Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

Tohya, Mari; Watanabe, Shin; Tada, Tatsuya; Tin, Htay Htay; Kirikae, Teruo

doi:10.1099/ijsem.0.004199

“…Bioinformatics calculations, such as the Average Nucleotide Identity (ANI) and digital DNA–DNA Hybridization (dDDH), are now commonly used to describe new species or to affiliate strains to a specific taxon [ 20 , 33 ]. Threshold values for species delineation are, respectively, between 95 and 96.5 for ANI and 70 for dDDH [ 13 , 34 , 35 , 36 , 37 ].…”

Section: Methodsmentioning

confidence: 99%

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

Girard

¹

,

Lood

²

,

Rokni‐Zadeh

³

et al. 2020

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The taxonomic affiliation of Pseudomonas isolates is currently assessed by using the 16S rRNA gene, MultiLocus Sequence Analysis (MLSA), or whole genome sequencing. Therefore, microbiologists are facing an arduous choice, either using the universal marker, knowing that these affiliations could be inaccurate, or engaging in more laborious and costly approaches. The rpoD gene, like the 16S rRNA gene, is included in most MLSA procedures and has already been suggested for the rapid identification of certain groups of Pseudomonas. However, a comprehensive overview of the rpoD-based phylogenetic relationships within the Pseudomonas genus is lacking. In this study, we present the rpoD-based phylogeny of 217 type strains of Pseudomonas and defined a cutoff value of 98% nucleotide identity to differentiate strains at the species level. To validate this approach, we sequenced the rpoD of 145 environmental isolates and complemented this analysis with whole genome sequencing. The rpoD sequence allowed us to accurately assign Pseudomonas isolates to 20 known species and represents an excellent first diagnostic tool to identify new Pseudomonas species. Finally, rpoD amplicon sequencing appears as a reliable and low-cost alternative, particularly in the case of large environmental studies with hundreds or thousands of isolates.

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“…Nearly identical syntenic BGCs are present in the genome of P. asplenii ATCC 23835 T , suggesting that these closely related species, have a very similar capacity to produce several (lipo)peptidic secondary metabolites (Hu et al 1998). It should be noted that Tohya et al (2020) recently suggested that P. fuscovaginae should be classified as a later heterotypic synonym of P. asplenii since the average nucleotide identity between the two type strains representing these species is 98.4%. A fuscopeptin-related compound, jessenipeptin, was recovered from Pseudomonas sp.…”

Section: P Fuscovaginae: Standing Out From the Phytopathogenic Crowdmentioning

confidence: 99%

“…QS1027, in line with changes in BGCs composition and organization that have occurred during their divergent evolutionary history ( Figure 2). Strain ES_PA-B8 has only 84% average nucleotide identity with P. asplenii ATCC 23835 T and needs to be reclassified (Tohya et al 2020).…”

Section: P Fuscovaginae: Standing Out From the Phytopathogenic Crowdmentioning

confidence: 99%

Lipopeptide families at the interface between pathogenic and beneficialPseudomonas-plant interactions

Girard

¹

,

Höfte

²

,

Mot

³

2020

Critical Reviews in Microbiology

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Lipopeptides (LPs) are a prominent class of molecules among the steadily growing spectrum of specialized metabolites retrieved from Pseudomonas, in particular soil-dwelling and plant-associated isolates. Among the multiple LP families, pioneering research focussed on phytotoxic and antimicrobial cyclic lipopeptides (CLPs) of the ubiquitous plant pathogen Pseudomonas syringae (syringomycin and syringopeptin). Their non-ribosomal peptide synthetases (NRPSs) are embedded in biosynthetic gene clusters (BGCs) that are tightly co-clustered on a pathogenicity island. Other members of the P. syringae group (Pseudomonas cichorii) and some species of the Pseudomonas asplenii group and Pseudomonas fluorescens complex have adopted these biosynthetic strategies to co-produce their own mycin and peptin variants, in some strains supplemented with an analogue of the P. syringae linear LP (LLP), syringafactin. This capacity is not confined to phytopathogens but also occurs in some biocontrol strains, which indicates that these LP families not solely function as general virulence factors. We address this issue by scrutinizing the structural diversity and bioactivities of LPs from the mycin, peptin, and factin families in a phylogenetic and evolutionary perspective. BGC functional organization (including associated regulatory and transport genes) and NRPS modular architectures in known and candidate LP producers were assessed by genome mining.

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“…Pseudomonas asiatica was recently proposed as a species belonging to the Pseudomonas putida group and is located close to P. putida and Pseudomonas monteilii [2]. The species was proposed as Pseudomonas shirazica [3], and was later reclassified as P. asiatica [4]. Carbapenem-resistant P. asiatica harbouring bla NDM-1 and bla VIM-2 were isolated from hospitalized patients in Myanmar [5], indicating that MBLproducing P. asiatica strains are spreading in Myanmar.…”

Section: Introductionmentioning

confidence: 99%

Emergence of clinical isolates of Pseudomonas asiatica and Pseudomonas monteilii from Japan harbouring an acquired gene encoding a carbapenemase VIM-2

Tohya

¹

,

Uechi

²

,

Tada

³

et al. 2021

Journal of Medical Microbiology

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Pseudomonas asiatica and Pseudomonas monteilii , belonging to the Pseudomonas putida phylogenetic group, are occasionally isolated from clinical samples, partly because they are often misidentified as P. putida in clinical laboratories. There are five reports describing carbapenem-resistant clinical isolates of these species. Carbapenem-resistant strains of P. asiatica and P. monteilii were isolated from stool samples. These isolates were sequenced using Illumina MiSeq and reidentified using average nucleotide identity (ANI) based on comparisons of their whole-genome sequences using the OrthoANI algorithm. The clonal relatedness of the isolates was assessed by pulse-field gel electrophoresis (PFGE). The size of plasmids conveying bla VIM-2 was examined by Southern blotting. A total of six carbapenem-resistant clinical isolates of P. asiatica (two isolates) and P. monteilii (four isolates) were obtained from stool samples from five patients in a Japanese hospital. All isolates harboured blaVIM-2 . The two isolates of P. asiatica had a different pattern in the PFGE analysis, with both having a 23 kb plasmid. Of the four isolates of P. monteilii with similar patterns in the PFGE analysis, three had 320 kb plasmids and one had a 240 kb plasmid. The genetic environments of the 320/240 kb and 23 kb plasmids differed. The results strongly indicated that carbapenem-resistant P. asiatica and P. monteilii producing metallo-β-lactamase are emerging in Japan. This is the first report of carbapenem-resistant P. asiatica and P. monteilii in Japan.

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Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

Abstract: This study was conducted to clarify the taxonomic status of the species Pseudomonas fuscovaginae and Show more

Cited by 20 publications

References 26 publications

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

Lipopeptide families at the interface between pathogenic and beneficialPseudomonas-plant interactions

Emergence of clinical isolates of Pseudomonas asiatica and Pseudomonas monteilii from Japan harbouring an acquired gene encoding a carbapenemase VIM-2

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