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.
The seventh cholera pandemic, caused by Vibrio cholerae O1 biotype El Tor (7PET), arrived in Africa during 1970 and became endemic in many countries on the continent (1). Cholera was first reported in South Africa in 1974 (2). However, South Africa is not considered a cholera-endemic area; outbreaks typically are associated with importation, particularly from neighboring countries. The last cholera outbreak in South Africa was triggered by imported cases from an outbreak in Zimbabwe during 2008; South Africa reported 12,706 cases during November 2008–April 2009 (3).
Globally, 7PET isolates are genetically homogeneous and linked to the Bay of Bengal in South Asia (4,5). Most 7PET isolates are multidrug-resistant sequence type (ST) 69 (6). Rarely, 7PET has a single-locus variant, ST515, in isolates from Africa belonging to lineage T10 (7). As of September 2021, all cholera isolates from South Africa have been characterized as 7PET ST69 by multilocus sequence typing (MLST).
South Africa actively surveils for cholera. Since the 2008–2009 outbreak, few cases have been identified: 5 during 2010–2014, most of which were imported, and none during 2015–2017. During 2008–2009, large outbreaks occurred in 3 provinces, Mpumalanga, Limpopo, and KwaZulu-Natal (3), but all were caused by imported cases from neighboring Zimbabwe and Mozambique. Therefore, given their experience, healthcare workers and laboratorians in these provinces typically will test for cholera in all cases of acute watery diarrhea.
In South Africa, the National Institute for Communicable Diseases (NICD) is notified of suspected cholera cases. NICD’s Centre for Enteric Diseases supports case investigations and receives all human and environmental V. cholerae isolates for further investigation. The case definition for confirmed cholera is isolation of V. cholerae O1 or O139 from a person with diarrhea. We investigated the molecular epidemiology of V. cholerae in South Africa during 2018–2020.