Characterization of by Whole-Genome Sequencing from a Clinical Sample: New Challenges in Identification.

The genus encompasses metabolically versatile bacteria widely distributed in diverse environments, including clinical settings. Among these, is a recently described environmental species with limited clinical characterization. In this study, we report the genomic and phenotypic characterization of a isolate, Pam1317368, recovered from a catheterized urine sample of a post-renal transplant patient without symptoms of urinary tract infection. Initial identification by MALDI-TOF MS misclassified the isolate as . Whole-genome sequencing and average nucleotide identity (ANI) analysis (≥95%) confirmed its identity as . The methodology included genomic DNA extraction, Illumina sequencing, genome assembly, ANI calculation, antimicrobial susceptibility testing, resistance gene identification and phylogenetic analysis. Antimicrobial susceptibility testing revealed multidrug resistance, including carbapenem resistance mediated by the metallo-β-lactamase gene . Additional resistance determinants included genes conferring resistance to fluoroquinolones and aminoglycosides. Phylogenetic analysis placed the isolate within the clade, closely related to environmental strains. Although the clinical significance of this finding remains unclear, the presence of clinically relevant resistance genes in an environmental species isolated from a human sample highlights the value of genomic surveillance and accurate species-level identification in clinical microbiology.