Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov.

Ma, Yuanyuan; Yao, Rong; Li, Yuanyuan; Wu, Xiulan; Li, Shuying; An, Qianli

doi:10.1007/s00284-020-02004-4

Cited by 17 publications

(5 citation statements)

References 42 publications

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“…The contig data used for ANI and core-gene analyses with all four isolates were matched with Kluyvera intestini GT-16 and P. diazotrophicus DSM 17806, with more than 80% digital DNA-DNA hybridization scores, which is sufficient for species identification ( 22 ). Given that K. intestini GT-16 was recently reclassified as P. diazotrophicus ( 10 , 21 ), these findings support the original identification of our isolates as P. diazotrophicus . Second, we reanalyzed our isolates after the database for the MALDI Biotyper system (the MBT Compass reference library, MBT-BDAL-10833, Bruker) was updated in our lab in April 2022.…”

Section: Observationsupporting

confidence: 85%

“…Metakosakonia sp. MRY16-398 ( 20 ), which was later identified as P. diazotrophicus ( 10 , 21 ), was closest to our four isolates. Besides the close epidemiological relationship such as their isolations within a week ( Table 1 ), the clonality observed in the pulsed-field gel analysis demonstrated that P. diazotrophicus have disseminated through nosocomial infections in the current cases ( Fig.…”

Section: Observationmentioning

confidence: 68%

“…MRY16-398 and Citrobacter sp. BDA59-3 are regarded as P. diazotrophicus MRY16-398 and P. diazotrophicus BDA59-3, respectively, and the reclassification of Metakosakonia massiliensis to Phytobacter massiliensis is included, according to recent studies ( 10 , 21 ). Scale bars = distance.…”

Section: Observationmentioning

confidence: 99%

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Emergence of Phytobacter diazotrophicus carrying an IncA/C ₂ plasmid harboring bla _NDM-1 in Tokyo, Japan

Kubota,

Nakayama,

Ariyoshi

et al. 2023

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Phytobacter diazotrophicus is an Enterobacterales species that was originally identified as a plant growth-promoting, Gram-negative bacterium. Recently, this species has been recognized as relevant to opportunistic human and nosocomial infections in clinical settings. Its frequent misidentification as other Enterobacterales species from clinical examination occasionally causes a delay in the identification of nosocomial outbreaks. Here, we report the emergence of New Delhi metallo-β-lactamase (NDM)-producing P. diazotrophicus isolated from hospitalized pediatric patients and hospital environments in Tokyo, Japan. In our case, these isolates were found during an investigation of carbapenem-resistant Enterobacterales in relation to nosocomial infections. Whole-genome sequencing is useful for overcoming the difficulty of species identification. Furthermore, we found that bla NDM-1 was carried by an IncA/C 2 plasmid (approximately 170 kbp), which was transferrable from the clinical isolates to the recipient strain Escherichia coli J53. Our study demonstrated that P. diazotrophicus behaves as a carrier of bla NDM -harboring plasmids, potentially disseminating resistance to carbapenems among Enterobacterales. IMPORTANCE Early detection of nosocomial outbreaks is important to minimize the spread of bacteria. When an outbreak is caused by multidrug-resistant bacteria such as carbapenem-resistant Enterobacterales, a delay in findings makes it difficult to control it because such bacteria often spread not only among human patients but also in hospital environments. Phytobacter diazotrophicus , an Enterobacterales species that has recently been found to be relevant to clinical settings, is often misidentified as other bacteria in clinical laboratories. Here, we found NDM-producing P. diazotrophicus in hospitalized pediatric patients and their environment in Tokyo, Japan. Given that the isolates carried bla NDM-1 -harboring transferrable plasmids, the influence of such bacteria could be greater with the mediation of horizontal transfer of carbapenem resistance. Our findings suggest that P. diazotrophicus should be recognized as an NDM-carrier, for which more attention should be paid in clinical settings.

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Section: Observationsupporting

confidence: 85%

Section: Observationmentioning

confidence: 68%

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Emergence of Phytobacter diazotrophicus carrying an IncA/C ₂ plasmid harboring bla _NDM-1 in Tokyo, Japan

Kubota,

Nakayama,

Ariyoshi

et al. 2023

mSphere

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“…[ 2 ] was mislabelled as Klebsiella michiganensis when it actually is Luteibacter rhizovicinus [ 32 ]. The genome assembly GCF_001022135.1 that we used for Phytobacter ursingii was originally identified as Kluyvera intermedia when it was first published but has since been reclassified [ 33 , 34 ]. The species names and NCBI reference IDs used in our analysis are: Blochmannia endosymbiont (GCF_000973545.1), Candidatus Doolittlea endobia (GCF_900039485.1), Candidatus Gullanella endobia (GCF_900048035.1), Candidatus Hoaglandella endobia (GCF_900044015.1), Candidatus Ishikawaella capsulata (GCF_000828515.1), Candidatus Riesia pediculicola (GCF_000093065.1), Candidatus Tachikawaea gelatinosa (GCF_000828815.1), Cedecea neteri (GCF_000757825.1), Citrobacter freundii (GCF_000648515.1), Cronobacter sakazakii (GCF_000982825.1, Enterobacter lignolyticus SCF1 (GCF_000164865.1), Escherichia coli (GCF_000299455.1), Luteibacter rhizovicinus (GCF_001887595.1), Phytobacter ursingii (GCF_001022135.1), Kosakonia sacchari (GCF_000300455.3), Pluralibacter gergoviae (GCF_000757785.1), Salmonella enterica (GCF_000195995.1), Shigella flexneri (GCF_000006925.2), and Shimwellia blattae (GCF_000262305.1).…”

