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Arbel-Groissman M, Menuhin-Gruman I, Yehezkeli H, Naki D, Bergman S, Udi Y, Tuller T. The Causes for Genomic Instability and How to Try and Reduce Them Through Rational Design of Synthetic DNA. Methods Mol Biol 2024; 2760:371-392. [PMID: 38468099 DOI: 10.1007/978-1-0716-3658-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Genetic engineering has revolutionized our ability to manipulate DNA and engineer organisms for various applications. However, this approach can lead to genomic instability, which can result in unwanted effects such as toxicity, mutagenesis, and reduced productivity. To overcome these challenges, smart design of synthetic DNA has emerged as a promising solution. By taking into consideration the intricate relationships between gene expression and cellular metabolism, researchers can design synthetic constructs that minimize metabolic stress on the host cell, reduce mutagenesis, and increase protein yield. In this chapter, we summarize the main challenges of genomic instability in genetic engineering and address the dangers of unknowingly incorporating genomically unstable sequences in synthetic DNA. We also demonstrate the instability of those sequences by the fact that they are selected against conserved sequences in nature. We highlight the benefits of using ESO, a tool for the rational design of DNA for avoiding genetically unstable sequences, and also summarize the main principles and working parameters of the software that allow maximizing its benefits and impact.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hader Yehezkeli
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Yarin Udi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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<i>Yersinia pestis</i> ssp. <i>pestis</i> Spatial MLVA25 Genotypic Structure in the Transboundary Saylyugem Natural Plague Focus. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2023. [DOI: 10.21055/0370-1069-2022-4-110-116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Advanced molecular-genetic methods for the diagnosis and typing of Yersinia pestis ssp. pestis in the field and clinical material are used for epidemiological surveillance of plague in the Saylyugem natural focus. The aim of the work was to study the spatial genotypic structure of Y. pestis ssp. pestis in the transboundary Saylyugem natural plague focus using MLVA25 typing. Materials and methods. The MLVA25 typing of 160 strains of Y. pestis ssp. Pestis isolated in the Saylyugem natural plague focus in 2012–2021 was carried out. Phylogenetic tree construction was performed with the help of UPGMA and MST methods. Results and discussion. The Y. pestis ssp. pestis strains isolated from the Saylyugem natural plague focus were differentiated into 15 MLVA types by the 25 VNTR loci cluster analysis. The studied strains form a homogeneous complex of MLVA25 types without marked geographical distribution across seven spatial groups. The analysis of the frequency of occurrence of the tandem repeats number for three variable loci of Y. pestis ssp. pestis strains shows the significant differences between the samples from the Mongolian and Russian parts of the Saylyugem natural plague focus. The most pronounced differences in spatial genotypic structure are traced through the yp4280ms62 locus.
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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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Menuhin-Gruman I, Arbel M, Amitay N, Sionov K, Naki D, Katzir I, Edgar O, Bergman S, Tuller T. Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels. ACS Synth Biol 2022; 11:1142-1151. [PMID: 34928133 PMCID: PMC8938948 DOI: 10.1021/acssynbio.1c00426] [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: 12/03/2022]
Abstract
![]()
Modern
synthetic biology procedures rely on the ability to generate
stable genetic constructs that keep their functionality over long
periods of time. However, maintenance of these constructs requires
energy from the cell and thus reduces the host’s fitness. Natural
selection results in loss-of-functionality mutations that negate the
expression of the construct in the population. Current approaches
for the prevention of this phenomenon focus on either small-scale,
manual design of evolutionary stable constructs or the detection of
mutational sites with unstable tendencies. We designed the Evolutionary
Stability Optimizer (ESO), a software tool that enables the large-scale
automatic design of evolutionarily stable constructs with respect
to both mutational and epigenetic hotspots and allows users to define
custom hotspots to avoid. Furthermore, our tool takes the expression
of the input constructs into account by considering the guanine-cytosine
(GC) content and codon usage of the host organism, balancing the trade-off
between stability and gene expression, allowing to increase evolutionary
stability while maintaining the high expression. In this study, we
present the many features of the ESO and show that it accurately predicts
the evolutionary stability of endogenous genes. The ESO was created
as an easy-to-use, flexible platform based on the notion that directed
genetic stability research will continue to evolve and revolutionize
current applications of synthetic biology. The ESO is available at
the following link: https://www.cs.tau.ac.il/~tamirtul/ESO/.
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Affiliation(s)
- Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Matan Arbel
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Niv Amitay
- School of Electrical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Karin Sionov
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Itai Katzir
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Omer Edgar
- School of Medicine, The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel 6997801
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel 6997801
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Belthoff JR, Elgin AA, Navock KA, Bernhardt SA. Burrowing owls as potential phoretic hosts of ground squirrel fleas during a plague epizootic. JOURNAL OF VECTOR ECOLOGY : JOURNAL OF THE SOCIETY FOR VECTOR ECOLOGY 2021; 46:48-56. [PMID: 35229581 DOI: 10.52707/1081-1710-46.1.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/30/2020] [Indexed: 06/14/2023]
Abstract
During the course of a plague epizootic, decimation of rodent host populations may result in the transfer of fleas to alternate or phoretic hosts, including to sympatric raptors that prey on rodents. We studied flea abundance and flea species assemblages on burrowing owls (Athene cunicularia hypugaea) in southwestern Idaho before (2012 - 2014), during (2015 - 2016), and after (2017) an epizootic of plague in Piute ground squirrels (Urocitellis mollis). We examined (1) if a larger proportion of burrowing owl nests contained fleas, (2) the likelihood that owls within a high flea abundance class increased, and (3) if owls harbored ground squirrel fleas during the epizootic. Using a flea abundance index assigned to 1,184 owls from 236 nests, the proportion of nests and the likelihood that owls had high flea abundance decreased rather than increased during epizootic years. Moreover, of 3,538 collected fleas from owls at 143 nests, no fleas were species that Piute ground squirrels typically harbor. Instead, Pulex irritans was the predominant flea collected in all study years (> 99%). Thus, although raptors may play a role in plague, there was no evidence that the die-off of ground squirrels resulted in higher flea intensity in burrowing owls or that they served as frequent accidental or phoretic hosts for ground squirrel fleas that could potentially be infectious with Yersinia pestis.
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Affiliation(s)
- James R Belthoff
- REU Site in Raptor Research, Raptor Research Center and Department of Biological Sciences, Boise State University, Boise, ID, U.S.A.,
| | - Andrew A Elgin
- REU Site in Raptor Research, Raptor Research Center and Department of Biological Sciences, Boise State University, Boise, ID, U.S.A
- Biology Department, William and Mary, Williamsburg, VA, U.S.A
| | - Kara A Navock
- REU Site in Raptor Research, Raptor Research Center and Department of Biological Sciences, Boise State University, Boise, ID, U.S.A
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Colman RE, Brinkerhoff RJ, Busch JD, Ray C, Doyle A, Sahl JW, Keim P, Collinge SK, Wagner DM. No evidence for enzootic plague within black-tailed prairie dog (Cynomys ludovicianus) populations. Integr Zool 2021; 16:834-851. [PMID: 33882192 PMCID: PMC9292313 DOI: 10.1111/1749-4877.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Yersinia pestis, causative agent of plague, occurs throughout the western United States in rodent populations and periodically causes epizootics in susceptible species, including black‐tailed prairie dogs (Cynomys ludovicianus). How Y. pestis persists long‐term in the environment between these epizootics is poorly understood but multiple mechanisms have been proposed, including, among others, a separate enzootic transmission cycle that maintains Y. pestis without involvement of epizootic hosts and persistence of Y. pestis within epizootic host populations without causing high mortality within those populations. We live‐trapped and collected fleas from black‐tailed prairie dogs and other mammal species from sites with and without black‐tailed prairie dogs in 2004 and 2005 and tested all fleas for presence of Y. pestis. Y. pestis was not detected in 2126 fleas collected in 2004 but was detected in 294 fleas collected from multiple sites in 2005, before and during a widespread epizootic that drastically reduced black‐tailed prairie dog populations in the affected colonies. Temporal and spatial patterns of Y. pestis occurrence in fleas and genotyping of Y. pestis present in some infected fleas suggest Y. pestis was introduced multiple times from sources outside the study area and once introduced, was dispersed between several sites. We conclude Y. pestis likely was not present in these black‐tailed prairie dog colonies prior to epizootic activity in these colonies. Although we did not identify likely enzootic hosts, we found evidence that deer mice (Peromyscus maniculatus) may serve as bridging hosts for Y. pestis between unknown enzootic hosts and black‐tailed prairie dogs.
