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Wood AJ, Benton CH, Delahay RJ, Marion G, Palkopoulou E, Pooley CM, Smith GC, Kao RR. The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution. Epidemics 2024; 48:100787. [PMID: 39197305 DOI: 10.1016/j.epidem.2024.100787] [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] [Received: 05/07/2024] [Revised: 07/03/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the "who-infected-whom" identification problem. We study samples from hosts (130 cattle, 111 badgers) with confirmed infection of M. bovis (causing bovine Tuberculosis), which has an estimated clock rate as slow as ∼0.1-1 variations per year. For each potential pathway between hosts, we calculate the relative likelihood that such a transmission event occurred. This is informed by an epidemiological model of transmission, and host life history data. By including WGS data, we shrink the number of plausible pathways significantly, relative to those deemed likely on the basis of life history data alone. Despite our uncertainty relating to the evolution of M. bovis, the WGS data are therefore a valuable adjunct to epidemiological investigations, especially for wildlife species whose life history data are sparse.
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Affiliation(s)
- A J Wood
- Roslin Institute, University of Edinburgh, United Kingdom
| | - C H Benton
- Animal & Plant Health Agency, United Kingdom
| | - R J Delahay
- Animal & Plant Health Agency, United Kingdom
| | - G Marion
- Biomathematics and Statistics Scotland, United Kingdom
| | | | - C M Pooley
- Biomathematics and Statistics Scotland, United Kingdom
| | - G C Smith
- Animal & Plant Health Agency, United Kingdom
| | - R R Kao
- Roslin Institute, University of Edinburgh, United Kingdom; Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom.
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2
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da Silva AF, da Silva Neto AM, Aksenen C, Jeronimo P, Dezordi F, Almeida S, Costa H, Salvato R, Campos TD, Wallau G, of the Fiocruz Genomic Network OB. ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance. NAR Genom Bioinform 2024; 6:lqae056. [PMID: 38800829 PMCID: PMC11127631 DOI: 10.1093/nargab/lqae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned ViralFlow into a general-purpose reference-based genome assembler for all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. ViralFlow v1.0 runs on a broad range of computational infrastructures, from laptop computers to high-performance computing (HPC) environments, and generates standard and well-formatted outputs suited for both public health reporting and scientific problem-solving. ViralFlow v1.0 is available at: https://viralflow.github.io/index-en.html.
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Affiliation(s)
- Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | - Antonio Marinho da Silva Neto
- Data Analysis and Engineering, Genomic Surveillance Unit, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | | | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | | | - Hudson Marques Paula Costa
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | - Richard Steiner Salvato
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, Rio Grande do Sul 90450-190, Brazil
| | - Tulio de Lima Campos
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Bernhard-Nocht-Strasse 74, D-20359 Hamburg, Germany
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3
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Montagud‐Martínez R, Márquez‐Costa R, Heras‐Hernández M, Dolcemascolo R, Rodrigo G. On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb Biotechnol 2024; 17:e14418. [PMID: 38381083 PMCID: PMC10880580 DOI: 10.1111/1751-7915.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology.
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Affiliation(s)
- Roser Montagud‐Martínez
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Rosa Márquez‐Costa
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - María Heras‐Hernández
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
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4
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Velasquez-Munoz A, Castro-Vargas R, Cullens-Nobis FM, Mani R, Abuelo A. Review: Salmonella Dublin in dairy cattle. Front Vet Sci 2024; 10:1331767. [PMID: 38264470 PMCID: PMC10803612 DOI: 10.3389/fvets.2023.1331767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
Salmonella enterica serovar Dublin (S. Dublin) is a bacterium host-adapted to cattle with increasing prevalence in dairy facilities. It can severely affect cattle health, producing high morbidity and mortality in young calves and reducing the performance of mature animals. Salmonella Dublin is difficult to control and eradicate from herds, as it can be shed from clinically normal animals. In addition, S. Dublin is a zoonotic bacterium that can be lethal for humans and pose a risk for human and animal health due to its multi-drug resistant characteristics. This review provides an overview of S. Dublin as a pathogen in dairy facilities, the risk factors associated with infection, and current strategies for preventing and controlling this disease. Furthermore, current gaps in knowledge are also discussed.
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Affiliation(s)
- Ana Velasquez-Munoz
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Departamento de Ciencias Veterinarias y Salud Pública, Universidad Católica de Temuco, Temuco, Chile
| | - Rafael Castro-Vargas
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Faith M. Cullens-Nobis
- Agriculture and Agribusiness Institute, Michigan State University Extension, Michigan State University, East Lansing, MI, United States
| | - Rinosh Mani
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Angel Abuelo
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Agriculture and Agribusiness Institute, Michigan State University Extension, Michigan State University, East Lansing, MI, United States
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5
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Wada T, Yoshida S, Yamamoto T, Nonaka L, Fukushima Y, Nakajima C, Suzuki Y, Imajoh M. Application of Genomic Epidemiology of Pathogens to Farmed Yellowtail Fish Mycobacteriosis in Kyushu, Japan. Microbes Environ 2024; 39:ME24011. [PMID: 38897967 PMCID: PMC11220446 DOI: 10.1264/jsme2.me24011] [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] [Received: 02/15/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
To investigate mycobacterial cases of farmed yellowtail fish in coastal areas of western Japan (Kagoshima, Kyushu), where aquaculture fisheries are active, Mycobacterium pseudoshottsii, the causative agent, was isolated from six neighboring fishing ports in 2012 and 2013. A phylogenetic ana-lysis revealed that the strains isolated from one fishing port were closely related to those isolated from other regions of Japan, suggesting the nationwide spread of a single strain. However, strains from Japan were phylogenetically distinct from those from the Mediterranean and the United States; therefore, worldwide transmission was not observed based on the limited data obtained on the strains exami-ned in this study. The present results demonstrate that a bacterial genomic ana-lysis of infected cases, a mole-cular epidemiology strategy for public health, provides useful data for estimating the prevalence and transmission pathways of M. pseudoshottsii in farmed fish. A bacterial genome ana-lysis of strains, such as that performed herein, may play an important role in monitoring the prevalence of this pathogen in fish farms and possible epidemics in the future as a result of international traffic, logistics, and trade in fisheries.
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Affiliation(s)
- Takayuki Wada
- Department of Microbiology, Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Takeshi Yamamoto
- Azuma-cho Fisheries Cooperative Association, Izumi, Kagoshima, Japan
| | - Lisa Nonaka
- Faculty of Human Life Sciences, Shokei University, Kumamoto, Kumamoto, Japan
| | - Yukari Fukushima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Masayuki Imajoh
- Laboratory of Fish Disease, Aquaculture Course, Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
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6
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Hopken MW, Piaggio AJ, Abdo Z, Chipman RB, Mankowski CP, Nelson KM, Hilton MS, Thurber C, Tsuchiya MTN, Maldonado JE, Gilbert AT. Are rabid raccoons ( Procyon lotor) ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes. Evol Appl 2023; 16:1937-1955. [PMID: 38143904 PMCID: PMC10739080 DOI: 10.1111/eva.13613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/06/2023] [Accepted: 10/18/2023] [Indexed: 12/26/2023] Open
Abstract
North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon (Procyon lotor) in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States. Understanding the spatial movement of RV by raccoon populations is important for monitoring and refining strategies supporting the landscape-level control and local elimination of this lethal zoonosis. We developed a high-throughput genotyping panel for raccoons based on hundreds of microhaplotypes to identify population structure and genetic diversity relevant to rabies management programs. Throughout the eastern United States, we identified hierarchical population genetic structure with clusters that were connected through isolation-by-distance. We also illustrate that this genotyping approach can be used to support real-time management priorities by identifying the geographic origin of a rabid raccoon that was collected in an area of the United States that had been raccoon RV-free for 8 years. The results from this study and the utility of the microhaplotype panel and genotyping method will provide managers with information on raccoon ecology that can be incorporated into future management decisions.
