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Lin D, Sutherland D, Aninta SI, Louie N, Nip KM, Li C, Yanai A, Coombe L, Warren RL, Helbing CC, Hoang LMN, Birol I. Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage. Antibiotics (Basel) 2022; 11:antibiotics11070952. [PMID: 35884206 PMCID: PMC9312091 DOI: 10.3390/antibiotics11070952] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Antibiotic resistance is a global health crisis increasing in prevalence every day. To combat this crisis, alternative antimicrobial therapeutics are urgently needed. Antimicrobial peptides (AMPs), a family of short defense proteins, are produced naturally by all organisms and hold great potential as effective alternatives to small molecule antibiotics. Here, we present rAMPage, a scalable bioinformatics discovery platform for identifying AMP sequences from RNA sequencing (RNA-seq) datasets. In our study, we demonstrate the utility and scalability of rAMPage, running it on 84 publicly available RNA-seq datasets from 75 amphibian and insect species—species known to have rich AMP repertoires. Across these datasets, we identified 1137 putative AMPs, 1024 of which were deemed novel by a homology search in cataloged AMPs in public databases. We selected 21 peptide sequences from this set for antimicrobial susceptibility testing against Escherichia coli and Staphylococcus aureus and observed that seven of them have high antimicrobial activity. Our study illustrates how in silico methods such as rAMPage can enable the fast and efficient discovery of novel antimicrobial peptides as an effective first step in the strenuous process of antimicrobial drug development.
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Affiliation(s)
- Diana Lin
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Darcy Sutherland
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, Canada;
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sambina Islam Aninta
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Nathan Louie
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Ka Ming Nip
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Chenkai Li
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Anat Yanai
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - René L. Warren
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
| | - Caren C. Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada;
| | - Linda M. N. Hoang
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, Canada;
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Inanc Birol
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada; (D.L.); (D.S.); (S.I.A.); (N.L.); (K.M.N.); (C.L.); (A.Y.); (L.C.); (R.L.W.)
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, BC V6Z R4R, Canada;
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence:
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Brannelly LA, Webb RJ, Jiang Z, Berger L, Skerratt LF, Grogan LF. Declining amphibians might be evolving increased reproductive effort in the face of devastating disease. Evolution 2021; 75:2555-2567. [PMID: 34383313 DOI: 10.1111/evo.14327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/08/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022]
Abstract
The devastating infectious disease chytridiomycosis has caused declines of amphibians across the globe, yet some populations are persisting and even recovering. One understudied effect of wildlife disease is changes in reproductive effort. Here, we aimed to understand if the disease has plastic effects on reproduction and if reproductive effort could evolve with disease endemism. We compared the effects of experimental pathogen exposure (trait plasticity) and population-level disease history (evolution in trait baseline) on reproductive effort using gametogenesis as a proxy in the declining and endangered frog Litoria verreauxii alpina. We found that unexposed males from disease-endemic populations had higher reproductive effort, which is consistent with an evolutionary response to chytridiomycosis. We also found evidence of trait plasticity, where males and females were affected differently by infection: pathogen exposed males had higher reproductive effort (larger testes), whereas females had reduced reproductive effort (smaller and fewer developed eggs) regardless of the population of origin. Infectious diseases can cause plastic changes in the reproductive effort at an individual level, and population-level disease exposure can result in changes to baseline reproductive effort; therefore, individual- and population-level effects of disease should be considered when designing management and conservation programs for threatened and declining species.
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Affiliation(s)
- Laura A Brannelly
- One Health Research Group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Rebecca J Webb
- One Health Research Group, School of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Zhixuan Jiang
- One Health Research Group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Lee Berger
- One Health Research Group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Lee F Skerratt
- One Health Research Group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Laura F Grogan
- Environmental Futures Research Institute, Griffith University, Southport, Queensland, Australia.,Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
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Grogan LF, Humphries JE, Robert J, Lanctôt CM, Nock CJ, Newell DA, McCallum HI. Immunological Aspects of Chytridiomycosis. J Fungi (Basel) 2020; 6:jof6040234. [PMID: 33086692 PMCID: PMC7712659 DOI: 10.3390/jof6040234] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Amphibians are currently the most threatened vertebrate class, with the disease chytridiomycosis being a major contributor to their global declines. Chytridiomycosis is a frequently fatal skin disease caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). The severity and extent of the impact of the infection caused by these pathogens across modern Amphibia are unprecedented in the history of vertebrate infectious diseases. The immune system of amphibians is thought to be largely similar to that of other jawed vertebrates, such as mammals. However, amphibian hosts are both ectothermic and water-dependent, which are characteristics favouring fungal proliferation. Although amphibians possess robust constitutive host defences, Bd/Bsal replicate within host cells once these defences have been breached. Intracellular fungal localisation may contribute to evasion of the induced innate immune response. Increasing evidence suggests that once the innate defences are surpassed, fungal virulence factors suppress the targeted adaptive immune responses whilst promoting an ineffectual inflammatory cascade, resulting in immunopathology and systemic metabolic disruption. Thus, although infections are contained within the integument, crucial homeostatic processes become compromised, leading to mortality. In this paper, we present an integrated synthesis of amphibian post-metamorphic immunological responses and the corresponding outcomes of infection with Bd, focusing on recent developments within the field and highlighting future directions.
