1
|
Shahi N, Prasartset T, Surachetpong W. A specific and sensitive droplet digital polymerase chain reaction assay for the detection of tilapia lake virus in fish tissue and environmental samples. JOURNAL OF FISH DISEASES 2023; 46:957-966. [PMID: 37294665 DOI: 10.1111/jfd.13816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/11/2023]
Abstract
Tilapia lake virus (TiLV) causes high mortality in farmed and wild tilapia in various countries. We developed a highly specific and sensitive droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify TiLV. The ddPCR assay could detect the virus at a lower threshold than the reverse transcription-quantitative polymerase reaction (RT-qPCR) method, and the sensitivity of the ddPCR assay was 10-fold higher. The diagnostic sensitivity and specificity of the ddPCR assay were 100% and did not cross-react with tilapia tissues infected with Tilapia parvovirus, Infectious spleen and kidney necrosis virus, Aeromonas hydrophila, Streptococcus agalactiae, S. iniae and Francisella noatunensis. The assay reproducibility was demonstrated by a high correlation coefficient of 0.998, and the inter-assay coefficients of variability indicated that the ddPCR assay exhibited low variability within and between measurements. The detection limit of the TiLV ddPCR assay was 100 fg cDNA, which is equal to 3.3 copies of TiLV. Furthermore, the ddPCR assay could detect TiLV in mucus, water and infected tissue samples and the lowest copy number of TiLV detected in water samples by the ddPCR assay was 7.9 ± 0.99 copies/reaction The results of the clinical samples tested for TiLV revealed that the ddPCR assay had a relatively higher detection rate than the RT-qPCR method. Overall, the ddPCR method offers a highly promising approach for the absolute quantification of TiLV in carrier fish and samples from the environment with low viral concentrations.
Collapse
Affiliation(s)
- Neetu Shahi
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Tharinthon Prasartset
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
2
|
Carella F, Palić D, Šarić T, Župan I, Gorgoglione B, Prado P, Andree KB, Giantsis IA, Michaelidis B, Lattos A, Theodorou JA, Luis Barja Perez J, Rodriguez S, Scarpa F, Casu M, Antuofermo E, Sanna D, Otranto D, Panarese R, Iaria C, Marino F, Vico GD. Multipathogen infections and multifactorial pathogenesis involved in noble pen shell ( Pinna nobilis) mass mortality events: Background and current pathologic approaches. Vet Pathol 2023; 60:560-577. [PMID: 37458195 DOI: 10.1177/03009858231186737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Disease outbreaks in several ecologically or commercially important invertebrate marine species have been reported in recent years all over the world. Mass mortality events (MMEs) have affected the noble pen shell (Pinna nobilis), causing its near extinction. Our knowledge of the dynamics of diseases affecting this species is still unclear. Early studies investigating the causative etiological agent focused on a novel protozoan parasite, Haplosporidium pinnae, although further investigations suggested that concurrent polymicrobial infections could have been pivotal in some MMEs, even in the absence of H. pinnae. Indeed, moribund specimens collected during MMEs in Italy, Greece, and Spain demonstrated the presence of a bacteria from within the Mycobacterium simiae complex and, in some cases, species similar to Vibrio mediterranei. The diagnostic processes used for investigation of MMEs are still not standardized and require the expertise of veterinary and para-veterinary pathologists, who could simultaneously evaluate a variety of factors, from clinical signs to environmental conditions. Here, we review the available literature on mortality events in P. nobilis and discuss approaches to define MMEs in P. nobilis. The proposed consensus approach should form the basis for establishing a foundation for future studies aimed at preserving populations in the wild.