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Affiliation(s)
- Matthew W. Hopken
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Antoinette J. Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Richard B. Chipman
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Clara P. Mankowski
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Kathleen M. Nelson
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Mikaela Samsel Hilton
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | - Christine Thurber
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Mirian T. N. Tsuchiya
- Data Science Lab, Office of the Chief Information OfficerSmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Amy T. Gilbert
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
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7
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Thorburn DMJ, Sagonas K, Binzer-Panchal M, Chain FJJ, Feulner PGD, Bornberg-Bauer E, Reusch TBH, Samonte-Padilla IE, Milinski M, Lenz TL, Eizaguirre C. Origin matters: Using a local reference genome improves measures in population genomics. Mol Ecol Resour 2023; 23:1706-1723. [PMID: 37489282 DOI: 10.1111/1755-0998.13838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 06/02/2023] [Indexed: 07/26/2023]
Abstract
Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST ), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.
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Affiliation(s)
- Doko-Miles J Thorburn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahesh Binzer-Panchal
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Uppsala University, Uppsala, Sweden
| | - Frederic J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Irene E Samonte-Padilla
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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9
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Rossi G, Shih BBJ, Egbe NF, Motta P, Duchatel F, Kelly RF, Ndip L, Sander M, Tanya VN, Lycett SJ, Bronsvoort BM, Muwonge A. Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data. Front Vet Sci 2023; 10:1086001. [PMID: 37266384 PMCID: PMC10230100 DOI: 10.3389/fvets.2023.1086001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/14/2023] [Indexed: 06/03/2023] Open
Abstract
When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies.
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Affiliation(s)
- Gianluigi Rossi
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barbara Bo-Ju Shih
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Nkongho Franklyn Egbe
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Paolo Motta
- The Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Bangkok, Thailand
| | - Florian Duchatel
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Robert Francis Kelly
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Lucy Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | | | | | - Samantha J. Lycett
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barend Mark Bronsvoort
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
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10
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Schrott J, Sodoma E, Dünser M, Tichy A, Khol JL. Mycobacterium avium subsp. paratuberculosis in Sheep and Goats in Austria: Seroprevalence, Risk Factors and Detection from Boot Swab Samples. Animals (Basel) 2023; 13:ani13091517. [PMID: 37174554 PMCID: PMC10177492 DOI: 10.3390/ani13091517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
This study aimed to investigate the prevalence of Mycobacterium avium subsp. paratuberculosis (MAP) in small ruminants in Austria by testing 22,019 serum samples with ELISA for the presence of specific antibodies. Furthermore, detailed investigations in five MAP-infected goat herds were carried out by ELISA, qPCR and bacterial culture. The found animal-level apparent MAP seroprevalence was 2.0% for goats and 0.7% for sheep (calculated true prevalence 3.5% and 1.2%, respectively). Herd-level apparent MAP seroprevalence was 11.1% for goat herds and 8.9% for sheep flocks. Significant risk factors for seropositivity in goat herds were: herd size, animal trading, farmed as a dairy herd, Animal Health Service membership and cohabitation with farmed game. For sheep flocks, seroprevalence was significantly higher in flocks with animal trading and where cattle or goats were kept in the flock, respectively. The overall apparent within-herd MAP seroprevalence in the five goat farms investigated was 21.8% (11.7%-28.0%, calculated true seroprevalence 38.6%) and an overall rate of MAP shedding of 12.3% was detected (5.0%-24.7%). It was possible to identify MAP by culture using boot swab samples in each herd. The results indicated a moderate MAP infection rate in small ruminants in Austria.
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Affiliation(s)
- Juliane Schrott
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Innsbruck, Technikerstraße 70, 6020 Innsbruck, Austria
| | - Eva Sodoma
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Innsbruck, Technikerstraße 70, 6020 Innsbruck, Austria
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Linz, Wieningerstraße 8, 4020 Linz, Austria
| | - Michael Dünser
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Innsbruck, Technikerstraße 70, 6020 Innsbruck, Austria
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Linz, Wieningerstraße 8, 4020 Linz, Austria
| | - Alexander Tichy
- Platform for Bioinformatics and Biostatistics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Johannes Lorenz Khol
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Wien, Austria
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11
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Bendall EE, Paz-Bailey G, Santiago GA, Porucznik CA, Stanford JB, Stockwell MS, Duque J, Jeddy Z, Veguilla V, Major C, Rivera-Amill V, Rolfes MA, Dawood FS, Lauring AS. SARS-CoV-2 Genomic Diversity in Households Highlights the Challenges of Sequence-Based Transmission Inference. mSphere 2022; 7:e0040022. [PMID: 36377913 PMCID: PMC9769559 DOI: 10.1128/msphere.00400-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
The reliability of sequence-based inference of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission is not clear. Sequence data from infections among household members can define the expected genomic diversity of a virus along a defined transmission chain. SARS-CoV-2 cases were identified prospectively among 2,369 participants in 706 households. Specimens with a reverse transcription-PCR cycle threshold of ≤30 underwent whole-genome sequencing. Intrahost single-nucleotide variants (iSNV) were identified at a ≥5% frequency. Phylogenetic trees were used to evaluate the relationship of household and community sequences. There were 178 SARS-CoV-2 cases in 706 households. Among 147 specimens sequenced, 106 yielded a whole-genome consensus with coverage suitable for identifying iSNV. Twenty-six households had sequences from multiple cases within 14 days. Consensus sequences were indistinguishable among cases in 15 households, while 11 had ≥1 consensus sequence that differed by 1 to 2 mutations. Sequences from households and the community were often interspersed on phylogenetic trees. Identification of iSNV improved inference in 2 of 15 households with indistinguishable consensus sequences and in 6 of 11 with distinct ones. In multiple-infection households, whole-genome consensus sequences differed by 0 to 1 mutations. Identification of shared iSNV occasionally resolved linkage, but the low genomic diversity of SARS-CoV-2 limits the utility of "sequence-only" transmission inference. IMPORTANCE We performed whole-genome sequencing of SARS-CoV-2 from prospectively identified cases in three longitudinal household cohorts. In a majority of multi-infection households, SARS-CoV-2 consensus sequences were indistinguishable, and they differed by 1 to 2 mutations in the rest. Importantly, even with modest genomic surveillance of the community (3 to 5% of cases sequenced), it was not uncommon to find community sequences interspersed with household sequences on phylogenetic trees. Identification of shared minority variants only occasionally resolved these ambiguities in transmission linkage. Overall, the low genomic diversity of SARS-CoV-2 limits the utility of "sequence-only" transmission inference. Our work highlights the need to carefully consider both epidemiologic linkage and sequence data to define transmission chains in households, hospitals, and other transmission settings.
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Affiliation(s)
- Emily E. Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Christina A. Porucznik
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Joseph B. Stanford
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Melissa S. Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Zuha Jeddy
- Abt Associates, Rockville, Maryland, USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chelsea Major
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vanessa Rivera-Amill
- Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico, USA
| | | | | | - Adam S. Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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12
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Dennis TPW, Mable BK, Brunelle B, Devault A, Carter RW, Ling CL, Mmbaga BT, Halliday JEB, Oravcova K, Forde TL. Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance. Microb Genom 2022; 8. [PMID: 35622897 PMCID: PMC9465068 DOI: 10.1099/mgen.0.000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole-genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1) Bacillus anthracis, which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2) Mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen. We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (>15×) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (Ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The Ct value had the highest predictive value, explaining 52 % of the variation in capture efficiency. Samples with Ct values ≤30 were over six times more likely to achieve the threshold coverage than those with a Ct > 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.
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Affiliation(s)
- Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K. Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ryan W. Carter
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jo E. B. Halliday
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- *Correspondence: Taya L. Forde,
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13
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Forde TL, Dennis TPW, Aminu OR, Harvey WT, Hassim A, Kiwelu I, Medvecky M, Mshanga D, Van Heerden H, Vogel A, Zadoks RN, Mmbaga BT, Lembo T, Biek R. Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity. Microb Genom 2022; 8:000759. [PMID: 35188453 PMCID: PMC8942019 DOI: 10.1099/mgen.0.000759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.
