Pangenome-GWAS analysis of Clostridioides difficile resistant traits from healthcare and non-healthcare associated settings

Clostridioides difficile (C. difficile) is a gastrointestinal pathogen that causes healthcare-associated infections with numerous mechanisms to acquire and confer antimicrobial resistance (AMR) and rapidly adapt to novel environments. These environments extend beyond healthcare, and encompass non-healthcare related settings, where antimicrobials engender distinct selection pressures. Employing a dataset of 3,870 whole-genome sequences of C. difficile from healthcare and non-healthcare environments, this study investigates the selection pressures associated with each setting and its impact on the prevalence of AMR genes of C.difficile. To achieve this, we used pangenome-wide association studies (pan-GWAS) and Generalized Linear Mixed Model to identify significant associations between AMR genes and the specific setting from which the isolates were collected. Our findings evidenced significant differences in the AMR gene repertoire between healthcare and non-healthcare associated C. difficile with antibiotics such as macrolides and fluoroquinolones being more linked with healthcare. Antibiotics commonly used in agriculture such as aminoglycosides or tetracyclines also presented associations with non-healthcare environments. Our work offers a comprehensive exploration of C. difficile AMR gene repertoire across healthcare and non-healthcare related settings shedding light on the selection pressures present in each environment, enhancing our understanding of C. difficile resistome and its influence on the bacterium's opportunistic colonization nature.