Genomic basis of antimicrobial resistance in non-toxigenic Clostridium difficile isolates from Southeast Asia

Despite being incapable of causing disease, non-toxigenic Clostridium difficile may still have clinical relevance. This study explored the role of non-toxigenic C. difficile as a reservoir of accessory antimicrobial resistance (AMR) genes by looking at the genomes of non-toxigenic C. difficile from various sources in Southeast Asia. This region has high rates of antimicrobial use, a high prevalence of non-toxigenic C. difficile and phenotypic AMR in such strains. More than half of the non-toxigenic C. difficile strains investigated had at least one accessory AMR genes. These genes were found on mobile genetic elements which were similar to the elements found in other bacteria, including Erysipelothrix rhusiopathiae and Streptococcus suis, both of which can be found in the gut of pigs. This suggests that non-toxigenic C. difficile can carry AMR genes between different hosts and can exchange these genes with a wide range of pathogenic bacteria. The concordance between MLSB resistance genotype and phenotype was low, suggesting multiple resistance mechanisms, many of which remain unknown. On the contrary, there was a high concordance between resistance genotype and phenotype for both fluoroquinolones and rifaximin. From an epidemiological perspective, non-toxigenic C. difficile populations in Southeast Asia comprised members of evolutionary clades 1 and 4, which are thought to originate from Europe and Asia, respectively. This population structure reflects the close relationship between the people of the two regions.