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Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B. Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling. Transbound Emerg Dis 2022; 69:e1734-e1748. [PMID: 35263501 DOI: 10.1111/tbed.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States (US) and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 Haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US sequences (n = 100) and US subset (n = 44) datasets. Discrete trait phylogeography analysis was used to estimate the transmission history of EIV using four global and US genome datasets. The North American lineage was the major source of globally dominant EIV variants and spread to other global regions. The US EIV strains generally spread from the southern and midwestern regions to other regions. The EIV H3N8 accumulated approximately three nucleotide substitutions per year in the HA gene under heterogenous local positive selection. Our findings will guide better decision making of target intervention strategies of EIV H3N8 infection and provide the better scheme of genomic surveillance in the US and global equine health. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Samantha M Barnum
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
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2
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Cánovas F, Domínguez-Godino JA, González-Wangüemert M. Epidemiology of skin ulceration disease in wild sea cucumber Holothuria arguinensis, a new aquaculture target species. DISEASES OF AQUATIC ORGANISMS 2019; 135:77-88. [PMID: 31294698 DOI: 10.3354/dao03373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Interest in wildlife epidemiology has increased in recent years. The control of diseases is critical for the survival of natural populations of economically valuable species. The present study is the first investigation of the etiology and epidemiology of skin ulceration disease in the sea cucumber Holothuria arguinensis, a new target species for fisheries and aquaculture in Europe. Bacterial cultures and molecular techniques were used to characterize this disease in animals collected during a survey across Ría Formosa Natural Park coastal lagoon in southern Portugal. Vibrio gigantis and V. crassostreae, which were both originally identified as disease agents in cultured oysters, were the most commonly isolated species of bacteria. Given that both sampling areas from which symptomatic H. arguinensis were collected were close to open oyster aquaculture facilities, this raises the possibility of an opportunistic infection, perhaps secondary to a decreased immune response caused by biotic or abiotic factors. An increase in prevalence of skin ulceration disease during the warmer season suggests that solar radiation and desiccation due to air exposure during low tide could be a cause of abiotic stress in the lagoon. Distributions of abundance and sizes of H. arguinensis in affected areas showed highest morbidity rates in adults. High fishery pressures throughout the study period could also cause elevations in prevalence and incidence rate of this disease. Skin ulcerative disease is endemic in this coastal lagoon. Disease monitoring is thus essential for the development of a conservation program to ensure the sustainability of fisheries and protection of natural resources.
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Affiliation(s)
- F Cánovas
- Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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3
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Grange ZL, Biggs PJ, Rose SP, Gartrell BD, Nelson NJ, French NP. Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation. MICROBIAL ECOLOGY 2017; 74:735-744. [PMID: 28361266 DOI: 10.1007/s00248-017-0959-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.
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Affiliation(s)
- Zoë L Grange
- Allan Wilson Centre, 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.
- One Health Institute, University of California Davis, Davis, CA, USA.
| | - Patrick J Biggs
- Allan Wilson Centre, 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
| | - Shanna P Rose
- Allan Wilson Centre, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Brett D Gartrell
- Allan Wilson Centre, 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
| | - Nicola J Nelson
- Allan Wilson Centre, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nigel P French
- Allan Wilson Centre, 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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Crispell J, Zadoks RN, Harris SR, Paterson B, Collins DM, de-Lisle GW, Livingstone P, Neill MA, Biek R, Lycett SJ, Kao RR, Price-Carter M. Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand. BMC Genomics 2017; 18:180. [PMID: 28209138 PMCID: PMC5314462 DOI: 10.1186/s12864-017-3569-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
Background Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being incorporated into routine bTB surveillance. Results A high rate of exchange was evident between the sampled wildlife and cattle populations but directional estimates of inter-species transmission were sensitive to the sampling strategy employed. A relatively high substitution rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing methods, acts to endorse WGS as a typing tool. Conclusions In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with the low prevalence of bTB in New Zealand’s cattle population it is likely that, currently, wildlife populations are acting as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular typing data. The substitution rates estimated here will be an important part of epidemiological investigations using WGS data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3569-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Crispell
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Brent Paterson
- TBfree New Zealand, PO Box 3412, Wellington, 6140, New Zealand
| | | | | | | | - Mark A Neill
- TBfree New Zealand, PO Box 3412, Wellington, 6140, New Zealand
| | - Roman Biek
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Samantha J Lycett
- Infection and Immunity Division, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Rowland R Kao
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK.
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Mather AE, Vaughan TG, French NP. Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa. Clin Infect Dis 2016; 61 Suppl 4:S259-65. [PMID: 26449940 DOI: 10.1093/cid/civ727] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) is a frequent cause of diarrhea around the world, yet in many African countries it is more commonly associated with invasive bacterial disease. Various source attribution models have been developed that utilize microbial subtyping data to assign cases of human NTS infection to different animal populations and foods of animal origin. Advances in molecular microbial subtyping approaches, in particular whole-genome sequencing, provide higher resolution data with which to investigate these sources. In this review, we provide updates on the source attribution models developed for Salmonella, and examine the application of whole-genome sequencing data combined with evolutionary modeling to investigate the putative sources and transmission pathways of NTS, with a focus on the epidemiology of NTS in Africa. This is essential information to decide where, what, and how control strategies might be applied most effectively.
