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 variable-number 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 multi-locus 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.
References
[1]
Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, et al. (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42: 1140–1143. doi: 10.1038/ng.705
[2]
Perry RD, Fetherston JD (1997) Yersinia pestis-etiologic agent of plague. Clin Microbiol Rev 10: 35–66.
[3]
Rotz LD, Khan AS, Lillibridge SR, Ostroff SM, Hughes JM (2002) Public health assessment of potential biological terrorism agents. Emerging infectious diseases 8: 225–230. doi: 10.3201/eid0802.010164
[4]
World Health Organization (WHO) (2010) Human plague: review of regional morbidity and mortality, 2004–2009. Wkly Epidemiol Rec 85: 40–45.
[5]
Galimand M, Guiyoule A, Gerbaud G, Rasoamanana B, Chanteau S, et al. (1997) Multidrug resistance in Yersinia pestis mediated by a transferable plasmid. N Engl J Med 337: 677–680. doi: 10.1056/NEJM199709043371004
[6]
Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, et al. (2007) Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS One 2: e309. doi: 10.1371/journal.pone.0000309
[7]
Brygoo ER (1966) Epidémiologie de la peste à Madagascar. Arch Inst Pasteur Madagascar 35: 9–147.
[8]
Chanteau S, Ratsifasoamanana L, Rasoamanana B, Rahalison L, Randriambelosoa J, et al. (1998) Plague, a reemerging disease in Madagascar. Emerg Infect Dis 4: 101–104. doi: 10.3201/eid0401.980114
[9]
Duplantier JM (2001) The black rat's role in spreading human plague in Madagascar. L'Institut de recherche pour le développement Scientific Bulletin 131: 1–3.
[10]
Duplantier JM, Rakotondravony D (1999) The rodent problem in Madagascar: agricultural pest and threat to human health. In: Singleton G, Hinds L, Leirs H, Zhang Z, editors. Ecologically-based management of rodent pests. Canberra: Australian Centre for International Agricultural Research. pp. 441–459.
[11]
Chanteau S, Ratsitorahina M, Rahalison L, Rasoamanana B, Chan F, et al. (2000) Current epidemiology of human plague in Madagascar. Microbes Infect 2: 25–31. doi: 10.1016/S1286-4579(00)00289-6
[12]
Migliani R, Chanteau S, Rahalison L, Ratsitorahina M, Boutin JP, et al. (2006) Epidemiological trends for human plague in Madagascar during the second half of the 20th century: a survey of 20,900 notified cases. Trop Med Int Health 11: 1228–1237. doi: 10.1111/j.1365-3156.2006.01677.x
[13]
Laventure S, Andrianaja V, Rasoamanana B (1991) Epidémie de peste à Majunga en 1991. Rapport de mission de l'Institut Pasteur de Madagascar 1991: 1-26. 1–26.
[14]
Boisier P, Rahalison L, Rasolomaharo M, Ratsitorahina M, Mahafaly M, et al. (2002) Epidemiologic features of four successive annual outbreaks of bubonic plague in Mahajanga, Madagascar. Emerg Infect Dis 8: 311–316. doi: 10.3201/eid0803.010250
[15]
Boisier P, Rasolomaharo M, Ranaivoson G, Rasoamanana B, Rakoto L, et al. (1997) Urban epidemic of bubonic plague in Majunga, Madagascar: epidemiological aspects. Trop Med Int Health 2: 422–427. doi: 10.1111/j.1365-3156.1997.tb00163.x
[16]
Rasolomaharo M, Rasoamanana B, Andrianirina Z, Buchy P, Rakotoarimanana N, et al. (1995) Plague in Majunga, Madagascar. Lancet 346: 1234. doi: 10.1016/S0140-6736(95)92944-4
[17]
Duplantier JM, Duchemin JB, Chanteau S, Carniel E (2005) From the recent lessons of the Malagasy foci towards a global understanding of the factors involved in plague reemergence. Vet Res 36: 437–453. doi: 10.1051/vetres:2005007
[18]
Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, et al. (1999) Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 96: 14043–14048. doi: 10.1073/pnas.96.24.14043
[19]
Achtman M, Morelli G, Zhu P, Wirth T, Diehl I, et al. (2004) Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A 101: 17837–17842. doi: 10.1073/pnas.0408026101
[20]
Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, et al. (2010) Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol 192: 1685–1699. doi: 10.1128/JB.01518-09
[21]
Guiyoule A, Grimont F, Iteman I, Grimont PA, Lefévre M, et al. (1994) Plague pandemics investigated by ribotyping of Yersinia pestis strains. J Clin Microbiol 32: 634–641.