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Affiliation(s)
- Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - O. Rhoda Aminu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - William T. Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Matej Medvecky
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Henriette Van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Adeline Vogel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ruth N. Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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14
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John Cremin C, Dash S, Huang X. Big Data: Historic Advances and Emerging Trends in Biomedical Research. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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15
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Lund AJ, Wade KJ, Nikolakis ZL, Ivey KN, Perry BW, Pike HNC, Paull SH, Liu Y, Castoe TA, Pollock DD, Carlton EJ. Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination. eLife 2022; 11:79320. [PMID: 36040013 PMCID: PMC9427098 DOI: 10.7554/elife.79320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.
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Affiliation(s)
- Andrea J Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Kristen J Wade
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Zachary L Nikolakis
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Kathleen N Ivey
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Blair W Perry
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Hamish NC Pike
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Sara H Paull
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Yang Liu
- Sichuan Centers for Disease Control and PreventionChengduChina
| | - Todd A Castoe
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - David D Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Elizabeth J Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
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16
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Macqueen DJ, Eve O, Gundappa MK, Daniels RR, Gallagher MD, Alexandersen S, Karlsen M. Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages. Viruses 2021; 13:2549. [PMID: 34960818 PMCID: PMC8705410 DOI: 10.3390/v13122549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022] Open
Abstract
Viral disease poses a major barrier to sustainable aquaculture, with outbreaks causing large economic losses and growing concerns for fish welfare. Genomic epidemiology can support disease control by providing rapid inferences on viral evolution and disease transmission. In this study, genomic epidemiology was used to investigate salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. Our aim was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. Using nanopore sequencing, we captured ~90% of the SAV2 genome for n = 68 field isolates from 10 aquaculture production regions sampled between 2018 and 2020. Using time-calibrated phylogenetics, we infer that, following its introduction to Norway around 2010, SAV2 split into two clades (SAV2a and 2b) around 2013. While co-present at the same sites near the boundary of Møre og Romsdal and Trøndelag, SAV2a and 2b were generally detected in non-overlapping locations at more Southern and Northern latitudes, respectively. We provide evidence for recent SAV2 transmission over large distances, revealing a strong connection between Møre og Romsdal and SAV2 detected in 2019/20 in Rogaland. We also demonstrate separate introductions of SAV2a and 2b outside the SAV2 zone in Sognefjorden (Vestland), connected to samples from Møre og Romsdal and Trøndelag, respectively, and a likely 100 km Northward transmission of SAV2b within Trøndelag. Finally, we recovered genomes of SAV2a and SAV3 co-infecting single fish in Rogaland, involving novel SAV3 lineages that diverged from previously characterized strains >25 years ago. Overall, this study demonstrates useful applications of genomic epidemiology for tracking viral disease spread in aquaculture.
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Affiliation(s)
- Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK; (O.E.); (M.K.G.); (R.R.D.)
| | - Oliver Eve
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK; (O.E.); (M.K.G.); (R.R.D.)
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK; (O.E.); (M.K.G.); (R.R.D.)
| | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK; (O.E.); (M.K.G.); (R.R.D.)
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17
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Rossi G, Crispell J, Brough T, Lycett SJ, White PCL, Allen A, Ellis RJ, Gordon SV, Harwood R, Palkopoulou E, Presho EL, Skuce R, Smith GC, Kao RR. Phylodynamic analysis of an emergent
Mycobacterium bovis
outbreak in an area with no previously known wildlife infections. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gianluigi Rossi
- Roslin Institute and R(D)SVS University of Edinburgh Edinburgh UK
| | - Joseph Crispell
- School of Veterinary Medicine University College Dublin Dublin Ireland
| | - Tanis Brough
- Advice Services Team Service Delivery Directorate APHA Penrith UK
| | | | | | - Adrian Allen
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department APHA Addlestone UK
| | - Stephen V. Gordon
- School of Veterinary Medicine University College Dublin Dublin Ireland
- Conway Institute University College Dublin Dublin Ireland
| | | | | | - Eleanor L. Presho
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | - Robin Skuce
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | | | - Rowland R. Kao
- Roslin Institute and R(D)SVS University of Edinburgh Edinburgh UK
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18
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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19
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Witte C, Fowler JH, Pfeiffer W, Hungerford LL, Braun J, Burchell J, Papendick R, Rideout BA. Social network analysis and whole-genome sequencing to evaluate disease transmission in a large, dynamic population: A study of avian mycobacteriosis in zoo birds. PLoS One 2021; 16:e0252152. [PMID: 34106953 PMCID: PMC8189513 DOI: 10.1371/journal.pone.0252152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/11/2021] [Indexed: 11/18/2022] Open
Abstract
This study combined a social network analysis and whole-genome sequencing (WGS) to test for general patterns of contagious spread of a mycobacterial infection for which pathways of disease acquisition are not well understood. Our population included 275 cases diagnosed with avian mycobacteriosis that were nested in a source population of 16,430 birds at San Diego Zoo Wildlife Alliance facilities from 1992 through mid-2014. Mycobacteria species were determined using conventional methods and whole genome sequencing (WGS). Mycobacterium avium avium (MAA) and Mycobacterium genavense were the most common species of mycobacteria identified and were present in different proportions across bird taxa. A social network for the birds was constructed from the source population to identify directly and indirectly connected cases during time periods relevant to disease transmission. Associations between network connectivity and genetic similarity of mycobacteria (as determined by clusters of genotypes separated by few single nucleotide polymorphisms, or SNPs) were then evaluated in observed and randomly generated network permutations. Findings showed that some genotypes clustered along pathways of bird connectivity, while others were dispersed throughout the network. The proportion of directly connected birds having a similar mycobacterial genotype was 0.36 and significant (p<0.05). This proportion was higher (0.58) and significant for MAA but not for M. genavense. Evaluations of SNP distributions also showed genotypes of MAA were more related in connected birds than expected by chance; however, no significant patterns of genetic relatedness were identified for M. genavense, although data were sparse. Integrating the WGS analysis of mycobacteria with a social network analysis of their host birds revealed significant genetic clustering along pathways of connectivity, namely for MAA. These findings are consistent with a contagious process occurring in some, but not all, case clusters.
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Affiliation(s)
- Carmel Witte
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, California, United States of America
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, United States of America
- Graduate School of Public Health, San Diego State University, San Diego, California, United States of America
| | - James H. Fowler
- Department of Political Science, University of California, San Diego, La Jolla, California, United States of America
| | - Wayne Pfeiffer
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America
| | - Laura L. Hungerford
- Department of Population Health Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, United States of America
| | - Josephine Braun
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, California, United States of America
| | - Jennifer Burchell
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, California, United States of America
| | - Rebecca Papendick
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, California, United States of America
| | - Bruce A. Rideout
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, California, United States of America
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20
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Guinat C, Vergne T, Kocher A, Chakraborty D, Paul MC, Ducatez M, Stadler T. What can phylodynamics bring to animal health research? Trends Ecol Evol 2021; 36:837-847. [PMID: 34034912 DOI: 10.1016/j.tree.2021.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 11/18/2022]
Abstract
Infectious diseases are a major burden to global economies, and public and animal health. To date, quantifying the spread of infectious diseases to inform policy making has traditionally relied on epidemiological data collected during epidemics. However, interest has grown in recent phylodynamic techniques to infer pathogen transmission dynamics from genetic data. Here, we provide examples of where this new discipline has enhanced disease management in public health and illustrate how it could be further applied in animal health. In particular, we describe how phylodynamics can address fundamental epidemiological questions, such as inferring key transmission parameters in animal populations and quantifying spillover events at the wildlife-livestock interface, and generate important insights for the design of more effective control strategies.