Collapse
Affiliation(s)
| | - Dušan Palić
- Ludwig-Maximilians-University Munich, Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | - Sergio Rodriguez
- University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | | | | | | | - Domenico Otranto
- University of Bari, Bari, Italy
- Bu-Ali Sina University, Hamedan, Iran
| | | | | | | | | |
Collapse
|
3
|
Moody NJG, Mohr PG, Williams LM, Cummins DM, Hoad J, Slater J, Valdeter ST, Colling A, Singanallur NB, Gardner IA, Gudkovs N, Crane MSJ. Performance characteristics of two real-time TaqMan polymerase chain reaction assays for the detection of WSSV in clinically diseased and apparently healthy prawns. DISEASES OF AQUATIC ORGANISMS 2022; 150:169-182. [PMID: 35979991 DOI: 10.3354/dao03687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study aimed to generate data on performance characteristics for 2 real-time TaqMan PCR assays (CSIRO and WOAH WSSV qPCRs) for the purposes of (1) detection of white spot syndrome virus (WSSV) in clinically diseased prawns and (2) detection of WSSV in apparently healthy prawns. Analytical sensitivity of both assays was 2 to 20 genome copies per reaction, and analytical specificity was 100% after testing nucleic acid from 9 heterologous prawn pathogens and 4 prawn species. Results obtained after testing more than 20 000 samples in up to 559 runs with the CSIRO WSSV qPCR and up to 293 runs with the WOAH WSSV qPCR demonstrated satisfactory repeatability for both assays. Both assays demonstrated median diagnostic sensitivity (DSe) 100% (95% CI: 94.9-100%) when testing clinically diseased prawns. When 1591 test results from apparently healthy prawns were analysed by Bayesian latent class analysis, median DSe and diagnostic specificity (DSp) were 82.9% (95% probability interval [PI]: 75.0-90.2%) and 99.7% (95% PI: 98.6-99.99%) for the CSIRO WSSV qPCR and 76.8% (95% PI: 68.9-84.9%) and 99.7% (95% PI: 98.7-99.99%) for the WOAH WSSV qPCR. When both assays were interpreted in parallel, median DSe increased to 98.3 (95% PI: 91.6-99.99%), and median DSp decreased slightly to 99.4% (95% PI: 97.9-99.99%). Routine testing of quantified positive controls by laboratories in the Australian laboratory network demonstrated satisfactory reproducibility of the CSIRO WSSV qPCR assay. Both assays demonstrated comparable performance characteristics, and the results contribute to the validation data required in the WOAH validation pathway for the purposes of detection of WSSV in clinically diseased and apparently healthy prawns.
Collapse
Affiliation(s)
- Nicholas J G Moody
- CSIRO Australian Centre for Disease Preparedness, 5 Portarlington Rd, East Geelong, Victoria 3220, Australia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Batts WN, Capps TR, Crosson LM, Powers RL, Breyta R, Purcell MK. Rapid Diagnostic Test to Detect and Discriminate Infectious Hematopoietic Necrosis Virus (IHNV) Genogroups U and M to Aid Management of Pacific Northwest Salmonid Populations. Animals (Basel) 2022; 12:ani12141761. [PMID: 35883308 PMCID: PMC9311590 DOI: 10.3390/ani12141761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious hematopoietic necrosis virus (IHNV) is an acute pathogen of salmonids in North America, Europe, and Asia that is phylogenetically classified into five major virus genogroups (U, M, L, E, and J). The geographic range of the U and M genogroup isolates overlap in the North American Columbia River Basin and Washington Coast region, where these genogroups pose different risks depending on the species of Pacific salmon (Oncorhynchus spp.). For certain management decisions, there is a need to both test for IHNV presence and rapidly determine the genogroup. Herein, we report the development and validation of a U/M multiplex reverse transcription, real-time PCR (RT-rPCR) assay targeting the IHNV nucleocapsid (N) protein gene. The new U/M RT-rPCR is a rapid, sensitive, and repeatable assay capable of specifically discriminating between North American U and M genogroup IHNV isolates. However, one M genogroup isolate obtained from commercially cultured Idaho rainbow trout (O. mykiss) showed reduced sensitivity with the RT-rPCR test, suggesting caution may be warranted before applying RT-rPCR as the sole surveillance test in areas associated with the Idaho trout industry. The new U/M assay had high diagnostic sensitivity (DSe > 94%) and specificity (DSp > 97%) in free-ranging adult Pacific salmon, when assessed relative to cell culture, the widely accepted reference standard, as well as the previously validated universal N RT-rPCR test. The high diagnostic performance of the new U/M assay indicates the test is suitable for surveillance, diagnosis, and confirmation of IHNV in Pacific salmon from the Pacific Northwest regions where the U and M genogroups overlap.
