What has molecular epidemiology ever done for wildlife disease research? Past contributions and future directions

Benton, Clare H.; Delahay, Richard J.; Trewby, Hannah; Hodgson, David J.

doi:10.1007/s10344-014-0882-4

Cited by 18 publications

(15 citation statements)

References 125 publications

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“…Historically, viral causes of disease in reptiles were likely to be under-reported for many reasons including the cost and bioinformatics support required to investigate novel diseases using NGS technologies, as well as co-infections with microbial species, and poor sampling techniques that obscure the true aetiologic agent [6]. Pathogen discovery tools, which are not reliant on targeting a specific organism, are increasingly being used in wildlife disease investigations [10,17,53,54], although uptake is considered slow comparative to health research in humans and domestic animals [54]. Thus we anticipate an increase in the number of viruses detected in wildlife taxa that have had few viral disease investigations, such as lizards, compared to well-studied mammals such as bats, rodents and primates where their capacity to host zoonotic pathogens arguably provides public health drivers for research as well as funding incentives [55,56].…”

Section: Discussionmentioning

confidence: 99%

Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa)

O’Dea

Jackson

et al. 2016

PLoS ONE

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A respiratory disease syndrome has been observed in large numbers of wild shingleback lizards (Tiliqua rugosa) admitted to wildlife care facilities in the Perth metropolitan region of Western Australia. Mortality rates are reportedly high without supportive treatment and care. Here we used next generation sequencing techniques to screen affected and unaffected individuals admitted to Kanyana Wildlife Rehabilitation Centre in Perth between April and December 2015, with the resultant discovery of a novel nidovirus significantly associated with cases of respiratory disease according to a case definition based on clinical signs. Interestingly this virus was also found in 12% of apparently healthy individuals, which may reflect testing during the incubation period or a carrier status, or it may be that this agent is not causative in the disease process. This is the first report of a nidovirus in lizards globally. In addition to detection of this virus, characterisation of a 23,832 nt segment of the viral genome revealed the presence of characteristic nidoviral genomic elements providing phylogenetic support for the inclusion of this virus in a novel genus alongside Ball Python nidovirus, within the Torovirinae sub-family of the Coronaviridae. This study highlights the importance of next generation sequencing technologies to detect and describe emerging infectious diseases in wildlife species, as well as the importance of rehabilitation centres to enhance early detection mechanisms through passive and targeted health surveillance. Further development of diagnostic tools from these findings will aid in detection and control of this agent across Australia, and potentially in wild lizard populations globally.

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Section: Discussionmentioning

confidence: 99%

Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa)

O’Dea

Jackson

et al. 2016

PLoS ONE

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“…While whole-genome sequencing (WGS) is increasingly being applied to human bacterial pathogens and is offering profound insight into their biology (21,22), few studies have utilized this approach for the study of bacterial infections in wildlife (23). Limited WGS data from passerine-derived S. Typhimurium isolates are available, and such information would offer considerable insight into the epidemiology and disease pathogenesis of these strains.…”

