One Health investigation of the antimicrobial resistome, genetic diversity and public health risk of toxigenic Clostridioides difficile isolated from humans and animals in Gauteng, South Africa

Abstract

Clostridioides difficile (C. difficile) is a Gram-positive pathogen that causes antimicrobial-associated diarrhoea in both high-income and low and middle-income countries. However, Africa lacks routine surveillance, strain typing and sufficient knowledge about the zoonotic potential of this pathogen. This study employed a One-Health (OH) approach to investigate antimicrobial resistome and genomic features of C. difficile isolated from human stool specimens (100) and animal (cattle and swine) faecal samples (200) using phenotypic and molecular techniques. Clinical and animal faecal samples were cultured on CCFA, with multiplex-PCR assays used for isolate identification and toxin gene detection. Animal isolates were further analyzed using MALDI-TOF MS. Whole genome sequencing (WGS) was conducted and data was analysed using various online tools including EnteroBase, pubMLST and CARD. Among clinical samples, 62% (62/100) were identified as C. difficile by M-PCR, with 97% (60/62) being toxigenic. The most dominant toxin profile was A+B+CDT+, linked to hypervirulence. The WGS of 43 C. difficile genomes revealed that 93% (40/43) clustered into clades 1-5, with epidemic hypervirulent strain sequence type (ST) 1 (clade 2) being the most prevalent [45%, 18/40]. Phenotypically, all isolates were susceptible to metronidazole and vancomycin. However, a chromosomal PnimBG promoter mutation, associated with reduced susceptibility to metronidazole was detected in ST1 strains raising concerns about future resistance. The success of epidemic strains such as ST1 and ST37 was linked to their antimicrobial resistance (AMR) genotypes. The gyrA mutation (Thr82IIe) associated with fluoroquinolone resistance was identified in all ST1 strains. The ST37 strains carried AMR determinants for five antimicrobial classes, confirming them as multidrug-resistant (MDR). Overall, 95% (40/43) of strains carried AMR determinants (AMR genes, mutations, efflux pumps, mobile genetic elements) for at least three antimicrobial classes, classifying them as MDR. This study is the first to report hypervirulent strains ST1 in Africa and ST11 in South Africa (SA), associated with zoonotic potential, severe symptoms and epidemic outbreaks. Phylogenetic analysis indicated an ongoing ST1 outbreak in both private and public healthcare settings. Additionally, strain ST54 was identified and harbouring multiple AMR determinants. The detection of zoonotic-associated sequence types (ST1, ST2, ST3, ST11, and ST37) in clinical samples highlights the importance of an OH approach. Although no animal isolates were identified as C. difficile, 31% (31/100), of swine isolates were culture - positive with 74% (23/31) being Clostridium perfringens, a pathogen of public health concern. Furthermore, 1% (1/100) of cattle isolates were Clostridium subterminales.

The findings suggest that C. difficile resistance to therapeutic antimicrobials remains rare, except for the PnimBG promoter mutation in ST1 strains. The high resistance rate of MDR C. difficile may be linked to extensive antimicrobial use, in immunocompromised individuals driven by the prevalence of HIV and TB in SA. Strengthened antimicrobial stewardship and infection control practices are critical to curbing AMR and improving patient outcomes. It is recommended that the C. difficile diagnostic algorithm used in SA be revised to include culture-based, AST and molecular epidemiology techniques, as current methods have failed to detect the ongoing outbreak of ST1 exposing a key diagnostic gap.