Molecular characterization of <i>Vibrio cholerae</i> responsible for cholera epidemics in Uganda by PCR, MLVA and WGS

<div><p>Background</p><p>For almost 50 years sub-Saharan Africa, including Uganda, has experienced several outbreaks due to V<i>ibrio cholerae</i>. Our aim was to determine the genetic relatedness and spread of strains responsible for cholera outbreaks in Uganda.</p><p>Methodology/Principal findings</p><p>Sixty-three <i>V</i>. <i>cholerae</i> isolates collected from outbreaks in Uganda between 2014 and 2016 were tested using multiplex polymerase chain reaction (PCR), multi-locus variable number of tandem repeat analysis <b>(</b>MLVA) and whole genome sequencing (WGS). Three closely related MLVA clonal complexes (CC) were identified: CC1, 32% (20/63); CC2, 40% (25/63) and CC3, 28% (18/63). Each CC contained isolates from a different WGS clade. These clades were contained in the third wave of the 7^th cholera pandemic strain, two clades were contained in the transmission event (T)10 lineage and other in T13. Analysing the dates and genetic relatedness revealed that <i>V</i>. <i>cholerae</i> genetic lineages spread between districts within Uganda and across national borders.</p><p>Conclusion</p><p>The <i>V</i>. <i>cholerae</i> strains showed local and regional transmission within Uganda and the East African region. To prevent, control and eliminate cholera, these countries should implement strong cross-border collaboration and regional coordination of preventive activities.</p>