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></div

MLVA CC for <i>V</i>. <i>cholerae</i> associated with outbreaks in Uganda.

<p>Each genotype is represented by five numbers indicating the number of repeats at the five loci, VC0147, VC0436-7 (intergenic), VC1650, VCA0171 and VCA0283. ‘N = ‘ reports the number of isolates with that genotype. The lines connecting the boxes indicate variation at a single locus. Part A is Clonal Complex 1, Part B is Clonal Complex 2, and Part C is Clonal Complex 3.</p

Phylogram of <i>V</i>. <i>cholerae</i> WGS data.

<p>Forty-one sequences from African isolates representing T10, T11 and T12 were included. Solid lines and black arrows demarcate the boundaries of the transmission events (T). Dotted lines and outlined arrows demarcate the boundaries of the clonal complexes (CC) in Uganda. Dashed arrows identify specific isolates from locations outside Uganda inferred to be examples of cross-border spread. The sequences within the Ugandan clades were less than five nucleotides apart. Those sequences in the Tanzanian clades were less than nine nucleotides from the Ugandan sequences of the closest clade. The radial lines are proportional to the number of nucleotide differences.</p

District of origin, number of isolates by year of isolate identification and serotype of <i>V</i>. <i>cholerae</i> isolates tested using PCR, MLVA and WGS.

<p>District of origin, number of isolates by year of isolate identification and serotype of <i>V</i>. <i>cholerae</i> isolates tested using PCR, MLVA and WGS.</p

Location of the fishing villages in Uganda that reported cholera outbreaks, 2011–2015.

<p>Location of the fishing villages in Uganda that reported cholera outbreaks, 2011–2015.</p

Cholera outbreaks that occurred in fishing villages along Lake Albert.

<p>Fig 4a-4c: Cholera outbreaks in Hoima district in 2012, 2013 and 2015, respectively.</p

Monthly reported cholera cases in fishing villages and average long term rainfall in Uganda, 2011–2015.

<p>Monthly reported cholera cases in fishing villages and average long term rainfall in Uganda, 2011–2015.</p

Location of the study districts, major lakes and rivers in Uganda, 2011–2015.

<p>Location of the study districts, major lakes and rivers in Uganda, 2011–2015.</p

Cholera outbreaks that occurred in fishing villages along Lake Edward.

<p>Fig 3a: Cholera outbreaks in Rukungiri and Kasese districts, 2011; Fig 3b: Cholera outbreak in Kasese district, 2015.</p

Description of cholera outbreaks in fishing villages in Uganda, 2011–2015.

<p>Description of cholera outbreaks in fishing villages in Uganda, 2011–2015.</p