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Bass D, Christison KW, Stentiford GD, Cook LSJ, Hartikainen H. Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology. Trends Parasitol 2023; 39:285-304. [PMID: 36759269 DOI: 10.1016/j.pt.2022.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 02/11/2023]
Abstract
Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host-symbiont-environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.
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Affiliation(s)
- David Bass
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Kevin W Christison
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa; Department of Forestry, Fisheries and the Environment, Private Bag X2, Vlaeberg, 8012, South Africa
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - Lauren S J Cook
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, UK
| | - Hanna Hartikainen
- University of Nottingham, School of Life Sciences, University Park, NG7 2RD, Nottingham, UK
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2
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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3
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Schilling AK, Mazzamuto MV, Romeo C. A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What's New? Animals (Basel) 2022; 12:1719. [PMID: 35804619 PMCID: PMC9265025 DOI: 10.3390/ani12131719] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
Abstract
In the last decades, wildlife diseases and the health status of animal populations have gained increasing attention from the scientific community as part of a One Health framework. Furthermore, the need for non-invasive sampling methods with a minimal impact on wildlife has become paramount in complying with modern ethical standards and regulations, and to collect high-quality and unbiased data. We analysed the publication trends on non-invasive sampling in wildlife health and disease research and offer a comprehensive review on the different samples that can be collected non-invasively. We retrieved 272 articles spanning from 1998 to 2021, with a rapid increase in number from 2010. Thirty-nine percent of the papers were focussed on diseases, 58% on other health-related topics, and 3% on both. Stress and other physiological parameters were the most addressed research topics, followed by viruses, helminths, and bacterial infections. Terrestrial mammals accounted for 75% of all publications, and faeces were the most widely used sample. Our review of the sampling materials and collection methods highlights that, although the use of some types of samples for specific applications is now consolidated, others are perhaps still underutilised and new technologies may offer future opportunities for an even wider use of non-invasively collected samples.
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Affiliation(s)
- Anna-Katarina Schilling
- Previously Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK;
| | - Maria Vittoria Mazzamuto
- Haub School of Environment and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, USA;
- Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Bianchi 9, 25124 Brescia, Italy
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4
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Dayaram A, Seeber PA, Greenwood AD. Environmental Detection and Potential Transmission of Equine Herpesviruses. Pathogens 2021; 10:pathogens10040423. [PMID: 33916280 PMCID: PMC8066653 DOI: 10.3390/pathogens10040423] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Equine herpesviruses (EHV) are a major health concern for domestic and wild equids and represent one of the most economically important disease agents of horses. Most known EHVs are transmitted directly between individuals as a result of direct exposure to exudates and aerosols. However, accumulating evidence suggests that environmental transmission may play a role including air, water, and fomites. Here, we reviewed studies on environmental stability and transmission of EHVs, which may influence viral dynamics and the use of environmental samples for monitoring EHV shedding.
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Affiliation(s)
- Anisha Dayaram
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany; (A.D.); (P.A.S.)
- Institute of Neurophysiology, Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter A. Seeber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany; (A.D.); (P.A.S.)
- Limnological Institute, University of Konstanz, 78464 Konstanz, Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany; (A.D.); (P.A.S.)
- Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Correspondence: ; Tel.: +49-(0)30-5168255
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5
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Seeber PA, Morrison T, Ortega A, East ML, Greenwood AD, Czirják GÁ. Immune differences in captive and free-ranging zebras (Equus zebra and E. quagga). Mamm Biol 2020. [DOI: 10.1007/s42991-020-00006-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractWild mammals in ex situ captivity experience substantially different environmental conditions compared to free-ranging conspecifics, e.g., in terms of diet, climatic conditions, social factors, movement space, and direct anthropogenic disturbance. Moreover, animals in captivity frequently undergo management interventions such as medical treatments which may influence pathogen pressure. Captivity is known to affect immunological responses in some terrestrial and marine mammals; however, it is unclear whether this can be generalized to other taxa. Furthermore, little is known about how energetically costly life history stages such as lactation influence the immune system in wildlife. We measured expression of components of the constitutive and induced innate immunity and of the adaptive immune system in plains and mountain zebras (Equus quagga and E. zebra), including lactating and non-lactating individuals. As a proxy for general immune function, we screened for lytic equine herpesvirus (EHV) infection, a common and often latent pathogen which is reactivated in response to stress and immune challenge. Both energetically cheap markers of the constitutive innate immunity were lower in captive than in wild zebras, whereas energetically costly markers of the induced innate immunity were more highly expressed in captive zebras. Lactation was associated with higher titers of natural antibodies and lysozyme. Lytic EHV infection was not significantly correlated with any of the measured immune markers. Our results suggest that captivity and lactation may influence immune functions in zebra mares.
