Fig. 2: Genetic relatedness of the V. cholerae isolates from the 2022–2023 outbreak and the historical isolates from the late 1980s and 1990s in Malawi.

a Maximum likelihood phylogenetic tree showing the genetic relatedness of all the Vc isolates from Malawi collected between 2022–2023 in the context of the historical Vc isolates from Malawi collected in the late 1980s and 1990s. Two genomes (LD04947912 and YA00436893) represent imported Vc into South Africa isolated from people infected in Malawi and are designated as Malawian sequences. b Maximum likelihood phylogenetic tree showing the genetic relatedness of the 7PET Vc isolates collected between 2022–2023 from Malawi. c Maximum likelihood phylogenetic tree showing the genetic relatedness of the 7PET Vc isolates collected between 2022–2023 in the context of the historical 7PET Vc isolates from Malawi. The circles with different colours at the tip of the phylogeny represent the year of isolation. All the Malawi 2022–2023 isolates were sampled from human clinical cases (coloured in blue) except one (coloured in red text), which was obtained from a water sample at a beach in the southern region of Malawi. The phylogeny is annotated by colour strips at the tips of each tree representing the sequence type (ST), year of isolation, and LPS O-antigen serogroup. The phylogeny was constructed based on the core-genome SNPs identified from the merged alignments of chromosomes 1 and 2, and rooted based on an outgroup Vibrio mimicus species, not shown in the tree. The isolates with taxon labels coloured in black in all the phylogenetic trees were sequenced and reported by previous studies (Supplementary Data 1).