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

PLoS Negl Trop Dis. 2015 Jun 25;9(6):e0003817. doi: 10.1371/journal.pntd.0003817. eCollection 2015.

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.

Publication types

  • Historical Article
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Africa South of the Sahara / epidemiology
  • Cholera / epidemiology*
  • Cholera / microbiology*
  • Cluster Analysis
  • DNA Primers / genetics
  • Epidemics / history*
  • Evolution, Molecular*
  • Gene Frequency
  • Genetics, Population
  • Haplotypes / genetics*
  • History, 20th Century
  • History, 21st Century
  • Humans
  • Minisatellite Repeats / genetics
  • Phylogeny
  • Phylogeography
  • Polymerase Chain Reaction
  • Vibrio cholerae / genetics*

Substances

  • DNA Primers

Grants and funding

The collection of strains and biological analyses were supported by many partners, including the WHO, the VEOLIA Environment Foundation and AFRICHOL project. Africhol (African Cholera Surveillance Network) (http://www.africhol.org/), is supported by a grant from the Bill & Melinda Gates Foundation, which had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Epidemiological surveillance including some field investigations was financially supported by the WHO, Epicentre, UNICEF and the CHOLTIC project (Belgian Science Policy). The project was also partly supported by the Directorate General of Development Cooperation of the Belgian Government through institutional collaboration INRB-ITM (project 2.01). This work was co-financed by Assistance Publique – Hôpitaux de Marseille. Sandra Moore was awarded a PhD contract from the public health doctoral network of the EHESP (École des hautes études en santé publique). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.