Temporal phylogeography of Yersinia pestis in Madagascar

Insights into the long-term maintenance of plague

Amy J. Vogler, Voahangy Andrianaivoarimanana, Sandra Telfer, Carina M. Hall, Jason W. Sahl, Crystal M. Hepp, Heather Centner, Genevieve Andersen, Dawn N. Birdsell, Lila Rahalison, Roxanne Nottingham, Paul S Keim, David M Wagner, Minoarisoa Rajerison

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background: Yersinia pestis appears to be maintained in multiple, geographically separate, and phylogenetically distinct subpopulations within the highlands of Madagascar. However, the dynamics of these locally differentiated subpopulations through time are mostly unknown. To address that gap and further inform our understanding of plague epidemiology, we investigated the phylogeography of Y. pestis in Madagascar over an 18 year period. Methodology/Principal findings: We generated whole genome sequences for 31 strains and discovered new SNPs that we used in conjunction with previously identified SNPs and variable-number tandem repeats (VNTRs) to genotype 773 Malagasy Y. pestis samples from 1995 to 2012. We mapped the locations where samples were obtained on a fine geographic scale to examine phylogeographic patterns through time. We identified 18 geographically separate and phylogenetically distinct subpopulations that display spatial and temporal stability, persisting in the same locations over a period of almost two decades. We found that geographic areas with higher levels of topographical relief are associated with greater levels of phylogenetic diversity and that sampling frequency can vary considerably among subpopulations and from year to year. We also found evidence of various Y. pestis dispersal events, including over long distances, but no evidence that any dispersal events resulted in successful establishment of a transferred genotype in a new location during the examined time period. Conclusions/Significance: Our analysis suggests that persistent endemic cycles of Y. pestis transmission within local areas are responsible for the long term maintenance of plague in Madagascar, rather than repeated episodes of wide scale epidemic spread. Landscape likely plays a role in maintaining Y. pestis subpopulations in Madagascar, with increased topographical relief associated with increased levels of localized differentiation. Local ecological factors likely affect the dynamics of individual subpopulations and the associated likelihood of observing human plague cases in a given year in a particular location.

Original languageEnglish (US)
Article numbere0005887
JournalPLoS Neglected Tropical Diseases
Volume11
Issue number9
DOIs
StatePublished - Sep 5 2017

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Phylogeography
Madagascar
Yersinia pestis
Plague
Single Nucleotide Polymorphism
Genotype
Minisatellite Repeats
Epidemiology
Genome

ASJC Scopus subject areas

  • Public Health, Environmental and Occupational Health
  • Infectious Diseases

Cite this

Vogler, A. J., Andrianaivoarimanana, V., Telfer, S., Hall, C. M., Sahl, J. W., Hepp, C. M., ... Rajerison, M. (2017). Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague. PLoS Neglected Tropical Diseases, 11(9), [e0005887]. https://doi.org/10.1371/journal.pntd.0005887

Temporal phylogeography of Yersinia pestis in Madagascar : Insights into the long-term maintenance of plague. / Vogler, Amy J.; Andrianaivoarimanana, Voahangy; Telfer, Sandra; Hall, Carina M.; Sahl, Jason W.; Hepp, Crystal M.; Centner, Heather; Andersen, Genevieve; Birdsell, Dawn N.; Rahalison, Lila; Nottingham, Roxanne; Keim, Paul S; Wagner, David M; Rajerison, Minoarisoa.

In: PLoS Neglected Tropical Diseases, Vol. 11, No. 9, e0005887, 05.09.2017.

Research output: Contribution to journalArticle

Vogler, AJ, Andrianaivoarimanana, V, Telfer, S, Hall, CM, Sahl, JW, Hepp, CM, Centner, H, Andersen, G, Birdsell, DN, Rahalison, L, Nottingham, R, Keim, PS, Wagner, DM & Rajerison, M 2017, 'Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague', PLoS Neglected Tropical Diseases, vol. 11, no. 9, e0005887. https://doi.org/10.1371/journal.pntd.0005887
Vogler, Amy J. ; Andrianaivoarimanana, Voahangy ; Telfer, Sandra ; Hall, Carina M. ; Sahl, Jason W. ; Hepp, Crystal M. ; Centner, Heather ; Andersen, Genevieve ; Birdsell, Dawn N. ; Rahalison, Lila ; Nottingham, Roxanne ; Keim, Paul S ; Wagner, David M ; Rajerison, Minoarisoa. / Temporal phylogeography of Yersinia pestis in Madagascar : Insights into the long-term maintenance of plague. In: PLoS Neglected Tropical Diseases. 2017 ; Vol. 11, No. 9.
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