Vibrio cholerae Outbreaks in Tanzania Exemplify Founder Flush: Simultaneous Increases in Population Size and Genetic Diversity.

Cholera is a major cause of morbidity and mortality in African countries includingTanzania. In August 2015, a major outbreak began in the Republic of Tanzania eventually affecting all 26 regions. This study sought to determine transmission patterns of cholera by determining the genetic relatedness of V. cholerae isolates from different locations in Tanzania.The epidemiology and genetic analysis are consistent with the spread of two MLVA clonal complexes (CCs) throughout Tanzania. Seven locations showed at least one genotype observed in a previous outbreak, possible founder genotype(s), and six locations had at least one and often more new genotypes related to the founder. Whole genome sequencing (WGS) revealed the isolates to be from the T10 and T13 transmission events between south Asia and east Africa. WGS confirmed the distinctness of the CCs and revealed that one CC was notmonophyletic. Close examination of the WGS revealed the examples of dinucleotide alleles at the same site in different isolate genomes being present in all four possible combinations.The V. cholerae isolates represented four distinct genetic lineages. There was evidence for recombination in the WGS. The largest MLVA CC (90% of isolates) revealed a founder-flush phenomenon with a small number of founder and numerous unique genotypes within a district. The cholera outbreaks were initiated by V. cholerae from other districts which then spread and evolved within Tanzania.