Clostridioides difficile (Clostridium difficile) infection (CDI) is a potentially significant cause of diarrhoeal illness in South Africa, particularly in TB patients who receive long-term intensive antimicrobial therapy. Previously C. difficile ribotype (RT) 017 was identified as the most commonly isolated RT in Cape Town hospitals. To investigate potential strain transmission, a selection of RT017 isolates was analysed by whole-genome shotgun sequencing (WGS) using the Illumina MiSeq platform. The analysis included 48 strains from patients attending nine Cape Town hospitals, including two specialist TB institutions, between September 2014 and September 2015, along with 10 strains isolated in 2012 and sequenced as part of an earlier study. Three different approaches were used to investigate strain relatedness – core genome single nucleotide variant analysis (cgSNV) based on a comparison of high-quality candidate SNVs, core genome multi-locus sequence typing (cgMLST), based on 2270 core genome loci and multi-locus variable-number tandem-repeat analysis (MLVA) based on 7 tandem repeat loci. The overall results of the different approaches were largely congruent with all three methods identifying clusters of related isolates according to previously published cut-offs. However, there were differences in the total number and size of clusters with five clusters of 7-18 isolates identified by cgMLST, eight clusters of 2-14 isolates identified by cgSNV and eleven clusters of 2-12 isolates identified by MLVA. Evidence of within-ward and inter-hospital transmission of clonally-related strains was observed, suggesting that patient movement and/or community sources played a role in strain transmission. In support of in vitro antimicrobial susceptibility testing, WGS predicted several antimicrobial resistance determinants, including mutations in the gyrA and gyrB (fluoroquinolone resistance) and rpoB (rifamycin resistance) genes. Transposons carrying tetM (Tn916, tetracycline resistance) and ermB (Tn6194, MLSB resistance) homologues were identified, with truncated forms of the latter (lacking the ermB gene) present in some strains. Taken together, the results suggest that multidrug resistant, clonally-related RT017 strains are circulating within patients attending public hospitals in the greater Cape Town area.