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Seeber PA, McEwen GK, Löber U, Förster DW, East ML, Melzheimer J, Greenwood AD. Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes. Mol Ecol Resour 2019; 19:1486-1496. [PMID: 31349392 DOI: 10.1111/1755-0998.13069] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/15/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022]
Abstract
Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.
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Affiliation(s)
- Peter Andreas Seeber
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gayle K McEwen
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany.,Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
| | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marion Linda East
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Jörg Melzheimer
- Department of Evolutionary Ecology, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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7
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Noninvasive Detection of Equid Herpesviruses in Fecal Samples. Appl Environ Microbiol 2019; 85:AEM.02234-18. [PMID: 30446563 DOI: 10.1128/aem.02234-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/09/2018] [Indexed: 12/23/2022] Open
Abstract
Equid herpesviruses (EHVs) are pathogens of equid and nonequid hosts that can cause disease and fatalities in captivity and in the wild. EHVs establish latent infections but can reactivate, and most EHVs are shed via the nasal passage. Therefore, nasal swabs are generally used for EHV monitoring. However, invasive sampling of wild equids is difficult. While feces is a commonly used substrate for detecting other pathogens, to our knowledge, EHVs have never been detected in feces of naturally infected equids. We systematically tested zebra feces for EHV presence by (i) establishing nested PCR conditions for fecal DNA extracts, (ii) controlling for environmental EHV contamination, and (iii) large-scale testing on a free-ranging zebra population. A dilution minimizing inhibition while maximizing viral DNA concentrations was determined in captive Grévy's zebra (Equus grevyi) fecal samples from individuals shedding EHV nasally. Sixteen of 42 fecal samples (38%) were EHV positive. To demonstrate that the EHV positivity was not a result of environmental contamination, rectal swabs of wild zebras were screened (n = 18 [Equus quagga and E. zebra]), and 50% were EHV positive, indicating that the source of EHV in feces is likely the intestinal mucosa and not postdefecation contamination. Out of 270 fecal samples of wild zebras, 26% were EHV positive. Quantitative PCRs showed that the amount of virus DNA in feces was not significantly smaller than that in other samples. In summary, fecal sampling facilitates large-scale screening and may be useful to noninvasively investigate phylogenetic EHV diversity in wild and domestic equids.IMPORTANCE Equid herpesviruses (EHVs) establish latent infections, and many EHVs are shed and transmitted via nasal discharge primarily through droplet and aerosol infection. Obtaining nasal swabs and other invasive samples from wildlife is often not possible without capture and physical restraint of individuals, which are resource intensive and a health risk for the captured animals. Fecal EHV shedding has never been demonstrated for naturally infected equids. We established the conditions for fecal EHV screening, and our results suggest that testing fecal samples is an effective noninvasive approach for monitoring acute EHV shedding in equids.
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8
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Seeber PA, Quintard B, Sicks F, Dehnhard M, Greenwood AD, Franz M. Environmental stressors may cause equine herpesvirus reactivation in captive Grévy's zebras ( Equus grevyi). PeerJ 2018; 6:e5422. [PMID: 30155350 PMCID: PMC6109370 DOI: 10.7717/peerj.5422] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022] Open
Abstract
Equine Herpesviruses (EHV) are common and often latent pathogens of equids which can cause fatalities when transmitted to non-equids. Stress and elevated glucocorticoids have been associated with EHV reactivation in domestic horses, but little is known about the correlation between stress and viral reactivation in wild equids. We investigated the effect of an environmental stressor (social group restructuring following a translocation event) on EHV reactivation in captive Grévy's zebras (Equus grevyi). A mare was translocated by road transport from Zoo Mulhouse, France, to join a resident group of three mares in Tierpark Berlin, Germany. We used an indirect sampling method to assess the frequency of EHV shedding for 14 days immediately after the translocation event (termed the 'experimental period'). The results were compared with those from two control periods, one preceding and one subsequent to the experimental period. In addition, we measured fecal glucocorticoid metabolite (fGCM) concentrations daily in all individuals from 6 days before, to 14 days after translocation. We found significantly higher EHV shedding frequencies during the experimental period, compared to each of the two control periods. All animals showed significantly elevated fGCM concentrations, compared to fGCM levels before translocation. Finally, we found that an increase in fGCM concentration was significantly associated with an increased likelihood of EHV shedding. Although the small number of animals in the study limits the conclusions that can be drawn from the study, taken together, our results support the hypothesis that environmental stressors induce viral reactivation in wild equids. Our results suggest that potentials stressors such as group restructuring and translocation should be considered in the management of zoological collections to reduce the risk of fatal EHV infections in novel hosts. Moreover, environmental stressors may play an important role in EHV reactivation and spread in wild equid populations.