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Affiliation(s)
- Rebecca E Colman
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - R Jory Brinkerhoff
- Environmental Studies Program, University of Colorado at Boulder, Boulder, Colorado, USA
| | - Joseph D Busch
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Chris Ray
- Environmental Studies Program, University of Colorado at Boulder, Boulder, Colorado, USA
| | - Adina Doyle
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Sharon K Collinge
- Environmental Studies Program, University of Colorado at Boulder, Boulder, Colorado, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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Mayo C, McDermott E, Kopanke J, Stenglein M, Lee J, Mathiason C, Carpenter M, Reed K, Perkins TA. Ecological Dynamics Impacting Bluetongue Virus Transmission in North America. Front Vet Sci 2020; 7:186. [PMID: 32426376 PMCID: PMC7212442 DOI: 10.3389/fvets.2020.00186] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Bluetongue virus (BTV) is an arbovirus transmitted to domestic and wild ruminants by certain species of Culicoides midges. The disease resulting from infection with BTV is economically important and can influence international trade and movement of livestock, the economics of livestock production, and animal welfare. Recent changes in the epidemiology of Culicoides-transmitted viruses, notably the emergence of exotic BTV genotypes in Europe, have demonstrated the devastating economic consequences of BTV epizootics and the complex nature of transmission across host-vector landscapes. Incursions of novel BTV serotypes into historically enzootic countries or regions, including the southeastern United States (US), Israel, Australia, and South America, have also occurred, suggesting diverse pathways for the transmission of these viruses. The abundance of BTV strains and multiple reassortant viruses circulating in Europe and the US in recent years demonstrates considerable genetic diversity of BTV strains and implies a history of reassortment events within the respective regions. While a great deal of emphasis is rightly placed on understanding the epidemiology and emergence of BTV beyond its natural ecosystem, the ecological contexts in which BTV maintains an enzootic cycle may also be of great significance. This review focuses on describing our current knowledge of ecological factors driving BTV transmission in North America. Information presented in this review can help inform future studies that may elucidate factors that are relevant to longstanding and emerging challenges associated with prevention of this disease.
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Affiliation(s)
- Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Emily McDermott
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Jennifer Kopanke
- Office of the Campus Veterinarian, Washington State University, Spokane, WA, United States
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Justin Lee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Candace Mathiason
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Molly Carpenter
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Kirsten Reed
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - T. Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
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8
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Biggins DE, Eads DA. Prairie Dogs, Persistent Plague, Flocking Fleas, and Pernicious Positive Feedback. Front Vet Sci 2019; 6:75. [PMID: 30984769 PMCID: PMC6447679 DOI: 10.3389/fvets.2019.00075] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 02/21/2019] [Indexed: 01/21/2023] Open
Abstract
Plague (caused by the bacterium Yersinia pestis) is a deadly flea-borne disease that remains a threat to public health nearly worldwide and is particularly disruptive ecologically where it has been introduced. We review hypotheses regarding maintenance and transmission of Y. pestis, emphasizing recent data from North America supporting maintenance by persistent transmission that results in sustained non-epizootic (but variable) rates of mortality in hosts. This maintenance mechanism may facilitate periodic epizootic eruptions "in place" because the need for repeated reinvasion from disjunct sources is eliminated. Resulting explosive outbreaks that spread rapidly in time and space are likely enhanced by synergistic positive feedback (PFB) cycles involving flea vectors, hosts, and the plague bacterium itself. Although PFB has been implied in plague literature for at least 50 years, we propose this mechanism, particularly with regard to flea responses, as central to epizootic plague rather than a phenomenon worthy of just peripheral mention. We also present new data on increases in flea:host ratios resulting from recreational shooting and poisoning as possible triggers for the transition from enzootic maintenance to PFB cycles and epizootic explosions. Although plague outbreaks have received much historic attention, PFB cycles that result in decimation of host populations lead to speculation that epizootic eruptions might not be part of the adaptive evolutionary strategy of Y. pestis but might instead be a tolerated intermittent cost of its modus operandi. We also speculate that there may be mammal communities where epizootics, as we define them, are rare or absent. Absence of plague epizootics might translate into reduced public health risk but does not necessarily equate to inconsequential ecologic impact.
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Affiliation(s)
- Dean E. Biggins
- United States Geological Survey, Fort Collins Science Center, Fort Collins, CO, United States
| | - David A. Eads
- United States Geological Survey, Fort Collins Science Center, Fort Collins, CO, United States
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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9
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Kendall LV, Owiny JR, Dohm ED, Knapek KJ, Lee ES, Kopanke JH, Fink M, Hansen SA, Ayers JD. Replacement, Refinement, and Reduction in Animal Studies With Biohazardous Agents. ILAR J 2019; 59:177-194. [DOI: 10.1093/ilar/ily021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 06/11/2018] [Indexed: 12/17/2022] Open
Abstract
Abstract
Animal models are critical to the advancement of our knowledge of infectious disease pathogenesis, diagnostics, therapeutics, and prevention strategies. The use of animal models requires thoughtful consideration for their well-being, as infections can significantly impact the general health of an animal and impair their welfare. Application of the 3Rs—replacement, refinement, and reduction—to animal models using biohazardous agents can improve the scientific merit and animal welfare. Replacement of animal models can use in vitro techniques such as cell culture systems, mathematical models, and engineered tissues or invertebrate animal hosts such as amoeba, worms, fruit flies, and cockroaches. Refinements can use a variety of techniques to more closely monitor the course of disease. These include the use of biomarkers, body temperature, behavioral observations, and clinical scoring systems. Reduction is possible using advanced technologies such as in vivo telemetry and imaging, allowing longitudinal assessment of animals during the course of disease. While there is no single method to universally replace, refine, or reduce animal models, the alternatives and techniques discussed are broadly applicable and they should be considered when infectious disease animal models are developed.
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Affiliation(s)
- Lon V Kendall
- Department of Microbiology, Immunology and Pathology, and Laboratory Animal Resources, Colorado State University, Fort Collins, Colorado
| | - James R Owiny
- Laboratory Animal Resources, Colorado State University, Fort Collins, Colorado
| | - Erik D Dohm
- Animal Resources Program, University of Alabama, Birmingham, Alabama
| | - Katie J Knapek
- Comparative Medicine Training Program, Colorado State University, Fort Collins, Colorado
| | - Erin S Lee
- Animal Resource Center, University of Texas Medical Branch, Galveston, Texas
| | - Jennifer H Kopanke
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Michael Fink
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri
| | - Sarah A Hansen
- Office of Animal Resources, University of Iowa, Iowa City, Iowa
| | - Jessica D Ayers
- Laboratory Animal Resources, Colorado State University, Fort Collins, Colorado
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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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11
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Gétaz M, Krijger M, Rezzonico F, Smits THM, van der Wolf JM, Pothier JF. Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description. Microb Genom 2018; 4:e000189. [PMID: 29874158 PMCID: PMC6113873 DOI: 10.1099/mgen.0.000189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Marjon Krijger
- Wageningen University and Research, Wageningen, the Netherlands
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | | | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
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12
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Markman DW, Antolin MF, Bowen RA, Wheat WH, Woods M, Gonzalez-Juarrero M, Jackson M. Yersinia pestis Survival and Replication in Potential Ameba Reservoir. Emerg Infect Dis 2018; 24:294-302. [PMID: 29350155 PMCID: PMC5782900 DOI: 10.3201/eid2402.171065] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Plague ecology is characterized by sporadic epizootics, then periods of dormancy. Building evidence suggests environmentally ubiquitous amebae act as feral macrophages and hosts to many intracellular pathogens. We conducted environmental genetic surveys and laboratory co-culture infection experiments to assess whether plague bacteria were resistant to digestion by 5 environmental ameba species. First, we demonstrated that Yersinia pestis is resistant or transiently resistant to various ameba species. Second, we showed that Y. pestis survives and replicates intracellularly within Dictyostelium discoideum amebae for ˃48 hours postinfection, whereas control bacteria were destroyed in <1 hour. Finally, we found that Y. pestis resides within ameba structures synonymous with those found in infected human macrophages, for which Y. pestis is a competent pathogen. Evidence supporting amebae as potential plague reservoirs stresses the importance of recognizing pathogen-harboring amebae as threats to public health, agriculture, conservation, and biodefense.
