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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete

Yuan Wu1,2, Lin Yang3, Wen-Ge Li4

  • 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. wuyuan@icdc.cn.

BMC Genomics
|November 1, 2019
PubMed
Summary
This summary is machine-generated.

Whole genome sequencing of Clostridioides difficile Clade 5 isolates reveals distinct mobile genetic elements and evolutionary pathways in RT078 strains. This highlights the importance of PCR-ribotyping for identifying these heterogeneous C. difficile strains.

Keywords:
CRISPR spacersCapillary electrophoresis-based PCR-ribotypingClostridioides difficileComplete whole genome sequencingMobile genetic elementstcdC deletion

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Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Clade 5 Clostridioides difficile exhibits significant heterogeneity, prompting increased research interest.
  • ST11 C. difficile isolates, including RT078 and novel ribotypes, were studied in hospitalized elderly patients receiving antibiotics.

Purpose of the Study:

  • To perform whole-genome sequencing of three ST11 C. difficile isolates.
  • To analyze and compare mobile genetic elements, antibiotic resistance, and virulence factors among these isolates.

Main Methods:

  • Third-generation sequencing for complete whole-genome sequencing.
  • Analysis of mobile genetic elements (MGEs), antibiotic-resistance genes, and virulent-related genes.
  • Comparison of genetic features including deletions, point mutations, plasmids, and CRISPR spacers.

Main Results:

  • Identical deletions and point mutations in tcdC were observed across all three isolates, challenging previous assumptions about RT078.
  • Isolate 21,062 (RT078) possessed a unique plasmid, distinct transposon content, and specialized CRISPR spacers.
  • All isolates maintained high drug sensitivity, but RT078 showed unique drug-resistance genes and a loss of flagellum-related genes.

Conclusions:

  • Capillary electrophoresis-based PCR-ribotyping is crucial for confirming RT078.
  • RT078 isolates demonstrate unique MGEs, suggesting an independent evolutionary trajectory.
  • Further studies with diverse RT078 isolates are recommended to validate these findings.