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Affiliation(s)
- Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Timothy G Vaughan
- Department of Computer Science, University of Auckland Allan Wilson Centre for Molecular Ecology and Evolution
| | - Nigel P French
- mEpiLab, Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand
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Kamath PL, Foster JT, Drees KP, Luikart G, Quance C, Anderson NJ, Clarke PR, Cole EK, Drew ML, Edwards WH, Rhyan JC, Treanor JJ, Wallen RL, White PJ, Robbe-Austerman S, Cross PC. Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock. Nat Commun 2016; 7:11448. [PMID: 27165544 PMCID: PMC4865865 DOI: 10.1038/ncomms11448] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/29/2016] [Indexed: 01/09/2023] Open
Abstract
Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (∼3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.
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Affiliation(s)
- Pauline L Kamath
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana 59715, USA
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Kevin P Drees
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Christine Quance
- USDA-APHIS, National Veterinary Services Laboratories, Ames, Iowa 50010, USA
| | - Neil J Anderson
- Montana Fish Wildlife and Parks, Bozeman, Montana 59718, USA
| | - P Ryan Clarke
- USDA-APHIS, Veterinary Services, Fort Collins, Colorado 80526, USA
| | - Eric K Cole
- USFWS, National Elk Refuge, Jackson, Wyoming 83001, USA
| | - Mark L Drew
- Wildlife Health Laboratory, Idaho Department of Fish and Game, Caldwell, Idaho 83607, USA
| | | | - Jack C Rhyan
- USDA-APHIS, Veterinary Services, Fort Collins, Colorado 80526, USA
| | - John J Treanor
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | - Rick L Wallen
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | - Patrick J White
- National Park Service, Yellowstone National Park, Mammoth, Wyoming 82190, USA
| | | | - Paul C Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana 59715, USA
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Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi. Trends Genet 2015; 31:201-7. [PMID: 25765920 DOI: 10.1016/j.tig.2015.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
Abstract
Population genomic studies have the potential to address many unresolved questions about microbial pathogens by facilitating the identification of genes underlying ecologically important traits, such as novel virulence factors and adaptations to humans or other host species. Additionally, this framework improves estimations of population demography and evolutionary history to accurately reconstruct recent epidemics and identify the molecular and environmental factors that resulted in the outbreak. The Lyme disease bacterium, Borrelia burgdorferi, exemplifies the power and promise of the application of population genomics to microbial pathogens. We discuss here the future of evolutionary studies in B. burgdorferi, focusing on the primary evolutionary forces of horizontal gene transfer, natural selection, and migration, as investigations transition from analyses of single genes to genomes.
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Vander Wal E, Garant D, Pelletier F. Evolutionary perspectives on wildlife disease: concepts and applications. Evol Appl 2014; 7:715-22. [PMID: 25469154 PMCID: PMC4227853 DOI: 10.1111/eva.12179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 05/21/2014] [Indexed: 12/21/2022] Open
Abstract
Wildlife disease has the potential to cause significant ecological, socioeconomic, and health impacts. As a result, all tools available need to be employed when host-pathogen dynamics merit conservation or management interventions. Evolutionary principles, such as evolutionary history, phenotypic and genetic variation, and selection, have the potential to unravel many of the complex ecological realities of infectious disease in the wild. Despite this, their application to wildlife disease ecology and management remains in its infancy. In this article, we outline the impetus behind applying evolutionary principles to disease ecology and management issues in the wild. We then introduce articles from this special issue on Evolutionary Perspectives on Wildlife Disease: Concepts and Applications, outlining how each is exemplar of a practical wildlife disease challenge that can be enlightened by applied evolution. Ultimately, we aim to bring new insights to wildlife disease ecology and its management using tools and techniques commonly employed in evolutionary ecology.
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Affiliation(s)
- Eric Vander Wal
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
| | - Dany Garant
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
| | - Fanie Pelletier
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
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Vander Wal E, Garant D, Calmé S, Chapman CA, Festa-Bianchet M, Millien V, Rioux-Paquette S, Pelletier F. Applying evolutionary concepts to wildlife disease ecology and management. Evol Appl 2014; 7:856-68. [PMID: 25469163 PMCID: PMC4227862 DOI: 10.1111/eva.12168] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/08/2014] [Indexed: 12/17/2022] Open
Abstract
Existing and emerging infectious diseases are among the most pressing global threats to biodiversity, food safety and human health. The complex interplay between host, pathogen and environment creates a challenge for conserving species, communities and ecosystem functions, while mediating the many known ecological and socio-economic negative effects of disease. Despite the clear ecological and evolutionary contexts of host-pathogen dynamics, approaches to managing wildlife disease remain predominantly reactionary, focusing on surveillance and some attempts at eradication. A few exceptional studies have heeded recent calls for better integration of ecological concepts in the study and management of wildlife disease; however, evolutionary concepts remain underused. Applied evolution consists of four principles: evolutionary history, genetic and phenotypic variation, selection and eco-evolutionary dynamics. In this article, we first update a classical framework for understanding wildlife disease to integrate better these principles. Within this framework, we explore the evolutionary implications of environment-disease interactions. Subsequently, we synthesize areas where applied evolution can be employed in wildlife disease management. Finally, we discuss some future directions and challenges. Here, we underscore that despite some evolutionary principles currently playing an important role in our understanding of disease in wild animals, considerable opportunities remain for fostering the practice of evolutionarily enlightened wildlife disease management.
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Affiliation(s)
- Eric Vander Wal
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
| | - Dany Garant
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
| | - Sophie Calmé
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
- El Colegio de la Frontera SurChetumal, Quintana Roo, Mexico
| | - Colin A Chapman
- Department of Anthropology and McGill School of Environment, McGill UniversityMontreal, QC, Canada
- Wildlife Conservation SocietyBronx, New York, NY, USA
| | | | | | | | - Fanie Pelletier
- Département de biologie, Université de SherbrookeSherbrooke, QC, Canada
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