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13
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Vogler AJ, Andrianaivoarimanana V, Telfer S, Hall CM, Sahl JW, Hepp CM, Centner H, Andersen G, Birdsell DN, Rahalison L, Nottingham R, Keim P, Wagner DM, Rajerison M. Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague. PLoS Negl Trop Dis 2017; 11:e0005887. [PMID: 28873412 PMCID: PMC5600411 DOI: 10.1371/journal.pntd.0005887] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/15/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Yersinia pestis appears to be maintained in multiple, geographically separate, and phylogenetically distinct subpopulations within the highlands of Madagascar. However, the dynamics of these locally differentiated subpopulations through time are mostly unknown. To address that gap and further inform our understanding of plague epidemiology, we investigated the phylogeography of Y. pestis in Madagascar over an 18 year period. METHODOLOGY/PRINCIPAL FINDINGS We generated whole genome sequences for 31 strains and discovered new SNPs that we used in conjunction with previously identified SNPs and variable-number tandem repeats (VNTRs) to genotype 773 Malagasy Y. pestis samples from 1995 to 2012. We mapped the locations where samples were obtained on a fine geographic scale to examine phylogeographic patterns through time. We identified 18 geographically separate and phylogenetically distinct subpopulations that display spatial and temporal stability, persisting in the same locations over a period of almost two decades. We found that geographic areas with higher levels of topographical relief are associated with greater levels of phylogenetic diversity and that sampling frequency can vary considerably among subpopulations and from year to year. We also found evidence of various Y. pestis dispersal events, including over long distances, but no evidence that any dispersal events resulted in successful establishment of a transferred genotype in a new location during the examined time period. CONCLUSIONS/SIGNIFICANCE Our analysis suggests that persistent endemic cycles of Y. pestis transmission within local areas are responsible for the long term maintenance of plague in Madagascar, rather than repeated episodes of wide scale epidemic spread. Landscape likely plays a role in maintaining Y. pestis subpopulations in Madagascar, with increased topographical relief associated with increased levels of localized differentiation. Local ecological factors likely affect the dynamics of individual subpopulations and the associated likelihood of observing human plague cases in a given year in a particular location.
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Affiliation(s)
- Amy J. Vogler
- 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
| | - Carina M. Hall
- 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
| | - Crystal M. Hepp
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heather Centner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Genevieve Andersen
- 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
| | - Lila Rahalison
- Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - 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
- Pathogen Genomics Division, 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
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14
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Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW. Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague. PLoS One 2017; 12:e0183478. [PMID: 28854255 PMCID: PMC5576697 DOI: 10.1371/journal.pone.0183478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/05/2017] [Indexed: 11/19/2022] Open
Abstract
The rapid pace of bacterial evolution enables organisms to adapt to the laboratory environment with repeated passage and thus diverge from naturally-occurring environmental ("wild") strains. Distinguishing wild and laboratory strains is clearly important for biodefense and bioforensics; however, DNA sequence data alone has thus far not provided a clear signature, perhaps due to lack of understanding of how diverse genome changes lead to convergent phenotypes, difficulty in detecting certain types of mutations, or perhaps because some adaptive modifications are epigenetic. Monitoring protein abundance, a molecular measure of phenotype, can overcome some of these difficulties. We have assembled a collection of Yersinia pestis proteomics datasets from our own published and unpublished work, and from a proteomics data archive, and demonstrated that protein abundance data can clearly distinguish laboratory-adapted from wild. We developed a lasso logistic regression classifier that uses binary (presence/absence) or quantitative protein abundance measures to predict whether a sample is laboratory-adapted or wild that proved to be ~98% accurate, as judged by replicated 10-fold cross-validation. Protein features selected by the classifier accord well with our previous study of laboratory adaptation in Y. pestis. The input data was derived from a variety of unrelated experiments and contained significant confounding variables. We show that the classifier is robust with respect to these variables. The methodology is able to discover signatures for laboratory facility and culture medium that are largely independent of the signature of laboratory adaptation. Going beyond our previous laboratory evolution study, this work suggests that proteomic differences between laboratory-adapted and wild Y. pestis are general, potentially pointing to a process that could apply to other species as well. Additionally, we show that proteomics datasets (even archived data collected for different purposes) contain the information necessary to distinguish wild and laboratory samples. This work has clear applications in biomarker detection as well as biodefense.
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Affiliation(s)
- Eric D. Merkley
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Landon H. Sego
- Applied Statistics and Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Andy Lin
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Owen P. Leiser
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Brooke L. Deatherage Kaiser
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Paul S. Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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15
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Eads DA, Biggins DE. Paltry past-precipitation: Predisposing prairie dogs to plague? J Wildl Manage 2017. [DOI: 10.1002/jwmg.21281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- David A. Eads
- Department of Biology, Colorado State University; U.S. Geological Survey, Fort Collins Science Center; 2150 Centre Avenue, Building C Fort Collins CO 80526 USA
| | - Dean E. Biggins
- U.S. Geological Survey; Fort Collins Science Center; 2150 Centre Avenue, Building C Fort Collins CO 80526 USA
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16
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Descamps T, De Smet L, Stragier P, De Vos P, de Graaf DC. Multiple Locus Variable number of tandem repeat Analysis: A molecular genotyping tool for Paenibacillus larvae. Microb Biotechnol 2016; 9:772-781. [PMID: 27365124 PMCID: PMC5072193 DOI: 10.1111/1751-7915.12375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/31/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022] Open
Abstract
American Foulbrood, caused by Paenibacillus larvae, is the most severe bacterial disease of honey bees (Apis mellifera). To perform genotyping of P. larvae in an epidemiological context, there is a need of a fast and cheap method with a high resolution. Here, we propose Multiple Locus Variable number of tandem repeat Analysis (MLVA). MLVA has been used for typing a collection of 209 P. larvae strains from which 23 different MLVA types could be identified. Moreover, the developed methodology not only permits the identification of the four Enterobacterial Repetitive Intergenic Consensus (ERIC) genotypes, but allows also a discriminatory subdivision of the most dominant ERIC type I and ERIC type II genotypes. A biogeographical study has been conducted showing a significant correlation between MLVA genotype and the geographical region where it was isolated.
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Affiliation(s)
- Tine Descamps
- Laboratory of Molecular Entomology and Bee Pathology, Faculty of Sciences, Ghent University, Ghent, Belgium.
| | - Lina De Smet
- Laboratory of Molecular Entomology and Bee Pathology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Pieter Stragier
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Faculty of Sciences, Ghent University, Ghent, Belgium
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17
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Vogler AJ, Nottingham R, Busch JD, Sahl JW, Shuey MM, Foster JT, Schupp JM, Smith SR, Rocke TE, Keim P, Wagner DM. VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation. INFECTION GENETICS AND EVOLUTION 2016; 45:297-302. [PMID: 27664903 DOI: 10.1016/j.meegid.2016.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
Abstract
Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Roxanne Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Medicine, Vanderbilt University, School of Medicine, Nashville, TN, United States
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - James M Schupp
- Translational Genomics Research Institute North, Flagstaff, AZ, United States
| | - Susan R Smith
- US Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Tonie E Rocke
- US Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Translational Genomics Research Institute North, Flagstaff, AZ, United States
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
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18
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Grange ZL, Gartrell BD, Biggs PJ, Nelson NJ, Anderson M, French NP. Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe. MICROBIAL ECOLOGY 2016; 71:1020-1029. [PMID: 26707136 DOI: 10.1007/s00248-015-0721-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/13/2015] [Indexed: 06/05/2023]
Abstract
Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations.
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Affiliation(s)
- Zoë L Grange
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
| | - Brett D Gartrell
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Nicola J Nelson
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Marti Anderson
- Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand
| | - Nigel P French
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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19
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Blanchong JA, Robinson SJ, Samuel MD, Foster JT. Application of genetics and genomics to wildlife epidemiology. J Wildl Manage 2016. [DOI: 10.1002/jwmg.1064] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Julie A. Blanchong
- Department of Natural Resource Ecology and Management; Iowa State University; 339 Science II Ames IA 50011 USA
| | | | - Michael D. Samuel
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit; University of Wisconsin; 204 Russell Labs, 1630 Linden Dr. Madison WI 53706 USA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular and Biomedical Sciences; University of New Hampshire; 291 Rudman Hall Durham NH 03824 USA
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20
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Cobble KR, Califf KJ, Stone NE, Shuey MM, Birdsell DN, Colman RE, Schupp JM, Aziz M, Van Andel R, Rocke TE, Wagner DM, Busch JD. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history. Ecol Evol 2016; 6:2624-51. [PMID: 27066243 PMCID: PMC4798151 DOI: 10.1002/ece3.2077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/16/2023] Open
Abstract
Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague‐related die‐offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two other DRB1 alleles appear to be trans‐species polymorphisms shared with the black‐tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an FST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.
