Klebsiella indica sp. nov., isolated from the surface of a tomato

Bacterial genomics is making an increasing contribution to the fields of medicine and public health microbiology. Consequently, accurate species identification of bacterial genomes is an important task, particularly as the number of genomes stored in online databases increases rapidly and new species are frequently discovered. Existing database entries require regular re-evaluation to ensure that species annotations are consistent with the latest species definitions. We have developed an automated method for bacterial species identification that is an extension of ribosomal multilocus sequence typing (rMLST). The method calculates an ‘rMLST nucleotide identity’ (rMLST-NI) based on the nucleotides present in the protein-encoding ribosomal genes derived from bacterial genomes. rMLST-NI was used to validate the species annotations of 11839 publicly available Klebsiella and Raoultella genomes based on a comparison with a library of type strain genomes. rMLST-NI was compared with two whole-genome average nucleotide identity methods (OrthoANIu and FastANI) and the k-mer based Kleborate software. The results of the four methods agreed across a dataset of 11839 bacterial genomes and identified a small number of entries (n=89) with species annotations that required updating. The rMLST-NI method was 3.5 times faster than Kleborate, 4.5 times faster than FastANI and 1600 times faster than OrthoANIu. rMLST-NI represents a fast and generic method for species identification using type strains as a reference.

show abstract

“… K. indica was defined in 2020 from the surface of a tomato collected in a vegetable market in India (sampled in 2014) [ 42 ].…”

Section: Introductionmentioning

confidence: 99%

Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation

et al. 2022

View full text Add to dashboard Cite

show abstract

Klebsiella

Rahi,

Rodrigues,

Brisse

2024

Bergey's Manual of Systematics of Archaea and Bacteria

View full text Add to dashboard Cite

Klebs.i.el' la . N.L. fem. dim. n. Klebsiella , named after Edwin Klebs (1834–1913), a German bacteriologist. Pseudomonadota / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Klebsiella Cells are Gram‐stain‐negative straight rods (0.3–1.0 × 0.6–6.0 μm), mostly nonmotile (except K. aerogenes ), and are capsulated. Grow on a variety of growth media including meat extract media (except K. granulomatis , which has not been cultured). Colonies are smooth, circular, more or less dome shaped, and glistening of varying degrees of stickiness, depending on the strain and the composition of the medium. Klebsiella are cytochrome oxidase‐negative, mesophilic, and facultatively anaerobic, having both a respiratory and a fermentative type of metabolism. The majority of Klebsiella fail to grow at 10 and 45°C, while the type strains of K. oxytoca , K. planticola , K. terrigena , K. ornithinolytica , K. michiganensis , and K. variicola show growth at 10°C. Klebsiella are usually positive for Voges–Proskauer test, except strains of K. spallanzanii , K. indica , and K. huaxiensis . Most Klebsiella members hydrolyze urea. Based on genomic sequence‐based phylogenetic analyses, Klebsiella species form higher‐level groups, called the K. pneumoniae species complex (KpSC), K. oxytoca species complex (KoSC), and K. planticola species complex (KplanSC). Additional species complexes may be defined in the future to accommodate other species such as K. aerogenes , K. terrigena , and K. indica . Some Klebsiella strains fix atmospheric nitrogen. Members of Klebsiella are considered ubiquitous and have been isolated from diverse sources including clinical specimens from humans and animals (e.g., cows, horses, and swine, monkeys), the mammalian gut, household items, soil, water, and plants. All Klebsiella species are considered opportunistic pathogens, except for a few specific pathovars, and may harbor a variety of antimicrobial resistance genes. Some strains of the KpSC, called hypervirulent strains, and some toxigenic strains of the KoSC are considered true pathogens. DNA G + C content (mol%) : 53–58 ( T m ). Type species : Klebsiella pneumoniae Trevisan 1887 AL (basonym: Hyalococcus pneumoniae Schroeter 1886).

show abstract

Metabacillus rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants

Wang

et al. 2022

Curr Microbiol

View full text Add to dashboard Cite

Klebsiella indica sp. nov., isolated from the surface of a tomato

Cited by 11 publications

References 30 publications

Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation

Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation

Klebsiella

Metabacillus rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants

Contact Info

Product

Resources

About