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Vogler AJ, Sahl JW, Leal NC, Sobreira M, Williamson CHD, Bollig MC, Birdsell DN, Rivera A, Thompson B, Nottingham R, Rezende AM, Keim P, Almeida AMP, Wagner DM. A single introduction of Yersinia pestis to Brazil during the 3rd plague pandemic. PLoS One 2019; 14:e0209478. [PMID: 30625164 PMCID: PMC6326411 DOI: 10.1371/journal.pone.0209478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/06/2018] [Indexed: 12/30/2022] Open
Abstract
Yersinia pestis was introduced to Brazil during the third plague pandemic and currently exists in several recognized foci. There is currently limited available phylogeographic data regarding Y. pestis in Brazil. We generated whole genome sequences for 411 Y. pestis strains from six Brazilian foci to investigate the phylogeography of Y. pestis in Brazil; these strains were isolated from 1966 to 1997. All 411 strains were assigned to a single monophyletic clade within the 1.ORI population, indicating a single Y. pestis introduction was responsible for the successful establishment of endemic foci in Brazil. There was a moderate level of genomic diversity but little population structure among the 411 Brazilian Y. pestis strains, consistent with a radial expansion wherein Y. pestis spread rapidly from the coast to the interior of Brazil and became ecologically established. Overall, there were no strong spatial or temporal patterns among the Brazilian strains. However, strains from the same focus tended to be more closely related and strains isolated from foci closer to the coast tended to fall in more basal positions in the whole genome phylogeny than strains from more interior foci. Overall, the patterns observed in Brazil are similar to other locations affected during the 3rd plague pandemic such as in North America and Madagascar.
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Affiliation(s)
- Amy J. Vogler
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nilma C. Leal
- Institute Aggeu Magalhães, Recife, Pernambuco, Brazil
| | | | - Charles H. D. Williamson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Molly C. Bollig
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Dawn N. Birdsell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Andrew Rivera
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Brian Thompson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne Nottingham
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | | | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail: (DMW); (AMPA)
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Qi Z, Cui Y, Zhang Q, Yang R. Taxonomy of Yersinia pestis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:35-78. [PMID: 27722860 DOI: 10.1007/978-94-024-0890-4_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This chapter summarized the taxonomy and typing works of Yersinia pestis since it's firstly identified in Hong Kong in 1894. Phenotyping methods that based on phenotypic characteristics, including biotyping, serotyping, antibiogram analysis, bacteriocin typing, phage typing, and plasmid typing, were firstly applied in classification of Y. pestis in subspecies level. And then, with the advancement of molecular biological technology, the methods based on outer membrane protein profiles, fatty acid composition, and bacterial mass fingerprinting were also used to identify the populations within Y. pestis. However, Y. pestis is a highly homogenous species; therefore, the above typing methods could only provide low resolution, e.g., only one serotype and one phage type were observed for the whole species. Since the 1990s, molecular typing based on DNA variations, including single-nucleotide polymorphism, gene gain/loss, variable-number tandem repeats, clustered regularly interspaced short palindromic repeat, etc., was introduced and improved the resolution and robust of typing result. Especially in recent years, genotyping-based whole-genome-wide variations were successfully employed in Y. pestis, which built the "gold standard" of typing scheme of the species and could distinguish the samples under the strain level. The taxonomy and typing works leaved us enormous polymorphism data; therefore, a comprehensive fingerprint database of Y. pestis was needed to collect and standardize these data, for facilitating future works on evolution, plague surveillance and control, anti-bioterrorism, and microbial forensic researches.
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Affiliation(s)
- Zhizhen Qi
- Qinghai Provincial Key Laboratory for Plague Control and Research, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai Province, 811602, China
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China
| | - Qingwen Zhang
- Qinghai Provincial Key Laboratory for Plague Control and Research, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai Province, 811602, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China.
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Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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Barros MPS, Silveira-Filho VM, Lins RHFB, Oliveira MBM, Almeida AMP, Leal-Balbino TC. Subtyping Brazilian Yersinia pestis strains by pulsed-field gel electrophoresis. GENETICS AND MOLECULAR RESEARCH 2013; 12:1294-302. [PMID: 23315882 DOI: 10.4238/2013.january.4.23] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We subtyped Brazilian Yersinia pestis strains by pulsed-field gel electrophoresis (PFGE). This was done with 22 Brazilian Y. pestis strains: 17 from an outbreak and 5 from endemic routine surveillance. The strains were divided into 2 groups (I and II), 8 subgroups (A-H) and 19 PFGE profiles or pulsotypes. PFGE did not separate outbreak from non-outbreak strains, as identical pulsotype patterns were found among outbreak strains and strains obtained from surveillance. However, it was able to detect intraspecific genetic diversity among Brazilian strains. This PFGE technique was able to differentiate a homogeneous group of Brazilian Y. pestis strains.
