Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA)

Brady, Carrie; Cleenwerck, Ilse; Venter, Stephanus N.; Vancanneyt, Marc; Swings, Jean; Coutinho, Teresa A.

doi:10.1016/j.syapm.2008.09.004

Cited by 329 publications

(291 citation statements)

References 43 publications

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“…Confirming the uncertainty of P. agglomerans identification, only 20 of the 53 strains received from culture collections as P. agglomerans, Pantoea spp., or E. agglomerans clustered with type strain LMG 1286 T according to gyrB sequencing. Seven strains previously assigned to P. agglomerans were found to fit in the MLSA groups of Pantoea recently described as new species (i.e., C9-1 as P. vagans; EM13cb and SC-1 as P. anthophila; LMG 5343 and ATCC 29001 as P. brenneri; and EM17cb as P. conspicua), or to belong to a novel subspecies of P. agglomerans (Eh252) (4,6,7,45). The remaining strains were reassigned to other Pantoea species or Enterobacteriaceae, although precise identification was not possible in all cases.…”

Section: Vol 76 2010mentioning

confidence: 97%

“…Accurate identification is complicated by the unsettled taxonomy of the "P. agglomerans-E. herbicola-E. agglomerans" complex (45). Recent analyses based on gyrB sequencing, multilocus sequence analysis (MLSA) (4), and fluorescent amplified fragment length polymorphisms (fAFLP) (45) indicate that strains belonging to Enterobacter or Erwinia archived in culture collections are often erroneously assigned to P. agglomerans and are likely also misidentified in clinical diagnostics. False classifications of environmental P. agglomerans strains as related Pantoea species, including human-or plant-pathogenic P. ananatis, are also common (45).…”

Section: P Agglomerans Is a Composite Taxon Conglomerating Formermentioning

confidence: 99%

“…Conversely, five strains belonging to other genera were incorrectly assigned to P. agglomerans using biochemical analysis: Erwinia persicina LMG 3622, Enterobacter sp. ATCC 27988 and ATCC 27991, Tatumella punctata LMG 22097, and Tatumella citrea LMG 23359, the latter two previously belonging to the former "Japanese species" of Pantoea (4,8). For the first three strains this outcome is the consequence of imprecise biochemical profiling, as 29 out of 45 reactions within the NMC/ID-51 panel are allowed to deliver a variable result while still retaining the identification as P. agglomerans (Fig.…”

Section: Vol 76 2010mentioning

confidence: 99%

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Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies

Rezzonico

Vogel²,

Duffy

et al. 2010

Appl Environ Microbiol

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Pantoea agglomerans is an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications of P. agglomerans, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification of P. agglomerans and related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based on gyrB sequencing, allowing rapid and reliable identification at the species level. (20) is a ubiquitous plant-epiphytic bacterium that belongs to the family Enterobacteriaceae. While several strains are commercialized for biological control of plant diseases (23), the species also includes two phytopathogenic pathovars that carry distinctive virulence plasmids (32). P. agglomerans has a Jekyll-Hyde nature, being described also as an opportunistic human pathogen (30), which raises biosafety regulatory issues for the utilization of beneficial isolates (45). Clinical reports predominantly involve septicemia following penetrating trauma (16, 56) or nosocomial infections (14,55). Clinical pathogenicity of this species has not been confidently confirmed (unfulfilled Koch's postulates). Infections attributed to P. agglomerans are typically of a polymicrobial nature involving patients affected by other diseases (14) and may represent secondary contamination of wounds. Standard clinical diagnostics and identification rely mainly on biochemical profiling analysis or alternatively on 16S rRNA gene sequencing, despite the inadequacy of these techniques for precise discrimination within the Enterobacter and Pantoea genera (5, 20, 39). Problems with correct identification have been observed for automated systems such as the API 20E (24, 39) and Vitek-2/GNIϩ (39, 40) (both from bioMerieux) or the Phoenix (11, 38) and Crystal identification systems (40, 48) (both from BD Diagnostic Systems). Pantoea agglomerans P. agglomerans is a composite taxon conglomerating formerEnterobacter agglomerans, Erwinia milletiae, and Erwinia herbicola strains. Accurate identification is complicated by the unsettled taxonomy of the "P. agglomerans-E. herbicola-E. agglomerans" complex (45). Recent analyses based on gyrB sequencing, multilocus sequence analysis (MLSA) (4), and fluorescent amplified fragment length polymorphisms (fAFLP) (45) indicate that strain...

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Section: Vol 76 2010mentioning

confidence: 97%

Section: P Agglomerans Is a Composite Taxon Conglomerating Formermentioning

confidence: 99%

Section: Vol 76 2010mentioning

confidence: 99%

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Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies

Rezzonico

Vogel²,

Duffy

et al. 2010

Appl Environ Microbiol

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“…Multilocus sequence analysis (MLSA) based on gyrB, rpoB, atpD and infB sequences was used in these studies as a supporting phylogenetic technique, since these genes were previously shown to be useful phylogenetic markers for Pantoea (Brady et al, 2008). In that study, strains from DNA HG II, IV and V (referred to as MLSA groups E, F, H and I) and Pectobacterium cypripedii were suggested to be members of the genus Pantoea.…”

mentioning

confidence: 99%

Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.

