Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018-2020

Abstract

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.

Figure

Maximum-likelihood phylogenomic tree for Vibrio cholerae O1 sequence type (ST) 75 isolates collected from South Africa, 2018–2020. The tree represents phylogeny for 7 V. cholerae O1 ST75 isolates from South Africa (red text); 144 sequences from a global collection of ST75, or closely related ST169, ST170, and ST182 isolates; and 1 7PET V. cholerae O1 sequence. The 7PET genome N16961 (ST69) was used as an outgroup. For each genome, its name; year of collection, when known; and country of isolation, plus province of isolation for isolate from South Africa, are shown at the tips of the tree. The lineages, presence of CTXɸ prophage or its variant form, and types of ctxB alleles are also shown. The 7PET outgroup genome, N16961, contains CTXɸ with a ctxB3 allele (not represented in the figure). Red dots indicate bootstrap values >95%. Scale bar indicates the number of nucleotide substitutions per variable site. 7PET, seventh pandemic V. cholerae O1 El Tor; CTXɸ, cholera toxin phi prophage; ctxB, cholera toxin B subunit gene.