Mutreja et al (2011): Evidence for several waves of global transmission in the seventh cholera pandemic

I have been reading the paper by Mutreja et al (2011): "Evidence for several waves of global transmission in the seventh cholera pandemic", by Ankur Mutreja, Gordon Dougan, my current group leader Nick Thomson, and their collaborators. 

Epidemiology

In this paper, they sequenced the genomes of 136 Vibrio cholerae isolates, and combined those with 18 previously published V. cholerae genomes, to make a phylogenetic analysis of 154 global isolates. Based on this, they showed that the current pandemic lineage of cholera (7PET lineage) has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s. Wave 1 spread in 1977-1992 and included the South American pandemic in the 1990s, Wave 2 in 1978-1984, and Wave 3 in 1986-1990. 

 Antimicrobial resistance

Wave 2 and 3 isolates have integrative conjugative element of the SXT family (an SXT/R391 ICE) carrying antimicrobial resistance genes, which they estimated to have been gained around 1978-1984. 

Cholera toxin subtype

They found that each wave had a particular cholera toxin (CTX) type.

Lineages of Vibrio cholerae

As well as investigating the spread of the current pandemic lineage (7PET lineage) of V. cholerae, Mutreja et al also put the 7PET lineage in context within the species. From phylogenetic analysis, they showed that the 7PET lineage is one of eight lineages of V. cholerae (L1-L8): 7PET is lineage L2, while the 'Classical' lineage (an earlier pandemic lineage) is lineage L1 in their classification, and isolates from the US Gulf Coast are L3. 

Pathogenwatch

I made a Pathogenwatch 'collection' for the isolates sequenced by Mutreja et al (2011), which you can see here. The collection contains 131 isolates, as I left out 5 relatively low-quality assemblies.