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Affiliation(s)
- Laura F. Grogan
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Southport, QLD 4222, Australia;
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia; (J.E.H.); (D.A.N.)
- Correspondence:
| | - Josephine E. Humphries
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia; (J.E.H.); (D.A.N.)
| | - Jacques Robert
- University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Chantal M. Lanctôt
- Australian Rivers Institute, Griffith University, Southport, QLD 4222, Australia;
| | - Catherine J. Nock
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia;
| | - David A. Newell
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia; (J.E.H.); (D.A.N.)
| | - Hamish I. McCallum
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Southport, QLD 4222, Australia;
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Brannelly LA, McCallum HI, Grogan LF, Briggs CJ, Ribas MP, Hollanders M, Sasso T, Familiar López M, Newell DA, Kilpatrick AM. Mechanisms underlying host persistence following amphibian disease emergence determine appropriate management strategies. Ecol Lett 2020; 24:130-148. [PMID: 33067922 DOI: 10.1111/ele.13621] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022]
Abstract
Emerging infectious diseases have caused many species declines, changes in communities and even extinctions. There are also many species that persist following devastating declines due to disease. The broad mechanisms that enable host persistence following declines include evolution of resistance or tolerance, changes in immunity and behaviour, compensatory recruitment, pathogen attenuation, environmental refugia, density-dependent transmission and changes in community composition. Here we examine the case of chytridiomycosis, the most important wildlife disease of the past century. We review the full breadth of mechanisms allowing host persistence, and synthesise research on host, pathogen, environmental and community factors driving persistence following chytridiomycosis-related declines and overview the current evidence and the information required to support each mechanism. We found that for most species the mechanisms facilitating persistence have not been identified. We illustrate how the mechanisms that drive long-term host population dynamics determine the most effective conservation management strategies. Therefore, understanding mechanisms of host persistence is important because many species continue to be threatened by disease, some of which will require intervention. The conceptual framework we describe is broadly applicable to other novel disease systems.
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Affiliation(s)
- Laura A Brannelly
- Veterinary BioSciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Vic, 3030, Australia
| | - Hamish I McCallum
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld., 4111, Australia
| | - Laura F Grogan
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld., 4111, Australia.,Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Cheryl J Briggs
- Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Maria P Ribas
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia.,Wildlife Conservation Medicine Research Group, Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Matthijs Hollanders
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Thais Sasso
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld., 4111, Australia
| | - Mariel Familiar López
- School of Environment and Sciences, Griffith University, Gold Coast, Qld., 4215, Australia
| | - David A Newell
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Auston M Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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The Influence of Human Interference on Zooplankton and Fungal Diversity in Poyang Lake Watershed in China. DIVERSITY 2020. [DOI: 10.3390/d12080296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Poyang water system in Jiangxi Province, China, is important for floodwater storage, diversity maintenance, and the economy of the Poyang Lake watershed. In recent years, pollution has destroyed the ecosystem and impacted human health and the related economy. The water quality of the Poyang Lake watershed and the impact of human interference must be assessed. Conventional analysis and high-throughput sequencing were used to evaluate the structure of both zooplankton and fungi in six sub-lakes of the Poyang Lake watershed under different anthropogenic influences. The sub-lakes included were Dahuchi Lake (in natural preserve, DHC), Shahu Lake (in natural reserve, SH), Nanhu Lake (out of natural preserve, NH), Zhelinhu Lake (artificial reservoir, ZLH), Sixiahu Lake (agricultural lake artificially isolated from Poyang Lake, SXH), and Qianhu Lake (urban lake, QH). The densities and biomass of the zooplankton in DHC, SH, NH were higher compared with those in SXH, ZLH and QH (p < 0.05). Zooplankton distribution of SXH was the most strongly associated with total nitrogen (TN), total phosphorus (TP) and chlorophyll a (Chl a), while QH was highly associated with pH, conductivity (Cond), and water temperature (WT). For fungal diversity, a large number of beneficial fungi, Basidiomycota (phylum level) and Massarina (genus level) were obtained from DHC (55.3% and 27.5%, respectively), SH (54.4% and 28.9%, respectively), and NH (48.6% and 1.4%, respectively), while a large number of pathogenic Chytridiomycota (at phylum level) were identified from SXH (21.0%), ZLH (5.5%), and QH (7.5%). Manmade pollutants have impacted the natural hydrology and water quality and promoted variation between the zooplankton and fungi in the six sub-lakes, reducing the relative abundance of beneficial fungi and increasing the number of pathogens in the environment, which threatens human health and economic production. Understanding the diversity among the zooplankton and fungi in the six sub-lakes of the Poyang Lake watershed may help guide future water management practices.