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Affiliation(s)
- Claire Guinat
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Timothee Vergne
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31300 Toulouse, France
| | - Arthur Kocher
- Transmission, Infection, Diversification & Evolution (tide) group, Max Planck Institute for the Science of Human History, Kahlaische str. 10, 07745 Jena, Germany
| | - Debapryio Chakraborty
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31300 Toulouse, France
| | - Mathilde C Paul
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31300 Toulouse, France
| | - Mariette Ducatez
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31300 Toulouse, France
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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21
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Nigsch A, Robbe-Austerman S, Stuber TP, Pavinski Bitar PD, Gröhn YT, Schukken YH. Who infects whom?-Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data. PLoS One 2021; 16:e0246983. [PMID: 33983941 PMCID: PMC8118464 DOI: 10.1371/journal.pone.0246983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022] Open
Abstract
Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johne’s disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1–4 other cows and spread infection to 0–17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.
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Affiliation(s)
- Annette Nigsch
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Suelee Robbe-Austerman
- USDA APHIS National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Tod P. Stuber
- USDA APHIS National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Paulina D. Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Yrjö T. Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Ynte H. Schukken
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Royal GD, Deventer, The Netherlands
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22
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Goic M, Bozanic-Leal MS, Badal M, Basso LJ. COVID-19: Short-term forecast of ICU beds in times of crisis. PLoS One 2021; 16:e0245272. [PMID: 33439917 PMCID: PMC7806165 DOI: 10.1371/journal.pone.0245272] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/27/2020] [Indexed: 11/19/2022] Open
Abstract
By early May 2020, the number of new COVID-19 infections started to increase rapidly in Chile, threatening the ability of health services to accommodate all incoming cases. Suddenly, ICU capacity planning became a first-order concern, and the health authorities were in urgent need of tools to estimate the demand for urgent care associated with the pandemic. In this article, we describe the approach we followed to provide such demand forecasts, and we show how the use of analytics can provide relevant support for decision making, even with incomplete data and without enough time to fully explore the numerical properties of all available forecasting methods. The solution combines autoregressive, machine learning and epidemiological models to provide a short-term forecast of ICU utilization at the regional level. These forecasts were made publicly available and were actively used to support capacity planning. Our predictions achieved average forecasting errors of 4% and 9% for one- and two-week horizons, respectively, outperforming several other competing forecasting models.
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Affiliation(s)
- Marcel Goic
- Department of Industrial Engineering, University of Chile, Santiago, Chile
| | - Mirko S. Bozanic-Leal
- Department of Industrial Engineering, University of Chile, Santiago, Chile
- Instituto de Sistemas Complejos de Ingeniería (ISCI), Santiago, Chile
| | - Magdalena Badal
- Department of Industrial Engineering, University of Chile, Santiago, Chile
- Instituto de Sistemas Complejos de Ingeniería (ISCI), Santiago, Chile
| | - Leonardo J. Basso
- Instituto de Sistemas Complejos de Ingeniería (ISCI), Santiago, Chile
- Department of Civil Engineering, University of Chile, Santiago, Chile
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23
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Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations. Sci Rep 2020; 10:21980. [PMID: 33319838 PMCID: PMC7738532 DOI: 10.1038/s41598-020-78900-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful methods include ‘phylodynamic approaches’ that integrate evolutionary and epidemiological data. However, they are typically computationally intensive, require extensive data, and are best applied when there is a strong molecular clock signal and substantial pathogen diversity. To determine how much transmission information can be inferred when pathogen genetic diversity is low and metadata limited, we propose an analytical approach that combines pathogen WGS data and sampling times from infected hosts. It accounts for ‘between-scale’ processes, in particular within-host pathogen evolution and between-host transmission. We applied this to a well-characterised population with an endemic Mycobacterium bovis (the causative agent of bovine/zoonotic tuberculosis, bTB) infection. Our results show that, even with such limited data and low diversity, the computation of the transmission probability between host pairs can help discriminate between likely and unlikely infection pathways and therefore help to identify potential transmission networks. However, the method can be sensitive to assumptions about within-host evolution.
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24
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Mining whole genome sequence data to efficiently attribute individuals to source populations. Sci Rep 2020; 10:12124. [PMID: 32699222 PMCID: PMC7376179 DOI: 10.1038/s41598-020-68740-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/15/2020] [Indexed: 11/27/2022] Open
Abstract
Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.
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25
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Firestone SM, Hayama Y, Lau MSY, Yamamoto T, Nishi T, Bradhurst RA, Demirhan H, Stevenson MA, Tsutsui T. Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates. PLoS One 2020; 15:e0235660. [PMID: 32667952 PMCID: PMC7363093 DOI: 10.1371/journal.pone.0235660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 06/22/2020] [Indexed: 11/19/2022] Open
Abstract
Transmission network modelling to infer 'who infected whom' in infectious disease outbreaks is a highly active area of research. Outbreaks of foot-and-mouth disease have been a key focus of transmission network models that integrate genomic and epidemiological data. The aim of this study was to extend Lau's systematic Bayesian inference framework to incorporate additional parameters representing predominant species and numbers of animals held on a farm. Lau's Bayesian Markov chain Monte Carlo algorithm was reformulated, verified and pseudo-validated on 100 simulated outbreaks populated with demographic data Japan and Australia. The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in BEAST2. The modified model achieved improvements in overall accuracy when tested on the simulated outbreaks. When implemented on the actual outbreak data from Japan, infected farms that held predominantly pigs were estimated to have five times the transmissibility of infected cattle farms and be 49% less susceptible. The farm-level incubation period was 1 day shorter than the latent period, the timing of the seeding of the outbreak in Japan was inferred, as were key linkages between clusters and features of farms involved in widespread dissemination of this outbreak. To improve accessibility the modified model has been implemented as the R package 'BORIS' for use in future outbreaks.
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Affiliation(s)
- Simon M. Firestone
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Max S. Y. Lau
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Takehisa Yamamoto
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Tatsuya Nishi
- Exotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Tokyo, Japan
| | - Richard A. Bradhurst
- Centre of Excellence for Biosecurity Risk Analysis, The University of Melbourne, Parkville, VIC, Australia
| | - Haydar Demirhan
- Mathematical Sciences Discipline, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Mark A. Stevenson
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
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26
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Yang S, Liu Q, Shen Z, Wang H, He L. Molecular Epidemiology of Myroides odoratimimus in Nosocomial Catheter-Related Infection at a General Hospital in China. Infect Drug Resist 2020; 13:1981-1993. [PMID: 32612373 PMCID: PMC7323792 DOI: 10.2147/idr.s251626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/14/2020] [Indexed: 11/30/2022] Open
Abstract
Purpose Catheter-related infection (CRI) is one of the most frequent causes of hospitalizations for immunocompromised patients. A major challenge is the increased prevalence of Myroides odoratimimus. The purpose of the present study was to evaluate the clinical features and molecular characteristics of M. odoratimimus collected from a general hospital in Shanghai, China. Patients and Methods From July 2015 to August 2016, a total of 22 isolates of M. odoratimimus were collected from inpatients respectively from the biliary and pancreatic surgery (6/22) and the urology department (16/22). Clonal relatedness among the isolates was assessed using pulsed-field gel electrophoresis (PFGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, the antimicrobial susceptibility tests were carried out using the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method. The presence of antibiotic resistance genes was screened using the polymerase chain reaction (PCR) assay. Additionally, protein structure prediction was analyzed using PSIPRED and RaptorX. Results PFGE differentiated these isolates into six possibly related clones from two different departments obtained during a distinct period, indicating clonal dissemination in the two departments. We compared the dendrograms of M. odoratimimus isolates obtained by MALDI-TOF MS with those obtained by PFGE and found that the coincidence rate between them was only 68.2%. All the M. odoratimimus isolates were highly resistant to most available antibiotics, including carbapenems. Furthermore, chromosome-encoded β-lactamases MUS-1 was confirmed by PCR in 6 of 22 Myroides odoratimimus isolates. Herein, we also reported a novel variant of blaMUS-1 in the remaining 16 isolates, which encodes MUS-3 protein at position 60 (Valine to Alanine), differing from the structure of MUS-1. Conclusion The opportunistic and extensively antibiotic-resistant Myroides odoratimimus has a small range of epidemics in these two different departments. Clinicians should be aware that M. odoratimimus may induce a severe nosocomial outbreak of catheter-related infections, particularly in immunocompromised patients.
