Genomic identification of nitrogen‐fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae

Abstract

It was difficult to differentiate Klebsiella pneumoniae, K. quasipneumoniae and K. variicola by biochemical and phenotypic tests. Genomics increase the resolution and credibility of taxonomy for closely-related species. Here, we obtained the complete genome sequence of the K. variicola type strain DSM 15968(T) (=F2R9(T)). The genome of the type strain is a circular chromosome of 5,521,203 bp with 57.56% GC content. From 540 Klebsiella strains whose genomes had been publicly available as at 3 March 2015, we identified 21 strains belonging to K. variicola and 8 strains belonging to K. quasipneumoniae based on the genome average nucleotide identities (ANI). All the K. variicola strains, one K. pneumoniae strain and five K. quasipneumoniae strains contained nitrogen-fixing genes. A phylogenomic analysis showed clear species demarcations for these nitrogen-fixing bacteria. In accordance with the key biochemical characteristics of K. variicola, the idnO gene encoding 5-keto-D-gluconate 5-reductase for utilization of 5-keto-D-gluconate and the sorCDFBAME operon for catabolism of L-sorbose were present whereas the rbtRDKT operon for catabolism of adonitol was absent in the genomes of K. variicola strains. Therefore, the genomic analyses supported the ANI-based species delineation; the genome sequence of the K. variicola type strain provides the reference genome for genomic identification of K. variicola, which is a nitrogen-fixing species.

Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans

“…We used an rpoB gene phylogenetic analysis and the results were validated by ANI. We identified the isolates misclassified previously described 5 and identified new isolates that corresponded to K. variicola and K. quasipneumoniae that were deposited as K. pneumoniae. Likewise, we identified one K. variicola genome misclassified that corresponds to K. quasipneumoniae subsp.…”

“…3,4 Subsequently by K. quasipneumoniae and other K. variicola genomes the misclassification was evidenced by Average Nucleotide Identity (ANI). 5 The aim of this work was detect misclassified K. variicola and K. quasipneumoniae genomes. We used an rpoB gene phylogenetic analysis and the results were validated by ANI.…”

Isolation and characterization of heterotrophic nitrifying and aerobic denitrifying Klebsiella pneumoniae and Klebsiella variicola strains from various environments

“…Furthermore, there is evidence to suggest the previous misclassification of K. variicola , i.e., there are numerous cases K. variicola misclassified as K. pneumoniae (Chen et al . ; Long et al . ).…”

Atypical Klebsiella Species in a Third Level Hospital as Cause of Neonatal Infection

“…This becomes more relevant because K. pneumoniae, K. variicola, and K. quasipneumoniae are difficult to differentiate phenotypically, leading to misinterpretation of their infection prevalence (6,15,16). In fact, to our knowledge, there is no biochemical test capable of differentiating these 3 Klebsiella species concomitantly during routines in clinical microbiology laboratories.…”

“…quasipneumoniae (KpII-A), K. quasipneumoniae subspp. similipneumoniae (KpII-B), and K. variicola (KpIII) (6). At present, K. oxytoca can cause infection in healthcare settings, with outbreaks of multidrug-resistant infection being increasingly reported in hospitalized patients (7)(8)(9)(10)(11)(12).…”