[22]
Motin VL, Georgescu AM, Elliott JM, Hu P, Worsham PL, et al. (2002) Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD). J Bacteriol 184: 1019–1027. doi: 10.1128/jb.184.4.1019-1027.2002
[23]
Lucier TS, Brubaker RR (1992) Determination of genome size, macrorestriction pattern polymorphism, and nonpigmentation-specific deletion in Yersinia pestis by pulsed-field gel electrophoresis. J Bacteriol 174: 2078–2086.
[24]
Guiyoule A, Rasoamanana B, Buchrieser C, Michel P, Chanteau S, et al. (1997) Recent emergence of new variants of Yersinia pestis in Madagascar. J Clin Microbiol 35: 2826–2833.
[25]
Huang XZ, Chu MC, Engelthaler DM, Lindler LE (2002) Genotyping of a homogeneous group of Yersinia pestis strains isolated in the United States. J Clin Microbiol 40: 1164–1173. doi: 10.1128/JCM.40.4.1164-1173.2002
[26]
Li Y, Dai E, Cui Y, Li M, Zhang Y, et al. (2008) Different region analysis for genotyping Yersinia pestis isolates from China. PLoS ONE 3: e2166. doi: 10.1371/journal.pone.0002166
[27]
Cui Y, Li Y, Gorgé O, Platonov ME, Yan Y, et al. (2008) Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS ONE 3: e2652. doi: 10.1371/journal.pone.0002652
[28]
Kingston JJ, Tuteja U, Kapil M, Murali HS, Batra HV (2009) Genotyping of Indian Yersinia pestis strains by MLVA and repetitive DNA sequence based PCRs. Antonie Van Leeuwenhoek 96: 303–312. doi: 10.1007/s10482-009-9347-2
[29]
Zhang Z, Hai R, Song Z, Xia L, Liang Y, et al. (2009) Spatial variation of Yersinia pestis from Yunnan Province of China. Am J Trop Med Hyg 81: 714–717. doi: 10.4269/ajtmh.2009.09-0174
[30]
Klevytska AM, Price LB, Schupp JM, Worsham PL, Wong J, et al. (2001) Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. J Clin Microbiol 39: 3179–3185. doi: 10.1128/JCM.39.9.3179-3185.2001
[31]
Pourcel C, André-Mazeaud F, Neubauer H, Ramisse F, Vergnaud G (2004) Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol 4: 22. doi: 10.1186/1471-2180-4-22
[32]
Girard JM, Wagner DM, Vogler AJ, Keys C, Allender CJ, et al. (2004) Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proc Natl Acad Sci U S A 101: 8408–8413. doi: 10.1073/pnas.0401561101
[33]
Li Y, Cui Y, Hauck Y, Platonov ME, Dai E, et al. (2009) Genotyping and phylogenetic analysis of Yersinia pestis by MLVA: insights into the worldwide expansion of Central Asia plague foci. PLoS One 4: e6000. doi: 10.1371/journal.pone.0006000
[34]
Lowell JL, Zhansarina A, Yockey B, Meka-Mechenko T, Stybayeva G, et al. (2007) Phenotypic and molecular characterizations of Yersinia pestis isolates from Kazakhstan and adjacent regions. Microbiology 153: 169–177. doi: 10.1099/mic.0.29059-0
[35]
Zhang X, Hai R, Wei J, Cui Z, Zhang E, et al. (2009) MLVA distribution characteristics of Yersinia pestis in China and the correlation analysis. BMC Microbiol 9: 205. doi: 10.1186/1471-2180-9-205
[36]
Keim P, Van Ert MN, Pearson T, Vogler AJ, Huynh LY, et al. (2004) Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect Genet Evol 4: 205–213. doi: 10.1016/j.meegid.2004.02.005
[37]
Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, et al. (2007) Global genetic population structure of Bacillus anthracis. PLoS One 2: e461. doi: 10.1371/journal.pone.0000461
[38]
Vogler AJ, Birdsell D, Price LB, Bowers JR, Beckstrom-Sternberg SM, et al. (2009) Phylogeography of Francisella tularensis: global expansion of a highly fit clone. J Bacteriol 191: 2474–2484. doi: 10.1128/JB.01786-08
