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Randriantseheno LN, Andrianaivoarimanana V, Pizarro-Cerdá J, Wagner DM, Rajerison M. Review of genotyping methods for Yersinia pestis in Madagascar. PLoS Negl Trop Dis 2024; 18:e0012252. [PMID: 38935608 PMCID: PMC11210753 DOI: 10.1371/journal.pntd.0012252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis. AIM This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches. METHODS Pubmed and Google Scholar were used to search for the keywords: "typing Yersinia pestis Madagascar," "evolution Yersinia pestis Madagascar," and "diversity Yersinia pestis Madagascar." Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications. RESULTS The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar. CONCLUSIONS Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.
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Affiliation(s)
- Lovasoa Nomena Randriantseheno
- Plague Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Ecole doctorale Sciences de la Vie et de l’Environnement, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | | | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, French National Reference Laboratory ‘Plague & Other Yersiniosis’, WHO Collaborating Centre for Plague FRA-140, Paris, France
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Andrianaivoarimanana V, Savin C, Birdsell DN, Vogler AJ, Le Guern AS, Rahajandraibe S, Brémont S, Rahelinirina S, Sahl JW, Ramasindrazana B, Rakotonanahary RJL, Rakotomanana F, Randremanana R, Maheriniaina V, Razafimbia V, Kwasiborski A, Balière C, Ratsitorahina M, Baril L, Keim P, Caro V, Rasolofo V, Spiegel A, Pizarro-Cerda J, Wagner DM, Rajerison M. Multiple Introductions of Yersinia pestis during Urban Pneumonic Plague Epidemic, Madagascar, 2017. Emerg Infect Dis 2024; 30:289-298. [PMID: 38270131 PMCID: PMC10826772 DOI: 10.3201/eid3002.230759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Pneumonic plague (PP) is characterized by high infection rate, person-to-person transmission, and rapid progression to severe disease. In 2017, a PP epidemic occurred in 2 Madagascar urban areas, Antananarivo and Toamasina. We used epidemiologic data and Yersinia pestis genomic characterization to determine the sources of this epidemic. Human plague emerged independently from environmental reservoirs in rural endemic foci >20 times during August-November 2017. Confirmed cases from 5 emergences, including 4 PP cases, were documented in urban areas. Epidemiologic and genetic analyses of cases associated with the first emergence event to reach urban areas confirmed that transmission started in August; spread to Antananarivo, Toamasina, and other locations; and persisted in Antananarivo until at least mid-November. Two other Y. pestis lineages may have caused persistent PP transmission chains in Antananarivo. Multiple Y. pestis lineages were independently introduced to urban areas from several rural foci via travel of infected persons during the epidemic.
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Affiliation(s)
| | | | | | - Amy J. Vogler
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Anne-Sophie Le Guern
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Soloandry Rahajandraibe
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Sylvie Brémont
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Soanandrasana Rahelinirina
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Jason W. Sahl
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Beza Ramasindrazana
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Rado Jean Luc Rakotonanahary
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Fanjasoa Rakotomanana
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Rindra Randremanana
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Viviane Maheriniaina
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Vaoary Razafimbia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Aurelia Kwasiborski
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Charlotte Balière
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Maherisoa Ratsitorahina
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Laurence Baril
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Paul Keim
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Valérie Caro
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - Voahangy Rasolofo
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
| | - André Spiegel
- Institut Pasteur de Madagascar, Antananarivo, Madagascar (V. Andrianaivoarimanana, S. Rahelinirina, B. Ramasindrazana, R.J.L. Rakotonanahary, F. Rakotomanana, R. Randremanana, M. Ratsitorahina, L. Baril, V. Rasolofo, A. Spiegel, M. Rajerison)
- Institut Pasteur, Paris, France (C. Savin, A.-S. Le Guern, S. Brémont, A. Kwasiborski, C. Balière, V. Caro, J. Pizarro-Cerda)
- Northern Arizona University, Flagstaff, Arizona, USA (D.N. Birdsell, A.J. Vogler, J.W. Sahl, P. Keim, D.M. Wagner)
- Madagascar Ministry of Public Health, Antananarivo (S. Rahajandraibe, V. Maheriniaina, V. Razafimbia)
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Anderson D, Pauling C, Beerntsen B, Song Q. Transovarial transmission of Yersinia pestis in its flea vector, Xenopsylla cheopis. RESEARCH SQUARE 2023:rs.3.rs-3397969. [PMID: 37961723 PMCID: PMC10635300 DOI: 10.21203/rs.3.rs-3397969/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Yersinia pestis is the causative agent of bubonic plague, a deadly flea-borne disease responsible for three historic pandemics. Today annual cases of human disease occur worldwide following exposure to Y. pestis infected fleas that can be found within the rodent population where plague activity cycles between epizootic outbreaks and extended periods of apparent quiescence. Flea transmission of Y. pestis is most efficient in "blocked" fleas that are unable to feed, whereas mammalian transmission to fleas requires a susceptible host with end-stage high titer bacteremia. These facts suggest alternative mechanisms of transmission must exist to support the persistence of Y. pestis between epizootic outbreaks. In this work, we addressed whether vertical transmission could be a mechanism for persistent low-infection across generations of fleas. We demonstrate that Y. pestis infection of the Oriental rat flea, Xenopyslla cheopis, spreads to the reproductive tissues and is found in eggs produced by infected adult fleas. We further show that vertical transmission of Y. pestis from eggs to adults results in midgut colonization indicating a strong probability that it can reenter the sylvatic plague cycle.
