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Chew XZ, Cobcroft J, Hutson KS. Fish ectoparasite detection, collection and curation. ADVANCES IN PARASITOLOGY 2024; 125:105-157. [PMID: 39095111 DOI: 10.1016/bs.apar.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Fish parasitology is a dynamic and internationally important discipline with numerous biological, ecological and practical applications. We reviewed optimal fish and parasite sampling methods for key ectoparasite phyla (i.e. Ciliophora, Platyhelminthes, Annelida and Arthropoda) as well as recent advances in molecular detection of ectoparasites in aquatic environments. Ideally, fish capture and anaesthesia as well as parasite recovery methods should be validated to eliminate potential sampling bias and inaccuracy in determining ectoparasite population parameters. There are considerable advantages to working with fresh samples and live parasites, when combined with appropriate fixation methods, as sampling using dead or decaying materials can lead to rapid decomposition of soft-bodied parasites and subsequent challenges for identification. Sampling methods differ between target phyla, and sometimes genera, with optimum techniques largely associated with identification of parasite microhabitat and the method of attachment. International advances in fish parasitology can be achieved through the accession of whole specimens and/or molecular voucher specimens (i.e. hologenophores) in curated collections for further study. This approach is now critical for data quality because of the increased application of environmental DNA (eDNA) for the detection and surveillance of parasites in aquatic environments where the whole organism may be unavailable. Optimal fish parasite sampling methods are emphasised to aid repeatability and reliability of parasitological studies that require accurate biodiversity and impact assessments, as well as precise surveillance and diagnostics.
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Affiliation(s)
- Xian Zhe Chew
- James Cook University Singapore, Singapore City, Singapore
| | - Jennifer Cobcroft
- James Cook University Singapore, Singapore City, Singapore; College of Science and Engineering, Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kate S Hutson
- College of Science and Engineering, Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia; Cawthron Institute, Nelson, New Zealand.
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Hu G, Huang K, Zhou W, Wang R, Zhao W, Zou H, Li W, Wu S, Li M, Wang G. Comparison of droplet digital PCR and real-time quantitative PCR for quantitative detection of the parasitic ciliate Ichthyophthirius multifiliis in the water environment. JOURNAL OF FISH DISEASES 2023; 46:357-367. [PMID: 36606558 DOI: 10.1111/jfd.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Ichthyophthiriasis, caused by the parasitic ciliate Ichthyophthirius multifiliis (Ich), is considered one of the most harmful diseases affecting freshwater fish globally. It can cause mass mortalities of fish in intensive farming systems. In such systems, it is thus necessary to detect and quantify the number of Ich in the water so that control measures can be implemented before Ichthyophthiriasis breaks out. In recent years, molecular diagnostic methods have become increasingly important in aquaculture. Real-time quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) have become robust assays for detecting pathogens. In this study, a set of specific primers and a TaqMan-minor groove binder probe targeting the small-subunit rDNA (SSU rDNA) of Ich were developed. They were used in qPCR and ddPCR assays to compare the performance of these two different methods in quantitatively detecting Ich. After optimizing the reaction conditions, both qPCR and ddPCR assays were found to have high linearity and quantitative correlations for standard plasmid DNA. When used for the detection of Ich eDNA in water samples, the qPCR assay had a wider detection range, making it a suitable method to screen for the prevalence of Ichthyophthiriasis. However, the ddPCR approach had higher sensitivity, which would help provide advance notice of the disease in complex water environmental samples.
