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Genomic history of the seventh pandemic of cholera in Africa

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Science  10 Nov 2017:
Vol. 358, Issue 6364, pp. 785-789
DOI: 10.1126/science.aad5901
  • Fig. 1 Phylogeny of seventh pandemic V. cholerae El Tor isolates.

    (A) Maximum likelihood phylogeny of the 1070 genomes studied, including M66 as an outgroup. Branches are color-coded according to their geographic location, inferred by stochastic mapping of the geographic origin of each isolate onto the tree. The N16961 reference genome is indicated by a black dashed line. (B) Maximum clade credibility tree produced with BEAST for a subset of 228 representative isolates. The 12 introduction events involving Africa are indicated by the letter T. The three previously described waves (3) are indicated by colored arrows. The clades containing O139 isolates and that containing isolates from the 2010 outbreak in Haiti are shown.

  • Fig. 2 Inferred propagation routes of seventh pandemic V. cholerae O1 El Tor populations to, from, and within Africa.

    The 12 introduction events involving Africa are indicated by the letter T. The date ranges shown for introductions are the median values for the most recent common ancestor (MRCA) in years (taken from BEAST) with the first number indicating the median MRCA of the African isolates and their closest relative from the source location, and the second number indicating the median MRCA of the African isolates. Introductions and inferred secondary transmission chains are indicated by thick and dashed arrows, respectively. Secondary transmission chains for West Africa in 1970 to 1971 are based on published records. The geographic presence of the various lineages is indicated by a circle, triangle, and diamond for waves 1, 2, and 3, respectively, and colored according to the inferred transmission events. The size of the shapes is proportional to the number of genomes analyzed (see fig. S3).

  • Fig. 3 Geographic and temporal distribution of seventh pandemic V. cholerae El Tor isolates from Africa according to their inferred introduction events (T1 to T12).

    The annual number of cholera cases reported to the World Health Organization (WHO) is shown in the upper panels. The United Nations subregion scheme was used for the geographic breakdown. The size of the circle scales with the number of genomes analyzed per year.

  • Fig. 4 Evolution of antibiotic resistance in seventh pandemic V. cholerae El Tor isolates from Africa.

    For each introduction into Africa (T1, T5 to T12), the proportion of genomes at different time periods following introduction that contain (A) an IncA/C plasmid, (B) a gyrA mutation, and (C) a SXT/R391 genomic island. (D) For wave 3, the mean number of antibiotic resistance genes (ARGs) per isolate at different time periods following introduction. Each value is calculated over a 10-year window, with the point plotted at the midpoint of the period. Sampling bias was prevented by randomly down-sampling the number of sequences to one sequence per country per year. In (A), (B), and (C), the color in the leftmost circle (at the value “X” on the x axis) represents the value for the closest genomic sequence obtained from outside Africa [for (A) to (C), a value of 1 implies that the sequence included the corresponding antibiotic resistance determinant, whereas 0 implies that the sequence lacked the determinant].

Supplementary Materials

  • Genomic history of the seventh pandemic of cholera in Africa

    François-Xavier Weill, Daryl Domman, Elisabeth Njamkepo, Cheryl Tarr, Jean Rauzier, Nizar Fawal, Karen H. Keddy, Henrik Salje, Sandra Moore, Asish K. Mukhopadhyay, Raymond Bercion, Francisco J. Luquero, Antoinette Ngandjio, Mireille Dosso, Elena Monakhova, Benoit Garin, Christiane Bouchier, Carlo Pazzani, Ankur Mutreja, Roland Grunow, Fati Sidikou, Laurence Bonte, Sébastien Breurec, Maria Damian, Berthe-Marie Njanpop-Lafourcade, Guillaume Sapriel, Anne-Laure Page, Monzer Hamze, Myriam Henkens, Goutam Chowdhury, Martin Mengel, Jean-Louis Koeck, Jean-Michel Fournier, Gordon Dougan, Patrick A. D. Grimont, Julian Parkhill, Kathryn E. Holt, Renaud Piarroux, Thandavarayan Ramamurthy, Marie-Laure Quilici, Nicholas R. Thomson

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Supplementary Text
    • Figs. S1 to S12
    • Tables S2 and S5 to S9
    • Captions for Tables S1, S3, and S4
    • References
    Table S1
    Details of Vibrio cholerae El Tor isolates and genomes used in this study.
    Table S3
    Number of cases reported to the World Health Organization and V. cholerae O1 lineages found in this study, per African country and year.
    Table S4
    SNPs used for phylogeny.

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