Collapse
Affiliation(s)
- William N. Batts
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (W.N.B.); (R.L.P.)
| | - Tony R. Capps
- Washington Department of Fish and Wildlife, Olympia, WA 98501, USA; (T.R.C.); (L.M.C.)
| | - Lisa M. Crosson
- Washington Department of Fish and Wildlife, Olympia, WA 98501, USA; (T.R.C.); (L.M.C.)
| | - Rachel L. Powers
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (W.N.B.); (R.L.P.)
| | - Rachel Breyta
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Maureen K. Purcell
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (W.N.B.); (R.L.P.)
- Correspondence:
| |
Collapse
|
5
|
Boerlage AS, Ashby A, Eze J, Gunn G, Reeves A. Field evaluation of diagnostic sensitivity (DSe) and specificity (DSp) of common tests for amoebic gill disease (AGD) and complex gill disease (CGD) in cultured Atlantic salmon (Salmo salar) in Scotland using Bayesian latent class models. Prev Vet Med 2022; 204:105654. [DOI: 10.1016/j.prevetmed.2022.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/15/2022] [Accepted: 04/18/2022] [Indexed: 11/25/2022]
|
6
|
Clouthier SC, McClure C, Schroeder T, Anderson ED. Bayesian latent class model estimates of diagnostic accuracy for three test methods designed to detect spring viremia of carp virus. Prev Vet Med 2021; 190:105338. [PMID: 33831815 DOI: 10.1016/j.prevetmed.2021.105338] [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: 12/06/2020] [Revised: 02/17/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
Spring viremia of carp virus (SVCV) causes a systemic hemorrhagic disease that poses a significant risk to wild and cultured fish and is listed as notifiable by the World Organization for Animal Health. Validated molecular diagnostic tools for SVCV are required to accurately describe and analyze the ecology of the virus. Here, the diagnostic specificity (DSp) and sensitivity (DSe) (i.e. accuracy) of three SVCV diagnostic tests - 2 reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays Q1G and Q2N and virus isolation by cell culture (VI) - were evaluated using 2-class latent class models run in maximum likelihood (ML) and Bayesian frameworks. Virus-free or experimentally-infected koi were sorted into three populations with low, moderate or high prevalence levels of SVCV (n = 269 fish in total). Koi kidney tissues were tested using Q2N and Q1G and for the VI assay, pools of kidney, spleen and gill tissues were used. All samples were blinded and analyzed in one laboratory. The ML and Bayesian approaches successfully estimated the diagnostic accuracy of the 3 tests with the exception of 1 ML model. The estimates were consistent across the two frameworks. The DSe estimates were higher for Q1G (>98 %) and Q2N (>96 %) compared to VI (>60 %). The DSp of all three tests varied by 12-15 % (79-91 % for Q1G, 79-94 % for Q2N and 81-97 % for VI) across same-fish samples revealing the potential range in test performance for one sample. The 3 fish populations had distinct SVCV prevalence levels estimated at 0-3 % (low), 70-73 % (moderate) and 95-96 % (high). The Bayesian covariance models revealed minor DSe dependence between Q1G and Q2N. The results suggested that SVCV diagnostic tests Q2N and Q1G are suitable for use as diagnostic assays and are fit for presumptive diagnosis, surveillance, and certification of populations or individuals as SVCV free.
