Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov.

Drancourt, Michel; Bollet, C.; Carta, Anne; Rousselier, P.

doi:10.1099/00207713-51-3-925

Cited by 422 publications

(327 citation statements)

References 41 publications

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“…For instance, the sequencing of the 16S rRNA gene has been widely used accurate species identification up to the genus level (Harris and Hartley 2003), including Klebsiella species (e.g., Drancourt et al 2001). Housekeeping genes are very useful in developing multilocus sequence typing (MLST) scheme for discriminating K. pneumoniae, which further provides unambiguous data useful for the epidemiology of K. pneumoniae.…”

Section: Introductionmentioning

confidence: 99%

Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

Guo

Shifei

et al. 2016

Antonie van Leeuwenhoek

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The present work aimed to evaluate 16S rRNA, khe and rpoB gene sequencing for the identification of Klebsiella pneumoniae in comparison with phenotypic methods. Fifteen clinical isolates were examined, which were initially identified as K. pneumoniae subsp. pneumoniae using the automated VITEK 32 system in two hospitals in Enshi City, China. Their identity was further supported by conventional phenotypic methods on the basis of morphological and biochemical characteristics. Using Bayesian phylogenetic analyses and haplotypes network reconstruction, 13 isolates were identified as K.pneumoniae, whereas the other two isolates (K19, K24) were classified as Shigella sp. and Enterobacter sp., respectively. Of the three genes, 16S rRNA and khe gene could discriminate the clinical isolates at the genus level, whereas rpoB could discriminate Klebsiella at the species and even subspecies level. Overall, the gene tree based on rpoB is more compatible with the currently accepted classification of Klebsiella than those based on 16S rRNA and khe genes, showing that rpoB can be a powerful tool for identification of K. pneumoniae isolates. Above all, our study challenges the utility of khe as a species-specific marker for identification of K. pneumoniae.Electronic supplementary material The online version of this article

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Section: Introductionmentioning

confidence: 99%

Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

Guo

Shifei

et al. 2016

Antonie van Leeuwenhoek

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“…Raoultella terrigena and R. planticola were considered Klebsiella species until they were renamed in 2001 (10). Phenotypic methods that are used in clinical laboratories in human medicine also fail to differentiate Raoultella spp.…”

Section: Vol 45 2007mentioning

confidence: 99%

Molecular Epidemiology of TwoKlebsiella pneumoniaeMastitis Outbreaks on a Dairy Farm in New York State

et al. 2007

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Klebsiella spp. have become an important cause of clinical mastitis in dairy cows in New York State. We describe the occurrence of two Klebsiella mastitis outbreaks on a single dairy farm. Klebsiella isolates from milk, feces, and environmental sources were compared using random amplified polymorphic DNA (RAPD)-PCR typing. The first mastitis outbreak was caused by a single strain of Klebsiella pneumoniae, RAPD type A, which was detected in milk from eight cows. RAPD type A was also isolated from the rubber liners of milking machine units after milking of infected cows and from bedding in the outbreak pen. Predominance of a single strain could indicate contagious transmission of the organism or exposure of multiple cows to an environmental point source. No new cases with RAPD type A were observed after implementation of intervention measures that targeted the prevention of transmission via the milking machine as well as improvement of environmental hygiene. A second outbreak of Klebsiella mastitis that occurred several weeks later was caused by multiple RAPD types, which rules out contagious transmission and indicates opportunistic infections originating from the environment. The diversity of Klebsiella strains as quantified with Simpson's index of discrimination was significantly higher for isolates from fecal, feed, and water samples than for isolates from milk samples. Several isolates from bedding material that had the phenotypic appearance of Klebsiella spp. were identified as being Raoultella planticola and Raoultella terrigena based on rpoB sequencing.

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“…For example, the type strain of Mangrovibacter plantisponsor (Rameshkumar et al, 2010) shares 97.2 % 16S rRNA gene sequence similarity with Cronobacter muytjensii E603 T . Moreover, the type strains of the type species of Klebsiella and Raoultella, which were described as two different genera (Drancourt et al, 2001), share 98.0 % 16S rRNA gene sequence similarity. Thus, it is probable that strains 8N4 T , 9N2 and 10N3 represent a novel species in a novel genus (Fig.…”

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confidence: 99%

Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar

Halpern

Fridman

Atamna-Ismaeel

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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Gram-negative, rod-shaped, oxidase-negative, facultatively anaerobic, yellow–orange-pigmented and motile bacterial strains, designated 8N4T, 9N2 and 10N3, were isolated from flower nectar of Amygdalus communis (almond) and Citrus paradisi (grapefruit). The 16S rRNA gene sequences of the strains shared highest sequence similarity of 97.0 % with that of Phaseolibacter flectens ATCC 12775T and lower similarity with sequences from other type strains of genera of the Enterobacteriaceae . A polyphasic approach that included determination of phenotypic properties and phylogenetic analysis based on 16S rRNA, gyrB, rpoB and atpD gene sequences supported the classification of strains 8N4T, 9N2 and 10N3 within a novel species in a novel genus in the family Enterobacteriaceae . Strain 8N4T, and the reference strains of the novel species, grew at 4–35 °C (optimum, 28–30 °C), with 0–5.0 % NaCl (optimum, 3 % NaCl) and with 0–60 % sucrose (optimum, 10–25 % sucrose). Their major cellular fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain 8N4T was 46.8 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the floral nectar isolates are classified within a novel species in a new genus in the family Enterobacteriaceae , for which the name Rosenbergiella nectarea gen. nov., sp. nov. is proposed. The type strain of Rosenbergiella nectarea is 8N4T ( = LMG 26121T = DSM 24150T).

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Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov.

Cited by 422 publications

References 41 publications

Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

Molecular Epidemiology of TwoKlebsiella pneumoniaeMastitis Outbreaks on a Dairy Farm in New York State

Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar

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