Vogler, Amy J., Chan, Fabien, Wagner, David M., Roumagnac, Philippe, Lee, Judy, Nera, Roxanne, Eppinger, Mark, Ravel, Jacques, Rahalison, Lila, Rasoamanana, Bruno W., Beckstrom-Sternberg, Stephen M., Achtman, Mark, Chanteau, Suzanne and Keim, Paul (2011) Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS Neglected Tropical Diseases, Volume 5 (Number 9). Article number e1319. doi:10.1371/journal.pntd.0001319

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Abstract

Background: Plague was introduced to Madagascar in 1898 and continues to be a significant human health problem. It
exists mainly in the central highlands, but in the 1990s was reintroduced to the port city of Mahajanga, where it caused
extensive human outbreaks. Despite its prevalence, the phylogeography and molecular epidemiology of Y. pestis in
Madagascar has been difficult to study due to the great genetic similarity among isolates. We examine island-wide
geographic-genetic patterns based upon whole-genome discovery of SNPs, SNP genotyping and hypervariable variablenumber
tandem repeat (VNTR) loci to gain insight into the maintenance and spread of Y. pestis in Madagascar.
Methodology/Principal Findings: We analyzed a set of 262 Malagasy isolates using a set of 56 SNPs and a 43-locus multilocus
VNTR analysis (MLVA) system. We then analyzed the geographic distribution of the subclades and identified patterns
related to the maintenance and spread of plague in Madagascar. We find relatively high levels of VNTR diversity in addition
to several SNP differences. We identify two major groups, Groups I and II, which are subsequently divided into 11 and 4
subclades, respectively. Y. pestis appears to be maintained in several geographically separate subpopulations. There is also
evidence for multiple long distance transfers of Y. pestis, likely human mediated. Such transfers have resulted in the
reintroduction and establishment of plague in the port city of Mahajanga, where there is evidence for multiple transfers
both from and to the central highlands.
Conclusions/Significance: The maintenance and spread of Y. pestis in Madagascar is a dynamic and highly active process
that relies on the natural cycle between the primary host, the black rat, and its flea vectors as well as human activity.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology R Medicine > RA Public aspects of medicine
Divisions:	Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Medicine > Warwick Medical School Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine
Library of Congress Subject Headings (LCSH):	Yersinia pestis , Plague , Molecular epidemiology -- Madagascar, Phylogeography
Journal or Publication Title:	PLoS Neglected Tropical Diseases
Publisher:	Public Library of Science
ISSN:	1935-2727
Official Date:	2011
Dates:	Date Event 2011 Published
Date of first compliant deposit:	26 December 2015
Date of first compliant Open Access:	26 December 2015
Volume:	Volume 5
Number:	Number 9
Page Range:	Article number e1319
DOI:	10.1371/journal.pntd.0001319
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access
Funder:	United States. Department of Homeland Security. Science and Technology Directorate, Northern Arizona University (NAU), National Institute of Allergy and Infectious Diseases (U.S.), National Institutes of Health (U.S.) (NIH), United States. Department of Health and Human Services (HHS), Science Foundation Ireland (SFI), Madagascar. Ministère de la santé (MMS), France (FR)
Grant number:	NBCH2070001, HSHQDC-08-C-00158 (USDHSSTD) ; AI065359, N01 AI-30071 (NIAID NIH HHS) ; 05/FE1/B882 (SFI) ; 01/95 IDA 2252-MAG (MMS) ; FAC Nu 94008 300 (FR)

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