We describe the molecular epidemiology of cholera in South Africa during 2018-2020. Vibrio cholerae O1 sequence type (ST) 75 recently emerged and became more prevalent than the V. cholerae O1 biotype El Tor pandemic clone. ST75 isolates were found across large spatial and temporal distances, suggesting local ST75 spread.
Keywords: O1; ST75; South Africa; Vibrio cholerae; antimicrobial resistance; bacteria; enteric infections; sequence type 75.