Deciphering the origin of the 2012 cholera epidemic in Guinea by integrating epidemiological and molecular analyses

Abstract

Cholera is typically considered endemic in West Africa, especially in the Republic of Guinea. However, a three-year lull period was observed from 2009 to 2011, before a new epidemic struck the country in 2012, which was officially responsible for 7,350 suspected cases and 133 deaths. To determine whether cholera re-emerged from the aquatic environment or was rather imported due to human migration, a comprehensive epidemiological and molecular survey was conducted. A spatiotemporal analysis of the national case databases established Kaback Island, located off the southern coast of Guinea, as the initial focus of the epidemic in early February. According to the field investigations, the index case was found to be a fisherman who had recently arrived from a coastal district of neighboring Sierra Leone, where a cholera outbreak had recently occurred. MLVA-based genotype mapping of 38 clinical Vibrio cholerae O1 El Tor isolates sampled throughout the epidemic demonstrated a progressive genetic diversification of the strains from a single genotype isolated on Kaback Island in February, which correlated with spatial epidemic spread. Whole-genome sequencing characterized this strain as an "atypical" El Tor variant. Furthermore, genome-wide SNP-based phylogeny analysis grouped the Guinean strain into a new clade of the third wave of the seventh pandemic, distinct from previously analyzed African strains and directly related to a Bangladeshi isolate. Overall, these results highly suggest that the Guinean 2012 epidemic was caused by a V. cholerae clone that was likely imported from Sierra Leone by an infected individual. These results indicate the importance of promoting the cross-border identification and surveillance of mobile and vulnerable populations, including fishermen, to prevent, detect and control future epidemics in the region. Comprehensive epidemiological investigations should be expanded to better understand cholera dynamics and improve disease control strategies throughout the African continent.

Figure 1. Evolution of the weekly cholera cases and rainfall in Guinea in 2012.

Accumulated rainfall data for the most affected areas of the country (Maritime and Middle Guinea) were obtained from satellite estimates (TMPA-RT 3B42RT derived), which was averaged on the position 9.00N-12.00N/15.00-11.75W and is available at: http://disc2.nascom.nasa.gov/Giovanni/tovas/realtime.3B42RT_daily.2.shtml. The blue bars indicate the weekly rainfall levels, and the red line indicates the number of suspected cholera cases per week.

Figure 2. Cumulated cholera attack rates and deaths per prefecture during the 2012 Guinean epidemic.

Figure 3. Cholera in Maritime Guinea between February and May 2012.

The map illustrates the early propagation of the outbreak along the coast and the cumulated attack rate per sub-prefecture. Village positions are available on the Index Mundi website (http://www.indexmundi.com/zp/gv/).

Figure 4. MLVA-based genotypes and relatedness of 38 clinical V. cholerae strains isolated in Guinea in 2012.

(A) Network of V. cholerae strain relatedness based on MLVA genotype. Following the genotype analysis of 38 V. cholerae strains using 6 different microsatellite loci, the strains were grouped according to the resulting MLVA genotype profiles. Each colored circle corresponds to a different genotype. The numbers indicate the sequential order when the first strain of the corresponding genotype was isolated. Circle diameter is relatively proportional to the number of isolates represented by each genotype (e.g., 14 strains displayed genotype #1, 7 isolates displayed genotype #8 and 1 strain displayed genotype #3). Each segment corresponds to a single mutation at 1 of the 6 assessed VNTRs. Bold segments represent primary and likely relatedness links between genotypes, while the dashed segments represent secondary and less likely genetic relationships. Genotype #1 was identified as the founder genotype using the eBURST algorithm. (B) Spatiotemporal repartition of genotyped V. cholerae strains. Prefecture-level maps of Guinea are displayed for each month from February to September 2012. The genotype color code described in Figure 4A was applied to spatially and temporarily localize the isolated strains. Therefore, the pie charts reflect the month and prefecture of strain isolation (represented by strain genotype) as well as the relative proportion of each genotype among them. Segments between different months spatially and temporarily illustrate the genetic relatedness displayed in Figure 4A. Only primary and sequentially earliest links between genotypes are represented.

Figure 5. (A) Maximum likelihood phylogenetic tree of the seventh pandemic lineage of V. cholerae based on the SNP differences across the whole core genome and including a strain isolated during the onset of the Guinean 2012 outbreak.

The pre-seventh pandemic isolate M66 was used as an outgroup to root the tree. Blue, green and red branches represent waves 1, 2 and 3, respectively. Purple and sky blue clade lineages represent the Kenyan clade and two South Asian clades within the third wave, respectively. Scale is provided as the number of substitutions per variable site. (B) Greater resolution of wave 3 of the seventh pandemic, in which the Guinean strain clustered distinctly from the two South Asian clades and the dominant Kenyan clade. Guinean isolate G298 is represented by the square while each colored circle indicates a spatially different isolate (as shown in the key). Scale is provided as the number of substitutions per variable site.