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Warren ME, Pickett BE, Adams BJ, Villalva C, Applegate A, Robison RA. Comparative sequence analysis elucidates the evolutionary patterns of Yersinia pestis in New Mexico over thirty-two years. PeerJ 2023; 11:e16007. [PMID: 37780382 PMCID: PMC10541020 DOI: 10.7717/peerj.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023] Open
Abstract
Background Yersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899. Methods To better understand evolutionary patterns in Y. pestis from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure. Results We identified four genes, including Yscp and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America.
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Affiliation(s)
- Mary E. Warren
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Byron J. Adams
- Department of Biology, Brigham Young University, Provo, UT, United States
- Monte L. Bean Life Science Museum, Provo, UT, United States
| | - Crystal Villalva
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Alyssa Applegate
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
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Esquivel Gomez LR, Savin C, Andrianaivoarimanana V, Rahajandraibe S, Randriantseheno LN, Zhou Z, Kocher A, Didelot X, Rajerison M, Kühnert D. Phylogenetic analysis of the origin and spread of plague in Madagascar. PLoS Negl Trop Dis 2023; 17:e0010362. [PMID: 37126517 PMCID: PMC10174576 DOI: 10.1371/journal.pntd.0010362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/11/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Plague is a zoonotic disease caused by the bacterium Yersinia pestis, highly prevalent in the Central Highlands, a mountainous region in the center of Madagascar. After a plague-free period of over 60 years in the northwestern coast city of Mahajanga, the disease reappeared in 1991 and caused several outbreaks until 1999. Previous research indicates that the disease was reintroduced to the city of Mahajanga from the Central Highlands instead of reemerging from a local reservoir. However, it is not clear how many reintroductions occurred and when they took place. METHODOLOGY/PRINCIPAL FINDINGS In this study we applied a Bayesian phylogeographic model to detect and date migrations of Y. pestis between the two locations that could be linked to the re-emergence of plague in Mahajanga. Genome sequences of 300 Y. pestis strains sampled between 1964 and 2012 were analyzed. Four migrations from the Central Highlands to Mahajanga were detected. Two resulted in persistent transmission in humans, one was responsible for most of the human cases recorded between 1995 and 1999, while the other produced plague cases in 1991 and 1992. We dated the emergence of the Y. pestis sub-branch 1.ORI3, which is only present in Madagascar and Turkey, to the beginning of the 20th century, using a Bayesian molecular dating analysis. The split between 1.ORI3 and its ancestor lineage 1.ORI2 was dated to the second half of the 19th century. CONCLUSIONS/SIGNIFICANCE Our results indicate that two independent migrations from the Central Highlands caused the plague outbreaks in Mahajanga during the 1990s, with both introductions occurring during the early 1980s. They happened over a decade before the detection of human cases, thus the pathogen likely survived in wild reservoirs until the spillover to humans was possible. This study demonstrates the value of Bayesian phylogenetics in elucidating the re-emergence of infectious diseases.
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Affiliation(s)
- Luis Roger Esquivel Gomez
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute for Geoanthropology (formerly MPI for the Science of Human History), Jena, Germany
| | - Cyril Savin
- Institut Pasteur, Université de Paris, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université de Paris, Yersinia National Reference Laboratory, Paris, France
- Institut Pasteur, Université de Paris, WHO Collaborative Reference & Research Center for Plague FRA-140, Paris, France
| | | | - Soloandry Rahajandraibe
- Plague Unit, Central Laboratory for Plague, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Zhemin Zhou
- Pasteurien College, Medical school of Soochow University, Soochow University, Suzhou, China
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Arthur Kocher
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute for Geoanthropology (formerly MPI for the Science of Human History), Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Minoarisoa Rajerison
- Plague Unit, Central Laboratory for Plague, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute for Geoanthropology (formerly MPI for the Science of Human History), Jena, Germany
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Epidemiological Characteristics of Human and Animal Plague in Yunnan Province, China, 1950 to 2020. Microbiol Spectr 2022; 10:e0166222. [PMID: 36219109 PMCID: PMC9784778 DOI: 10.1128/spectrum.01662-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This study analyzed the epidemiological characteristics of 3,464 human plague cases and the distribution pattern of 4,968 Yersinia pestis isolates from humans, hosts, and vector insects from 1950 to 2020 among two natural plague foci in Yunnan Province, China. These foci include the Rattus flavipectus plague focus of the Yunnan, Guangdong, and Fujian provinces and the Apodemus chevrieri-Eothenomys miletus plague focus of the highlands of northwestern Yunnan Province. The case fatality rate for plague in humans was 18.39% (637/3,464), and the total isolation rate of Y. pestis was 0.17% (4,968/2,975,288). Despite that the frequency of human cases declined rapidly, the animal plague fluctuated greatly, alternating between activity and inactivity in these foci. The tendency among human cases can be divided into 4 stages, 1950 to 1955, 1956 to 1989, 1990 to 2005, and 2006 to 2020. Bubonic plague accounted for the majority of cases in Yunnan, where pneumonic and septicemic plague rarely occurred. The natural plague foci have been in a relatively active state due to the stability of local ecology. Dense human population and frequent contact with host animals contribute to the high risk of human infection. This study systematically analyzed the epidemic pattern of human plague and the distribution characteristics of Y. pestis in the natural plague foci in Yunnan, providing a scientific basis for further development and adjustment of plague prevention and control strategies. IMPORTANCE Yunnan is the origin of the third plague pandemic. The analysis of human and animal plague characteristics of plague foci in Yunnan enlightens the prevention and control of the next plague pandemics. The plague characteristics of Yunnan show that human plague occurred when animal plague reached a certain scale, and strengthened surveillance of animal plague and reducing the density of host animals and transmission vectors contribute to the prevention and control of human plague outbreaks. The phenomenon of alternation between the resting period and active period of plague foci in Yunnan further proves the endogenous preservation mechanism of plague.