Section: Methodsmentioning

confidence: 99%

Annotation-free delineation of prokaryotic homology groups

2022

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Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate homology groups in a set of bacterial genomes without relying on gene annotations to define the boundaries of homologous regions. To solve this problem, we have developed a graph-based algorithm to partition a set of bacterial genomes into Maximal Homologous Groups of sequences (MHGs) where each MHG is a maximal set of maximum-length sequences which are homologous across the entire sequence alignment. We applied our algorithm to a dataset of 19 Enterobacteriaceae species and found that MHGs cover much greater proportions of genomes than markers and, relatedly, are less biased in terms of the functions of the genes they cover. We zoomed in on the correlation between each individual marker and their overlapping MHGs, and show that few phylogenetic splits supported by the markers are supported by the MHGs while many marker-supported splits are contradicted by the MHGs. A comparison of the species tree inferred from marker genes with the species tree inferred from MHGs suggests that the increased bias and lack of genome coverage by markers causes incorrect inferences as to the overall relationship between bacterial taxa.

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“…MRY16-398 and cluster with a group of strains that, in spite of the names under which the sequences were deposited, also belong to P. diazotrophicus. As a matter of fact, based on genomic comparisons, a recommendation to unite Metakosakonia and Phytobacter under the latter genus name was recently proposed by Ma et al [27] and misidentification of Phytobacter isolates as Klyuvera, Citrobacter or 'Grimontella' has been reported before [28]. It is interesting to note that the genus Phytobacter does not appear to be monophyletic with respect to FliC, as other clusters contain a mix of several Phytobacter species and are interspersed among sequences belonging to other genera (Figure 2).…”

Section: Cloning Of the Gene And Sequence Analysismentioning

confidence: 99%

Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor

et al. 2022

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Symbiotic microorganisms in the intestinal tract can influence the general fitness of their hosts and contribute to protecting them against invading pathogens. In this study, we obtained isolate Phytobacter diazotrophicus SCO41 from the gut of free-living nematode Caenorhabditis elegans that displayed strong colonization-resistance against invading biocontrol bacterium Bacillus nematocida B16. The colonization-resistance phenotype was found to be mediated by a 37-kDa extracellular protein that was identified as flagellin (FliC). With the help of genome information, the fliC gene was cloned and heterologously expressed in E. coli. It could be shown that the B. nematocida B16 grows in chains rather than in planktonic form in the presence of FliC. Scanning Electronic Microscopy results showed that protein FliC-treated B16 bacterial cells are thinner and longer than normal cells. Localization experiments confirmed that the protein FliC is localized in both the cytoplasm and the cell membrane of B16 strain, in the latter especially at the position of cell division. ZDOCK analysis showed that FliC could bind with serine/threonine protein kinase, membrane protein insertase YidC and redox membrane protein CydB. It was inferred that FliC interferes with cell division of B. nematocidal B16, therefore inhibiting its colonization of C. elegans intestines in vivo. The isolation of P. diazotrophicus as part of the gut microbiome of C. elegans not only provides interesting insights about the lifestyle of this nitrogen-fixing bacterium, but also reveals how the composition of the natural gut microbiota of nematodes can affect biological control efforts by protecting the host from its natural enemies.

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Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov.

Cited by 17 publications

References 42 publications

Emergence of Phytobacter diazotrophicus carrying an IncA/C ₂ plasmid harboring bla _NDM-1 in Tokyo, Japan

Emergence of Phytobacter diazotrophicus carrying an IncA/C ₂ plasmid harboring bla _NDM-1 in Tokyo, Japan

Annotation-free delineation of prokaryotic homology groups

Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor

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Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov.

Cited by 17 publications

References 42 publications

Emergence of Phytobacter diazotrophicus carrying an IncA/C 2 plasmid harboring bla NDM-1 in Tokyo, Japan

Emergence of Phytobacter diazotrophicus carrying an IncA/C 2 plasmid harboring bla NDM-1 in Tokyo, Japan

Annotation-free delineation of prokaryotic homology groups

Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor

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Emergence of Phytobacter diazotrophicus carrying an IncA/C ₂ plasmid harboring bla _NDM-1 in Tokyo, Japan

Emergence of Phytobacter diazotrophicus carrying an IncA/C ₂ plasmid harboring bla _NDM-1 in Tokyo, Japan