Founder-flush effect found in Vibrio cholerae by MLVA of Nigerian samples

Introduction: We analyzed the multilocus variable tandem repeat analysis (MLVA) genotypes from DNA of toxigenic Vibrio cholerae O1 patient isolates from Nigeria collected by the Nigerian Institute of Medical Research between 2016 to 2021. Findings: Sixty distinct MLVA genotypes were observed among the 144 Isolates. There were two large clonal complexes (CC) of related genotypes that differed by change at a single locus. The locus with the most alleles was P5. Each genotype is represented by the number of repeats at each of the five loci, in order. The first CC was observed from 2016 to 2019, but not afterwards. A single genotype of the first CC was observed in 2016, 5 genotypes in 2017, 6 in 2018 including 2 previously observed in 2017 and 1 in 2019. The second CC was observed only in 2021. Three genotypes - 8,4,6,18,y where y = 33, 34 or 35 – were observed in isolates collected at multiple locations. These genotypes were observed in 8, 7 and 7 of the 11 outbreaks, respectively. All three genotypes were present in Gombe, Plateau and Jigawa. Only one outbreak did not have any of these three genotypes. 15 of 18 other genotypes were unique to a location. In Gombe, Katsina, Kebbi, Lagos, Niger, Plateau and Taraba, an isolate with a founder genotype (8,4,6,18,y) was collected prior to isolates with genotypes unique to that site. Discussion: The genotypes of V. cholerae isolates collected from the outbreaks of cholera follow a founder-flush pattern. One or more genotype(s) [the founders] give(s) rise to multiple other genotypes as the outbreak expands and spreads [the flush] over time and space in Nigeria. Our data and analyses are consistent with the founder-flush phenomena. Keywords: cholera, MLVA, founder-flush, Nigeria, surveillance, Africa, Vibrio cholerae