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7
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Exploring and Mitigating Plague for One Health Purposes. CURRENT TROPICAL MEDICINE REPORTS 2022. [DOI: 10.1007/s40475-022-00265-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Eads D, Livieri T, Tretten T, Hughes J, Kaczor N, Halsell E, Grassel S, Dobesh P, Childers E, Lucas D, Noble L, Vasquez M, Grady AC, Biggins D. Assembling a safe and effective toolbox for integrated flea control and plague mitigation: Fipronil experiments with prairie dogs. PLoS One 2022; 17:e0272419. [PMID: 35939486 PMCID: PMC9359584 DOI: 10.1371/journal.pone.0272419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/19/2022] [Indexed: 11/19/2022] Open
Abstract
Background Plague, a widely distributed zoonotic disease of mammalian hosts and flea vectors, poses a significant risk to ecosystems throughout much of Earth. Conservation biologists use insecticides for flea control and plague mitigation. Here, we evaluate the use of an insecticide grain bait, laced with 0.005% fipronil (FIP) by weight, with black-tailed prairie dogs (BTPDs, Cynomys ludovicianus). We consider safety measures, flea control, BTPD body condition, BTPD survival, efficacy of plague mitigation, and the speed of FIP grain application vs. infusing BTPD burrows with insecticide dusts. We also explore conservation implications for endangered black-footed ferrets (Mustela nigripes), which are specialized predators of Cynomys. Principal findings During 5- and 10-day laboratory trials in Colorado, USA, 2016–2017, FIP grain had no detectable acute toxic effect on 20 BTPDs that readily consumed the grain. During field experiments in South Dakota, USA, 2016–2020, FIP grain suppressed fleas on BTPDs for at least 12 months and up to 24 months in many cases; short-term flea control on a few sites was poor for unknown reasons. In an area of South Dakota where plague circulation appeared low or absent, FIP grain had no detectable effect, positive or negative, on BTPD survival. Experimental results suggest FIP grain may have improved BTPD body condition (mass:foot) and reproduction (juveniles:adults). During a 2019 plague epizootic in Colorado, BTPDs on 238 ha habitat were protected by FIP grain, whereas BTPDs were nearly eliminated on non-treated habitat. Applications of FIP grain were 2–4 times faster than dusting BTPD burrows. Significance Deltamethrin dust is the most commonly used insecticide for plague mitigation on Cynomys colonies. Fleas on BTPD colonies exhibit the ability to evolve resistance to deltamethrin after repeated annual treatments. Thus, more tools are needed. Accumulating data show orally-delivered FIP is safe and usually effective for flea control with BTPDs, though potential acute toxic effects cannot be ruled out. With continued study and refinement, FIP might be used in rotation with, or even replace deltamethrin, and serve an important role in Cynomys and black-footed ferret conservation. More broadly, our stepwise approach to research on FIP may function as a template or guide for evaluations of insecticides in the context of wildlife conservation.
