Sequence similarity of Clostridium difficile strains by analysis of conserved genes and genome content is reflected by their ribotype affiliation
Autor: | Marc Monot, Hedwig Kurka, Maja Rupnik, Frédéric Barbut, Armin Ehrenreich, Wolfgang Ludwig, Bruno Dupuy, Wolfgang Liebl, Alexander Indra |
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Přispěvatelé: | Department of Microbiology [Freising], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), CipKeBiP - The Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institute for Medical Microbiology and Hygiene [Vienna], Austrian Agency for Health and Food Safety (AGES), Financial support of this work (collaborative project CDIFFGEN – Pathogenomics of increased Clostridium difficile virulence) within the framework ERA-NET PathoGenoMics 2 by the German Federal Ministry of Education and Research (BMBF) is gratefully acknowledged., Technische Universität München [München] (TUM), National reference laboratory for clostridium difficile, Université Pierre et Marie Curie - Paris 6 (UPMC)-AP-HP - Hôpital Saint-Antoine, Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7) |
Jazyk: | angličtina |
Rok vydání: | 2014 |
Předmět: |
Bacterial Diseases
MESH: Sequence Analysis DNA Gene Identification and Analysis lcsh:Medicine MESH: Virulence MESH: Genome Bacterial Genome Ribotyping Conserved sequence Cluster Analysis Genome Sequencing MESH: Genetic Variation lcsh:Science MESH: Phylogeny Conserved Sequence Phylogeny Genetics Multidisciplinary MESH: Conserved Sequence Phylogenetic tree Virulence Genomics Clostridium difficile Phylogenetics Infectious Diseases Phenotype DNA Gyrase Medicine Research Article MESH: DNA Gyrase DNA Bacterial Clostridium Difficile Bacterial Toxins Biology MESH: Phenotype MESH: Sequence Homology Nucleic Acid Molecular Genetics Genome Analysis Tools Sequence Homology Nucleic Acid Evolutionary Systematics Gene MESH: Clostridium difficile Comparative genomics Evolutionary Biology Evolutionary Developmental Biology Clostridioides difficile lcsh:R Computational Biology Genetic Variation MESH: Ribotyping [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biology Sequence Analysis DNA Comparative Genomics MESH: Cluster Analysis MESH: DNA Bacterial MESH: Bacterial Toxins lcsh:Q Genome Bacterial |
Zdroj: | PLoS ONE PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e86535. ⟨10.1371/journal.pone.0086535⟩ PLoS ONE, 2014, 9 (1), pp.e86535. ⟨10.1371/journal.pone.0086535⟩ PLoS ONE, Vol 9, Iss 1, p e86535 (2014) |
ISSN: | 1932-6203 |
DOI: | 10.1371/journal.pone.0086535⟩ |
Popis: | International audience; PCR-ribotyping is a broadly used method for the classification of isolates of Clostridium difficile, an emerging intestinal pathogen, causing infections with increased disease severity and incidence in several European and North American countries. We have now carried out clustering analysis with selected genes of numerous C. difficile strains as well as gene content comparisons of their genomes in order to broaden our view of the relatedness of strains assigned to different ribotypes. We analyzed the genomic content of 48 C. difficile strains representing 21 different ribotypes. The calculation of distance matrix-based dendrograms using the neighbor joining method for 14 conserved genes (standard phylogenetic marker genes) from the genomes of the C. difficile strains demonstrated that the genes from strains with the same ribotype generally clustered together. Further, certain ribotypes always clustered together and formed ribotype groups, i.e. ribotypes 078, 033 and 126, as well as ribotypes 002 and 017, indicating their relatedness. Comparisons of the gene contents of the genomes of ribotypes that clustered according to the conserved gene analysis revealed that the number of common genes of the ribotypes belonging to each of these three ribotype groups were very similar for the 078/033/126 group (at most 69 specific genes between the different strains with the same ribotype) but less similar for the 002/017 group (86 genes difference). It appears that the ribotype is indicative not only of a specific pattern of the amplified 16S-23S rRNA intergenic spacer but also reflects specific differences in the nucleotide sequences of the conserved genes studied here. It can be anticipated that the sequence deviations of more genes of C. difficile strains are correlated with their PCR-ribotype. In conclusion, the results of this study corroborate and extend the concept of clonal C. difficile lineages, which correlate with ribotypes affiliation. |
Databáze: | OpenAIRE |
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