Genomic Microevolution of Vibrio cholerae O1, Lake Tanganyika Basin, Africa

Abstract

Africa's Lake Tanganyika basin is a cholera hotspot. During 2001-2020, Vibrio cholerae O1 isolates obtained from the Democratic Republic of the Congo side of the lake belonged to 2 of the 5 clades of the AFR10 sublineage. One clade became predominant after acquiring a parC mutation that decreased susceptibility to ciprofloxacin.

Keywords: Africa. Emerg Infect Dis. 2023 Jan [date cited]. https://doi.org/10.3201/eid2901.220641; African Great Lakes Region; Burundi; Democratic Republic of Congo; Gallandat K; Jeandron A; Kamwiziku G; Lake Tanganyika; Lake Tanganyika Basin; Njamkepo E; Rauzier J; Suggested citation for this article: Hounmanou YMG; Tanzania; Vibrio cholerae; Zambia; bacteria; cholera; et al. Genomic microevolution of Vibrio cholerae O1; genomics; neglected tropical diseases.

Figure 1

Phylogenomics of clinical and environmental Vibrio cholerae O1 El Tor isolates from the Lake Tanganyika basin, Africa. A) Maximum-likelihood phylogeny of 1,366 seventh pandemic V. cholerae O1 El Tor (7PET) genomes with strain A6 as the outgroup. The different sublineages introduced into Africa are indicated. Light blue indicates AFR10 sublineage. Rings 1 and 2 show geographic origin of isolates; ring 3 shows isolates sequenced in this study. B) Maximum-likelihood tree for 357 AFR10 isolates, with strain N16961 as an outgroup. The 5 clades are color-coded: AFR10a, brown; AFR10b, yellow; AFR10c, green; AFR10d, pink; and AFR10e, blue. The outermost ring indicates the geographic locations of the different isolates in the tree. Filled circles indicate the presence of ST69 or ST515, Ogawa and Inaba serotypes, IncA/C plasmid, and the S85L mutation in parC; open circles indicate their absence. MLST, multilocus sequence typing; ST, sequence type.

Figure 2

A) Spatiotemporal dynamics of the AFR10 clades of Vibrio cholerae O1 in the African Great Lakes Region, Africa, 1998–2020. Circle size indicates the number of isolates at the location concerned. The 5 AFR10 clades are color-coded: AFR10a, brown; AFR10b, yellow; AFR10c, green; AFR10d, pink; and AFR10e, blue. B) V. cholerae O1 isolates from the Lake Tanganyika basin. All AFR10 isolates from Bujumbura (Burundi), Kigoma (Tanzania) and the South-Kivu province (DRC) were considered to be Lake Tanganyika basin isolates.