Collapse
Affiliation(s)
- Sharon C Clouthier
- Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba, R3T 2N6, Canada.
| | - Carol McClure
- AquaEpi Research, RR3, 300 Heartz Road, Charlottetown, Prince Edward Island, C1C 0H8, Canada.
| | - Tamara Schroeder
- Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba, R3T 2N6, Canada.
| | | |
Collapse
|
7
|
Laurin E, Gardner IA, Peña A, Rozas-Serri M, Gayosa J, Neumann Heise J, Mardones FO. Bayesian estimation of diagnostic sensitivity and specificity of a qPCR and a bacteriological culture method for Piscirickettsia salmonis in farmed Atlantic salmon (Salmo salar L.) in Chile. JOURNAL OF FISH DISEASES 2020; 43:1167-1175. [PMID: 32716071 DOI: 10.1111/jfd.13226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Early detection of piscirickettsiosis is an important purpose of government- and industry-based surveillance for the disease in Atlantic salmon farms in Chile. Real-time qPCRs are currently used for surveillance because bacterial isolation is inadequately sensitive or rapid enough for routine use. Since no perfect tests exist, we used Bayesian latent class models to estimate diagnostic sensitivity (DSe) and specificity (DSp) of qPCR and culture using separate two-test, single-population models for three farms (n = 148, 151, 44). Informative priors were used for DSp (culture (beta(999,1); qPCR (beta(98,2)), and flat priors (beta 1,1) for DSe and prevalence. Models were run for liver and kidney tissues combined and separately, based on the presence of selected gross-pathological signs. Across all models, qPCR DSe was 5- to 30-fold greater than for culture. Combined-tissue qPCR median DSe was highest in Farm 3 (sampled during P. salmonis outbreak (DSe = 97.6%)) versus Farm 1 (DSe = 85.6%) or Farm 2 (DSe = 83.5%), both sampled before clinical disease. Median DSe of qPCR was similar for liver and kidney, but higher when gross-pathological signs were evident at necropsy. High DSe and DSp and rapid turnaround-time indicate that the qPCR is fit for surveillance programmes and diagnosis during an outbreak. Targeted testing of salmon with gross-pathological signs can enhance DSe.
Collapse
Affiliation(s)
- Emilie Laurin
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ian A Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Andrea Peña
- Pathovet Laboratory Ltd, Puerto Montt, Chile
| | | | | | | | - Fernando O Mardones
- School of Veterinary Medicine, Pontifical Catholic University, Santiago, Chile
| |
Collapse
|
8
|
Canier L, Dubreuil C, Noyer M, Serpin D, Chollet B, Garcia C, Arzul I. A new multiplex real-time PCR assay to improve the diagnosis of shellfish regulated parasites of the genus Marteilia and Bonamia. Prev Vet Med 2020; 183:105126. [PMID: 32919320 DOI: 10.1016/j.prevetmed.2020.105126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Aquaculture including shellfish production is an important food resource worldwide which is particularly vulnerable to infectious diseases. Marteilia refringens, Bonamia ostreae and Bonamia exitiosa are regulated protozoan parasites infecting flat oysters Ostrea edulis that are endemic in Europe. Although some PCR assays have been already developed for their detection, a formal validation to assess the performances of those tools is often lacking. In order to facilitate the diagnosis of flat oyster regulated diseases, we have developed and evaluated a new multiplex Taqman® PCR allowing the detection of both M. refringens and Bonamia sp. parasites in one step. First part of this work consisted in assessing analytical sensitivity and specificity of the new PCR assay. Then, diagnostic performances were assessed by testing a panel of field samples with the new real-time PCR and currently recommended conventional PCR methods for the detection of M. refringens and Bonamia sp. Samples were collected from the main flat oyster production sites in France (N = 386 for M. refringens and N = 349 for B. ostreae). In the absence of gold standard, diagnostic sensitivity and specificity of the new PCR were estimated through Bayesian latent class analysis (DSe 87,2% and DSp 98,4% for the detection M. refringens, DSe 77,5% and DSp 98,4% for the detection of Bonamia sp.). Those results suggest equivalent performances for the detection of Bonamia sp. and an improved sensitivity for the detection of M. refringens compared to commonly used conventional protocols. Finally, the new PCR was evaluated in the context of an inter-laboratory comparison study including 17 European laboratories. Results revealed a very good reproducibility with a global accordance (intra-laboratory precision) >96% and a global concordance (inter-laboratory precision) >93% for both targets, demonstrating that this new tool is easily transferable to different laboratory settings. This is the first assay designed to detect both Marteilia refringens and Bonamia sp. in a single step and it should allow reducing the number of analysis to monitor both diseases, and where relevant to demonstrate freedom from infection.