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Affiliation(s)
- David Eads
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
- * E-mail:
| | - Travis Livieri
- Prairie Wildlife Research, Stevens Point, Wisconsin, United States of America
| | - Tyler Tretten
- U.S. Fish and Wildlife Service, National Black-Footed Ferret Conservation Center, Carr, Colorado, United States of America
| | - John Hughes
- U.S. Fish and Wildlife Service, National Black-Footed Ferret Conservation Center, Carr, Colorado, United States of America
| | - Nick Kaczor
- U.S. Fish and Wildlife Service, Colorado Front Range National Wildlife Refuge Complex, Arvada, Colorado, United States of America
| | - Emily Halsell
- U.S. Fish and Wildlife Service, Colorado Front Range National Wildlife Refuge Complex, Arvada, Colorado, United States of America
| | - Shaun Grassel
- Lower Brule Sioux Tribe, Lower Brule, South Dakota, United States of America
| | - Phillip Dobesh
- U.S. Forest Service, Wall Ranger District, Wall, South Dakota, United States of America
| | - Eddie Childers
- National Park Service, Badlands National Park, Rapid City, South Dakota, United States of America
| | - David Lucas
- U.S. Fish and Wildlife Service, Colorado Front Range National Wildlife Refuge Complex, Arvada, Colorado, United States of America
| | - Lauren Noble
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Michele Vasquez
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Anna Catherine Grady
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Dean Biggins
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
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Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis. Microbiol Spectr 2022; 10:e0224221. [PMID: 35438532 PMCID: PMC9248902 DOI: 10.1128/spectrum.02242-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The life cycle of Yersinia pestis has changed a lot to adapt to flea-borne transmission since it evolved from an enteric pathogen, Yersinia pseudotuberculosis. Small insertions and deletions (indels), especially frameshift mutations, can have major effects on phenotypes and contribute to virulence and host adaptation through gene disruption and inactivation. Here, we analyzed 365 Y. pestis genomes and identified 2,092 genome-wide indels on the core genome. As recently reported in Mycobacterium tuberculosis, we also detected "indel pockets" in Y. pestis, with average complexity scores declining around indel positions, which we speculate might also exist in other prokaryotes. Phylogenic analysis showed that indel-based phylogenic tree could basically reflect the phylogenetic relationships of major phylogroups in Y. pestis, except some inconsistency around the Big Bang polytomy. We observed 83 indels arising in the trunk of the phylogeny, which played a role in accumulation of pseudogenes related to key metabolism and putatively pathogenicity. We also discovered 32 homoplasies at the level of phylogroups and 7 frameshift scars (i.e., disrupted reading frame being rescued by a second frameshift). Additionally, our analysis showed evidence of parallel evolution at the level of genes, with sspA, rpoS, rnd, and YPO0624, having enriched mutations in Brazilian isolates, which might be advantageous for Y. pestis to cope with fluctuating environments. The diversified selection signals observed here demonstrates that indels are important contributors to the adaptive evolution of Y. pestis. Meanwhile, we provide potential targets for further exploration, as some genes/pseudogenes with indels we focus on remain uncharacterized. IMPORTANCE Yersinia pestis, the causative agent of plague, is a highly pathogenic clone of Yersinia pseudotuberculosis. Previous genome-wide SNP analysis provided few adaptive signatures during its evolution. Here by investigating 365 public genomes of Y. pestis, we give a comprehensive overview of general features of genome-wide indels on the core genome and their roles in Y. pestis evolution. Detection of "indel pockets," with average complexity scores declining around indel positions, in both Mycobacterium tuberculosis and Y. pestis, gives us a clue that this phenomenon might appear in other bacterial genomes. Importantly, the identification of four different forms of selection signals in indels would improve our understanding on adaptive evolution of Y. pestis, and provide targets for further physiological mechanism researches of this pathogen. As evolutionary research based on genome-wide indels is still rare in bacteria, our study would be a helpful reference in deciphering the role of indels in other species.
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10
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Ramasindrazana B, Parany MNJ, Rasoamalala F, Rasoanoro M, Rahajandraibe S, Vogler AJ, Sahl JW, Andrianaivoarimanana V, Rajerison M, Wagner DM. Local-scale diversity of Yersinia pestis: A case study from Ambohitromby, Ankazobe District, Madagascar. Zoonoses Public Health 2022; 69:61-70. [PMID: 34480413 DOI: 10.1111/zph.12892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
Plague is a re-emerging zoonotic disease and a major public health concern in several portions of the world, especially in Madagascar. We report on the presence of different subtypes of Yersinia pestis co-occurring in the same locality. After confirmation of a human plague case in Ambohitromby Commune (Ankazobe District) via isolation of Y. pestis, we undertook small mammal trapping to identify the circulation of Y. pestis amongst rodents in this locality; blood samples were collected from rodents for seroprevalence analysis. Of the 60 individuals of Rattus rattus captured, one yielded an isolate of Y. pestis, 13 others were positive for F1 antigen of Y. pestis using a rapid diagnostic test, and 4 were PCR positive targeting the caf1 and pla genes; 28/60 (46.7%) of the captured R. rattus were seropositive for Y. pestis. Whole-genome SNP analyses revealed that the two isolates obtained from the human case, and the R. rattus belonged to two different subtypes of Y. pestis (s05 and s13, respectively) that were circulating concurrently in Ambohitromby in 2016. Three Y. pestis subtypes (s03, s05 and s13) have now been isolated from Ambohitromby. Subtype s05 had been persisting there for >10 years but one or both of the other subtypes may have been introduced from the Central Highlands region as they were not observed in previous years (s13) or only observed once previously (s03). High seroprevalence against Y. pestis in R. rattus suggests that a portion of the local murine population may have acquired resistance to Y. pestis. Future research should focus on genomically characterizing Y. pestis strains circulating in Ankazobe District and other plague-endemic regions of Madagascar to better understand the overall phylogeography of Y. pestis.
