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

Backgoround: The genus Pseudomonas encompasses metabolically versatile bacteria widely distributed in diverse environments, including clinical settings. Among these, Pseudomonas kurunegalensis is a recently described environmental species with limited clinical characterization. Objective and

Methods

In this study, we report the genomic and phenotypic characterization of a P. kurunegalensis 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 Pseudomonas monteilii. Whole-genome sequencing and average nucleotide identity (ANI) analysis (≥95%) confirmed its identity as P. kurunegalensis. The methodology included genomic DNA extraction, Illumina sequencing, genome assembly, ANI calculation, antimicrobial susceptibility testing, resistance gene identification and phylogenetic analysis.

Results

Antimicrobial susceptibility testing revealed multidrug resistance, including carbapenem resistance mediated by the metallo-β-lactamase gene VIM-2. Additional resistance determinants included genes conferring resistance to fluoroquinolones and aminoglycosides. Phylogenetic analysis placed the isolate within the P. kurunegalensis clade, closely related to environmental strains.

Conclusions

Although the clinical significance of this finding remains unclear, the presence of clinically relevant resistance genes in an environmental Pseudomonas species isolated from a human sample highlights the value of genomic surveillance and accurate species-level identification in clinical microbiology.