Imported Cholera Cases, South Africa, 2023

Abstract

Since February 2022, Malawi has experienced a cholera outbreak of >54,000 cases. We investigated 6 cases in South Africa and found that isolates linked to the outbreak were Vibrio cholerae O1 serotype Ogawa from seventh pandemic El Tor sublineage AFR15, indicating a new introduction of cholera into Africa from south Asia.

Keywords: Malawi; South Africa; Vibrio cholerae; Vibrio cholerae serogroup O1; bacteria; cholera; enteric infections; sequence type 69.

Figure

Maximum-likelihood phylogeny of Vibrio cholerae O1 El Tor isolates collected in South Africa, 2023, compared with 1,443 reference seventh pandemic V. cholerae El Tor (7PET) genomic sequences. A6 was used as the outgroup. The genomic waves and acquisition of the ctxB7 allele are indicated. Color coding indicates the geographic origins of the isolates; sublineages previously introduced into Africa (AFR1, AFR3–AFR14) are shown at right. A magnification of the clade containing the 6 isolates from South Africa (red text) is shown at right. For each genome, name (or accession number), country where contamination occurred, and year of sample collection are shown at the tips of the tree. The 6 isolates collected in South Africa belong to a new 7PET wave 3 sublineage called AFR15. Blue dots indicate bootstrap values ≥90%. Scale bars indicate number of nucleotide substitutions per variable site.