[39]
Pearson T, Busch JD, Ravel J, Read TD, Rhoton SD, et al. (2004) Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc Natl Acad Sci U S A 101: 13536–13541. doi: 10.1073/pnas.0403844101
[40]
Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413: 523–527. doi: 10.1038/35097083
[41]
Touchman JW, Wagner DM, Hao J, Mastrian SD, Shah MK, et al. (2007) A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS One 2: e220. doi: 10.1371/journal.pone.0000220
[42]
Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, et al. (2007) Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS One 2: e770. doi: 10.1371/journal.pone.0000770
[43]
Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, et al. (2006) Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol 188: 4453–4463. doi: 10.1128/JB.00124-06
[44]
Deng W, Burland V, Plunkett G, 3rd , Boutin A, Mayhew GF, et al. (2002) Genome sequence of Yersinia pestis KIM. J Bacteriol 184: 4601–4611. doi: 10.1128/JB.184.16.4601-4611.2002
[45]
Eppinger M, Guo Z, Sebastian Y, Song Y, Lindler LE, et al. (2009) Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. J Bacteriol 191: 7628–7629. doi: 10.1128/JB.01227-09
[46]
Garcia E, Worsham P, Bearden S, Malfatti S, Lang D, et al. (2007) Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union. Adv Exp Med Biol 603: 17–22. doi: 10.1007/978-0-387-72124-8_2
[47]
Song Y, Tong Z, Wang J, Wang L, Guo Z, et al. (2004) Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res 11: 179–197. doi: 10.1093/dnares/11.3.179
[48]
Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30: 2478–2483. doi: 10.1093/nar/30.11.2478
[49]
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175–185. doi: 10.1101/gr.8.3.175
[50]
Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244–1245. doi: 10.1093/bioinformatics/17.12.1244
[51]
Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18: 117–143. doi: 10.1111/j.1442-9993.1993.tb00438.x
[52]
Johansson A, Farlow J, Larsson P, Dukerich M, Chambers E, et al. (2004) Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J Bacteriol 186: 5808–5818. doi: 10.1128/JB.186.17.5808-5818.2004
[53]
Migliani R, Ratsitorahina M, Rahalison L, Rakotoarivony I, Duchemin JB, et al. (2001) [Resurgence of the plague in the Ikongo district of Madagascar in 1998. 1. Epidemiological aspects in the human population]. Bull Soc Pathol Exot 94: 115–118.
[54]
Gilabert A, Loiseau A, Duplantier JM, Rahelinirina S, Rahalison L, et al. (2007) Genetic structure of black rat populations in a rural plague focus in Madagascar. Can J Zool 85: 965–972. doi: 10.1139/z07-083
[55]
Rahelinirina S, Duplantier JM, Ratovonjato J, Ramilijaona O, Ratsimba M, et al. (2010) Study on the movement of Rattus rattus and evaluation of the plague dispersion in Madagascar. Vector Borne Zoonotic Dis 10: 77–84. doi: 10.1089/vbz.2009.0019
[56]
Tollenaere C, Rahalison L, Ranjalahy M, Duplantier JM, Rahelinirina S, et al. (2010) Susceptibility to Yersinia pestis experimental infection in wild Rattus rattus, reservoir of plague in Madagascar. Ecohealth 7: 242–247. doi: 10.1007/s10393-010-0312-3
[57]
Keim PS, Wagner DM (2009) Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nat Rev Microbiol 7: 813–821. doi: 10.1038/nrmicro2219
