The genome of a clinical<i>Klebsiella variicola</i>strain reveals virulence-associated traits and a pl9-like plasmid

Andrade, Bruno de Bezerril; Ramos, Nilcéia de Veiga; Marin, Michel F. Abanto; Fonseca, Érica L.; Vicente, Ana Carolina Paulo

doi:10.1111/1574-6968.12583

Cited by 33 publications

(28 citation statements)

References 18 publications

(19 reference statements)

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“…There is full support, with a bootstrap value of 1,000 for the group composed of the K. variicola isolates and K. pneumoniae 342. The K. pneumoniae 342 endophytic strain clearly is a strain of K. variicola ; this assumption was hypothesized when K. variicola was described as a new bacterial species [ 4 ] and was recently confirmed in other studies [ 9 , 20 , 21 ]. Thus, in the present study, this bacterium was considered to belong to the K. variicola species for the rest of the analysis.…”

Section: Resultsmentioning

confidence: 86%

Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola

Garza–Ramos¹,

Silva-Sánchez²,

Martı́nez-Romero

et al. 2015

BMC Microbiol

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BackgroundKlebsiella variicola was very recently described as a new bacterial species and is very closely related to Klebsiella pneumoniae; in fact, K. variicola isolates were first identified as K. pneumoniae. Therefore, it might be the case that some isolates, which were initially classified as K. pneumoniae, are actually K. variicola. The aim of this study was to devise a multiplex-PCR probe that can differentiate isolates from these sister species.ResultThis work describes the development of a multiplex-PCR method to identify K. variicola. This development was based on sequencing a K. variicola clinical isolate (801) and comparing it to other K. variicola and K. pneumoniae genomes. The phylogenetic analysis showed that K. variicola isolates form a monophyletic group that is well differentiated from K. pneumoniae. Notably, the isolate K. pneumoniae 342 and K. pneumoniae KP5-1 might have been misclassified because in our analysis, both clustered with K. variicola isolates rather than with K. pneumoniae. The multiplex-PCR (M-PCR-1 to 3) probe system could identify K. variicola with high accuracy using the shared unique genes of K. variicola and K. pneumoniae genomes, respectively. M-PCR-1 was used to assay a collection of multidrug-resistant (503) and antimicrobial-sensitive (557) K. pneumoniae clinical isolates. We found K. variicola with a prevalence of 2.1% (23/1,060), of them a 56.5% (13/23) of the isolates were multidrug resistant, and 43.5% (10/23) of the isolates were antimicrobial sensitive. The phylogenetic analysis of rpoB of K. variicola-positive isolates identified by multiplex-PCR support the correct identification and differentiation of K. variicola from K. pneumoniae clinical isolates.ConclusionsThis multiplex-PCR provides the means to reliably identify and genotype K. variicola. This tool could be very helpful for clinical, epidemiological, and population genetics studies of this species. A low but significant prevalence of K. variicola isolates was found, implying that misclassification had occurred previously. We believe that our multiplex-PCR assay could be of paramount importance to understand the population dynamics of K. variicola in both clinical and environmental settings.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0396-6) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 86%

Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola

Garza–Ramos¹,

Silva-Sánchez²,

Martı́nez-Romero

et al. 2015

BMC Microbiol

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“…13 Additionally, K. pneumoniae and K. variicola shared some virulence determinants that cause infections in humans. 14,15 Some Klebsiella isolates have been misclassified 16,17 and consequently the taxonomic descriptions of their genome sequences in NCBI repositories are inaccurate. Here we used correctly identified K. variicola and K. quasipneumoniae genomes for the comparison of virulence and plant colonization determinants of this genus of enterobacteria.…”