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Affiliation(s)
- Kacy R Cobble
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Katy J Califf
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Nathan E Stone
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Dawn N Birdsell
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Rebecca E Colman
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - James M Schupp
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Maliha Aziz
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Roger Van Andel
- University of California Berkeley MC 7150 Berkeley California 94720 USA
| | - Tonie E Rocke
- United States Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison Wisconsin 53711 USA
| | - David M Wagner
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
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21
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Two Distinct Yersinia pestis Populations Causing Plague among Humans in the West Nile Region of Uganda. PLoS Negl Trop Dis 2016; 10:e0004360. [PMID: 26866815 PMCID: PMC4750964 DOI: 10.1371/journal.pntd.0004360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023] Open
Abstract
Background Plague is a life-threatening disease caused by the bacterium, Yersinia pestis. Since the 1990s, Africa has accounted for the majority of reported human cases. In Uganda, plague cases occur in the West Nile region, near the border with Democratic Republic of Congo. Despite the ongoing risk of contracting plague in this region, little is known about Y. pestis genotypes causing human disease. Methodology/Principal Findings During January 2004–December 2012, 1,092 suspect human plague cases were recorded in the West Nile region of Uganda. Sixty-one cases were culture-confirmed. Recovered Y. pestis isolates were analyzed using three typing methods, single nucleotide polymorphisms (SNPs), pulsed field gel electrophoresis (PFGE), and multiple variable number of tandem repeat analysis (MLVA) and subpopulations analyzed in the context of associated geographic, temporal, and clinical data for source patients. All three methods separated the 61 isolates into two distinct 1.ANT lineages, which persisted throughout the 9 year period and were associated with differences in elevation and geographic distribution. Conclusions/Significance We demonstrate that human cases of plague in the West Nile region of Uganda are caused by two distinct 1.ANT genetic subpopulations. Notably, all three typing methods used, SNPs, PFGE, and MLVA, identified the two genetic subpopulations, despite recognizing different mutation types in the Y. pestis genome. The geographic and elevation differences between the two subpopulations is suggestive of their maintenance in highly localized enzootic cycles, potentially with differing vector-host community composition. This improved understanding of Y. pestis subpopulations in the West Nile region will be useful for identifying ecologic and environmental factors associated with elevated plague risk. Plague, a severe and often fatal zoonotic disease, is caused by the bacterium Yersinia pestis. Currently, the majority of human cases have been reported from resource limited areas of Africa, where the proximity to commensal rats and other small mammals increases the likelihood for human contact with infected animals or their fleas. Over a 9 year time period, >1000 suspect cases were recorded in the West Nile region of Uganda within the districts of Arua and Zombo. Culture-confirmed cases were shown by three independent typing methods to be due to two distinct 1.ANT genetic subpopulations of Y. pestis. The two genetic subpopulations persisted throughout the 9 year time period, consistent with their ongoing maintenance in local enzootic cycles. Additionally, the two subpopulations were found to differ with respect to geographic location and elevation, with SNP Group 1 strains being found further north and at lower elevations as compared to SNP Group 2. The relative independence of the two Y. pestis subpopulations is suggestive of their maintenance in distinct foci involving enzootic cycles with differing vector-host community composition.
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22
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Salkeld DJ, Stapp P, Tripp DW, Gage KL, Lowell J, Webb CT, Brinkerhoff RJ, Antolin MF. Ecological Traits Driving the Outbreaks and Emergence of Zoonotic Pathogens. Bioscience 2016; 66:118-129. [PMID: 32287347 PMCID: PMC7109792 DOI: 10.1093/biosci/biv179] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Infectious diseases that are transmitted from wildlife hosts to humans, such as the Ebola virus and MERS virus, can be difficult to understand because the pathogens emerge from complex multifaceted ecological interactions. We use a wildlife–pathogen system—prairie dogs (Cynomys ludovicianus) and the plague bacterium (Yersinia pestis)—to describe aspects of disease ecology that apply to many cases of emerging infectious disease. We show that the monitoring and surveillance of hosts and vectors during the buildup to disease outbreaks are crucial for understanding pathogen-transmission dynamics and that a community-ecology framework is important to identify reservoir hosts. Incorporating multidisciplinary approaches and frameworks may improve wildlife–pathogen surveillance and our understanding of seemingly sporadic and rare pathogen outbreaks.
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Affiliation(s)
- Daniel J Salkeld
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - Paul Stapp
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - Daniel W Tripp
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - Kenneth L Gage
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - Jennifer Lowell
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - Colleen T Webb
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - R Jory Brinkerhoff
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
| | - Michael F Antolin
- Dan Salkeld is an ecologist and epidemiologist affiliated with the Department of Biology at Colorado State University. Paul Stapp is a professor in the Department of Biological Science at California State University, in Fullerton. Dan Tripp is a biologist at the Colorado Division of Parks and Wildlife, in Fort Collins. Ken Gage is the chief of the Flea-Borne Diseases Laboratory, of CDC's Bacterial Zoonoses Branch, Division of Vector-Borne Infectious Diseases, in Fort Collins, Colorado. Jen Lowell is a professor of Health Sciences at Carroll College, in Helena, Montana. Colleen Webb and Michael Antolin are professors in the Department of Biology at Colorado State University, with interests in disease ecology and evolution. Jory Brinkerhoff is a professor at the Department of Biology at the University of Richmond, in Virginia
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Abstract
This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.
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Leiser OP, Merkley ED, Clowers BH, Deatherage Kaiser BL, Lin A, Hutchison JR, Melville AM, Wagner DM, Keim PS, Foster JT, Kreuzer HW. Investigation of Yersinia pestis Laboratory Adaptation through a Combined Genomics and Proteomics Approach. PLoS One 2015; 10:e0142997. [PMID: 26599979 PMCID: PMC4658026 DOI: 10.1371/journal.pone.0142997] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
The bacterial pathogen Yersinia pestis, the cause of plague in humans and animals, normally has a sylvatic lifestyle, cycling between fleas and mammals. In contrast, laboratory-grown Y. pestis experiences a more constant environment and conditions that it would not normally encounter. The transition from the natural environment to the laboratory results in a vastly different set of selective pressures, and represents what could be considered domestication. Understanding the kinds of adaptations Y. pestis undergoes as it becomes domesticated will contribute to understanding the basic biology of this important pathogen. In this study, we performed a parallel serial passage experiment (PSPE) to explore the mechanisms by which Y. pestis adapts to laboratory conditions, hypothesizing that cells would undergo significant changes in virulence and nutrient acquisition systems. Two wild strains were serially passaged in 12 independent populations each for ~750 generations, after which each population was analyzed using whole-genome sequencing, LC-MS/MS proteomic analysis, and GC/MS metabolomics. We observed considerable parallel evolution in the endpoint populations, detecting multiple independent mutations in ail, pepA, and zwf, suggesting that specific selective pressures are shaping evolutionary responses. Complementary LC-MS/MS proteomic data provide physiological context to the observed mutations, and reveal regulatory changes not necessarily associated with specific mutations, including changes in amino acid metabolism and cell envelope biogenesis. Proteomic data support hypotheses generated by genomic data in addition to suggesting future mechanistic studies, indicating that future whole-genome sequencing studies be designed to leverage proteomics as a critical complement.