Collapse
Affiliation(s)
- Lydie Canier
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France.
| | - Christine Dubreuil
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France
| | - Mathilde Noyer
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France
| | - Delphine Serpin
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France
| | - Bruno Chollet
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France
| | - Céline Garcia
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France
| | - Isabelle Arzul
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France
| |
Collapse
|
9
|
Jia B, Colling A, Stallknecht DE, Blehert D, Bingham J, Crossley B, Eagles D, Gardner IA. Validation of laboratory tests for infectious diseases in wild mammals: review and recommendations. J Vet Diagn Invest 2020; 32:776-792. [PMID: 32468923 DOI: 10.1177/1040638720920346] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Evaluation of the diagnostic sensitivity (DSe) and specificity (DSp) of tests for infectious diseases in wild animals is challenging, and some of the limitations may affect compliance with the OIE-recommended test validation pathway. We conducted a methodologic review of test validation studies for OIE-listed diseases in wild mammals published between 2008 and 2017 and focused on study design, statistical analysis, and reporting of results. Most published papers addressed Mycobacterium bovis infection in one or more wildlife species. Our review revealed limitations or missing information about sampled animals, identification criteria for positive and negative samples (case definition), representativeness of source and target populations, and species in the study, as well as information identifying animals sampled for calculations of DSe and DSp as naturally infected captive, free-ranging, or experimentally challenged animals. The deficiencies may have reflected omissions in reporting rather than design flaws, although lack of random sampling might have induced bias in estimates of DSe and DSp. We used case studies of validation of tests for hemorrhagic diseases in deer and white-nose syndrome in hibernating bats to demonstrate approaches for validation when new pathogen serotypes or genotypes are detected and diagnostic algorithms are changed, and how purposes of tests evolve together with the evolution of the pathogen after identification. We describe potential benefits of experimental challenge studies for obtaining DSe and DSp estimates, methods to maintain sample integrity, and Bayesian latent class models for statistical analysis. We make recommendations for improvements in future studies of detection test accuracy in wild mammals.
Collapse
Affiliation(s)
- Beibei Jia
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Axel Colling
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - David E Stallknecht
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - David Blehert
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - John Bingham
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Beate Crossley
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Debbie Eagles
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Ian A Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| |
Collapse
|
10
|
Laurin E, Thakur K, Mohr PG, Hick P, Crane MSJ, Gardner IA, Moody NJG, Colling A, Ernst I. To pool or not to pool? Guidelines for pooling samples for use in surveillance testing of infectious diseases in aquatic animals. JOURNAL OF FISH DISEASES 2019; 42:1471-1491. [PMID: 31637760 DOI: 10.1111/jfd.13083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
Samples from multiple animals may be pooled and tested to reduce costs of surveillance for infectious agents in aquatic animal populations. The primary advantage of pooling is increased population-level coverage when prevalence is low (<10%) and the number of tests is fixed, because of increased likelihood of including target analyte from at least one infected animal in a tested pool. Important questions and a priori design considerations need to be addressed. Unfortunately, pooling recommendations in disease-specific chapters of the 2018 OIE Aquatic Manual are incomplete and, except for amphibian chytrid fungus, are not supported by peer-reviewed research. A systematic review identified only 12 peer-reviewed aquatic diagnostic accuracy and surveillance studies using pooled samples. No clear patterns for pooling methods and characteristics were evident across reviewed studies, although most authors agreed there is a negative effect on detection. Therefore, our purpose was to review pooling procedures used in published aquatic infectious disease research, present evidence-based guidelines, and provide simulated data examples for white spot syndrome virus in shrimp. A decision tree of pooling guidelines was developed for use by peer-reviewed journals and research institutions for the design, statistical analysis and reporting of comparative accuracy studies of individual and pooled tests for surveillance purposes.
