Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases

Claudia Marina Muñoz, Dora Inés Ríos-Chaparro, Manuel Alfonso Patarroyo, Juan David Ramírez

Resultado de la investigación: Contribución a RevistaArtículo

4 Citas (Scopus)

Resumen

Background: Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Results: Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. Conclusions: This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.

Idioma originalEnglish (US)
Número de artículo62
Páginas (desde-hasta)1-12
Número de páginas12
PublicaciónBMC Microbiology
Volumen17
N.º1
DOI
EstadoPublished - mar 14 2017

Huella dactilar

Multilocus Sequence Typing
Clostridium difficile
Databases
Essential Genes
Population
Genes
Multigene Family
Bacillus
Genetic Recombination
Gastrointestinal Tract
Alleles
Demography
Pathology

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Microbiology (medical)

Citar esto

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abstract = "Background: Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Results: Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7{\%}), followed by C2 (29.1{\%}). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0{\%}). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. Conclusions: This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.",
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Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases. / Muñoz, Claudia Marina; Ríos-Chaparro, Dora Inés; Patarroyo, Manuel Alfonso; Ramírez, Juan David.

En: BMC Microbiology, Vol. 17, N.º 1, 62, 14.03.2017, p. 1-12.

Resultado de la investigación: Contribución a RevistaArtículo

TY - JOUR

T1 - Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases

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AU - Ríos-Chaparro, Dora Inés

AU - Patarroyo, Manuel Alfonso

AU - Ramírez, Juan David

PY - 2017/3/14

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