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Affiliation(s)
- Owen P. Leiser
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Eric D. Merkley
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, WA, 99354, United States of America
| | - Brooke L. Deatherage Kaiser
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Andy Lin
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Janine R. Hutchison
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - Angela M. Melville
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Paul S. Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86001, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, 99352, United States of America
- * E-mail:
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25
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Wilder AP, Kunz TH, Sorenson MD. Population genetic structure of a common host predicts the spread of white-nose syndrome, an emerging infectious disease in bats. Mol Ecol 2015; 24:5495-506. [PMID: 26407297 DOI: 10.1111/mec.13396] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/27/2023]
Abstract
Landscape complexity influences patterns of animal dispersal, which in turn may affect both gene flow and the spread of pathogens. White-nose syndrome (WNS) is an introduced fungal disease that has spread rapidly throughout eastern North America, causing massive mortality in bat populations. We tested for a relationship between the population genetic structure of the most common host, the little brown myotis (Myotis lucifugus), and the geographic spread of WNS to date by evaluating logistic regression models of WNS risk among hibernating colonies in eastern North America. We hypothesized that risk of WNS to susceptible host colonies should increase with both geographic proximity and genetic similarity, reflecting historical connectivity, to infected colonies. Consistent with this hypothesis, inclusion of genetic distance between infected and susceptible colonies significantly improved models of disease spread, capturing heterogeneity in the spatial expansion of WNS despite low levels of genetic differentiation among eastern populations. Expanding our genetic analysis to the continental range of little brown myotis reveals strongly contrasting patterns of population structure between eastern and western North America. Genetic structure increases markedly moving westward into the northern Great Plains, beyond the current distribution of WNS. In western North America, genetic differentiation of geographically proximate populations often exceeds levels observed across the entire eastern region, suggesting infrequent and/or locally restricted dispersal, and thus relatively limited opportunities for pathogen introduction in western North America. Taken together, our analyses suggest a possibly slower future rate of spread of the WNS pathogen, at least as mediated by little brown myotis.
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Affiliation(s)
- Aryn P Wilder
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Thomas H Kunz
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Michael D Sorenson
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
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26
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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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27
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Jack BR, Leonard SP, Mishler DM, Renda BA, Leon D, Suárez GA, Barrick JE. Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator. ACS Synth Biol 2015; 4:939-43. [PMID: 26096262 DOI: 10.1021/acssynbio.5b00068] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unwanted evolution can rapidly degrade the performance of genetically engineered circuits and metabolic pathways installed in living organisms. We created the Evolutionary Failure Mode (EFM) Calculator to computationally detect common sources of genetic instability in an input DNA sequence. It predicts two types of mutational hotspots: deletions mediated by homologous recombination and indels caused by replication slippage on simple sequence repeats. We tested the performance of our algorithm on genetic circuits that were previously redesigned for greater evolutionary reliability and analyzed the stability of sequences in the iGEM Registry of Standard Biological Parts. More than half of the parts in the Registry are predicted to experience >100-fold elevated mutation rates due to the inclusion of unstable sequence configurations. We anticipate that the EFM Calculator will be a useful negative design tool for avoiding volatile DNA encodings, thereby increasing the evolutionary lifetimes of synthetic biology devices.
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Affiliation(s)
- Benjamin R. Jack
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sean P. Leonard
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dennis M. Mishler
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian A. Renda
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dacia Leon
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Gabriel A. Suárez
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeffrey E. Barrick
- Center for Systems and Synthetic
Biology, Center for Computational Biology and Bioinformatics, Institute
for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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28
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Riehm JM, Projahn M, Vogler AJ, Rajerison M, Andersen G, Hall CM, Zimmermann T, Soanandrasana R, Andrianaivoarimanana V, Straubinger RK, Nottingham R, Keim P, Wagner DM, Scholz HC. Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007. PLoS Negl Trop Dis 2015; 9:e0003844. [PMID: 26069964 PMCID: PMC4466568 DOI: 10.1371/journal.pntd.0003844] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 05/22/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Yersinia pestis is the causative agent of human plague and is endemic in various African, Asian and American countries. In Madagascar, the disease represents a significant public health problem with hundreds of human cases a year. Unfortunately, poor infrastructure makes outbreak investigations challenging. METHODOLOGY/PRINCIPAL FINDINGS DNA was extracted directly from 93 clinical samples from patients with a clinical diagnosis of plague in Madagascar in 2007. The extracted DNAs were then genotyped using three molecular genotyping methods, including, single nucleotide polymorphism (SNP) typing, multi-locus variable-number tandem repeat analysis (MLVA), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) analysis. These methods provided increasing resolution, respectively. The results of these analyses revealed that, in 2007, ten molecular groups, two newly described here and eight previously identified, were responsible for causing human plague in geographically distinct areas of Madagascar. CONCLUSIONS/SIGNIFICANCE Plague in Madagascar is caused by numerous distinct types of Y. pestis. Genotyping method choice should be based upon the discriminatory power needed, expense, and available data for any desired comparisons. We conclude that genotyping should be a standard tool used in epidemiological investigations of plague outbreaks.
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Affiliation(s)
- Julia M. Riehm
- Central Institute of the Bundeswehr Medical Service, Munich, Germany
- * E-mail:
| | - Michaela Projahn
- Bundeswehr Institute of Microbiology & German Center for Infectious Diseases, Munich, Germany
| | - Amy J. Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Genevieve Andersen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carina M. Hall
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Thomas Zimmermann
- Central Institute of the Bundeswehr Medical Service, Munich, Germany
| | | | | | | | - Roxanne Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Holger C. Scholz
- Bundeswehr Institute of Microbiology & German Center for Infectious Diseases, Munich, Germany
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29
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Rocke TE, Tripp D, Lorenzsonn F, Falendysz E, Smith S, Williamson J, Abbott R. Age at Vaccination May Influence Response to Sylvatic Plague Vaccine (SPV) in Gunnison's Prairie Dogs (Cynomys gunnisoni). ECOHEALTH 2015; 12:278-87. [PMID: 25589000 DOI: 10.1007/s10393-014-1002-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 11/17/2014] [Accepted: 12/03/2014] [Indexed: 05/24/2023]
Abstract
Gunnison's prairie dogs (Cynomys gunnisoni) have been considered at greater risk from Yersinia pestis (plague) infection in the montane portion of their range compared to populations at lower elevations, possibly due to factors related to flea transmission of the bacteria or greater host susceptibility. To test the latter hypothesis and determine whether vaccination against plague with an oral sylvatic plague vaccine (SPV) improved survival, we captured prairie dogs from a C. g. gunnisoni or "montane" population and a C. g. zuniensis or "prairie" population for vaccine efficacy and challenge studies. No differences (P = 0.63) were found in plague susceptibility in non-vaccinated animals between these two populations; however, vaccinates from the prairie population survived plague challenge at significantly higher rates (P < 0.01) than those from the montane population. Upon further analysis, we determined that response to immunization was most likely associated with differences in age, as the prairie group was much younger on average than the montane group. Vaccinates that were juveniles or young adults survived plague challenge at a much higher rate than adults (P < 0.01 and P = 0.02, respectively), but no difference (P = 0.83) was detected in survival rates between control animals of different ages. These results suggest that host susceptibility is probably not related to the assumed greater risk from plague in the C. g. gunnisoni or "montane" populations of Gunnison's prairie dogs, and that SPV could be a useful plague management tool for this species, particularly if targeted at younger cohorts.
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Affiliation(s)
- Tonie E Rocke
- USGS National Wildlife Health Center, 6006 Schroeder Rd., Madison, WI, 53711, USA.
| | - Dan Tripp
- Wildlife Health Program, Colorado Parks and Wildlife, 317 West Prospect Road, Fort Collins, CO, 80526-2097, USA
| | - Faye Lorenzsonn
- USGS National Wildlife Health Center, 6006 Schroeder Rd., Madison, WI, 53711, USA
| | - Elizabeth Falendysz
- USGS National Wildlife Health Center, 6006 Schroeder Rd., Madison, WI, 53711, USA
| | - Susan Smith
- USGS National Wildlife Health Center, 6006 Schroeder Rd., Madison, WI, 53711, USA
| | - Judy Williamson
- USGS National Wildlife Health Center, 6006 Schroeder Rd., Madison, WI, 53711, USA
| | - Rachel Abbott
- USGS National Wildlife Health Center, 6006 Schroeder Rd., Madison, WI, 53711, USA
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30
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Lowell JL, Antolin MF, Andersen GL, Hu P, Stokowski RP, Gage KL. Single-Nucleotide Polymorphisms Reveal Spatial Diversity Among Clones of Yersinia pestis During Plague Outbreaks in Colorado and the Western United States. Vector Borne Zoonotic Dis 2015; 15:291-302. [PMID: 25988438 PMCID: PMC4449629 DOI: 10.1089/vbz.2014.1714] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND In western North America, plague epizootics caused by Yersinia pestis appear to sweep across landscapes, primarily infecting and killing rodents, especially ground squirrels and prairie dogs. During these epizootics, the risk of Y. pestis transmission to humans is highest. While empirical models that include climatic conditions and densities of rodent hosts and fleas can predict when epizootics are triggered, bacterial transmission patterns across landscapes, and the scale at which Y. pestis is maintained in nature during inter-epizootic periods, are poorly defined. Elucidating the spatial extent of Y. pestis clones during epizootics can determine whether bacteria are propagated across landscapes or arise independently from local inter-epizootic maintenance reservoirs. MATERIAL AND METHODS We used DNA microarray technology to identify single-nucleotide polymorphisms (SNPs) in 34 Y. pestis isolates collected in the western United States from 1980 to 2006, 21 of which were collected during plague epizootics in Colorado. Phylogenetic comparisons were used to elucidate the hypothesized spread of Y. pestis between the mountainous Front Range and the eastern plains of northern Colorado during epizootics. Isolates collected from across the western United States were included for regional comparisons. RESULTS By identifying SNPs that mark individual clones, our results strongly suggest that Y. pestis is maintained locally and that widespread epizootic activity is caused by multiple clones arising independently at small geographic scales. This is in contrast to propagation of individual clones being transported widely across landscapes. Regionally, our data are consistent with the notion that Y. pestis diversifies at relatively local scales following long-range translocation events. We recommend that surveillance and prediction by public health and wildlife management professionals focus more on models of local or regional weather patterns and ecological factors that may increase risk of widespread epizootics, rather than predicting or attempting to explain epizootics on the basis of movement of host species that may transport plague.