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Affiliation(s)
- Shuang Yang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhen Shen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hua Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lei He
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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27
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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28
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Lu L, Robertson G, Ashworth J, Pham Hong A, Shi T, Ivens A, Thwaites G, Baker S, Woolhouse M. Epidemiology and Phylogenetic Analysis of Viral Respiratory Infections in Vietnam. Front Microbiol 2020; 11:833. [PMID: 32499763 PMCID: PMC7242649 DOI: 10.3389/fmicb.2020.00833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
Acute respiratory infections (ARIs) impose a major public health burden on fragile healthcare systems of developing Southeast Asian countries such as Vietnam. The epidemiology, genetic diversity and transmission patterns of respiratory viral pathogens that circulate in this region are not well characterized. We used RT-PCR to screen for 14 common respiratory viruses in nasal/throat samples from 4326 ARI patients from 5 sites in Vietnam during 2012-2016. 64% of patients tested positive for viruses; 14% tested positive multiple co-infecting viruses. The most frequently detected viruses were Respiratory syncytial virus (RSV, 23%), Human Rhinovirus (HRV, 13%), Influenza A virus (IAV, 11%) and Human Bocavirus (HBoV, 7%). RSV infections peaked in July to October, were relatively more common in children <1 year and in the northernmost hospital. IAV infections peaked in December to February and were relatively more common in patients >5 years in the central region. Coinfection with IAV or RSV was associated with increased disease severity compared with patients only infected with HBoV or HRV. Over a hundred genomes belonging to 13 families and 24 genera were obtained via metagenomic sequencing, including novel viruses and viruses less commonly associated with ARIs. Phylogenetic and phylogeographic analyses further indicated that neighboring countries were the most likely source of many virus lineages causing ARIs in Vietnam and estimated the period that specific lineages have been circulating. Our study illustrates the value of applying the state-of-the-art virus diagnostic methods (multiplex RT-PCR and metagenomic sequencing) and phylodynamic analyses at a national level to generate an integrated picture of viral ARI epidemiology.
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Affiliation(s)
- Lu Lu
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gail Robertson
- Statistical Consultancy Unit, School of Mathematics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jordan Ashworth
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anh Pham Hong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ting Shi
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Guy Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark Woolhouse
- Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
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29
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Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions. Viruses 2020; 12:v12050516. [PMID: 32392864 PMCID: PMC7290424 DOI: 10.3390/v12050516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022] Open
Abstract
Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.
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30
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Kleczkowski A, Hoyle A, McMenemy P. One model to rule them all? Modelling approaches across OneHealth for human, animal and plant epidemics. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180255. [PMID: 31056049 DOI: 10.1098/rstb.2018.0255] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
One hundred years after the 1918 influenza outbreak, are we ready for the next pandemic? This paper addresses the need to identify and develop collaborative, interdisciplinary and cross-sectoral approaches to modelling of infectious diseases including the fields of not only human and veterinary medicine, but also plant epidemiology. Firstly, the paper explains the concepts on which the most common epidemiological modelling approaches are based, namely the division of a host population into susceptible, infected and removed (SIR) classes and the proportionality of the infection rate to the size of the susceptible and infected populations. It then demonstrates how these simple concepts have been developed into a vast and successful modelling framework that has been used in predicting and controlling disease outbreaks for over 100 years. Secondly, it considers the compartmental models based on the SIR paradigm within the broader concept of a 'disease tetrahedron' (comprising host, pathogen, environment and man) and uses it to review the similarities and differences among the fields comprising the 'OneHealth' approach. Finally, the paper advocates interactions between all fields and explores the future challenges facing modellers. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
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Affiliation(s)
- Adam Kleczkowski
- 1 Department of Mathematics and Statistics, University of Strathclyde , Glasgow G1 1XH , UK
| | - Andy Hoyle
- 2 Computing Science and Mathematics, University of Stirling , Stirling FK9 4LA , UK
| | - Paul McMenemy
- 2 Computing Science and Mathematics, University of Stirling , Stirling FK9 4LA , UK
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31
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Vandenberg O, Durand G, Hallin M, Diefenbach A, Gant V, Murray P, Kozlakidis Z, van Belkum A. Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies. Clin Microbiol Rev 2020; 33:e00057-19. [PMID: 32102900 PMCID: PMC7048017 DOI: 10.1128/cmr.00057-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Géraldine Durand
- bioMérieux, Microbiology Research and Development, La Balme Les Grottes, France
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Andreas Diefenbach
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Labor Berlin, Charité-Vivantes GmbH, Berlin, Germany
| | - Vanya Gant
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Patrick Murray
- BD Life Sciences Integrated Diagnostic Solutions, Scientific Affairs, Sparks, Maryland, USA
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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32
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Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G. In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses 2020; 12:v12020182. [PMID: 32033422 PMCID: PMC7077180 DOI: 10.3390/v12020182] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004-2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.
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Affiliation(s)
- Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Correspondence:
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA;
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Michael T. Pyne
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA;
| | - David R. Hillyard
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA;
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
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33
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Gupta P, Robin VV, Dharmarajan G. Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2020; 99:65. [PMID: 33622992 PMCID: PMC7371965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/23/2020] [Accepted: 05/25/2020] [Indexed: 08/23/2024]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease mediated extinctions and wildlife epidemics. We then focus on elucidating how host-parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Affiliation(s)
- Pooja Gupta
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29801, USA.
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Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR. Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system. eLife 2019; 8:e45833. [PMID: 31843054 PMCID: PMC6917503 DOI: 10.7554/elife.45833] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023] Open
Abstract
Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown. In Britain, the role of badgers in infection persistence in cattle is highly contentious, despite decades of research and control efforts. We applied Bayesian phylogenetic and machine-learning approaches to bacterial genome data to quantify the roles of badgers and cattle in M. bovis infection dynamics in the presence of data biases. Our results suggest that transmission occurs more frequently from badgers to cattle than vice versa (10.4x in the most likely model) and that within-species transmission occurs at higher rates than between-species transmission for both. If representative, our results suggest that control operations should target both cattle and badgers.
