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
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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