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Affiliation(s)
- Jennifer L. Lowell
- Department of Health Sciences, Carroll College, Helena, Montana
- Department of Biology, Colorado State University, Fort Collins, Colorado
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Gary L. Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Ping Hu
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - Kenneth L. Gage
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
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31
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Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons. J Bacteriol 2014; 196:3036-44. [PMID: 24957617 DOI: 10.1128/jb.01820-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Variable-number tandem repeats (VNTRs) mutate rapidly and can be useful markers for genotyping. While multilocus VNTR analysis (MLVA) is increasingly used in the detection and investigation of food-borne outbreaks caused by Salmonella enterica serovar Typhimurium (S. Typhimurium) and other bacterial pathogens, MLVA data analysis usually relies on simple clustering approaches that may lead to incorrect interpretations. Here, we estimated the rates of copy number change at each of the five loci commonly used for S. Typhimurium MLVA, during in vitro and in vivo passage. We found that loci STTR5, STTR6, and STTR10 changed during passage but STTR3 and STTR9 did not. Relative rates of change were consistent across in vitro and in vivo growth and could be accurately estimated from diversity measures of natural variation observed during large outbreaks. Using a set of 203 isolates from a series of linked outbreaks and whole-genome sequencing of 12 representative isolates, we assessed the accuracy and utility of several alternative methods for analyzing and interpreting S. Typhimurium MLVA data. We show that eBURST analysis was accurate and informative. For construction of MLVA-based trees, a novel distance metric, based on the geometric model of VNTR evolution coupled with locus-specific weights, performed better than the commonly used simple or categorical distance metrics. The data suggest that, for the purpose of identifying potential transmission clusters for further investigation, isolates whose profiles differ at one of the rapidly changing STTR5, STTR6, and STTR10 loci should be collapsed into the same cluster.
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32
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Yan Y, Wang H, Li D, Yang X, Wang Z, Qi Z, Zhang Q, Cui B, Guo Z, Yu C, Wang J, Wang J, Liu G, Song Y, Li Y, Cui Y, Yang R. Two-step source tracing strategy of Yersinia pestis and its historical epidemiology in a specific region. PLoS One 2014; 9:e85374. [PMID: 24416399 PMCID: PMC3887043 DOI: 10.1371/journal.pone.0085374] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/26/2013] [Indexed: 11/24/2022] Open
Abstract
Source tracing of pathogens is critical for the control and prevention of infectious diseases. Genome sequencing by high throughput technologies is currently feasible and popular, leading to the burst of deciphered bacterial genome sequences. Utilizing the flooding genomic data for source tracing of pathogens in outbreaks is promising, and challenging as well. Here, we employed Yersinia pestis genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives. Through this strategy, we observed that the Xinghai plague outbreak was caused by Y. pestis that circulated in the local plague focus, where the majority of historical plague epidemics in the Qinghai-Tibet Plateau may originate from. The analytical strategy developed here will be of great help in fighting against the outbreaks of emerging infectious diseases, by pinpointing the source of pathogens rapidly with genomic epidemiological data and microbial forensics information.
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Affiliation(s)
- Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Hu Wang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | | | - Xianwei Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuyun Wang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Qingwen Zhang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Baizhong Cui
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Zhaobiao Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | | | | | - Guangming Liu
- School of Computer Science, National University of Defense Technology, Changsha, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (RY); (YC)
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (RY); (YC)
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Bühlmann A, Dreo T, Rezzonico F, Pothier JF, Smits THM, Ravnikar M, Frey JE, Duffy B. Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites. Environ Microbiol 2013; 16:2112-25. [PMID: 24112873 DOI: 10.1111/1462-2920.12289] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/14/2013] [Indexed: 01/08/2023]
Abstract
Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficiently high resolution. We report a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. Repeats in the E. amylovora genome were identified with comparative genomic tools, and VNTR markers were developed and validated. A Multiple-Locus VNTR Analysis (MLVA) was applied to E. amylovora isolates from bacterial collections representing global and regional distribution of the pathogen. Based on six repeats, MLVA allowed the distinction of 227 haplotypes among a collection of 833 isolates of worldwide origin. Three geographically separated groups were recognized among global isolates using Bayesian clustering methods. Analysis of regional outbreaks confirmed presence of diverse haplotypes but also high representation of certain haplotypes during outbreaks. MLVA analysis is a practical method for epidemiological studies of E. amylovora, identifying previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region.
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Affiliation(s)
- Andreas Bühlmann
- Plant Protection Division, Agroscope Changins-Wädenswil Research Station ACW, CH-8820, Wädenswil, Switzerland
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THE INNATE IMMUNE RESPONSE MAY BE IMPORTANT FOR SURVIVING PLAGUE IN WILD GUNNISON'S PRAIRIE DOGS. J Wildl Dis 2013; 49:920-31. [DOI: 10.7589/2012-08-209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dynamic of mutational events in variable number tandem repeats of Escherichia coli O157:H7. BIOMED RESEARCH INTERNATIONAL 2013; 2013:390354. [PMID: 24093095 PMCID: PMC3777172 DOI: 10.1155/2013/390354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 07/22/2013] [Indexed: 11/30/2022]
Abstract
VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenic E. coli O157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05 to 1.8 × 10−03 mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03 mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.
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St Romain K, Tripp DW, Salkeld DJ, Antolin MF. Duration of plague (Yersinia pestis) outbreaks in black-tailed prairie dog (Cynomys ludovicianus) colonies of northern Colorado. ECOHEALTH 2013; 10:241-5. [PMID: 24057801 DOI: 10.1007/s10393-013-0860-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/21/2013] [Accepted: 06/21/2013] [Indexed: 05/24/2023]
Abstract
Plague, caused by the bacterium Yersinia pestis, triggers die-offs in colonies of black-tailed prairie dogs (Cynomys ludovicianus), but the time-frame of plague activity is not well understood. We document plague activity in fleas from prairie dogs and their burrows on three prairie dog colonies that suffered die-offs. We demonstrate that Y. pestis transmission occurs over periods from several months to over a year in prairie dog populations before observed die-offs.
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Affiliation(s)
- Krista St Romain
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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Li Y, Cui Y, Cui B, Yan Y, Yang X, Wang H, Qi Z, Zhang Q, Xiao X, Guo Z, Ma C, Wang J, Song Y, Yang R. Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme. PLoS One 2013; 8:e66567. [PMID: 23805236 PMCID: PMC3689786 DOI: 10.1371/journal.pone.0066567] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/09/2013] [Indexed: 01/14/2023] Open
Abstract
Background Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci. Methodology/Principal Findings Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a “14+12” loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established. Conclusions/Significance Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized “14+12” loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.
