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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.

SUBMITTER: Rebaudet S

PROVIDER: S-EPMC4046952 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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

Rebaudet Stanislas S Mengel Martin A MA Koivogui Lamine L Moore Sandra S Mutreja Ankur A Kande Yacouba Y Yattara Ousmane O Sarr Keita Véronique V Njanpop-Lafourcade Berthe-Marie BM Fournier Pierre-Edouard PE Garnotel Eric E Keita Sakoba S Piarroux Renaud R

PLoS neglected tropical diseases 20140605 6

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 th ...[more]

PMID: 24901522

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Project description:Cholera is endemic in Guinea, having suffered consecutive outbreaks from 2004 to 2008 followed by a lull until the 2012 epidemic. Here we describe the temporal-spatial and behavioural characteristics of cholera cases in Conakry during a three-year period, including the large-scale 2012 epidemic.We used the national and African Cholera Surveillance Network (Africhol) surveillance data collected from every cholera treatment centre in Conakry city from August 2011 to December 2013. The prevalence of suspect and confirmed cholera cases, the case fatality ratio (CFR), and the factors associated with suspected cholera were described according to three periods: pre-epidemic (A), epidemic 2012 (B) and post epidemic (C). Weekly attack rates and temporal-spatial clustering were calculated at municipality level for period B. Cholera was confirmed by culture at the cholera national reference laboratory.A total of 4559 suspect cases were reported: 66, 4437, and 66 suspect cases in periods A, B and C, respectively. Among the 204 suspect cases with culture results available, 6%, 60%, and 70% were confirmed in periods A, B, and C, respectively. With 0.3%, the CFR was significantly lower in period B than in periods A (7.6%) and C (7.1%). The overall attack rate was 0.28% in period B, ranging from 0.17% to 0.31% across municipalities. Concomitantly, a cluster of cases was identified in two districts in the northern part of Conakry. At 14%, rice water stools were less frequent in period A than in period B and C (78% and 84%). Dehydration (31% vs 94% and 89%) and coma (0.4% vs 3.1% and 2.9%) were lower during period B than in periods A and C. The treatment of drinking water was less frequent in period A, while there were more reports of recent travel in period C.The epidemic dynamic and the sociological description of suspect cases before, during, and after the large-scale epidemic revealed that the Vibrio cholerae was already present before the epidemic. However, it appeared that infected individuals reacted differently in terms of disease severity as well as their access to treated water and travel habits. Such an in-depth description of cholera epidemics should be systematically carried out in cholera endemic settings in order to prioritize higher risk areas, identify transmission factors, and optimize preventive interventions.

Project description:BackgroundBetween 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting.MethodsIn this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports.FindingsThe 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016-17 epidemic (20?438 cases) spread among settlements along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1-2·3) higher attack rates than those where vaccination occurred before the peak.InterpretationPandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging.FundingThe Bill & Melinda Gates Foundation.

Project description:BackgroundDespite World Health Organization (WHO) prequalification of two safe and effective oral cholera vaccines (OCV), concerns about the acceptability, potential diversion of resources, cost and feasibility of implementing timely campaigns has discouraged their use. In 2012, the Ministry of Health of Guinea, with the support of Médecins Sans Frontières organized the first mass vaccination campaign using a two-dose OCV (Shanchol) as an additional control measure to respond to the on-going nationwide epidemic. Overall, 316,250 vaccines were delivered. Here, we present the results of vaccination coverage, acceptability and surveillance of adverse events.Methodology/principal findingsWe performed a cross-sectional cluster survey and implemented adverse event surveillance. The study population included individuals older than 12 months, eligible for vaccination, and residing in the areas targeted for vaccination (Forécariah and Boffa, Guinea). Data sources were household interviews with verification by vaccination card and notifications of adverse events from surveillance at vaccination posts and health centres. In total 5,248 people were included in the survey, 3,993 in Boffa and 1,255 in Forécariah. Overall, 89.4% [95%CI:86.4-91.8%] and 87.7% [95%CI:84.2-90.6%] were vaccinated during the first round and 79.8% [95%CI:75.6-83.4%] and 82.9% [95%CI:76.6-87.7%] during the second round in Boffa and Forécariah respectively. The two dose vaccine coverage (including card and oral reporting) was 75.8% [95%CI: 71.2-75.9%] in Boffa and 75.9% [95%CI: 69.8-80.9%] in Forécariah respectively. Vaccination coverage was higher in children. The main reason for non-vaccination was absence. No severe adverse events were notified.Conclusions/significanceThe well-accepted mass vaccination campaign reached high coverage in a remote area with a mobile population. Although OCV should not be foreseen as the long-term solution for global cholera control, they should be integrated as an additional tool into the response.

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

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

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