Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status

Nguyen, Scott V.; Cunningham, Scott A.; Jeraldo, Patricio; Tran, Anthony; Patel, Robin

doi:10.1099/ijsem.0.004626

“…In order to explore the genetic relationship of the Y. ruckeri strains with the genus Yersinia, we additionally downloaded the genome sequence data of 90 strains representing the 26 currently validated Yersinia species (Savin et al, 2019;Le Guern et al, 2020;Nguyen et al, 2021). Reference genomes in the RefSeq database and the genomes of the species type strains were prioritized during data retrieval from NCBI.…”

Section: Comparative Analysis Of Y Ruckeri To the Genus Yersiniamentioning

confidence: 99%

Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis

Abdel-Glil

¹

,

Fischer

²

,

Steinhagen

³

et al. 2021

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Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark. In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.

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“…In order to explore the genetic relationship of the Y. ruckeri strains with the genus Yersinia, we additionally downloaded the genome sequence data of 90 strains representing the 26 currently validated Yersinia species (Savin et al, 2019;Le Guern et al, 2020;Nguyen et al, 2021). Reference genomes in the RefSeq database and the genomes of the species type strains were prioritized during data retrieval from NCBI.…”

Section: Comparative Analysis Of Y Ruckeri To the Genus Yersiniamentioning

confidence: 99%

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“…In order to explore the genetic relationship of the Y. ruckeri strains with the genus Yersinia, we additionally downloaded the genome sequence data of 90 strains representing the 26 currently validated Yersinia species (Savin et al, 2019;Le Guern et al, 2020;Nguyen et al, 2021). Reference genomes in the RefSeq database and the genomes of the species type strains were prioritized during data retrieval from NCBI.…”

Section: Comparative Analysis Of Y Ruckeri To the Genus Yersiniamentioning

confidence: 99%

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0

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Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status

Abstract: The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA–DNA hybridization values, and phylogenetic analyses of the type strains … Show more

Cited by 11 publications

References 21 publications

Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis

Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis

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