Phenotypic and genotypic antimicrobial resistance profiles of clinical Clostridioides difficile isolates collected from private and public health settings in South Africa.

Purpose: Antimicrobial resistance (AMR) is important in the pathogenesis and spread of Clostridioides difficile infection (CDI). However, very little is known about the association of AMR and C. difficile in South Africa. The present study aimed to investigate the phenotypic and genotypic antimicrobial profiles of clinical C. difficile isolates.

Methods: Phenotypic antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS) were used to characterize the isolates.

Results: The AST showed that 43 isolates were susceptible to metronidazole and vancomycin. The WGS revealed a PnimB promoter mutation associated with reduced metronidazole susceptibility in all sequence type (ST) 1 strains (42%, 18/43). No vancomycin resistance determinants were found. Distinct lineages displayed specific resistance traits, such as fluoroquinolone resistance in ST1 strains due to a DNA gyrase (gyrA) mutation (Thr82Ile) and multidrug resistance (MDR) in ST37 strains, which contained resistance determinants for five antimicrobial classes. Overall, 95% (40/43) of strains had AMR determinants for at least three antimicrobial classes, indicating MDR. A qacG efflux pump gene, conferring resistance to disinfectants, was found in all strains.

Conclusion: Antimicrobial resistance to metronidazole and vancomycin remains rare, however, high MDR prevalence particularly among ST1 and ST37 strains, suggests a risk of AMR gene transmission to other pathogens. The high rate of MDR C. difficile may reflect extensive antimicrobial use driven by comorbidities in immunocompromised individuals, contributing to AMR. These findings underscore the importance of ongoing AMR surveillance, effective antimicrobial stewardship and infection control to manage CDI and mitigate AMR spread.