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Affiliation(s)
- M P S Barros
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães, FIOCRUZ, Recife, PE, Brasil
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Abstract
Increased interest in the pathogenic potential of Yersinia pestis has emerged because of the potential threats from bioterrorism. Pathogenic potential is based on genetic factors present in a population of microbes, yet most studies evaluating the role of specific genes in virulence have used a limited number of strains. For Y. pestis this issue is complicated by the fact that most strains available for study in the Americas are clonally derived and thus genetically restricted, emanating from a strain of Y. pestis introduced into the United States in 1902 via marine shipping and subsequent spread of this strain throughout North and South America. In countries from the former Soviet Union (FSU), Mongolia, and China there are large areas of enzootic foci of Y. pestis infection containing genetically diverse strains that have been intensely studied by scientists in these countries. However, the results of these investigations are not generally known outside of these countries. Here we describe the variety of methods used in the FSU to classify Y. pestis strains based on genetic and phenotypic variation and show that there is a high level of diversity in these strains not reflected by ones obtained from sylvatic areas and patients in the Americas.
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Affiliation(s)
- Andrey P Anisimov
- Department of Infectious Diseases, State Research Center for Applied Microbiology, 142279 Obolensk, Serpukhov District, Moscow Region, Russia
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Abstract
AIMS To determine the effectiveness of multiplex-PCR in Yersinia pestis identification in samples preserved in Cary & Blair medium and to evaluate if this technique would uncover Y. pestis-positives among culture-negative samples. METHODS AND RESULTS Multiplex-PCR was used to detect Y. pestis in Cary & Blair preserved bubo aspirates from experimentally infected guinea pigs and to re-analyze samples from a plague outbreak after prolonged storage in Cary & Blair. Variation in the target genes amplification was observed over time. CONCLUSIONS Multiplex-PCR proved to be more effective than culture for plague diagnosis, both for old and recent samples. This technique would be a valuable tool for the plague control programme. SIGNIFICANCE AND IMPACT OF THE STUDY The multiplex-PCR technique can be useful for the detection and characterization of Y. pestis even when the bacteria are no longer viable and when culture diagnosis has been hampered by the growth of contaminants.
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Affiliation(s)
- A C Melo
- Centro de Pesquisas Aggeu Magalhães/FIOCRUZ/MS, Recife, PE, Brazil
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Leal NC, Almeida AM. Diagnosis of plague and identification of virulence markers in Yersinia pestis by multiplex-PCR. Rev Inst Med Trop Sao Paulo 1999; 41:339-42. [PMID: 10671286 DOI: 10.1590/s0036-46651999000600002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have developed a procedure for the rapid diagnosis of plague that also allows the identification of prominent virulence markers of Y. pestis strains. This procedure is based upon the use of a single polymerase chain reaction with multiple pairs of primers directed at genes present in the three virulence plasmids as well as in the chromosomal pathogenicity island of the bacterium. The technique allowed the discrimination of strains which lacked one or more of the known pathogenic loci, using as template total DNA obtained from bacterial cultures and from simulated blood cultures containing diluted concentration of bacteria. It also proved effective in confirming the disease in a blood culture from a plague suspected patient. As the results are obtained in a few hours this technique will be useful in the methodology of the Plague Control Program.
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Affiliation(s)
- N C Leal
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães, Recife, PE, Brazil.
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Abath FG, Almeida AM, Ferreira LC. Surface-exposed antigenic determinants in outer membranes of wild Yersinia pestis isolates. ZENTRALBLATT FUR BAKTERIOLOGIE : INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY 1991; 276:73-85. [PMID: 1724154 DOI: 10.1016/s0934-8840(11)80221-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Immunogenic surface exposed envelope proteins of Yersinia pestis strains were investigated with SDS-PAGE and immunoblots with antisera of immunized guinea pigs and convalescent patients. The sarkosyl-insoluble outer membrane proteins (OMPs) of three human isolates and one laboratory strain of Y. pestis grown in different rich media to exponential or stationary phase, and cultivated at 28 degrees C or 37 degrees C, were assayed for the presence of immunogenic peptides. Seven guinea-pig sera immunized with one of the four Y. pestis strains and four human sera from plague-infected patients indicated that at least four outer membrane proteins with molecular weights of 45 KDal, 42 KDal, 21 KDal and 16.5 KDal were strongly recognized by at least one of them. All but one of the guinea-pig serum and one human serum recognized the 45 KDal protein. The 42 KDal was identified only in outer membrane isolated from Y. pestis cells grown at 28 degrees C. All immunogenic OMPs were found in the four strains investigated. Labelling of intact Y. pestis cells with Iodogen and 131I further demonstrated the surface-exposed location of the immunogenic OMPs.
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Affiliation(s)
- F G Abath
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, Brazil
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