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confidence: 99%

Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales

Mather

Lawson

Pinna

et al. 2016

Appl Environ Microbiol

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Passerine salmonellosis is a well-recognized disease of birds in the order Passeriformes, which includes common songbirds such as finches and sparrows, caused by infection with Salmonella enterica serovar Typhimurium. Previous research has suggested that some subtypes of S. Typhimurium-definitive phage types (DTs) 40, 56 variant, and 160 -are host adapted to passerines and that these birds may represent a reservoir of infection for humans and other animals. Here, we have used the whole-genome sequences of 11 isolates from British passerines, five isolates of similar DTs from humans and a domestic cat, and previously published S. Typhimurium genomes that include similar DTs from other hosts to investigate the phylogenetic relatedness of passerine salmonellae to other S. Typhimurium isolates and investigate possible genetic features of the distinct disease pathogenesis of S. Typhimurium in passerines. Our results demonstrate that the 11 passerine isolates and 13 other isolates, including those from nonpasserine hosts, were genetically closely related, with a median pairwise single nucleotide polymorphism (SNP) difference of 130 SNPs. These 24 isolates did not carry antimicrobial resistance genetic determinants or the S. Typhimurium virulence plasmid. Although our study does not provide evidence of Salmonella transmission from passerines to other hosts, our results are consistent with the hypothesis that wild birds represent a potential reservoir of these Salmonella subtypes, and thus, sensible personal hygiene precautions should be taken when feeding or handling garden birds. IMPORTANCEPasserine salmonellosis, caused by certain definitive phage types (DTs) of Salmonella Typhimurium, has been documented as a cause of wild passerine mortality since the 1950s in many countries, often in the vicinity of garden bird feeding stations. To gain better insight into its epidemiology and host-pathogen interactions, we sequenced the genomes of a collection of 11 isolates from wild passerine salmonellosis in England and Wales. Phylogenetic analysis showed these passerine isolates to be closely related to each other and to form a clade that is distinct from other strains of S. Typhimurium, which included a multidrug-resistant isolate from invasive nontyphoidal Salmonella disease that shares the same phage type as several of the passerine isolates. Closely related to wild passerine isolates and within the same clade were four S. Typhimurium isolates from humans as well as isolates from horses, poultry, cattle, an unspecified wild bird, and a domestic cat and dog with similar DTs and/or multilocus sequence types. This suggests the potential for cross-species transmission, and the genome sequences provide a valuable resource to investigate passerine salmonellosis further. P asserine salmonellosis is a well-described disease caused by Salmonella enterica subsp. enterica serovar Typhimurium that has been reported in Europe, North America, Asia, and Australasia, with the earliest reports in the 1950s (1-9). While the disease ...

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“…These PCR‐based methods require knowing which pathogens are likely present, but disease etiology is not always known. Merely detecting the presence of a pathogen is not sufficient for many wildlife disease studies, particularly for understanding epidemiological questions related to disease transmission, rate of infection, dispersal, and evolution (Benton et al ). The foundation for genetic comparison of pathogens is fairly simple: find mutations in conserved nucleotide sequences that can be used to determine how samples are related to each other.…”

Section: Pathogen Detection and Characterizationmentioning

confidence: 99%

Application of genetics and genomics to wildlife epidemiology

et al. 2016

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Wildlife diseases can have significant impacts on wildlife conservation and management. Many of the pathogens that affect wildlife also have important implications for domestic animal and human health. However, management interventions to prevent or control wildlife disease are hampered by uncertainties about the complex interactions between pathogens and free-ranging wildlife. We often lack crucial knowledge about host ecology, pathogen characteristics, and host-pathogen dynamics. The purpose of this review is to familiarize wildlife biologists and managers with the application of genetic and genomic methodologies for investigating pathogen and host biology to better understand and manage wildlife diseases. The genesis of this review was a symposium at the 2013 annual Wildlife Society Conference. We reviewed the scientific literature and used our personal experiences to identify studies that illustrate the application of genetic and genomic methods to advance our understanding of wildlife epidemiology, focusing on recent research, new techniques, and innovative approaches. Using examples from a variety of pathogen types and a broad array of vertebrate taxa, we describe how genetics and genomics can provide tools to detect and characterize pathogens, uncover routes of disease transmission and spread, shed light on the ways that disease susceptibility is influenced by both host and pathogen attributes, and elucidate the impacts of disease on wildlife populations. Genetic and increasingly genomic methodologies will continue to contribute important insights into pathogen and host biology that will aid efforts to assess and mitigate the impacts of wildlife diseases on global health and conservation of biodiversity. ABSTRACT Wildlife diseases can have significant impacts on wildlife conservation and management. Many of the pathogens that affect wildlife also have important implications for domestic animal and human health. However, management interventions to prevent or control wildlife disease are hampered by uncertainties about the complex interactions between pathogens and free-ranging wildlife. We often lack crucial knowledge about host ecology, pathogen characteristics, and host-pathogen dynamics. The purpose of this review is to familiarize wildlife biologists and managers with the application of genetic and genomic methodologies for investigating pathogen and host biology to better understand and manage wildlife diseases. The genesis of this review was a symposium at the 2013 annual Wildlife Society Conference. We reviewed the scientific literature and used our personal experiences to identify studies that illustrate the application of genetic and genomic methods to advance our understanding of wildlife epidemiology, focusing on recent research, new techniques, and innovative approaches. Using examples from a variety of pathogen types and a broad array of vertebrate taxa, we describe how genetics and genomics can provide tools to detect and characterize pathogens, uncover routes of disease transmissio...

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What has molecular epidemiology ever done for wildlife disease research? Past contributions and future directions

Cited by 18 publications

References 125 publications

Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa)

Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa)

Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales

Application of genetics and genomics to wildlife epidemiology

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