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Affiliation(s)
- Beza Ramasindrazana
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Domaine Sciences et Technologies, Université d'Antananarivo, Antananarivo, Madagascar
| | - Mamionah N J Parany
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Domaine Sciences et Technologies, Université d'Antananarivo, Antananarivo, Madagascar
| | - Fanohinjanaharinirina Rasoamalala
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Domaine Sciences et Technologies, Université d'Antananarivo, Antananarivo, Madagascar
| | - Mercia Rasoanoro
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Domaine Sciences et Technologies, Université d'Antananarivo, Antananarivo, Madagascar
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11
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Matchett MR, Stanley TR, Mccollister MF, Eads DA, Boulerice JT, Biggins DE. Oral Sylvatic Plague Vaccine Does Not Adequately Protect Prairie Dogs ( Cynomys spp.) for Endangered Black-Footed Ferret ( Mustela nigripes) Conservation. Vector Borne Zoonotic Dis 2021; 21:921-940. [PMID: 34757815 PMCID: PMC8742283 DOI: 10.1089/vbz.2021.0049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The plague bacterium Yersinia pestis is lethal to endangered black-footed ferrets (Mustela nigripes, BFF) and the prairie dogs (Cynomys spp., PD) on which they depend for habitat and prey. We assessed the effectiveness of an oral sylvatic plague vaccine delivered in baits to black-tailed PD (Cynomys ludovicianus, BTPD) from 2013 to 2017 on the Charles M. Russell National Wildlife Refuge (CMR) in northcentral Montana. We permanently marked BTPD on four paired vaccine (N = 1,349 individuals) and placebo plots (N = 926; 7,027 total captures). We analyzed capture–recapture data under a Cormack–Jolly–Seber model to estimate annual apparent survival. Overall, survival averaged 0.05 lower on vaccine plots than on paired placebo plots. Immediately before noticeable die-offs and detecting plague on pairs CMR1 and CMR2, 89% of BTPD sampled on vaccine plots had consumed at least one bait and the immune systems of 40% were likely boosted by consuming baits over multiple years. Survival to the following year was 0.16 and 0.05 on the vaccine plots and 0.19 and 0.06 on the placebo plots for pairs CMR1 and CMR2, respectively. These rates were markedly lower than 0.63, the overall average estimate on those same plots during the previous 3 years. PD populations subjected to such large die-offs would not be expected to sustain a BFF population. An overriding limitation to achieving sufficient protection rests with vaccine delivery constraints. Late summer/fall bait distribution results in the highest bait uptake rates. However, the PD birth pulse each spring can double the size of populations in most years, greatly reducing the proportion of vaccinates in populations and diminishing potential herd immunity benefits. In addition to nonvaccinated juveniles and PD that do not consume bait, incomplete vaccine protection and time required for immunity to develop leaves a large majority of PD populations vulnerable to plague for 6–7 months or more each year.
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Affiliation(s)
- Marc R Matchett
- Charles M. Russell National Wildlife Refuge, U.S. Fish and Wildlife Service, Lewistown, Montana, USA
| | - Thomas R Stanley
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Matthew F Mccollister
- Charles M. Russell National Wildlife Refuge, U.S. Fish and Wildlife Service, Lewistown, Montana, USA
| | - David A Eads
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | | | - Dean E Biggins
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
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12
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Andrianaivoarimanana V, Wagner DM, Birdsell DN, Nikolay B, Rakotoarimanana F, Randriantseheno LN, Vogler AJ, Sahl JW, Hall CM, Somprasong N, Cauchemez S, Schweizer HP, Razafimandimby H, Rogier C, Rajerison M. Transmission of antimicrobial resistant Yersinia pestis during a pneumonic plague outbreak. Clin Infect Dis 2021; 74:695-702. [PMID: 34244722 PMCID: PMC8886911 DOI: 10.1093/cid/ciab606] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Pneumonic plague (PP), caused by Yersinia pestis, is the most feared clinical form of plague due to its rapid lethality and potential to cause outbreaks. PP outbreaks are now rare due to antimicrobial therapy. METHODS A PP outbreak in Madagascar involving transmission of a Y. pestis strain resistant to streptomycin, the current recommended first-line treatment in Madagascar, was retrospectively characterized using epidemiology, clinical diagnostics, molecular characterization, and animal studies. RESULTS The outbreak occurred in February 2013 in the Faratsiho district of Madagascar and involved 22 cases, including three untreated fatalities. The 19 other cases participated in funeral practices for the fatal cases and fully recovered after combination antimicrobial therapy: intramuscular streptomycin followed by oral co-trimoxazole. The Y. pestis strain that circulated during this outbreak is resistant to streptomycin resulting from a spontaneous point mutation in the 30S ribosomal protein S12 (rpsL) gene. This same mutation causes streptomycin resistance in two unrelated Y. pestis strains, one isolated from a fatal PP case in a different region of Madagascar in 1987 and another isolated from a fatal PP case in China in 1996, documenting this mutation has occurred independently at least three times in Y. pestis. Laboratory experiments revealed this mutation has no detectable impact on fitness or virulence, and revertants to wild-type are rare in other species containing it, suggesting Y. pestis strains containing it could persist in the environment. CONCLUSION Unique AMR strains of Y. pestis continue to arise in Madagascar and can be transmitted during PP outbreaks.