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Affiliation(s)
- Yanjun Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Laboratory Department, Navy General Hospital, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Baizhong Cui
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xianwei Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Haidong Wang
- Laboratory Department, Navy General Hospital, Beijing, China
| | - Zhizhen Qi
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Qingwen Zhang
- Qinghai Institute for Endemic Diseases Prevention and Control, Xining, China
| | - Xiao Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhaobiao Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Cong Ma
- Laboratory Department, Navy General Hospital, Beijing, China
| | - Jing Wang
- Institute of Health Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (RY); (YS)
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail: (RY); (YS)
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Brouat C, Rahelinirina S, Loiseau A, Rahalison L, Rajerison M, Laffly D, Handschumacher P, Duplantier JM. Plague circulation and population genetics of the reservoir Rattus rattus: the influence of topographic relief on the distribution of the disease within the Madagascan focus. PLoS Negl Trop Dis 2013; 7:e2266. [PMID: 23755317 PMCID: PMC3674990 DOI: 10.1371/journal.pntd.0002266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 04/29/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. METHODOLOGY/PRINCIPAL FINDINGS We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150-200 km(2) within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. CONCLUSIONS/SIGNIFICANCE Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations.
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Pilosof S, Fortuna MA, Vinarski MV, Korallo-Vinarskaya NP, Krasnov BR. Temporal dynamics of direct reciprocal and indirect effects in a host-parasite network. J Anim Ecol 2013; 82:987-96. [DOI: 10.1111/1365-2656.12090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/22/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Shai Pilosof
- Albert Katz International School for Desert Studies and Mitrani Department of Desert Ecology; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion; Israel
| | - Miguel A. Fortuna
- Integrative Ecology Group; Estación Biológica de Doñana (EBD-CSIC); Seville; Spain
| | - Maxim V. Vinarski
- Department of Zoology; Faculty of Chemistry and Biology; Omsk State Pedagogical University; Tukhachevskogo emb. 14; 644099; Omsk; Russia
| | - Natalia P. Korallo-Vinarskaya
- Laboratory of Arthropod-Borne Viral Infections; Omsk Research Institute of Natural Foci Infections; Mira str. 7; 644080; Omsk; Russia
| | - Boris R. Krasnov
- Albert Katz International School for Desert Studies and Mitrani Department of Desert Ecology; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion; Israel
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Gascuel F, Choisy M, Duplantier JM, Débarre F, Brouat C. Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus. PLoS Comput Biol 2013; 9:e1003039. [PMID: 23675291 PMCID: PMC3649974 DOI: 10.1371/journal.pcbi.1003039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/04/2013] [Indexed: 11/23/2022] Open
Abstract
Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar. Bubonic plague, known to have marked human history by three deadly pandemics, is an infectious disease which mainly circulates in wild rodent populations and is transmitted by fleas. Although this disease can be quickly lethal to its host, it has persisted on long-term in many rodent populations around the world. The reasons for this persistence remain poorly known. Two mechanisms have been invoked, but not yet explicitly and independently tested: first, the spatial structure of rodent populations (subdivision into several subpopulations) and secondly, the presence of, not only plague-susceptible rodents, but also plague-resistant ones. To gain insight into the role of the above two factors in plague persistence, we analysed a mathematical model of plague propagation. We applied our analyses to the case of Madagascar, where plague has persisted on central highlands since the 1920s and is responsible for about 30% of the human cases worldwide. We found that the long-term persistence of plague can be explained by the presence of any of the above two factors. These results allowed us to propose scenarios to explain the localized presence of plague in the Malagasy highlands, and help understand the persistence of plague in many wild foci.
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Affiliation(s)
- Fanny Gascuel
- IRD, CBGP (UMR IRD/INRA/CIRAD/MontpellierSupAgro), Montferrier-sur-Lez, France.
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Gyuranecz M, Rannals BD, Allen CA, Jánosi S, Keim PS, Foster JT. Within-host evolution of Brucella canis during a canine brucellosis outbreak in a kennel. BMC Vet Res 2013; 9:76. [PMID: 23587163 PMCID: PMC3637509 DOI: 10.1186/1746-6148-9-76] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/09/2013] [Indexed: 11/30/2022] Open
Abstract
Background Little is currently known about Brucella evolution within the host during infection. The current study is the first to employ fine-scale genotyping on an isolate collection derived from a Brucella canis outbreak. Eight isolates of B. canis, cultured from different tissues of three dogs (female, stud dog, puppy of another female) from a single kennel over three months were genetically characterized with a 15-marker multi-locus, variable-number tandem repeat (VNTR) analysis (MLVA) to assess the genetic relatedness of isolates and potential rapid mutational changes. Results MLVA discriminated among the otherwise indistinguishable isolates from different animals and from isolates collected at different time points within each host, with different VNTR alleles being detected at multiple dates and tissue sites. We suspect that all isolates cultured from the female, puppy, and stud dogs originated from the same strain, with subsequent rapid in vivo mutations. However, high mutation rates and apparent in several of the loci prevented making definitive epidemiological relationships among isolates. Conclusions This investigation highlights the rapid in vivo genetic mutations of several VNTRs of B. canis over a short time period in the host and the emergence of alternate alleles. However, this work also suggests the challenges of using highly mutable VNTRs to infer epidemiological relationships of strains within a short duration outbreak.
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Affiliation(s)
- Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest 1143, Hungária körút 21, Hungary
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Turingan RS, Thomann HU, Zolotova A, Tan E, Selden RF. Rapid focused sequencing: a multiplexed assay for simultaneous detection and strain typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One 2013; 8:e56093. [PMID: 23418519 PMCID: PMC3572037 DOI: 10.1371/journal.pone.0056093] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 01/08/2013] [Indexed: 01/29/2023] Open
Abstract
Background The intentional release of Bacillus anthracis in the United States in 2001 has heightened concern about the use of pathogenic microorganisms in bioterrorism attacks. Many of the deadliest bacteria, including the Class A Select Agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis, are highly infectious via the pulmonary route when released in aerosolized form. Hence, rapid, sensitive, and reliable methods for detection of these biothreats and characterization of their potential impact on the exposed population are of critical importance to initiate and support rapid military, public health, and clinical responses. Methodology/Principal Findings We have developed microfluidic multiplexed PCR and sequencing assays based on the simultaneous interrogation of three pathogens per assay and ten loci per pathogen. Microfluidic separation of amplified fluorescently labeled fragments generated characteristic electrophoretic signatures for identification of each agent. The three sets of primers allowed significant strain typing and discrimination from non-pathogenic closely-related species and environmental background strains based on amplicon sizes alone. Furthermore, sequencing of the 10 amplicons per pathogen, termed “Rapid Focused Sequencing,” allowed an even greater degree of strain discrimination and, in some cases, can be used to determine virulence. Both amplification and sequencing assays were performed in microfluidic biochips developed for fast thermal cycling and requiring 7 µL per reaction. The 30-plex sequencing assay resulted in genotypic resolution of 84 representative strains belonging to each of the three biothreat species. Conclusions/Significance The microfluidic multiplexed assays allowed identification and strain differentiation of the biothreat agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis and clear discrimination from closely-related species and several environmental background strains. The assays may be extended to detect a large number of pathogens, are applicable to the evaluation of both environmental and clinical samples, and have the potential to be applied in military, public health, and clinical diagnostic settings.
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Affiliation(s)
| | | | - Anna Zolotova
- NetBio, Waltham, Massachusetts, United States of America
| | - Eugene Tan
- NetBio, Waltham, Massachusetts, United States of America
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A decade of plague in Mahajanga, Madagascar: insights into the global maritime spread of pandemic plague. mBio 2013; 4:e00623-12. [PMID: 23404402 PMCID: PMC3573667 DOI: 10.1128/mbio.00623-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A cluster of human plague cases occurred in the seaport city of Mahajanga, Madagascar, from 1991 to 1999 following 62 years with no evidence of plague, which offered insights into plague pathogen dynamics in an urban environment. We analyzed a set of 44 Mahajanga isolates from this 9-year outbreak, as well as an additional 218 Malagasy isolates from the highland foci. We sequenced the genomes of four Mahajanga strains, performed whole-genome sequence single-nucleotide polymorphism (SNP) discovery on those strains, screened the discovered SNPs, and performed a high-resolution 43-locus multilocus variable-number tandem-repeat analysis of the isolate panel. Twenty-two new SNPs were identified and defined a new phylogenetic lineage among the Malagasy isolates. Phylogeographic analysis suggests that the Mahajanga lineage likely originated in the Ambositra district in the highlands, spread throughout the northern central highlands, and was then introduced into and became transiently established in Mahajanga. Although multiple transfers between the central highlands and Mahajanga occurred, there was a locally differentiating and dominant subpopulation that was primarily responsible for the 1991-to-1999 Mahajanga outbreaks. Phylotemporal analysis of this Mahajanga subpopulation revealed a cycling pattern of diversity generation and loss that occurred during and after each outbreak. This pattern is consistent with severe interseasonal genetic bottlenecks along with large seasonal population expansions. The ultimate extinction of plague pathogens in Mahajanga suggests that, in this environment, the plague pathogen niche is tenuous at best. However, the temporary large pathogen population expansion provides the means for plague pathogens to disperse and become ecologically established in more suitable nonurban environments. Maritime spread of plague led to the global dissemination of this disease and affected the course of human history. Multiple historical plague waves resulted in massive human mortalities in three classical plague pandemics: Justinian (6th and 7th centuries), Middle Ages (14th to 17th centuries), and third (mid-1800s to the present). Key to these events was the pathogen’s entry into new lands by “plague ships” via seaport cities. Although initial disease outbreaks in ports were common, they were almost never sustained for long and plague pathogens survived only if they could become established in ecologically suitable habitats. Although plague pathogens’ ability to invade port cities has been essential for intercontinental spread, these regions have not proven to be a suitable long-term niche. The disease dynamics in port cities such as Mahajanga are thus critical to plague pathogen amplification and dispersal into new suitable ecological niches for the observed global long-term maintenance of plague pathogens.
