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

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.

Fig 1. Phylogeny of seventh pandemic (7PET) V. cholerae O1 isolates associated with cholera outbreaks in DR Congo between 2014 and 2017.

The 7PET V. cholerae O1 biotype El Tor N19691 belonging to wave 1 was used as outgroup. The scale bar represents substitutions per variable site in the core genome. Green, blue, yellow, purple and red isolates represent 7PET wave 3 clades from Central Africa, East Africa, West Africa, Haiti and Asia regions.

Fig 2. Geographical location of the sequenced V. cholerae isolates.

Fig 3. Phylogeny of the five V. cholerae non-O1/non-O139 from eastern DRC and their potential relationship with V. cholerae O1 and V. cholerae non-O1/non-O139 from other regions of the world.