Isolation of a novel species in the genus Cupriavidus from a patient with sepsis using whole genome sequencing

Abstract

Whole genome sequencing (WGS) has become an accessible tool in clinical microbiology, and it allowed us to identify a novel Cupriavidus species. We isolated Gram-negative bacillus from the blood of an immunocompromised patient, and phenotypical and molecular identifications were performed. Phenotypic identification discrepancies were noted between the Vitek 2 (bioMérieux, Marcy-l’Étoile, France) and Vitek MS systems (bioMérieux). Using 16S rRNA gene sequencing, it was impossible to identify the pathogen to the species levels. WGS was performed using the Illumina MiSeq platform (Illumina, San Diego, CA), and genomic sequence database searching with a TrueBacTM ID-Genome system (ChunLab, Inc., Seoul, Republic of Korea) showed no strains with average nucleotide identity values higher than 95.0%, which is the cut-off for species-level identification. Phylogenetic analysis indicated that the bacteria was a new Cupriavidus species that formed a subcluster with Cupriavidus gilardii. WGS holds great promise for accurate molecular identification beyond 16S rRNA gene sequencing in clinical microbiology.