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Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A 2012; 110:577-82. [PMID: 23271803 DOI: 10.1073/pnas.1205750110] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.
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Riehm JM, Vergnaud G, Kiefer D, Damdindorj T, Dashdavaa O, Khurelsukh T, Zöller L, Wölfel R, Le Flèche P, Scholz HC. Yersinia pestis lineages in Mongolia. PLoS One 2012; 7:e30624. [PMID: 22363455 PMCID: PMC3281858 DOI: 10.1371/journal.pone.0030624] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 12/19/2011] [Indexed: 11/26/2022] Open
Abstract
Background Whole genome sequencing allowed the development of a number of high resolution sequence based typing tools for Yersinia (Y.) pestis. The application of these methods on isolates from most known foci worldwide and in particular from China and the Former Soviet Union has dramatically improved our understanding of the population structure of this species. In the current view, Y. pestis including the non or moderate human pathogen Y. pestis subspecies microtus emerged from Yersinia pseudotuberculosis about 2,600 to 28,600 years ago in central Asia. The majority of central Asia natural foci have been investigated. However these investigations included only few strains from Mongolia. Methodology/Principal Findings Clustered Regularly Interspaced Short Prokaryotic Repeats (CRISPR) analysis and Multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) with 25 loci was performed on 100 Y. pestis strains, isolated from 37 sampling areas in Mongolia. The resulting data were compared with previously published data from more than 500 plague strains, 130 of which had also been previously genotyped by single nucleotide polymorphism (SNP) analysis. The comparison revealed six main clusters including the three microtus biovars Ulegeica, Altaica, and Xilingolensis. The largest cluster comprises 78 isolates, with unique and new genotypes seen so far in Mongolia only. Typing of selected isolates by key SNPs was used to robustly assign the corresponding clusters to previously defined SNP branches. Conclusions/Significance We show that Mongolia hosts the most recent microtus clade (Ulegeica). Interestingly no representatives of the ancestral Y. pestis subspecies pestis nodes previously identified in North-western China were identified in this study. This observation suggests that the subsequent evolution steps within Y. pestis pestis did not occur in Mongolia. Rather, Mongolia was most likely re-colonized by more recent clades coming back from China contemporary of the black death pandemic, or more recently in the past 600 years.
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Affiliation(s)
- Julia M Riehm
- Bundeswehr Institute of Microbiology, Munich, Germany.
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Gibbons HS, Krepps MD, Ouellette G, Karavis M, Onischuk L, Leonard P, Broomall S, Sickler T, Betters JL, McGregor P, Donarum G, Liem A, Fochler E, McNew L, Rosenzweig CN, Skowronski E. Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico. PLoS One 2012; 7:e31604. [PMID: 22359605 PMCID: PMC3281092 DOI: 10.1371/journal.pone.0031604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/10/2012] [Indexed: 02/07/2023] Open
Abstract
Plague disease caused by the Gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19th century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.
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Affiliation(s)
- Henry S Gibbons
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America.
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García K, Gavilán RG, Höfle MG, Martínez-Urtaza J, Espejo RT. Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions. PLoS One 2012; 7:e30823. [PMID: 22292049 PMCID: PMC3265528 DOI: 10.1371/journal.pone.0030823] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 12/22/2011] [Indexed: 11/18/2022] Open
Abstract
The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10(-4) mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered.
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Affiliation(s)
- Katherine García
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Ronnie G. Gavilán
- Instituto de Acuicultura, Universidad de Santiago de Compostela, Campus Universitario Sur, Santiago de Compostela, Spain
| | - Manfred G. Höfle
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Jaime Martínez-Urtaza
- Instituto de Acuicultura, Universidad de Santiago de Compostela, Campus Universitario Sur, Santiago de Compostela, Spain
| | - Romilio T. Espejo
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- * E-mail:
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Oliveira M, Barros M, Silveira-Filho V, Araújo-Nepomuceno M, Balbino V, Leal N, Almeida A, Leal-Balbino T. Genetic diversity of Yersinia pestis in Brazil. GENETICS AND MOLECULAR RESEARCH 2012; 11:3414-24. [DOI: 10.4238/2012.september.25.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Vogler AJ, Chan F, Wagner DM, Roumagnac P, Lee J, Nera R, Eppinger M, Ravel J, Rahalison L, Rasoamanana BW, Beckstrom-Sternberg SM, Achtman M, Chanteau S, Keim P. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS Negl Trop Dis 2011; 5:e1319. [PMID: 21931876 PMCID: PMC3172189 DOI: 10.1371/journal.pntd.0001319] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/30/2011] [Indexed: 11/18/2022] Open
Abstract
Background Plague was introduced to Madagascar in 1898 and continues to be a significant human health problem. It exists mainly in the central highlands, but in the 1990s was reintroduced to the port city of Mahajanga, where it caused extensive human outbreaks. Despite its prevalence, the phylogeography and molecular epidemiology of Y. pestis in Madagascar has been difficult to study due to the great genetic similarity among isolates. We examine island-wide geographic-genetic patterns based upon whole-genome discovery of SNPs, SNP genotyping and hypervariable 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. Plague, caused by the bacterium Yersinia pestis, has been a problem in Madagascar since it was introduced in 1898. It mainly affects the central highlands, but also has caused several large outbreaks in the port city of Mahajanga, after it was reintroduced there in the 1990s. Despite its prevalence, the genetic diversity and related geographic distribution of different genetic groups of Y. pestis in Madagascar has been difficult to study due to the great genetic similarity among isolates. We subtyped a set of Malagasy isolates and identified two major genetic groups that were subsequently divided into 11 and 4 subgroups, 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. 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.
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Affiliation(s)
- Amy J. Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Fabien Chan
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Judy Lee
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne Nera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mark Eppinger
- Institute for Genomic Sciences (IGS), School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genomic Sciences (IGS), School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Lila Rahalison
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Stephen M. Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Mark Achtman
- Max Planck Institut für Infektionsbiologie, Berlin, Germany
- Environmental Research Institute, University College Cork, Cork, Ireland
| | | | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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Vogler AJ, Birdsell DN, Lee J, Vaissaire J, Doujet CL, Lapalus M, Wagner DM, Keim P. Phylogeography of Francisella tularensis ssp. holarctica in France. Lett Appl Microbiol 2011; 52:177-80. [PMID: 21214606 DOI: 10.1111/j.1472-765x.2010.02977.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To investigate the phylogeography of French Francisella tularensis ssp. holarctica isolates. METHODS AND RESULTS Canonical SNPs and MLVA were used to genotype 103 French F. tularensis ssp. holarctica isolates. We confirmed the presence of one subclade, the central and western European group (B.Br.FTNF002-00), and identified four major MLVA genotypes with no obvious geographical differentiation. CONCLUSIONS The lack of geographical resolution among MLVA genotypes suggests rapid dispersal, convergent evolution or a combination of the two. SIGNIFICANCE AND IMPACT OF THE STUDY This study expands knowledge of the phylogeography of one of the two dominant European F. tularensis ssp. holarctica subclades and illustrates the need for additional SNP discovery within this subclade.
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Affiliation(s)
- A J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
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