A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile | Microbiology Society
Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of   Clostridioides difficile   infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few ‘epidemic’ strains in specific geographical regions. Here, through detailed analysis of 10 330 publicly-available   C. difficile   genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in   C. difficile  . Of the 10 330   C  .   difficile   genomes, 4532 (43.9 %) in 89 STs across clades 1–5 carried at least one genotypic AMR determinant, with 901 genomes (8.7 %) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades.   C. difficile   from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (P