Genomic study of European Clostridioides difficile ribotype 002/sequence type 8

Area of Science:

• Microbiology
• Genomics
• Epidemiology

Background:

• Clostridioides difficile is a major cause of healthcare-associated infections.
• Clostridioides difficile ribotype 002, linked to sequence type 8 (ST8), is a prevalent human pathogen.

Purpose of the Study:

• To investigate the genetic characteristics of 537 Clostridioides difficile ST8/RT002 genomes.
• To analyze antimicrobial resistance genes and mobile elements within this lineage.
• To explore the One Health implications of ST8/RT002 epidemiology.

Main Methods:

• Whole-genome sequencing of 298 C. difficile strains from a European collection.
• Bioinformatic analysis integrating a global dataset of 1,437 ST8 genomes from Enterobase.
• Pangenome analysis and core genome multilocus sequence typing (cgMLST) clustering.

Main Results:

• ST8/RT002 genomes exhibit close genetic relatedness and low overall variation.
• A diverse range of antimicrobial resistance genes and mobile elements were identified.
• Clonal isolates were detected across human, animal, environmental, and food sectors, indicating a stable lineage with a potential universal environmental source.
• Nine cross-sectoral cgMLST clusters were identified, despite a low percentage of non-human isolates.

Conclusions:

• Clostridioides difficile ST8 is a prominent, genetically stable lineage with significant One Health implications.
• The adaptability of ST8 in acquiring antimicrobial resistance genes underscores the need for vigilance.
• Continued surveillance of non-human sources is crucial for a comprehensive understanding of C. difficile epidemiology.