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Affiliation(s)
| | | | | | | | | | | | - Amy J Vogler
- Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Northern Arizona University, Flagstaff, Arizona, USA
| | - Carina M Hall
- Northern Arizona University, Flagstaff, Arizona, USA
| | - Nawarat Somprasong
- Northern Arizona University, Flagstaff, Arizona, USA.,University of Florida, Gainesville, Florida, USA
| | | | - Herbert P Schweizer
- Northern Arizona University, Flagstaff, Arizona, USA.,University of Florida, Gainesville, Florida, USA
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Vallès X, Stenseth NC, Demeure C, Horby P, Mead PS, Cabanillas O, Ratsitorahina M, Rajerison M, Andrianaivoarimanana V, Ramasindrazana B, Pizarro-Cerda J, Scholz HC, Girod R, Hinnebusch BJ, Vigan-Womas I, Fontanet A, Wagner DM, Telfer S, Yazdanpanah Y, Tortosa P, Carrara G, Deuve J, Belmain SR, D’Ortenzio E, Baril L. Human plague: An old scourge that needs new answers. PLoS Negl Trop Dis 2020; 14:e0008251. [PMID: 32853251 PMCID: PMC7451524 DOI: 10.1371/journal.pntd.0008251] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague's resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a "One Health" approach.
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Affiliation(s)
- Xavier Vallès
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- Key Laboratory for Earth System Modelling, Department of Earth System Science, Tsinghua University, Beijing, China
| | - Christian Demeure
- Yersinia Research Unit, National Reference Centre “Plague & Other Yersinioses,” WHO Collaborating Research and Reference Centre for Yersinia, Institut Pasteur, Paris, France
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul S. Mead
- Bacterial Diseases Branch, Division of Vector Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Oswaldo Cabanillas
- Control de Epidemia Desastres y Otras Emergencias Sanitarias, Oficina General de Epidemiologia, Ministerio de Salud, Perúu
| | - Mahery Ratsitorahina
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Minoarisoa Rajerison
- Plague Unit, Central Laboratory for Plague, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Beza Ramasindrazana
- Plague Unit, Central Laboratory for Plague, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Javier Pizarro-Cerda
- Yersinia Research Unit, National Reference Centre “Plague & Other Yersinioses,” WHO Collaborating Research and Reference Centre for Yersinia, Institut Pasteur, Paris, France
| | - Holger C. Scholz
- Reference Laboratory for Plague, Bundeswehr Institute of Microbiology, Munich, Germany
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - B. Joseph Hinnebusch
- Rocky Mountain Laboratories, National Institute of Health, National Institutes of Allergy and Infectious Diseases, Hamilton, Montana, United States of America
| | - Ines Vigan-Womas
- Immunology of Infectious Diseases Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
- PACRI unit, Conservatoire National des Arts et Métiers, Paris, France
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sandra Telfer
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Yazdan Yazdanpanah
- REACTing, Inserm, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
- Service de Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Pablo Tortosa
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical, La Réunion, France
| | - Guia Carrara
- REACTing, Inserm, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Jane Deuve
- Department of International Affairs, Institut Pasteur, Paris, France
| | - Steven R. Belmain
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Eric D’Ortenzio
- REACTing, Inserm, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
- Service de Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Laurence Baril
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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Spyrou MA, Keller M, Tukhbatova RI, Scheib CL, Nelson EA, Andrades Valtueña A, Neumann GU, Walker D, Alterauge A, Carty N, Cessford C, Fetz H, Gourvennec M, Hartle R, Henderson M, von Heyking K, Inskip SA, Kacki S, Key FM, Knox EL, Later C, Maheshwari-Aplin P, Peters J, Robb JE, Schreiber J, Kivisild T, Castex D, Lösch S, Harbeck M, Herbig A, Bos KI, Krause J. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat Commun 2019; 10:4470. [PMID: 31578321 PMCID: PMC6775055 DOI: 10.1038/s41467-019-12154-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.
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Affiliation(s)
- Maria A Spyrou
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany.
| | - Marcel Keller
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation, 420008
| | | | - Elizabeth A Nelson
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany
| | | | - Gunnar U Neumann
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Don Walker
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | - Amelie Alterauge
- Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland
| | - Niamh Carty
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | - Craig Cessford
- Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | - Hermann Fetz
- Archaeological Service, State Archive Nidwalden, 6371, Nidwalden, Switzerland
| | - Michaël Gourvennec
- Archeodunum SAS, Agency Toulouse, 8 allée Michel de Montaigne, 31770, Colomiers, France
| | - Robert Hartle
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | - Sacha Kacki
- PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France
- Department of Archaeology, Durham University, South Rd, Durham, DH1 3LE, UK
| | - Felix M Key
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Christian Later
- Bavarian State Department of Monuments and Sites, 80539, Munich, Germany
| | | | - Joris Peters
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, Kaulbachstr. 37/III, 80539, Munich, Germany
| | - John E Robb
- Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | | | - Toomas Kivisild
- Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Dominique Castex
- PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France
| | - Sandra Lösch
- Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland
| | - Michaela Harbeck
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany.
