Bacterial
Vibrio cholerae
Vibrio cholerae, for the most part, is a natural inhabitant of aquatic ecosystems, where it is found in association with many different organisms that live in or interact with the aquatic environment, such as birds, fish, copepods and crustaceans. Members of this species can be serotyped based on the O-antigens associated with polysaccharides found on the outer membrane of the cell. Of the more than 200 known serogroups of Vibrio cholerae only two, O1 and O139, are associated with the gastroentistinal disease cholera.
The pathogenic strains of V. cholerae have, integrated in their genomes, genes of the CTXϕ phage that include the ctxA and ctxB genes that together assemble the cholera toxin. Pathogenic V. cholerae strains also contain the tcpA gene (part of the Vibrio pathogenicity island 1 - VPI-1) and others genes that assemble the toxin-coregulated pilus (TCP), a structure essential for the formation of V. cholerae microcolonies and colonisation of the human gut.
The current outbreaks of cholera that occur around the world are caused by a strain of V. cholerae that evolved in the 1950s and sparked the 7th cholera pandemic, which started in Indonesia. The evolutionary history of this strain leads back to the El Tor strain of cholera that emerged in Egypt in the early 20th century, but several evolutionary stages took place before the final pandemic strain arose.
Hu et al describe in detail the stages of evolution of the 7th pandemic strain, which happened through a series of recombination events, infection with the CTXϕ phage and acquisition of two new pathogenicity islands (VSP-I and VSP-II). The 7th pandemic itself has progressed in several overlapping waves, which have also involved genetic changes such as the acquisition of the SXT integrating conjugative element. We are currently in the 3rd wave of the 7th cholera pandemic.
The following figure (from Montero et al) graphically illustrates the evolution and classification of V. cholerae:
Since its emergence in the 1960s, 7th pandemic cholera has been imported into Africa 13 different times, with each introduced by identified as T1 up until T13 (see Weill et al and Bwire et al). The particular strains of V. cholerae that made up the T12 import into Africa are also associated with the reemergence of cholera in Haiti from 2010 onwards.
As is illustrated by the above short history, V. cholerae is highly diverse species of baceteria whose genomic evolution involves both recombination and horizontal gene transfer (sometimes mediated by phages) and clonal expansion of evolutionarily successful strains. This pattern of diversity and clonality is common to several bacteria, where a species can involve remarkable diversity and an outbreak (even a large one) clonal expansion of a successful clone.
For the purposes of our practical study we will be working with some sequences associated with cholera in Haiti. These are drawn from BioProject PRJNA510624, whose analysis was published in two papers by Mavian et al and Paisie et al.