Evolutionary Dynamics of the Yersinia enterocolitica Complex

Reuter, Sandra; Thomson, Nicholas R.; McNally, Alan

doi:10.1007/978-1-4614-3561-7_2

Cited by 5 publications

(5 citation statements)

References 169 publications

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“…5, S1). Core-based and pan-based-genome analysis showed Y. pestis and Y. pseudotuberculosis closely related to each other, similar to previously published data (Duan et al 2014;Reuter et al 2012), and Y. enterocolitica was as an independent branch including the strain LC20 (Fig. 6).…”

Section: Discussionsupporting

confidence: 85%

“…Previous reports suggest Y. enterocolitica is genetically split into distinct biotypes, with non-pathogenic biotype 1A displaying increased heterogeneity compared to the other biotypes (1B, 2-5) and a phylogeny inferring that biotype 1A is the progenitor for modern Y. enterocolitica (Reuter et al 2012). The emergence of the pathogenic biotypes occurred by gaining the pYV plasmid (Chain et al 2006), and further showing extensive gene decay within operons encoding metabolic functions, the same evolutionary process occurred in Y. pseudotuberculosis and Y. pestis (Achtman et al 1999).…”

Section: Discussionmentioning

confidence: 98%

“…The high-pathogenic biotype 1B and the non-pathogenic biotype 1A are distinct from the low-pathogenic biotype and each has >500 unique CDSs. However, they also share 86 CDSs related to metabolic functions that are absent from the low-pathogenic biotype (Reuter et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Shi

Liang

et al. 2016

Arch Microbiol

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Yersinia enterocolitica is the most diverse species among the Yersinia genera and shows more polymorphism, especially for the non-pathogenic strains. Individual non-pathogenic Y. enterocolitica strains are wrongly identified because of atypical phenotypes. In this study, we isolated an unusual Y. enterocolitica strain LC20 from Rattus norvegicus. The strain did not utilize urea and could not be classified as the biotype. API 20E identified Escherichia coli; however, it grew well at 25 °C, but E. coli grew well at 37 °C. We analyzed the genome of LC20 and found the whole chromosome of LC20 was collinear with Y. enterocolitica 8081, and the urease gene did not exist on the genome which is consistent with the result of API 20E. Also, the 16 S and 23 SrRNA gene of LC20 lay on a branch of Y. enterocolitica. Furthermore, the core-based and pan-based phylogenetic trees showed that LC20 was classified into the Y. enterocolitica cluster. Two plasmids (80 and 50 k) from LC20 shared low genetic homology with pYV from the Yersinia genus, one was an ancestral Yersinia plasmid and the other was novel encoding a number of transposases. Some pathogenic and non-pathogenic Y. enterocolitica-specific genes coexisted in LC20. Thus, although it could not be classified into any Y. enterocolitica biotype due to its special biochemical metabolism, we concluded the LC20 was a Y. enterocolitica strain because its genome was similar to other Y. enterocolitica and it might be a strain with many mutations and combinations emerging in the processes of its evolution.

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Section: Discussionsupporting

confidence: 85%

Section: Discussionmentioning

confidence: 98%

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Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Shi

Liang

et al. 2016

Arch Microbiol

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“…Another possible explanation for universal activity of colicin F Y against Y. enterocolitica involves a close relationship between Y. enterocolitica and colicin F Y producers, with little or no contact between them. A phylogenetic analysis showed that Y. enterocolitica was clearly related to other environmental enterocolitica-like species including Y. frederiksenii [59], [60]. In addition, contact between the two bacterial species appears to be quite rare despite the sporadic co-occurrence of both species [61]–[63].…”

