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

Marina Muñoz1,2, Dora Inés Ríos-Chaparro1, Manuel Alfonso Patarroyo3,4

  • 1Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia.

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Multilocus sequence typing (MLST) analysis of Clostridium difficile (CD) reveals common strains and clades globally. The study suggests revising housekeeping genes like sodA and indicates more CD clades may exist.

Keywords:
Clostridium difficileDistribution patternMultilocus sequence typing (MLST)Population structure

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Area of Science:

  • Microbiology
  • Genetics
  • Epidemiology

Background:

  • Clostridium difficile (CD) causes various gastrointestinal pathologies.
  • Multilocus sequence typing (MLST) is a robust method for bacterial strain identification.
  • A specific MLST scheme exists for CD, crucial for tracking its diversity.

Purpose of the Study:

  • To describe the frequency of Clostridium difficile sequence types (STs) and Clades (C).
  • To evaluate the intra-taxa diversity within the CD MLST database (CD-MLST-db).
  • To assess the utility of an MLSA approach for CD population structure analysis.

Main Methods:

  • Analysis of 1778 Clostridium difficile isolates from 17 countries.
  • Utilized Multilocus Sequence Typing (MLST) and Multilocus Sequence Analysis (MLSA).
  • Evaluated the diversity of seven housekeeping genes within the MLST scheme.

Main Results:

  • Clade 1 (C1) was the most frequent worldwide (57.7%), followed by Clade 2 (C2) (29.1%).
  • Sequence Type 1 (ST-1), belonging to C2, was the most common ST.
  • Genes like sodA showed high diversity, suggesting a need for revision in the MLST scheme; a distinct group of STs indicated potential for more CD clades.

Conclusions:

  • The CD-MLST-db is valuable for studying CD distribution and population structure.
  • The housekeeping gene sodA may require re-evaluation within the CD MLST scheme.
  • Evidence suggests a greater number of Clostridium difficile clades than currently defined, with genetic material exchange contributing to diversity.