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15
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Andrianaivoarimanana V, Piola P, Wagner DM, Rakotomanana F, Maheriniaina V, Andrianalimanana S, Chanteau S, Rahalison L, Ratsitorahina M, Rajerison M. Trends of Human Plague, Madagascar, 1998-2016. Emerg Infect Dis 2019; 25:220-228. [PMID: 30666930 PMCID: PMC6346457 DOI: 10.3201/eid2502.171974] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Madagascar is more seriously affected by plague, a zoonosis caused by Yersinia pestis, than any other country. The Plague National Control Program was established in 1993 and includes human surveillance. During 1998-2016, a total of 13,234 suspected cases were recorded, mainly from the central highlands; 27% were confirmed cases, and 17% were presumptive cases. Patients with bubonic plague (median age 13 years) represented 93% of confirmed and presumptive cases, and patients with pneumonic plague (median age 29 years) represented 7%. Deaths were associated with delay of consultation, pneumonic form, contact with other cases, occurrence after 2009, and not reporting dead rats. A seasonal pattern was observed with recrudescence during September-March. Annual cases peaked in 2004 and decreased to the lowest incidence in 2016. This overall reduction occurred primarily for suspected cases and might be caused by improved adherence to case criteria during widespread implementation of the F1 rapid diagnostic test in 2002.
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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17
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Demeure C, Dussurget O, Fiol GM, Le Guern AS, Savin C, Pizarro-Cerdá J. Yersinia pestis and plague: an updated view on evolution, virulence determinants, immune subversion, vaccination and diagnostics. Microbes Infect 2019; 21:202-212. [DOI: 10.1016/j.micinf.2019.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/18/2019] [Indexed: 01/08/2023]
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18
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Demeure CE, Dussurget O, Mas Fiol G, Le Guern AS, Savin C, Pizarro-Cerdá J. Yersinia pestis and plague: an updated view on evolution, virulence determinants, immune subversion, vaccination, and diagnostics. Genes Immun 2019; 20:357-370. [PMID: 30940874 PMCID: PMC6760536 DOI: 10.1038/s41435-019-0065-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/18/2019] [Indexed: 12/30/2022]
Abstract
Plague is a vector-borne disease caused by Yersinia pestis. Transmitted by fleas from rodent reservoirs, Y. pestis emerged <6000 years ago from an enteric bacterial ancestor through events of gene gain and genome reduction. It is a highly remarkable model for the understanding of pathogenic bacteria evolution, and a major concern for public health as highlighted by recent human outbreaks. A complex set of virulence determinants, including the Yersinia outer-membrane proteins (Yops), the broad-range protease Pla, pathogen-associated molecular patterns (PAMPs), and iron capture systems play critical roles in the molecular strategies that Y. pestis employs to subvert the human immune system, allowing unrestricted bacterial replication in lymph nodes (bubonic plague) and in lungs (pneumonic plague). Some of these immunogenic proteins as well as the capsular antigen F1 are exploited for diagnostic purposes, which are critical in the context of the rapid onset of death in the absence of antibiotic treatment (less than a week for bubonic plague and <48 h for pneumonic plague). Here, we review recent research advances on Y. pestis evolution, virulence factor function, bacterial strategies to subvert mammalian innate immune responses, vaccination, and problems associated with pneumonic plague diagnosis.
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Affiliation(s)
| | - Olivier Dussurget
- Yersinia Research Unit, Institut Pasteur, F-75724, Paris, France
- Université Paris-Diderot, Sorbonne Paris Cité, F-75013, Paris, France
| | - Guillem Mas Fiol
- Yersinia Research Unit, Institut Pasteur, F-75724, Paris, France
- Université Paris-Diderot, Sorbonne Paris Cité, F-75013, Paris, France
| | - Anne-Sophie Le Guern
- Yersinia Research Unit, Institut Pasteur, F-75724, Paris, France
- National Reference Laboratory 'Plague & Other Yersiniosis', Institut Pasteur, F-75724, Paris, France
- World Health Organization Collaborating Research & Reference Centre for Yersinia, Institut Pasteur, F-75724, Paris, France
| | - Cyril Savin
- Yersinia Research Unit, Institut Pasteur, F-75724, Paris, France
- National Reference Laboratory 'Plague & Other Yersiniosis', Institut Pasteur, F-75724, Paris, France
- World Health Organization Collaborating Research & Reference Centre for Yersinia, Institut Pasteur, F-75724, Paris, France
| | - Javier Pizarro-Cerdá
- Yersinia Research Unit, Institut Pasteur, F-75724, Paris, France.
- National Reference Laboratory 'Plague & Other Yersiniosis', Institut Pasteur, F-75724, Paris, France.
- World Health Organization Collaborating Research & Reference Centre for Yersinia, Institut Pasteur, F-75724, Paris, France.
