The Lake Chad Basin, an Isolated and Persistent Reservoir of Vibrio cholerae O1: A Genomic Insight into the Outbreak in Cameroon, 2010

Abstract

The prevalence of reported cholera was relatively low around the Lake Chad basin until 1991. Since then, cholera outbreaks have been reported every couple of years. The objective of this study was to investigate the 2010/2011 Vibrio cholerae outbreak in Cameroon to gain insight into the genomic make-up of the V. cholerae strains responsible for the outbreak. Twenty-four strains were isolated and whole genome sequenced. Known virulence genes, resistance genes and integrating conjugative element (ICE) elements were identified and annotated. A global phylogeny (378 genomes) was inferred using a single nucleotide polymorphism (SNP) analysis. The Cameroon outbreak was found to be clonal and clustered distant from the other African strains. In addition, a subset of the strains contained a deletion that was found in the ICE element causing less resistance. These results suggest that V. cholerae is endemic in the Lake Chad basin and different from other African strains.

Fig 1. Reported cholera cases around the Lake Chad basin.

The number of cases per year (1970–2012) presented in a cumulative graph. The following colors represent each country: Purple represents Nigeria, green represents Chad, red represents Cameroon, and blue represents Niger.

Fig 2. The inferred phylogeny based on SNPs for the Cameroon isolates.

Each isolate is presented with a strain name followed by the city of origin and year of isolation. The vertical lines divide the isolates into two groups, representing the two different resistance profiles. The resistance genes that differ are marked in brown.

Fig 3. Location of Vibrio cholerae cases in Cameroon and around Lake Chad basin.

Red dots in Cameroon indicate the location of the cities from where the isolates originate.

Fig 4. A graphical representation of the ICE fragment ICEVchInd5.

The arrows represent the genes. The numbers indicate bp. position on the ICE fragment, with position 1 starting at the first bp of the fragment. The brown arrows represent the genes that were missing from the less-resistant sub-clone.

Fig 5. The Cameroon outbreak in a global perspective and phylogeny.

Fig A. Map of Africa presenting the origin of the sequenced V. cholerae from the African continent. Green indicates Cameroon and Benin and brown indicates the rest of Africa. Fig B. Global phylogeny inferred from SNPs of 376 V. cholerae lineage 2 isolates. The origin of the majority of isolates in each cluster is indicated by the vertical lines to the right of the figure. The tree is rooted on the non-7^th pandemic strain M66-2. Ten branches have been shortened to fit the figure; this is indicated with a small gap flanked by vertical lines near the end of the branch.