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Affiliation(s)
- Guangran Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weitian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runqiu Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Weishan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shangong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Schuster CJ, Murray KN, Sanders JL, Kent ML. Application of an eDNA assay for the detection of Pseudoloma neurophilia (Microsporidia) in zebrafish ( Danio rerio) facilities. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2023; 564:739044. [PMID: 38562455 PMCID: PMC10983818 DOI: 10.1016/j.aquaculture.2022.739044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Environmental DNA (eDNA) water assays are beginning to be implemented for many important pathogens in confined aquaculture systems. Recirculating systems are rapidly being developed for fin fish aquaculture. Zebrafish (Danio rerio) are reared in these systems, and Pseudoloma neurophilia (Microsporidia) represents a serious challenge for zebrafish research facilities. Diagnosis of the pathogen has traditionally used histology or PCR of tissues with lethal sampling. However, with the development of a nonlethal assay to detect P. neurophilia in tank water, facilities will be able to integrate the assay into routine surveillance efforts to couple with their established protocols. Here, we first describe a modified protocol to extract and quantify parasite DNA from the environment for nonlethal detection of P. neurophilia in adult zebrafish populations. Using this modified assay, we then evaluated water samples from a longitudinal experimental infection study, targeting timepoints during initial infection. The parasite was detectable in the water immediately after initial exposure until week 4 post exposure (pe), when the parasite was undetectable until 7 weeks pe. After that time, the parasite was sporadically detected in the water for the 10-month study, likely correlating with the lifecycle of the parasite. Using water samples from the Zebrafish International Resource Center, we also validated the clinical relevance of the assay in a large zebrafish facility. The integration of this assay at ZIRC will significantly compliment surveillance and control efforts for the microsporidian parasite.
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Affiliation(s)
- Corbin J. Schuster
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
- Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403, USA
| | - Katrina N. Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403, USA
| | - Justin L. Sanders
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Michael L. Kent
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
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Schuster CJ, Kent ML, Peterson JT, Sanders JL. MULTI-STATE OCCUPANCY MODEL ESTIMATES PROBABILITY OF DETECTION OF AN AQUATIC PARASITE USING ENVIRONMENTAL DNA: PSEUDOLOMA NEUROPHILIA IN ZEBRAFISH AQUARIA. J Parasitol 2022; 108:527-538. [PMID: 36326809 PMCID: PMC9811945 DOI: 10.1645/22-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Detecting the presence of important parasites within a host and its environment is critical to understanding the dynamics that influence a pathogen's ability to persist, while accurate detection is also essential for the implementation of effective control strategies. Pseudoloma neurophilia is the most common pathogen reported in zebrafish (Danio rerio) research facilities. The only assays currently available for P. neurophilia are through lethal sampling, often requiring euthanasia of the entire population for accurate estimates of prevalence in small populations. We present a non-lethal screening method to detect P. neurophilia in tank water based on the detection of environmental DNA (eDNA) from this microsporidium, using a previously developed qPCR assay that was adapted to the digital PCR (dPCR) platform to complement current surveillance protocols. Using the generated dPCR data, a multi-state occupancy model was also implemented to predict the probability of detecting the microsporidium in tank water under different flow regimes and pathogen prevalence. The occupancy model revealed that samples collected in static conditions were more informative than samples collected from flow-through conditions, with a probability of detection at 80% and 47%, respectively. There was also a positive correlation between the frequency of detection in water and prevalence in fish based on qPCR.
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Affiliation(s)
- Corbin J Schuster
- Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, Oregon 97331
- Zebrafish International Resource Center, University of Oregon, 1100 Johnson Lane, Eugene, Oregon 97403
| | - Michael L Kent
- Department of Microbiology, Oregon State University, 2820 SW Campus Way, Corvallis, Oregon 97331
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, 700 SW 30th St., Corvallis, Oregon 97331
| | - James T Peterson
- U.S. Geological Survey, Oregon Cooperative Fish and Wildlife Unit, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, 2820 SW Campus Way, Corvallis, Oregon 97331
| | - Justin L Sanders
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, 700 SW 30th St., Corvallis, Oregon 97331
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Shea D, Bateman A, Li S, Tabata A, Schulze A, Mordecai G, Ogston L, Volpe JP, Neil Frazer L, Connors B, Miller KM, Short S, Krkošek M. Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms. Proc Biol Sci 2020; 287:20202010. [PMID: 33081614 PMCID: PMC7661312 DOI: 10.1098/rspb.2020.2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.
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Affiliation(s)
- Dylan Shea
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Andrew Bateman
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada.,Pacific Salmon Foundation, Vancouver, British Columbia, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Angela Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsey Ogston
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - John P Volpe
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, Canada
| | - L Neil Frazer
- Department of Earth Sciences, University of Hawaii at Mānoa, Honolulu, Hawaii, Canada
| | - Brendan Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, British Columbia, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Steven Short
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, British Columbia, Canada
| | - Martin Krkošek
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada
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