Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates

Abstract

Background: Since cholera appeared in Africa during the 1970s, cases have been reported on the continent every year. In Sub-Saharan Africa, cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa.

Methodology/principal findings: In this study, we applied MLVA (Multi-Locus Variable Number Tandem Repeat Analysis) typing of 337 Vibrio cholerae isolates from recent cholera epidemics in the Democratic Republic of the Congo (DRC), Zambia, Guinea and Togo. We aimed to assess the relationship between outbreaks. Applying this method, we identified 89 unique MLVA haplotypes across our isolate collection. MLVA typing revealed the short-term divergence and microevolution of these Vibrio cholerae populations to provide insight into the dynamics of cholera outbreaks in each country. Our analyses also revealed strong geographical clustering. Isolates from the African Great Lakes Region (DRC and Zambia) formed a closely related group, while West African isolates (Togo and Guinea) constituted a separate cluster. At a country-level scale our analyses revealed several distinct MLVA groups, most notably DRC 2011/2012, DRC 2009, Zambia 2012 and Guinea 2012. We also found that certain MLVA types collected in the DRC persisted in the country for several years, occasionally giving rise to expansive epidemics. Finally, we found that the six environmental isolates in our panel were unrelated to the epidemic isolates.

Conclusions/significance: To effectively combat the disease, it is critical to understand the mechanisms of cholera emergence and diffusion in a region-specific manner. Overall, these findings demonstrate the relationship between distinct epidemics in West Africa and the African Great Lakes Region. This study also highlights the importance of monitoring and analyzing Vibrio cholerae isolates.

Fig 1. Map of African countries implicated in study.

Upper panel: the four countries from which V. cholerae isolates were collected are indicated in different colors on the map of Africa (i.e., Guinea, green; Togo, red; Democratic Republic of the Congo (DRC), violet and Zambia: blue). Ghana and Nigeria are also labeled. Lower panel: detailed maps of Guinea and the DRC are shown. Lower right: DRC; the cities (red squares) and provinces mentioned are indicated on the map. The Congo River and Lake Tanganyika are also shown (in blue). Lower left: Guinea; the capital, Conakry, and Kaback Island are indicated along the Atlantic coast.

Fig 2. Minimum Spanning Tree based on the MLVA types of 337 V. cholerae isolates derived from several recent African epidemics.

Each MLVA type is represented by a node, and the size of the nodes reflects the number of isolates with the indicated MLVA type. The relationships between isolate MLVA types are indicated by the type of connecting segments and the length of the segment between nodes. The solid lines indicate the most likely SLV, and the dashed lines represent DLV. The distance between the nodes represents the number of varying VNTRs. The colors reflect the distinct country and period of isolate origin (grouped by epidemic populations). Pie charts were used to indicate the distribution of strains isolated from different time periods or countries displaying identical an MLVA type.