Section: Discussionmentioning

confidence: 99%

Unique Activity Spectrum of Colicin FY: All 110 Characterized Yersinia enterocolitica Isolates Were Colicin FY Susceptible

et al. 2013

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Colicin FY is a plasmid encoded toxin that recognizes a yersinia-specific outer membrane protein (YiuR) as a receptor molecule. We have previously shown that the activity spectrum of colicin FY comprises strains of the genus Yersinia. In this study, we analyzed the activity of colicin FY against 110 Yersinia enterocolitica isolates differing in geographical origin and source. All isolates were characterized through analysis of 16S rRNA genes, serotyping, biotyping, restriction profiling of genomic DNA, detection of virulence markers and susceptibility to antibiotics. This confirmed the broad variability of the collection, in which all 110 Y. enterocolitica isolates, representing 77 various strains, were inhibited by colicin FY. Although isolates showed variable levels of susceptibility to colicin FY, it was not associated with any strain characteristic. The universal susceptibility of Y. enterocolitica strains to colicin FY together with the absence of activity towards strains outside the Yersinia genus suggests potential therapeutic applications for colicin FY.

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“…enterocolitica can be isolated from the intestinal tract of cattle sheep and pigs, serotype O:8/phylogroup 2 strains have rarely been isolated from humans and livestock and have been shown to have a higher level of virulence in mouse infection models. Moreover, results of analyses of the core and accessory genes and of the gene flow across the phylogroups suggest that the different phylogroups are ecologically separated and do not share common niches (6, 70).…”

Section: Resultsmentioning

confidence: 99%

Comparative Transcriptomic Profiling of Yersinia enterocolitica O:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation

et al. 2019

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Yersinia enterocolitica is a zoonotic pathogen and an important cause of bacterial gastrointestinal infections in humans. Large-scale population genomic analyses revealed genetic and phenotypic diversity of this bacterial species, but little is known about the differences in the transcriptome organization, small RNA (sRNA) repertoire, and transcriptional output. Here, we present the first comparative high-resolution transcriptome analysis of Y. enterocolitica strains representing highly pathogenic phylogroup 2 (serotype O:8) and moderately pathogenic phylogroup 3 (serotype O:3) grown under four infection-relevant conditions. Our transcriptome sequencing (RNA-seq) approach revealed 1,299 and 1,076 transcriptional start sites and identified strain-specific sRNAs that could contribute to differential regulation among the phylogroups. Comparative transcriptomics further uncovered major gene expression differences, in particular, in the temperature-responsive regulon. Multiple virulence-relevant genes are differentially regulated between the two strains, supporting an ecological separation of phylogroups with certain niche-adapted properties. Strong upregulation of the ystA enterotoxin gene in combination with constitutive high expression of cell invasion factor InvA further showed that the toxicity of recent outbreak O:3 strains has increased. Overall, our report provides new insights into the specific transcriptome organization of phylogroups 2 and 3 and reveals gene expression differences contributing to the substantial phenotypic differences that exist between the lineages. IMPORTANCE Yersinia enterocolitica is a major diarrheal pathogen and is associated with a large range of gut-associated diseases. Members of this species have evolved into different phylogroups with genotypic variations. We performed the first characterization of the Y. enterocolitica transcriptional landscape and tracked the consequences of the genomic variations between two different pathogenic phylogroups by comparing their RNA repertoire, promoter usage, and expression profiles under four different virulence-relevant conditions. Our analysis revealed major differences in the transcriptional outputs of the closely related strains, pointing to an ecological separation in which one is more adapted to an environmental lifestyle and the other to a mostly mammal-associated lifestyle. Moreover, a variety of pathoadaptive alterations, including alterations in acid resistance genes, colonization factors, and toxins, were identified which affect virulence and host specificity. This illustrates that comparative transcriptomics is an excellent approach to discover differences in the functional output from closely related genomes affecting niche adaptation and virulence, which cannot be directly inferred from DNA sequences.

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Evolutionary Dynamics of the Yersinia enterocolitica Complex

Cited by 5 publications

References 169 publications

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica

Unique Activity Spectrum of Colicin FY: All 110 Characterized Yersinia enterocolitica Isolates Were Colicin FY Susceptible

Comparative Transcriptomic Profiling of Yersinia enterocolitica O:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation

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