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Prophage Carriage and Genetic Diversity within Environmental Isolates of Clostridioides difficile

Khald Blau1, Claudia Gallert1

  • 1Department of Microbiology-Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany.

International Journal of Molecular Sciences
|January 11, 2024
PubMed

Insights

Environmental Clostridioides difficile strains carry diverse prophages, some with CRISPR arrays. These integrated prophages may influence bacterial biology and fitness.

Area of Science:

  • Microbiology
  • Genomics
  • Bacteriophage Biology

Background:

  • Clostridioides difficile causes antibiotic-associated diarrhea globally.
  • Bacteriophages are explored as alternative therapeutics.
  • Prophage carriage in environmental C. difficile is understudied.

Purpose of the Study:

  • To investigate the prevalence and genetic diversity of integrated prophages in environmental C. difficile isolates.
  • To identify CRISPR-Cas systems within prophage regions.
  • To analyze phylogenetic relationships of identified prophages.

Main Methods:

  • Genomic analysis of 166 environmental C. difficile isolates.
  • Utilized PHASTER web server for prophage prediction.
  • Employed CRISPRCasFinder for CRISPR-Cas system identification.
  • Phylogenetic analysis based on phage-related genes (TerL, LysM).

Main Results:

  • Identified 372 intact prophages, with phiCDHM1 and phiCDHM19 being predominant.
  • Discovered two novel siphoviruses: phiSM101- and phivB_CpeS-CP51-like Clostridium phages.
  • Found a correlation between prophage types and sequence types (STs)/ribotypes.
  • Observed that most prophages carry CRISPR arrays and accessory genes (Agr, Abi).

Conclusions:

  • Environmental C. difficile strains harbor a diverse range of prophages.
  • Prophage carriage, genetic diversity, and CRISPR arrays may impact host strain biology, lifestyle, and fitness.
  • Findings contribute to understanding phage-host interactions in environmental settings.
Keywords:
CRISPR-Cas systemsClostridioides difficileintact prophagesphage-related genesprophagesribotypessequence types

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