Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.

Rodrigues, Carla; Passet, Virginie; Rakotondrasoa, Andriniaina; Diallo, Thierno Abdoulaye; Criscuolo, Alexis; Brisse, Sylvain

doi:10.1016/j.resmic.2019.02.003

Cited by 105 publications

(73 citation statements)

References 24 publications

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“…We therefore aimed to develop a novel real-time PCR assay, and used an intergenic region located adjacent to the previously proposed target gene khe . Using well-defined reference strains representative of current taxonomy (20, 31, 32), we show that the novel ZKIR PCR real-time assay allows the accurate detection of all members of the Kp complex. We found complete specificity and sensitivity ( i.e ., phylogenetic coverage) of this assay based on our reference strains panel.…”

Section: Discussionmentioning

confidence: 99%

“…The phylogenetic distribution of molecular targets that were previously described in the literature for Kp detection, were investigated in silico . All available Klebsiella genomes were downloaded from the NCBI database (February 2018) and combined with the ones of Institut Pasteur’s internal reference collection (n=66) (20, 31, 32), representing a total of 4,222 genomes which included Klebsiella species and closely related Raoultella species. The average nucleotide identity (ANI) metric was used to classify the genomes in each of the phylogroups.…”

Section: Methodsmentioning

confidence: 99%

“…variicola (Kp3) and subsp. tropica (Kp5)], ‘ K. quasivariicola’ (Kp6) and K. africana (Kp7) (8, 18–20). Most of these taxa are still often misidentified as “ K. pneumoniae” or “K.…”

Section: Introductionmentioning

confidence: 99%

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The ZKIR Assay, a novel Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

Barbier

Rodrigues

Depret

et al. 2019

Preprint

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Klebsiella pneumoniae (Kp) is of growing public health concern due to the emergence of strains that are multidrug-resistant, virulent, or both. Taxonomically, Kp includes seven phylogroups, with Kp1 (K. pneumoniae sensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here we analysed 4222 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR assay, was developed and used to detect Kp in 96 environmental samples. Results were compared to a culture-based method using SCAI agar medium coupled to MALDI-TOF mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10-1 CFU g-1 after enrichment for 24 h in LB supplemented with ampicillin, and 1.5 × 103 to 1.5 × 104 CFU g-1 directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 MLST sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific and sensitive novel method to detect the presence of Kp in complex matrices, and indicates that Kp isolates from environmental samples differ from clinical isolates.IMPORTANCEThe Klebsiella pneumoniae species complex (Kp) includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR, which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content, from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The ZKIR Assay, a novel Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

Barbier

Rodrigues

Depret

et al. 2019

Preprint

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“…The members of Klebsiella and Raoultella are rod-shaped, Gram-negative and capsule-forming bacteria. Recently, four novel species of the genus have been described viz., Klebsiella michiganensis [3], Klebsiella quasipneumoniae [4], Klebsiella africana [5] and Klebsiella huaxiensis [6]. The strains previously identified as Klebsiella oxytoca phylogroup Ko6 have been reclassified into a new species Klebsiella grimontii [7], Ko3 as Klebsiella spallanzanii and Ko4 as Klebsiella pasteurii [8].…”

Section: Introductionmentioning

confidence: 99%

“…The strains previously identified as Klebsiella oxytoca phylogroup Ko6 have been reclassified into a new species Klebsiella grimontii [7], Ko3 as Klebsiella spallanzanii and Ko4 as Klebsiella pasteurii [8]. Members of this genus have been isolated from varied sources including clinical specimens [4][5][6][7][8], soil [9,10], water samples [11], household toothbrush holder [3] and mammalian gut [12].…”

Section: Introductionmentioning

confidence: 99%

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

Gujarati

Chaudhari

Hagir

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A novel bacterial strain, designated TOUT106T, was isolated from the surface of a tomato. The cells were rod-shaped, Gram-negative, encapsulated and non-motile. Strain TOUT106T grows best at 28 °C and pH 7.0 and can tolerate up to 2 % (w/v) NaCl. Based on 16S rRNA gene phylogeny, strain TOUT106T was placed close to the Salmonella clade, with close similarity to Salmonella enterica subsp. arizonae strain NCTC 8297T (98.42 %). Results of genome-based phylogenetic analysis revealed that strain TOUT106T is placed well in the Klebsiella–Raoultella clade, by forming a distinct branch with Klebsiella michiganensis DSM25444T, Klebsiella oxytoca NCTC132727T, Klebsiella grimontii 06D021T and Klebsiella pasteurii SB6412T. The genomic DNA G+C content of strain TOUT106T is 53.53 mol%. The average nucleotide identity values of TOUT106T were less than 86.5 % with closely related members of the family Enterobacteriaceae . The major fatty acids of strain TOUT106T were C16 : 0, C17:0 cyclo, C14:0 3OH/C16:1 iso, C14 : 0, C19:0 cyclo ω8c, C18:1 ω6c/C18:1 ω7c, C12 : 0 and C16:1 ω7c/C16:1 ω6c. Strain TOUT106T showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS compared to its closest relatives. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain TOUT106T could be distinguished from the recognized species of the genus Klebsiella . It is suggested to represent a novel species of this genus, for which the name Klebsiella indica sp. nov. is proposed. The type strain is TOUT106T (=MCC 2901T=KACC 21384T=JCM 33718T).

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Klebsiella

Rahi,

Rodrigues,

Brisse

2024

Bergey's Manual of Systematics of Archaea and Bacteria

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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).

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Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.

Cited by 105 publications

References 24 publications

The ZKIR Assay, a novel Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

The ZKIR Assay, a novel Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

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

Klebsiella

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