Section: Salud Pública De México / Vol 60 No 1 Enero-febrero De 2018mentioning

confidence: 99%

Klebsiella variicola and Klebsiella quasipneumoniae with capacity to adapt to clinical and plant settings

et al. 2017

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“…A total of 174 genes associated to virulence in Klebsiella were aligned with the metagenome assembly using blastn (29–35). According to it, 38 putative virulence genes were found in the metagenome assembly using as selection criteria an identity up to 95% throughout all the gene sequence (Table 3), of which 22 correspond to K. variicola , 15 belong to K. pneumoniae and 1 to K. aerogenes .…”

Section: Resultsmentioning

confidence: 99%

Nitrogen-fixing Klebsiella variicola in feces from herbivorous tortoises

Montes-Grajales

Jiménez

Rogel

et al. 2019

Preprint

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2 25 Abstract 26 Animals feeding on plants (herbivorous) may have nutritional deficiencies and 27 use bacterial nitrogen fixation in guts to compensate unbalanced diets with high carbon 28 and low nitrogen. Using the acetylene reduction assay we searched for nitrogen fixation 29 in the feces from several herbivorous animals in captivity. We detected acetylene 30 reduction in feces from two African spurred tortoises, Centrochelys sulcata and in feces 31 from six Gopherus berlandieri tortoises and isolated nitrogen-fixing klebsiellas from 32 them. Additionally, we performed a gut metagenomic study with Illumina sequencing 33 from a healthy Mexican G. berlandieri tortoise, and the nif genes identified in the feces 34 microbiome matched those from Klebsiella variicola. Fecal bacterial composition from 35 tortoises was similar to that reported from other reptilian guts. 36 3 37 Introduction 38 Nitrogen fixation is a unique biochemical process carried out by nitrogenases 39 encoded by nif genes, which are found in only a few prokaryotes (1). Nitrogen fixation 40 is energetically expensive and nitrogen-fixing bacteria are in many cases minor 41 components of the microbial community that nevertheless provide a valuable ecological 42 service (2). Nitrogen-fixing bacteria are called diazotrophs (3). 43 When associated with nitrogen-fixing bacteria, insects or plants may inhabit in 44 nitrogen poor conditions. Termites contain nitrogen-fixing bacteria in their guts that 45 allow them to grow in wood, similarly wood eating beetles contain nitrogen-fixing 46 bacteria (4). Nitrogen fixation by Klebsiella variicola occurs in the fungal garden of 47 ants (5). A novel betaproteobacterium capable of fixing nitrogen is a recently described 48 symbiont that is transmitted by eggs of carmine cochineals which feed on cacti as the 49 Gopherus berlandieri tortoise does (6). Cacti have high sugar content and are nitrogen 50 poor, conditions that would be favorable for nitrogen fixation in animals that use cacti 51 for food, such as the carmine cochineal or the G. berlandieri tortoise. 52 G. berlandieri, is distributed from North Mexico (states of Coahuila, Nuevo 53 Leon and Tamaulipas) to South-central Texas in United States (7). This species 54 generally maintains restricted mobility by living for prolonged times in the same 55 burrow (8) and its diet is mainly composed of grasses, weeds and cacti. On the other 56 hand, the African spurred tortoise, Centrochelys sulcata, which is also vegetarian, lives 57 in West Africa (9). 58 Metagenomic analyses have contributed to gain a better insight on taxonomic 59 composition and functions of the gut microbiota of various species, including non-60 model organisms, such as sea turtles (10). Gut microbiota may confer adaptability to 61 herbivorous tortoises such as G. berlandieri and C. sulcata naturally exposed to low 4 62 nitrogen-content diets. The aim of this research was to identify nitrogen-fixing species 63 in the gut microbiota of G. berlandieri and C. sulcata. In addition we present one G...

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The genome of a clinicalKlebsiella variicolastrain reveals virulence-associated traits and a pl9-like plasmid

Cited by 33 publications

References 18 publications

Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola

Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola

Klebsiella variicola and Klebsiella quasipneumoniae with capacity to adapt to clinical and plant settings

Nitrogen-fixing Klebsiella variicola in feces from herbivorous tortoises

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