Mixta gen. nov., a new genus in the Erwiniaceae

Palmer, Marike; Steenkamp, Emma Theodora; Coetzee, Martin Petrus Albertus; Avontuur, Juanita R.; Chan, Wai; Zyl, Elritha Van; Blom, Jochen; Venter, Stephanus N.

doi:10.1099/ijsem.0.002540

Cited by 53 publications

(19 citation statements)

References 88 publications

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“…Because these strains were classified prior to the description of the proposed Mixta calida , we considered the single M . calida strain found in our study to be correctly identified [38]. Three non- Pantoea strains, 07–703, 12BT205805, and B012497 are sufficiently divergent that they remain unclassified.…”

Section: Discussionmentioning

confidence: 53%

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

Soutar

Stavrinides

2019

PLoS ONE

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The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.

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Section: Discussionmentioning

confidence: 53%

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

Soutar

Stavrinides

2019

PLoS ONE

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“…Previously, P. citrea , P. terrea , and P. punctata were transferred to the genus Tatumella (Brady et al, 2010). Recently, Pantoea calida , Pantoea gaviniae , Pantoea theicola , and Pantoea intestinalis were moved to a new genus Mixta (Palmer et al, 2018). This suggests that the taxonomy of the genus is evolving probably due to the use of improved taxonomic methodologies.…”

Section: Introductionmentioning

confidence: 99%

Taxogenomics and Systematics of the Genus Pantoea

Tambong

2019

Front. Microbiol.

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Members of the genus Pantoea are Gram-negative bacteria isolated from various environments. Taxonomic affiliation based on multilocus sequence analysis (MLSA) is used routinely for inferring accurate phylogeny and identification of bacterial species and genera. Partial sequences of five housekeeping genes (fusA, gyrB, leuS, rpoB, and pyrG) were extracted from 206 draft or complete genomes of Pantoea strains publicly available in databases and analyzed together with the representative sequences of the 25 validly published Pantoea type strains to verify and assess their phylogenetic assignations. Of a total of 159 strains assigned to species level, 11.3% of the non-type strains were incorrectly assigned within suitable Pantoea species. The highest proportion of misidentified strains was recorded in Pantoea vagans, 8 out of 15 (53.3%) inaccurate assignations at the species level. One probable reason for this incorrect classification could be the method previously used for strain identification. Forty-seven (22.8%) genome sequences were from strains identified at the genus level only (Pantoea sp.). A combination of MLSA, average nucleotide identities [ANI and MuMmer-based ANI (ANIm)], tetranucleotide usage pattern (TETRA), and genome-based DNA-DNA hybridization (gDDH) data was used to accurately assign 25 of the 47 strains to validly published Pantoea species, while 17 strains could be assigned as putative novel species within the genus Pantoea. Four genomes designed as Pantoea sp. were identified as Mixta calida. Positive and significant correlation coefficients were computed between MLSA and all the indices derived from whole-genome sequences being proposed for species delimitation. gDDH exhibited the best correlation with MLSA while TETRA was the worst. Accurate species-level identification is key to a better understanding of bacterial diversity and evolution. The MLSA scheme used here could be instrumental to determine the correct taxonomic status of new whole-genome sequenced Pantoea strains, especially non-type strains, before depositing into public databases.

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“…The genera Coetzeea and Thorsellia, are the only genera described for the Thorselliaceae family. Even though this review focuses only on genera within the family Enterobacteriaceae described during the 21th century, Table 1 shows all the families and genera that belong to the order Enterobacteriales [13][14][15][16][17][18][19][20][21] , in order to show the genera related to Enterobacteriaceae.…”

Section: Resultsmentioning

confidence: 99%

Enterobacteria in the 21st century: a review focused on taxonomic changes

Morales-López

Yepes

Prada-Herrera

et al. 2019

J Infect Dev Ctries

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Introduction: Enterobacteria are the main group causing infections in humans. The aim of this review is to present the new genera and the taxonomic changes that the Enterobacteriacea family has experienced in recent years. Methodology: a systematic search of papers published in databases from January 2000 to July 2018 was done. Additionally, the bibliographic references of each document were reviewed and each paper citing the article was reviewed in search of clinical cases. Results: Nineteen new genera of Enterobacteria have been described since 2000. The genera Yersinia, Morganella and Erwinia do not belong to the family Enterobacteriacea anymore. Conclusions: for an adequate clinical and epidemiological interpretation, it is advisable to update the libraries of the commercial systems used for the identification of the microorganisms, as well as to train the staff in the taxonomic changes of microorganisms.

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Mixta gen. nov., a new genus in the Erwiniaceae

Cited by 53 publications

References 88 publications

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

Taxogenomics and Systematics of the Genus Pantoea

Enterobacteria in the 21st century: a review focused on taxonomic changes

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