Brady

Cleenwerck

Venter

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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Bacterial strains belonging to DNA hybridization groups (HG) II, IV and V, in the Erwinia herbicola-Enterobacter agglomerans complex, of Brenner et al. [Int J Syst Bacteriol 34 (1984), [45][46][47][48][49][50][51][52][53][54][55] were suggested previously to belong to the genus Pantoea, but have never been formally described and classified. Additionally, it has been shown in several studies that Pectobacterium cypripedii is more closely related to species of Pantoea than to those of Pectobacterium. In this study, the phylogenetic positions of Brenner's DNA HG II, IV and V and Pectobacterium cypripedii were re-examined by both 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) based on the gyrB, rpoB, atpD and infB genes. The analyses revealed that DNA HG II, IV and V and Pectobacterium cypripedii form five separate branches within the genus Pantoea (strains from HG V were split into two branches). DNA-DNA hybridization data further confirmed that DNA HG II, IV and V constitute four separate species. Pectobacterium cypripedii was shown to be a close phylogenetic relative of Pantoea dispersa and DNA HG IV by both 16S rRNA gene sequence and MLSA analyses. Biochemical analyses performed on strains from DNA HG II, IV and V and Pectobacterium cypripedii confirmed their taxonomic position within the genus Pantoea and revealed phenotypic characteristics that allow the differentiation of these species from each other and from their closest phylogenetic neighbours. It is proposed to emend the description of the genus Pantoea and to describe Pantoea septica sp. nov. for DNA HG II (type strain LMG 5345 T 5BD 874 T 5CDC 3123-70 T ), Pantoea eucrina sp. nov. for DNA HG IV (type strain LMG 2781 T 5BD 872 T 5CDC 1741-71 T 5LMG 5346 T ), Pantoea brenneri sp. nov. for strains of DNA HG V excluding LMG 24534 (type strain LMG 5343 T 5BD 873 T 5CDC 3482-71 T ) and Pantoea conspicua sp. nov. for the remaining strain of DNA HG V (type strain LMG 24534 T 5BD 805 T 5CDC 3527-71 T ) and to transfer Pectobacterium cypripedii to the genus as Pantoea cypripedii comb. nov. (type strain LMG 2657 T 5ATCC 29267 T 5DSM 3873 T 5LMG 2655 T ).Abbreviations: HG, hybridization group; MLSA, multilocus sequence analysis.

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“…of Brady et al (2008). Purification and sequencing (Sanger method) of PCR products were carried out by the Shenggong Company in Shanghai, China.…”

mentioning

confidence: 99%

Reclassification of Enterobacter oryziphilus and Enterobacter oryzendophyticus as Kosakonia oryziphila comb. nov. and Kosakonia oryzendophytica comb. nov.

Zhou

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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The taxonomic positions of Enterobacter oryziphilus and Enterobacter oryzendophyticus were re-examined on the basis of concatenated partial rpoB, atpD, gyrB and infB gene sequence analysis. The reconstructed phylogenetic tree based upon concatenated partial rpoB, atpD, gyrB and infB gene sequences clearly showed that E. oryziphilus and E. oryzendophyticus and all defined species of the genus Kosakonia form a clade separate from other genera of the family Enterobacteriaceae, and, therefore, these species of the genus Enterobacter should be transferred to the genus Kosakonia. E. oryziphilus and E. oryzendophyticus are reclassified as K. oryziphila comb. nov. 166;Oren & Garrity, 2015). A maximum-likelihood tree based on 16S rRNA gene sequences indicated that E. oryziphilus and E. oryzendophyticus were related phylogenetically to E. arachidis, E. oryzae, E. radicincitans, Enterobacter cloacae subsp. cloacae, Enterobacter cloacae subsp. dissolvens and E. cowanii (Hardoim et al., 2013). rpoB gene sequence analysis also showed that E. oryziphilus was related phylogenetically to E. radicincitans, E. arachidis and E. cowanii (Hardoim et al., 2013). E. arachidis, E. oryzae, E. radicincitans and E. cowanii had already been transferred into a novel genus, Kosakonia, by Brady et al. (2013) on the basis of multilocus sequence analysis (concatenated partial rpoB, atpD, gyrB and infB gene sequence analysis). According to the results presented by Hardoim et al. (2013), E. oryziphilus and E. oryzendophyticus were probably members of the novel genus Kosakonia, so their taxonomic status was re-evaluated.In the present study, the taxonomic status of E. oryziphilus and E. oryzendophyticus was re-examined on the basis of concatenated partial rpoB, atpD, gyrB and infB gene sequence analysis. Strains LMG 26429 T and LMG 26432 T were incubated aerobically at 30 C on nutrient agar (pH 7.0) consisting of 0.5 % peptone, 0.3 % meat extract and 0.5 % NaCl.The DNA for gene amplification was prepared using bacterial genomic DNA extraction kits (TIANGEN). The RNA polymerase b subunit (rpoB), DNA gyrase (gyrB), initiation translation factor 2 (infB) and ATP synthase b subunit (atpD) genes were amplified using the primers and protocolThe GenBank/EMBL/DDBJ accession numbers for the atpD, gyrB, infB and rpoB gene sequences of strains LMG 26429 T and LMG 26432 T are LN873150-LN873157.

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Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA)

Cited by 329 publications

References 43 publications

Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies

Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis ofPantoeaSpecies

Reclassification of Enterobacter oryziphilus and Enterobacter oryzendophyticus as Kosakonia oryziphila comb. nov. and Kosakonia oryzendophytica comb. nov.

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