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19
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Rabaan AA, Al-Ahmed SH, Alsuliman SA, Aldrazi FA, Alfouzan WA, Haque S. The rise of pneumonic plague in Madagascar: current plague outbreak breaks usual seasonal mould. J Med Microbiol 2019; 68:292-302. [PMID: 30632956 DOI: 10.1099/jmm.0.000915] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Madagascar has just emerged from the grip of an acute urban pneumonic plague outbreak, which began in August 2017, before the usual plague season of October-April and outside the traditional plague foci in the northern and central highlands. The World Health Organization reported a total of 2417 confirmed, probable and suspected cases, including 209 deaths between 1 August and 26 November 2017. The severity and scope of this outbreak, which has affected those in higher socioeconomic groups as well as those living in poverty, along with factors including the potential for use of multi-drug-resistant strains of plague in bioterrorism, highlights the ongoing threat posed by this ancient disease. Factors likely to have contributed to transmission include human behaviour, including burial practices and movement of people, poor urban planning leading to overcrowding and ready transmission by airborne droplets, climatic factors and genomic subtypes. The outbreak demonstrates the importance of identifying targeted pneumonic plague therapies and of developing vaccines that can be administered in planned programmes in developing countries such as Madagascar where plague is endemic. The dominance of pneumonic plague in this outbreak suggests that we need to focus more urgently on the danger of person-to-person transmission, as well as the problem of transmission of plague from zoonotic sources.
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Affiliation(s)
- Ali A Rabaan
- 1Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- 2Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Shahab A Alsuliman
- 3Internal Medicine and Infectious Disease Department, Dammam Medical Complex, Dammam, Saudi Arabia
| | - Fatimah A Aldrazi
- 4Infection Control Department, Dammam Medical Complex, Dammam, Saudi Arabia
| | - Wadha A Alfouzan
- 5Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Shafiul Haque
- 6Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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20
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D’Ortenzio E, Lemaître N, Brouat C, Loubet P, Sebbane F, Rajerison M, Baril L, Yazdanpanah Y. Plague: Bridging gaps towards better disease control. Med Mal Infect 2018; 48:307-317. [DOI: 10.1016/j.medmal.2018.04.393] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/13/2018] [Indexed: 01/14/2023]
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21
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Tsuzuki S, Lee H, Miura F, Chan YH, Jung SM, Akhmetzhanov AR, Nishiura H. Dynamics of the pneumonic plague epidemic in Madagascar, August to October 2017. ACTA ACUST UNITED AC 2018; 22. [PMID: 29162211 PMCID: PMC5718396 DOI: 10.2807/1560-7917.es.2017.22.46.17-00710] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transmission potential and severity of pneumonic plague in Madagascar were assessed. Accounting for reporting delay, the reproduction number was estimated at 1.73. The case fatality risk was estimated as 5.5%. Expected numbers of exported cases from Madagascar were estimated across the world and all estimates were below 1 person from August to October, 2017.
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Affiliation(s)
- Shinya Tsuzuki
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyojung Lee
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Fuminari Miura
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.,Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yat Hin Chan
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Sung-Mok Jung
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | | | - Hiroshi Nishiura
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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22
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Mitchell CL, Andrianaivoarimanana V, Colman RE, Busch J, Hornstra-O’Neill H, Keim PS, Wagner DM, Rajerison M, Birdsell DN. Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model. PLoS Negl Trop Dis 2017; 11:e0006077. [PMID: 29227994 PMCID: PMC5739503 DOI: 10.1371/journal.pntd.0006077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 12/21/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genetic analysis of pathogenic organisms is a useful tool for linking human cases together and/or to potential environmental sources. The resulting data can also provide information on evolutionary patterns within a targeted species and phenotypic traits. However, the instruments often used to generate genotyping data, such as single nucleotide polymorphisms (SNPs), can be expensive and sometimes require advanced technologies to implement. This places many genotyping tools out of reach for laboratories that do not specialize in genetic studies and/or lack the requisite financial and technological resources. To address this issue, we developed a low cost and low tech genotyping system, termed agarose-MAMA, which combines traditional PCR and agarose gel electrophoresis to target phylogenetically informative SNPs. METHODOLOGY/PRINCIPAL FINDINGS To demonstrate the utility of this approach for generating genotype data in a resource-constrained area (Madagascar), we designed an agarose-MAMA system targeting previously characterized SNPs within Yersinia pestis, the causative agent of plague. We then used this system to genetically type pathogenic strains of Y. pestis in a Malagasy laboratory not specialized in genetic studies, the Institut Pasteur de Madagascar (IPM). We conducted rigorous assay performance validations to assess potential variation introduced by differing research facilities, reagents, and personnel and found no difference in SNP genotyping results. These agarose-MAMA PCR assays are currently employed as an investigative tool at IPM, providing Malagasy researchers a means to improve the value of their plague epidemiological investigations by linking outbreaks to potential sources through genetic characterization of isolates and to improve understanding of disease ecology that may contribute to a long-term control effort. CONCLUSIONS The success of our study demonstrates that the SNP-based genotyping capacity of laboratories in developing countries can be expanded with manageable financial cost for resource constraint laboratories. This is a practical formula that reduces resource-driven limitations to genetic research and promises to advance global collective knowledge of infectious diseases emanating from resource limited regions of the world.
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Affiliation(s)
- Cedar L. Mitchell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Rebecca E. Colman
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra-O’Neill
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Minoarisoa Rajerison
- Plague Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- * E-mail: (MR); (DNB)
| | - Dawn N. Birdsell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail: (MR); (DNB)
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