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Affiliation(s)
- Joseph Crispell
- School of Veterinary Medicine, Veterinary Sciences CentreUniversity College DublinDublinIreland
| | - Clare H Benton
- National Wildlife Management CentreAnimal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Daniel Balaz
- Roslin InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)CambridgeUnited Kingdom
| | - Assel Ahkmetova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Adrian Allen
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Eleanor L Presho
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | - James Dale
- Animal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Glyn Hewinson
- Centre for Bovine Tuberculosis, Institute of Biological, Environmental and Rural SciencesUniversity of AberystwythAberystwythUnited Kingdom
| | | | | | - Robin A Skuce
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | | | - Daniel J Wilson
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population HealthUniversity of OxfordOxfordUnited Kingdom
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Richard J Delahay
- National Wildlife Management CentreAnimal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Rowland Raymond Kao
- Roslin InstituteUniversity of EdinburghEdinburghUnited Kingdom
- Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUnited Kingdom
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Abdo Z. Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs. J Virol Methods 2019; 276:113777. [PMID: 31730870 DOI: 10.1016/j.jviromet.2019.113777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Long-term viral archives are valuable sources of research data. Each archive can store hundreds of thousands of diverse sample types. In the current era of whole genome sequencing, archived samples become a rich source of evolutionary and epidemiological data that can span years, and even decades. However, the ability to obtain high quality viral whole genome sequences from samples of various types, age, and quality is inconsistent. A minimum quality threshold that helps predict the best success of obtaining high quality genomic sequences for both recent and archived samples is highly valuable. Real-time reverse transcription PCR (rrt-PCR) and droplet digital PCR (ddPCR) are useful tools to evaluate nucleic acid integrity. We hypothesized that diagnostic rrt-PCR and ddPCR data for avian influenza virus (AIV) can predict viral whole genome sequencing success. To test this hypothesis we used RNA extracted from cloacal and oropharyngeal swabs stored in the USDA-APHIS National Wildlife Disease Program Wildlife Tissue Archive. We determined that a specific rrt-PCR Cq value or ddPCR copies/μL resulted in recovery of complete sequences of all eight AIV gene segments. We used logistic regression to estimate probabilities of whole genome recovery at 0.95 (Cq = 15, copies/μL = 49,350), 0.75 (Cq = 24, copies/μL = 16,800), 0.50 (Cq = 29, copies/μL = <1), and 0.25 (Cq = 235, copies/μL = <1). We also identified values at which we predictably recovered HA and NA segments for diagnosing subtypes (Cq = 27.29; copies/μL = 757.50). This approach will allow researchers to assess the potential success of AIV whole genome recovery from diagnostic samples collected in routine AIV surveillance.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
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Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
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Chaters GL, Johnson PCD, Cleaveland S, Crispell J, de Glanville WA, Doherty T, Matthews L, Mohr S, Nyasebwa OM, Rossi G, Salvador LCM, Swai E, Kao RR. Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180264. [PMID: 31104601 PMCID: PMC6558568 DOI: 10.1098/rstb.2018.0264] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2019] [Indexed: 11/12/2022] Open
Abstract
Livestock movements are an important mechanism of infectious disease transmission. Where these are well recorded, network analysis tools have been used to successfully identify system properties, highlight vulnerabilities to transmission, and inform targeted surveillance and control. Here we highlight the main uses of network properties in understanding livestock disease epidemiology and discuss statistical approaches to infer network characteristics from biased or fragmented datasets. We use a 'hurdle model' approach that predicts (i) the probability of movement and (ii) the number of livestock moved to generate synthetic 'complete' networks of movements between administrative wards, exploiting routinely collected government movement permit data from northern Tanzania. We demonstrate that this model captures a significant amount of the observed variation. Combining the cattle movement network with a spatial between-ward contact layer, we create a multiplex, over which we simulated the spread of 'fast' ( R0 = 3) and 'slow' ( R0 = 1.5) pathogens, and assess the effects of random versus targeted disease control interventions (vaccination and movement ban). The targeted interventions substantially outperform those randomly implemented for both fast and slow pathogens. Our findings provide motivation to encourage routine collection and centralization of movement data to construct representative networks. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
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Affiliation(s)
- G. L. Chaters
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - P. C. D. Johnson
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - S. Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - J. Crispell
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - W. A. de Glanville
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - T. Doherty
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - L. Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - S. Mohr
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - O. M. Nyasebwa
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Nelson Mandela Road, Dar Es Salaam, Tanzania
| | - G. Rossi
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - L. C. M. Salvador
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - E. Swai
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Nelson Mandela Road, Dar Es Salaam, Tanzania
| | - R. R. Kao
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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Hayama Y, Firestone SM, Stevenson MA, Yamamoto T, Nishi T, Shimizu Y, Tsutsui T. Reconstructing a transmission network and identifying risk factors of secondary transmissions in the 2010 foot-and-mouth disease outbreak in Japan. Transbound Emerg Dis 2019; 66:2074-2086. [PMID: 31131968 DOI: 10.1111/tbed.13256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 11/27/2022]
Abstract
Research aimed at understanding transmission networks, representing a network of "who infected whom" for an infectious disease outbreak, have been actively conducted in recent years. Transmission network models incorporating epidemiological and genetic data are valuable for elucidating disease transmission pathways. In this study, we reconstructed the transmission network of the foot-and-mouth disease (FMD) epidemic in Japan in 2010, and explored farm-level risk factors associated with increased risk of secondary transmission. A published, systematic Bayesian transmission network model was applied to epidemiological data of 292 infected farms and whole genome sequence data of 104 of the infected farms. This model can make inferences for known infected farms even lacking genetic data. After estimating the consensus network, the accuracy of the network was examined by comparison with epidemiological data. Then, risk factors inferred to have been sources of secondary transmission were explored using zero-inflated Poisson regression model. As far as we are aware, this study represents the largest FMD outbreak transmission network to be published by such means combining epidemiological and genetic data. The consensus network reasonably generated the epidemiological links, which were estimated from the actual epidemiological investigation. Among 292 farms, 101 farms (35%) were inferred to have been the sources of secondary transmission, and amongst these farms, the median number of secondary cases was 2 (min:1-max:18) farms. The farm-type (small and large -sized pig farms), the number of days from onset to notification, and the number of susceptible farms within a 1-km radius were significantly associated with secondary transmission. Transmission network modelling enabled inference of the connections between infected farms during the FMD epidemic and identified important factors for controlling the risk of secondary transmission. This study demonstrated that the predominant susceptible species held on a farm, farm size, and animal density were associated with increased onwards transmission.
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Affiliation(s)
- Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
| | - Simon M Firestone
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark A Stevenson
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Takehisa Yamamoto
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
| | - Tatsuya Nishi
- Exotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Yumiko Shimizu
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
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Mayr A, Weinhold L, Hofner B, Titze S, Gefeller O, Schmid M. The betaboost package-a software tool for modelling bounded outcome variables in potentially high-dimensional epidemiological data. Int J Epidemiol 2019; 47:1383-1388. [PMID: 30380092 DOI: 10.1093/ije/dyy093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/11/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation To provide an integrated software environment for model fitting and variable selection in regression models with a bounded outcome variable. Implementation The proposed modelling framework is implemented in the add-on package betaboost of the statistical software environment R. General features The betaboost methodology is based on beta-regression, which is a state-of-the-art method for modelling bounded outcome variables. By combining traditional model fitting techniques with recent advances in statistical learning and distributional regression, betaboost allows users to carry out data-driven variable and/or confounder selection in potentially high-dimensional epidemiological data. The software package implements a flexible routine to incorporate linear and non-linear predictor effects in both the mean and the precision parameter (relating inversely to the variance) of a beta-regression model. Availability The software is hosted publicly at [http://github.com/boost-R/betaboost] and has been published under General Public License (GPL) version 3 or newer.
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Affiliation(s)
- Andreas Mayr
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Leonie Weinhold
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Benjamin Hofner
- Section Biostatistics, Paul-Ehrlich-Institut, Langen, Germany
| | - Stephanie Titze
- Department of Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Olaf Gefeller
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias Schmid
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
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Salvador LCM, O'Brien DJ, Cosgrove MK, Stuber TP, Schooley AM, Crispell J, Church SV, Gröhn YT, Robbe-Austerman S, Kao RR. Disease management at the wildlife-livestock interface: Using whole-genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan, USA. Mol Ecol 2019; 28:2192-2205. [PMID: 30807679 DOI: 10.1111/mec.15061] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 01/16/2019] [Accepted: 02/14/2019] [Indexed: 12/30/2022]
Abstract
The role of wildlife in the persistence and spread of livestock diseases is difficult to quantify and control. These difficulties are exacerbated when several wildlife species are potentially involved. Bovine tuberculosis (bTB), caused by Mycobacterium bovis, has experienced an ecological shift in Michigan, with spillover from cattle leading to an endemically infected white-tailed deer (deer) population. It has potentially substantial implications for the health and well-being of both wildlife and livestock and incurs a significant economic cost to industry and government. Deer are known to act as a reservoir of infection, with evidence of M. bovis transmission to sympatric elk and cattle populations. However, the role of elk in the circulation of M. bovis is uncertain; they are few in number, but range further than deer, so may enable long distance spread. Combining Whole Genome Sequences (WGS) for M. bovis isolates from exceptionally well-observed populations of elk, deer and cattle with spatiotemporal locations, we use spatial and Bayesian phylogenetic analyses to show strong spatiotemporal admixture of M. bovis isolates. Clustering of bTB in elk and cattle suggests either intraspecies transmission within the two populations, or exposure to a common source. However, there is no support for significant pathogen transfer amongst elk and cattle, and our data are in accordance with existing evidence that interspecies transmission in Michigan is likely only maintained by deer. This study demonstrates the value of whole genome population studies of M. bovis transmission at the wildlife-livestock interface, providing insights into bTB management in an endemic system.