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Claytor SC, Gummer JPA, Grogan LF, Skerratt LF, Webb RJ, Brannelly LA, Berger L, Roberts AA. Susceptibility of frogs to chytridiomycosis correlates with increased levels of immunomodulatory serotonin in the skin. Cell Microbiol 2019; 21:e13089. [PMID: 31373151 DOI: 10.1111/cmi.13089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/03/2019] [Accepted: 07/16/2019] [Indexed: 11/28/2022]
Abstract
Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a skin disease responsible for the global decline of amphibians. Frog species and populations can vary in susceptibility, but this phenomenon remains poorly understood. Here, we investigated serotonin in the skin of infected and uninfected frogs. In more susceptible frog populations, skin serotonin rose with increasing infection intensity, but decreased in later stages of the disease. The more resistant population maintained a basal level of skin serotonin. Serotonin inhibited both Bd sporangial growth and Jurkat lymphocyte proliferation in vitro. However, serotonin accumulates in skin granular glands, and this compartmentalisation may prevent inhibition of Bd growth in vivo. We suggest that skin serotonin increases in susceptible frogs due to pathogen excretion of precursor tryptophan, but that resistant frogs are able to control the levels of serotonin. Overall, the immunosuppressive effects of serotonin may contribute to the susceptibility of frogs to chytridiomycosis.
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Affiliation(s)
- Sieara C Claytor
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Joel P A Gummer
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, Australia.,Metabolomics Australia, Western Australia Node, Murdoch University, Perth, Australia
| | - Laura F Grogan
- Griffith Wildlife Disease Ecology Group, Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan, Australia
| | - Lee F Skerratt
- One Health Research Group, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, Australia
| | - Rebecca J Webb
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Laura A Brannelly
- One Health Research Group, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, Australia
| | - Lee Berger
- One Health Research Group, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, Australia
| | - Alexandra A Roberts
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
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Chytridiomycosis causes catastrophic organism-wide metabolic dysregulation including profound failure of cellular energy pathways. Sci Rep 2018; 8:8188. [PMID: 29844538 PMCID: PMC5974026 DOI: 10.1038/s41598-018-26427-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023] Open
Abstract
Chytridiomycosis is among several recently emerged fungal diseases of wildlife that have caused decline or extinction of naïve populations. Despite recent advances in understanding pathogenesis, host response to infection remains poorly understood. Here we modelled a total of 162 metabolites across skin and liver tissues of 61 frogs from four populations (three long-exposed and one naïve to the fungus) of the Australian alpine tree frog (Litoria verreauxii alpina) throughout a longitudinal exposure experiment involving both infected and negative control individuals. We found that chytridiomycosis dramatically altered the organism-wide metabolism of clinically diseased frogs. Chytridiomycosis caused catastrophic failure of normal homeostatic mechanisms (interruption of biosynthetic and degradation metabolic pathways), and pronounced dysregulation of cellular energy metabolism. Key intermediates of the tricarboxylic acid cycle were markedly depleted, including in particular α-ketoglutarate and glutamate that together constitute a key nutrient pathway for immune processes. This study was the first to apply a non-targeted metabolomics approach to a fungal wildlife disease and specifically to dissect the host-pathogen interface of Bd-infected frogs. The patterns of metabolite accumulation we have identified reveal whole-body metabolic dysfunction induced by a fungal skin infection, and these findings have broad relevance for other fungal diseases.
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Grogan LF, Cashins SD, Skerratt LF, Berger L, McFadden MS, Harlow P, Hunter DA, Scheele BC, Mulvenna J. Evolution of resistance to chytridiomycosis is associated with a robust early immune response. Mol Ecol 2018; 27:919-934. [DOI: 10.1111/mec.14493] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/30/2017] [Accepted: 09/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Laura F. Grogan
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
- Griffith Wildlife Disease Ecology Group Environmental Futures Research Institute School of Environment Griffith University Nathan QLD Australia
- Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane QLD Australia
| | - Scott D. Cashins
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
| | - Lee F. Skerratt
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
| | - Lee Berger
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
| | | | - Peter Harlow
- Taronga Conservation Society Australia Mosman NSW Australia
| | - David A. Hunter
- Ecosystems and Threatened Species South West Region Office of Environment and Heritage NSW Department of Premier and Cabinet Queanbeyan NSW Australia
| | - Ben C. Scheele
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville QLD Australia
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
| | - Jason Mulvenna
- Genetics and Computational Biology QIMR Berghofer Medical Research Institute Brisbane QLD Australia
- School of Biomedical Sciences The University of Queensland Brisbane QLD Australia
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