Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)

PLoS Negl Trop Dis. 2020 Apr 20;14(4):e0007642. doi: 10.1371/journal.pntd.0007642. eCollection 2020 Apr.

Abstract

Background: Over the past recent years, Vibrio cholerae has been associated with outbreaks in sub-Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries.

Methods/principal findings: Phenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of V. cholerae associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to V. cholerae isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other V. cholerae isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates.

Conclusions/significance: Current data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Child
  • Child, Preschool
  • Cholera / epidemiology
  • Cholera / microbiology*
  • Cluster Analysis
  • DNA, Bacterial / genetics
  • Democratic Republic of the Congo / epidemiology
  • Female
  • Genotype*
  • Humans
  • Infant
  • Male
  • Middle Aged
  • Molecular Epidemiology
  • Phylogeny
  • Prophages / genetics
  • Vibrio cholerae / classification*
  • Vibrio cholerae / genetics*
  • Vibrio cholerae / isolation & purification
  • Whole Genome Sequencing
  • Young Adult

Substances

  • DNA, Bacterial

Grants and funding

This project has been supported by the Belgian Cooperation Agency through the grant COOP-CONV-20-022 of the ARES (Académie de Recherche et d’Enseignement Supérieur). It was also supported by a grant (HFM/18-10 - 2019-2022) from the Department Management of Scientific & Technological Research of Defence (IRSD-RSTD; Royal High Institute for Defence, Belgium). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.