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Affiliation(s)
- Liliana C M Salvador
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Ecology and Evolutionary Biology Department, Princeton University, Princeton, New Jersey.,Royal (Dick) Veterinary School of Veterinary Studies, University of Edinburgh, Midlothian, UK.,Department of Infectious Diseases, College of Veterinary Medicine, Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Daniel J O'Brien
- Wildlife Disease Laboratory, Michigan Department of Natural Resources, Lansing, Michigan
| | - Melinda K Cosgrove
- Wildlife Disease Laboratory, Michigan Department of Natural Resources, Lansing, Michigan
| | - Tod P Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa
| | - Angie M Schooley
- Mycobacteriology Laboratory, Infectious Disease Division, Michigan Department of Health and Human Services, Lansing, Michigan
| | - Joseph Crispell
- School of Veterinary Medicine, College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Steven V Church
- Mycobacteriology Laboratory, Infectious Disease Division, Michigan Department of Health and Human Services, Lansing, Michigan
| | - Yrjö T Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa
| | - Rowland R Kao
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Royal (Dick) Veterinary School of Veterinary Studies, University of Edinburgh, Midlothian, UK
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Lewnard JA, Reingold AL. Emerging Challenges and Opportunities in Infectious Disease Epidemiology. Am J Epidemiol 2019; 188:873-882. [PMID: 30877295 PMCID: PMC7109842 DOI: 10.1093/aje/kwy264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Much of the intellectual tradition of modern epidemiology stems from efforts to understand and combat chronic diseases persisting through the 20th century epidemiologic transition of countries such as the United States and United Kingdom. After decades of relative obscurity, infectious disease epidemiology has undergone an intellectual rebirth in recent years amid increasing recognition of the threat posed by both new and familiar pathogens. Here, we review the emerging coalescence of infectious disease epidemiology around a core set of study designs and statistical methods bearing little resemblance to the chronic disease epidemiology toolkit. We offer our outlook on challenges and opportunities facing the field, including the integration of novel molecular and digital information sources into disease surveillance, the assimilation of such data into models of pathogen spread, and the increasing contribution of models to public health practice. We next consider emerging paradigms in causal inference for infectious diseases, ranging from approaches to evaluating vaccines and antimicrobial therapies to the task of ascribing clinical syndromes to etiologic microorganisms, an age-old problem transformed by our increasing ability to characterize human-associated microbiota. These areas represent an increasingly important component of epidemiology training programs for future generations of researchers and practitioners.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California
- Correspondence to Dr. Joseph A. Lewnard, Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, 2121 Berkeley Way, Berkeley, CA 94720 (e-mail: )
| | - Arthur L Reingold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California
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More SJ. Can bovine TB be eradicated from the Republic of Ireland? Could this be achieved by 2030? Ir Vet J 2019; 72:3. [PMID: 31057791 PMCID: PMC6485114 DOI: 10.1186/s13620-019-0140-x] [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: 03/01/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
Background There has been an ongoing decline in bovine tuberculosis (TB) in the Republic of Ireland, however, TB has yet to be eradicated. Further to a recent commitment by the Irish government to eradicate TB by 2030, this paper considers two questions, ‘Can bovine TB be eradicated from the Republic of Ireland?’ and ‘Could this be achieved by 2030?’, given current knowledge from research. Main body of the abstract Until very recently, Ireland has lacked key tools required for eradication. This gap has substantially been filled with the national roll-out of badger vaccination. Nonetheless, there is robust evidence, drawn from general national research, international experiences, and results of a recent modelling study, to suggest that all current strategies plus badger vaccination will not be sufficient to successfully eradicate TB from Ireland by 2030. We face a critical decision point in the programme, specifically the scope and intensity of control measures from this point forward. Adequate information is available, both from research and international experience, to indicate that these additional measures should broadly focus on adequately addressing TB risks from wildlife, implementing additional risk-based cattle controls, and enhancing industry engagement. These three areas are considered in some detail. Conclusion Based on current knowledge, it will not be possible to eradicate TB by 2030 with current control strategies plus national badger vaccination. Additional measures will be needed if Ireland is to eradicate TB within a reasonable time frame. Decisions made now will have long-term implications both in terms of time-to-eradication and cumulative programme costs.
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Affiliation(s)
- Simon J More
- Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 W6F6 Ireland
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43
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Gilbertson MLJ, Fountain-Jones NM, Craft ME. Incorporating genomic methods into contact networks to reveal new insights into animal behavior and infectious disease dynamics. BEHAVIOUR 2019; 155:759-791. [PMID: 31680698 DOI: 10.1163/1568539x-00003471] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behavior. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic approaches means more researchers may seek out these tools. The integration of network and genomic approaches provides opportunities to examine the interaction between behavior and pathogen transmission in new ways and with greater resolution. While a number of studies have begun to incorporate both contact network and genomic approaches, a great deal of work has yet to be done to better integrate these techniques. In this review, we give a broad overview of how network and genomic approaches have each been used to address questions regarding the interaction of social behavior and infectious disease, and then discuss current work and future horizons for the merging of these techniques.
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Affiliation(s)
- Marie L J Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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44
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Firestone SM, Hayama Y, Bradhurst R, Yamamoto T, Tsutsui T, Stevenson MA. Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models. Sci Rep 2019; 9:4809. [PMID: 30886211 PMCID: PMC6423326 DOI: 10.1038/s41598-019-41103-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 02/28/2019] [Indexed: 12/22/2022] Open
Abstract
A number of transmission network models are available that combine genomic and epidemiological data to reconstruct networks of who infected whom during infectious disease outbreaks. For such models to reliably inform decision-making they must be transparently validated, robust, and capable of producing accurate predictions within the short data collection and inference timeframes typical of outbreak responses. A lack of transparent multi-model comparisons reduces confidence in the accuracy of transmission network model outputs, negatively impacting on their more widespread use as decision-support tools. We undertook a formal comparison of the performance of nine published transmission network models based on a set of foot-and-mouth disease outbreaks simulated in a previously free country, with corresponding simulated phylogenies and genomic samples from animals on infected premises. Of the transmission network models tested, Lau’s systematic Bayesian integration framework was found to be the most accurate for inferring the transmission network and timing of exposures, correctly identifying the source of 73% of the infected premises (with 91% accuracy for sources with model support >0.80). The Structured COalescent Transmission Tree Inference provided the most accurate inference of molecular clock rates. This validation study points to which models might be reliably used to reconstruct similar future outbreaks and how to interpret the outputs to inform control. Further research could involve extending the best-performing models to explicitly represent within-host diversity so they can handle next-generation sequencing data, incorporating additional animal and farm-level covariates and combining predictions using Ensemble methods and other approaches.
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Affiliation(s)
- Simon M Firestone
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Richard Bradhurst
- Centre of Excellence for Biosecurity Risk Analysis, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Takehisa Yamamoto
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Mark A Stevenson
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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45
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Altizer S, Becker DJ, Epstein JH, Forbes KM, Gillespie TR, Hall RJ, Hawley DM, Hernandez SM, Martin LB, Plowright RK, Satterfield DA, Streicker DG. Food for contagion: synthesis and future directions for studying host-parasite responses to resource shifts in anthropogenic environments. Philos Trans R Soc Lond B Biol Sci 2019. [PMID: 29531154 DOI: 10.1098/rstb.2017.0102] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human-provided resource subsidies for wildlife are diverse, common and have profound consequences for wildlife-pathogen interactions, as demonstrated by papers in this themed issue spanning empirical, theoretical and management perspectives from a range of study systems. Contributions cut across scales of organization, from the within-host dynamics of immune function, to population-level impacts on parasite transmission, to landscape- and regional-scale patterns of infection. In this concluding paper, we identify common threads and key findings from author contributions, including the consequences of resource subsidies for (i) host immunity; (ii) animal aggregation and contact rates; (iii) host movement and landscape-level infection patterns; and (iv) interspecific contacts and cross-species transmission. Exciting avenues for future work include studies that integrate mechanistic modelling and empirical approaches to better explore cross-scale processes, and experimental manipulations of food resources to quantify host and pathogen responses. Work is also needed to examine evolutionary responses to provisioning, and ask how diet-altered changes to the host microbiome influence infection processes. Given the massive public health and conservation implications of anthropogenic resource shifts, we end by underscoring the need for practical recommendations to manage supplemental feeding practices, limit human-wildlife conflicts over shared food resources and reduce cross-species transmission risks, including to humans.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'.
