Discovery and whole genome sequencing of a human clinical isolate of the novel species Klebsiella quasivariicola sp. nov.

Abstract

Originally thought to be a single species, Klebsiella pneumoniae has been divided into three distinct species: K. pneumoniae, K. quasipneumoniae and K. variicola. In a recent study of 1,777 extended-spectrum beta-lactamase (ESBL)-producing Klebsiella strains recovered from human infections in Houston, we discovered one strain (KPN1705) causing a wound infection that was phylogenetically distinct from all currently recognized Klebsiella species. Whole genome sequencing of strain KPN1705 revealed that it was single locus variant of the multilocus sequence type ST-1155. This sequence type was reported only once previously. To further investigate the phylogeny of these two organisms, we sequenced the genome of strain KPN1705 to closure and compared its genetic features to Klebsiella reference strains. Results demonstrated strain KPN1705 extensively shares core gene content, antimicrobial resistance genes, and plasmids with K. pneumoniae, K. quasipneumoniae and K. variicola. Since strain KPN1705 and the previously reported novel strain are phylogenetically most closely related to K. variicola, we propose the name K. quasivariicola sp. nov.