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Affiliation(s)
- Peter A. Seeber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | | | - Martin Dehnhard
- Department of Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Mathias Franz
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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9
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Costantini D, Seeber PA, Soilemetzidou SE, Azab W, Bohner J, Buuveibaatar B, Czirják GÁ, East ML, Greunz EM, Kaczensky P, Lamglait B, Melzheimer J, Uiseb K, Ortega A, Osterrieder N, Sandgreen DM, Simon M, Walzer C, Greenwood AD. Physiological costs of infection: herpesvirus replication is linked to blood oxidative stress in equids. Sci Rep 2018; 8:10347. [PMID: 29985431 PMCID: PMC6037783 DOI: 10.1038/s41598-018-28688-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/22/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses may have a dramatic impact on the health of their animal hosts. The patho-physiological mechanisms underlying viral infections in animals are, however, not well understood. It is increasingly recognized that oxidative stress may be a major physiological cost of viral infections. Here we compare three blood-based markers of oxidative status in herpes positive and negative individuals of the domestic horse (Equus ferus caballus) and of both captive and free-ranging Mongolian khulan (Equus hemionus hemionus) and plains zebra (Equus quagga). Herpes positive free-ranging animals had significantly more protein oxidative damage and lower glutathione peroxidase (antioxidant enzyme) than negative ones, providing correlative support for a link between oxidative stress and herpesvirus infection in free-living equids. Conversely, we found weak evidence for oxidative stress in herpes positive captive animals. Hence our work indicates that environment (captive versus free living) might affect the physiological response of equids to herpesvirus infection. The Mongolian khulan and the plains zebra are currently classified as near threatened by the International Union for Conservation of Nature. Thus, understanding health impacts of pathogens on these species is critical to maintaining viable captive and wild populations.
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Affiliation(s)
- David Costantini
- UMR 7221 CNRS/MNHN, Muséum National d'Histoire Naturelle, Sorbonne Universités, 7 rue Cuvier, 75005, Paris, France.
- Institute for Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, Scotland, UK.
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
| | - Peter A Seeber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Sanatana-Eirini Soilemetzidou
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Walid Azab
- Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Julia Bohner
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | | | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Marion L East
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Eva Maria Greunz
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
- Parc Zoologique de Thoiry, Rue du Pavillon de Montreuil, 78770, Thoiry, France
| | - Petra Kaczensky
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstrasse 1, A-1160, Vienna, Austria
- Norwegian Institute for Nature Research - NINA, Sluppen, NO-7485, Trondheim, Norway
| | - Benjamin Lamglait
- Faculty of Veterinary Medicine, Université de Montréal, 3200 Rue Sicotte, Saint-Hyacinthe, Québec, J2S 2N4, Canada
- Réserve Africaine de Sigean, 19 Chemin Hameau du Lac, RD 6009, 11130, Sigean, France
| | - Jörg Melzheimer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Kenneth Uiseb
- Ministry of Environment and Tourism, Private Bag 13301, Windhoek, Namibia
| | - Alix Ortega
- Réserve Africaine de Sigean, 19 Chemin Hameau du Lac, RD 6009, 11130, Sigean, France
| | - Nikolaus Osterrieder
- Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | | | - Marie Simon
- Parc Zoologique de Thoiry, Rue du Pavillon de Montreuil, 78770, Thoiry, France
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstrasse 1, A-1160, Vienna, Austria
- Wildlife Conservation Society, 2300 Southern Blvd., 10460, Bronx, New York, USA
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Oertzenweg 19, Berlin, 14163, Germany
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