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Affiliation(s)
- Sonia Altizer
- Odum School of Ecology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA .,Center for the Ecology of Infectious Disease, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Daniel J Becker
- Odum School of Ecology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Center for the Ecology of Infectious Disease, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Kristian M Forbes
- Department of Virology, University of Helsinki, Helsinki, Finland.,Department of Biology, The Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
| | - Thomas R Gillespie
- Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Richard J Hall
- Odum School of Ecology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Center for the Ecology of Infectious Disease, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Department of Infectious Disease, College of Veterinary Medicine, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Dana M Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Sonia M Hernandez
- Warnell School of Forestry and Natural Resources, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Lynn B Martin
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Raina K Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Dara A Satterfield
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Daniel G Streicker
- Odum School of Ecology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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46
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Babayan SA, Orton RJ, Streicker DG. Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes. Science 2018; 362:577-580. [PMID: 30385576 DOI: 10.1126/science.aap9072] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 05/21/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022]
Abstract
Identifying the animal origins of RNA viruses requires years of field and laboratory studies that stall responses to emerging infectious diseases. Using large genomic and ecological datasets, we demonstrate that animal reservoirs and the existence and identity of arthropod vectors can be predicted directly from viral genome sequences via machine learning. We illustrate the ability of these models to predict the epidemiology of diverse viruses across most human-infective families of single-stranded RNA viruses, including 69 viruses with previously elusive or never-investigated reservoirs or vectors. Models such as these, which capitalize on the proliferation of low-cost genomic sequencing, can narrow the time lag between virus discovery and targeted research, surveillance, and management.
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Affiliation(s)
- Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.,The Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, Scotland, UK
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, Scotland, UK. .,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
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47
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Tsairidou S, Allen A, Banos G, Coffey M, Anacleto O, Byrne AW, Skuce RA, Glass EJ, Woolliams JA, Doeschl-Wilson AB. Can We Breed Cattle for Lower Bovine TB Infectivity? Front Vet Sci 2018; 5:310. [PMID: 30581821 PMCID: PMC6292866 DOI: 10.3389/fvets.2018.00310] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/22/2018] [Indexed: 11/13/2022] Open
Abstract
Host resistance and infectivity are genetic traits affecting infectious disease transmission. This Perspective discusses the potential exploitation of genetic variation in cattle infectivity, in addition to resistance, to reduce the risk, and prevalence of bovine tuberculosis (bTB). In bTB, variability in M. bovis shedding has been previously reported in cattle and wildlife hosts (badgers and wild boars), but the observed differences were attributed to dose and route of infection, rather than host genetics. This article addresses the extent to which cattle infectivity may play a role in bTB transmission, and discusses the feasibility, and potential benefits from incorporating infectivity into breeding programmes. The underlying hypothesis is that bTB infectivity, like resistance, is partly controlled by genetics. Identifying and reducing the number of cattle with high genetic infectivity, could reduce further a major risk factor for herds exposed to bTB. We outline evidence in support of this hypothesis and describe methodologies for detecting and estimating genetic parameters for infectivity. Using genetic-epidemiological prediction models we discuss the potential benefits of selection for reduced infectivity and increased resistance in terms of practical field measures of epidemic risk and severity. Simulations predict that adding infectivity to the breeding programme could enhance and accelerate the reduction in breakdown risk compared to selection on resistance alone. Therefore, given the recent launch of genetic evaluations for bTB resistance and the UK government's goal to eradicate bTB, it is timely to consider the potential of integrating infectivity into breeding schemes.
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Affiliation(s)
- Smaragda Tsairidou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Allen
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Scotland's Rural College, Midlothian, United Kingdom
| | - Mike Coffey
- Scotland's Rural College, Midlothian, United Kingdom
| | - Osvaldo Anacleto
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil
| | - Andrew W. Byrne
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Robin A. Skuce
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Elizabeth J. Glass
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - John A. Woolliams
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrea B. Doeschl-Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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48
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Kozakiewicz CP, Burridge CP, Funk WC, VandeWoude S, Craft ME, Crooks KR, Ernest HB, Fountain‐Jones NM, Carver S. Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol Appl 2018; 11:1763-1778. [PMID: 30459828 PMCID: PMC6231466 DOI: 10.1111/eva.12678] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/24/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free-living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host-vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross-disciplinary advances.
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Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyGraduate Degree Program in EcologyColorado State UniversityFort CollinsColorado
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColorado
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt. PaulMinnesota
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryDepartment of Veterinary SciencesUniversity of WyomingLaramieWyoming
| | | | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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49
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Pozo P, VanderWaal K, Grau A, de la Cruz ML, Nacar J, Bezos J, Perez A, Minguez O, Alvarez J. Analysis of the cattle movement network and its association with the risk of bovine tuberculosis at the farm level in Castilla y Leon, Spain. Transbound Emerg Dis 2018; 66:327-340. [DOI: 10.1111/tbed.13025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Pilar Pozo
- VISAVET Health Surveillance Centre Universidad Complutense de Madrid Madrid Spain
- MAEVA SERVET, S.L. Madrid Spain
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine University of Minnesota St. Paul Minnesota
| | - Anna Grau
- Dirección General de Producción Agropecuaria e Infraestructuras Agrarias Consejería de Agricultura y Ganadería de la Junta de Castilla y León Valladolid Spain
| | | | - Jesus Nacar
- Dirección General de Producción Agropecuaria e Infraestructuras Agrarias Consejería de Agricultura y Ganadería de la Junta de Castilla y León Valladolid Spain
| | - Javier Bezos
- VISAVET Health Surveillance Centre Universidad Complutense de Madrid Madrid Spain
- Departamento de Sanidad Animal Facultad de Veterinaria Universidad Complutense de Madrid Madrid Spain
| | - Andres Perez
- Department of Veterinary Population Medicine University of Minnesota St. Paul Minnesota
| | - Olga Minguez
- Dirección General de Producción Agropecuaria e Infraestructuras Agrarias Consejería de Agricultura y Ganadería de la Junta de Castilla y León Valladolid Spain
| | - Julio Alvarez
- VISAVET Health Surveillance Centre Universidad Complutense de Madrid Madrid Spain
- Department of Veterinary Population Medicine University of Minnesota St. Paul Minnesota
- Departamento de Sanidad Animal Facultad de Veterinaria Universidad Complutense de Madrid Madrid Spain
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50
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Abstract
In this study, we sought to apply recent advances in informetrics to the analysis of literature related to big data in the field of medicine. Our aim was to elucidate research trends, identify knowledge clusters and decipher the links between them. We also sought to ascertain the theories most commonly applied in the processing of medical data and identify potential research gaps. The most important keywords over the last 10 years have been ‘big data’, ‘data mining’, ‘healthcare’, ‘cloud computing’, ‘machine learning’ and ‘electronic health record system’. These could be viewed as the core issues of research associated with big data in the field of medicine. We also identified a number of keywords that are expected to play a pivotal role in this field in the near future. These terms include the ‘internet of things’, ‘e-health’, ‘sensors’, ‘predictive modeling’, ‘quantified self’, ‘smart city’, ‘wearable device’ and ‘m-health’. Finally, we compiled co-word networks indicating the degree of connectivity between keywords, for use in locating knowledge gaps by revealing the overall context of issues commonly encountered when investigating big data. Our findings form a solid academic foundation on which to develop medical technologies, managerial strategies and theory related to big data.
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Affiliation(s)
- Wen-Chin Hsu
- Department of Information Management, National Central University, Taiwan (R.O.C.)
| | - Jia-Huan Li
- Department of Information Management, National Central University, Taiwan (R.O.C.)
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