Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping.

Brisse, Sylvain; Verhoef, J.

doi:10.1099/00207713-51-3-915

Cited by 240 publications

(240 citation statements)

References 39 publications

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“…This finding is in accordance with the study of Brisse et al (2001), which had shown, using other genes (namely gyrA and parC) and different typing methods (RAPD and ribotyping), that six clinical isolates of K. oxytoca and reference strain K. oxytoca NCTC 49131 were classified into two clusters. The new relevant point in our study is the demonstration that this genetic delineation was also obtained from the chromosomal b-lactamase gene of K. oxytoca, which does not belong to the housekeeping gene family.…”

Section: Oxy-2 Groupssupporting

confidence: 78%

Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal β-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing

Granier

Plaisance

Leflon‐Guibout

et al. 2003

International Journal of Systematic and Evolutionary Microbiology

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Section: Oxy-2 Groupssupporting

confidence: 78%

Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal β-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing

Granier

Plaisance

Leflon‐Guibout

et al. 2003

International Journal of Systematic and Evolutionary Microbiology

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“…Notably, all the publicly available genomes of K. pneumoniae clinical isolates that we analyzed, including the K. pneumoniae subsp. rhinoscleromatis reference genome, clustered within KpI (15).…”

Section: Resultsmentioning

confidence: 99%

“…Although it is clear that K. pneumoniae is genetically and phenotypically diverse (12,13), previous efforts to identify specific features that can distinguish human clinical isolates from plant, animal, or environmental isolates have yielded no markers of humanspecific lineages (14). Three distinct phylogroups of K. pneumoniaeKpI, KpII, and KpIII-have been defined based on sequencing of a small number of genes (15,16), and it has been proposed that these phylogroups be redesignated as distinct species, namely, K. pneumoniae (KpI), K. quasipneumoniae (KpII) (17), and K. variicola (KpIII) (18); however, all three cause infections in humans (15,19).…”

Section: Significancementioning

confidence: 99%

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

Holt

Wertheim

Zadoks

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

1,042

1,123

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Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

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“…For instance, sequences of seven housekeeping genes, i.e., rpoB, gapA, mdh, pgi, phoE, infB and tonB, have been successfully used to develop a MLST scheme for K. pneumoniae (Diancourt et al 2005). On the other hand, the identification of K. pneumoniae strains were generally confirmed in more simple ways, e.g., by rpoB and/or gyrA gene sequences (Brisse and Duijkeren 2005;Brisse and Verhoef 2001;Brisse et al 2004). Subsequently, the rpoB gene, encoding the bsubunit of RNA polymerase, has emerged as a core gene candidate for phylogenetic analyses allowing discrimination of closely related isolates (Adékambi et al 2009;Martínez et al 2004;Mollet et al 1997).…”

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

show abstract

Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping.

Cited by 240 publications

References 39 publications

Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal β-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing

Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal β-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

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

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