chromosomal from isolates and assigned the plasmid-encoded genes. The study allowed us to propose a new genomospecies and to better define genomosp. 5. Two new CTX-M sub-groups could also be suggested. Even if no chromosomal gene can be found in and 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 species proposals, but a rigorous analysis of these sequences is needed for a better definition, including preexisting, and even established species. genomosp. 5 could be more clearly defined, and, among isolates that do not produce a chromosome-encoded CTX-M enzyme, true should be kept within the genus as well as a new genomospecies ( genomosp. 6) different from . We could clean up true from those that deserved transfer to other genera, and some deposits as , , , and several sp. to the real species. Two new sub-groups of CTX-M enzymes could be proposed. The accurate identification of the chromosome-encoded gene in isolates could be a useful taxonomic tool to guide the species classification.