Mobile genetic elements mediating antimicrobial resistance drive the evolutionary process of Clostridioides difficile ST37/RT017

Clostridioides difficile (C. difficile) ST37/RT017 is one of the most prevalent genotypes, exhibiting resistance to multiple antimicrobial agents and widespread dissemination, particularly in East Asia. However, its evolutionary history and genetic adaptation remains limited. Here, we aimed to systematically assess the genetic diversity, key evolutionary events, and potential driving forces of C. difficile ST37/RT017. To explored dynamic trends in the genomic characterization, diversity and changes, both phylogenetic and Bayesian evolutionary analyses revealed that the C. difficile ST37/RT017 strains were clustered into three variant lineages as a directed bus-like topology, from VL I, to VL II, and VL III. An incremental increase in the median number of resistance genes was observed, with one in VL I, five in VL II, and six in VL III. Distinguishing features included variations in resistance genes or fluoroquinolone resistance mutation, such as erm(B), tet(M), aac(6’)-Ie-aph(2’’)-Ia, ant(6)-Ia and gyrA (T82I). Further analysis of evolutionary mechanisms revealed that Tn916, carrying tet(M), was present in 87.9% (160/182) of VL III and 92.6% (163/176) of VL II, but only 4.1% (5/122) of VL I. The Tn6194-like element, carrying erm(B), was found in 25.3% (46/182) of VL II and 84.7% (149/176) of VL III, with none detected in VL I. Furthermore, other functional genes, especially srtB, were notable in C. difficile ST37/RT017, which gradually acquired resistance genes from VL I to VL II and VL III. The systematically analysis in this study suggests that the acquisition of antibiotic resistance genes was the primary driver of adaptive evolution in C. difficile ST37/RT017. Horizontal gene transfer, particularly through mobile genetic elements is a key genetic mechanism in the adaptive evolution of C. difficile ST37/RT017. Based on these genetic profiles, the active establishment and optimization of a rational system for antibiotic use will be crucial to prevent the emergence of a C. difficile ST37/RT017 variant.