Collapse
Affiliation(s)
- Emilie Laurin
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Krishna Thakur
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Peter G Mohr
- CSIRO Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Paul Hick
- School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Mark St J Crane
- CSIRO Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Ian A Gardner
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Axel Colling
- CSIRO Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Ingo Ernst
- Department of Agriculture, Canberra, ACT, Australia
| |
Collapse
|
11
|
Caraguel CGB, Ellard K, Moody NJG, Corbeil S, Williams LM, Mohr PG, Cummins DM, Hoad J, Slater J, Crane MSJ. Diagnostic test accuracy when screening for Haliotid herpesvirus 1 (AbHV) in apparently healthy populations of Australian abalone Haliotis spp. DISEASES OF AQUATIC ORGANISMS 2019; 136:199-207. [PMID: 31621653 DOI: 10.3354/dao03405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The accuracy of 3 real-time PCR assays (ORF49, ORF66 and ORF77) and histopathology was evaluated for the purpose of demonstrating or certifying abalone free from Haliotid herpesvirus 1 (AbHV), the causative agent of abalone viral ganglioneuritis. Analytically, all 3 qPCRs showed equivalent limit of detection (20 copies per reaction); however, ORF49 could not detect 2 of the AbHV genotypes. A selection of 1452 archive specimens sourced from apparently healthy abalone populations was screened using all 4 tests. In the absence of a perfect reference standard, a Bayesian latent class analysis was built to estimate diagnostic sensitivity (DSe), diagnostic specificity (DSp) and likelihood ratios of a positive (LR+) and negative test result (LR-) for each individual test and for all possible combinations of test pairs interpreted either in series or in parallel. The pair ORF49/ORF66 interpreted in parallel performed the best both analytically and diagnostically to demonstrate freedom from AbHV in an established population of abalone and to certify individual abalone free from AbHV for trade or movement purposes (DSe = 96.0%, 95% posterior credibility interval [PCI]: 82.6 to 99.9; DSp = 97.7%, 95% PCI: 96.4 to 99.4; LR+ = 41.4, 95% PCI: 27.4 to 148.7; LR- = 0.041, 95% PCI: 0.001 to 0.176). Histopathology showed very poor DSe (DSe = 6.3%, 95% PCI: 2.4 to 13.1) as expected since most infected abalone in the study were likely sub-clinical with limited pathological change. Nevertheless, we recommend histopathology when clinically investigating outbreaks to find potential, new, emerging AbHV genotype(s) that may not be detectable by either ORF49 or ORF66.
Collapse
Affiliation(s)
- Charles G B Caraguel
- School of Animal & Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Roseworthy, South Australia 5371, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Laurin E, Morrison D, Gardner IA, Siah A, Powell JFF, Kamaitis M. Bayesian latent class analysis of ELISA and RT-rPCR diagnostic accuracy for subclinical Renibacterium salmoninarum infection in Atlantic salmon (Salmo salar) broodstock. JOURNAL OF FISH DISEASES 2019; 42:303-313. [PMID: 30549278 DOI: 10.1111/jfd.12933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/10/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
Renibacterium salmoninarum infection causes bacterial kidney disease (BKD) in salmonid freshwater and saltwater life stages, with potentially severe financial loss for the aquaculture industry. Preventing vertical transmission, from infected broodstock to eggs, is key to disease management. As there is no perfect reference standard for detecting R. salmoninarum, we used Bayesian latent class analyses to compare real-time reverse transcriptase PCR (RT-rPCR, mRNA target) and enzyme-linked immunosorbent assay (ELISA; p57 antigen target) diagnostic accuracy for detection in Atlantic salmon broodstock from British Columbia, Canada, and assessed ELISA repeatability. In 2016, 4,544 Atlantic salmon broodstock (no clinical signs of BKD or gross lesions) were sampled for ELISA testing of kidney tissue. Two groups of ELISA positives (n = 132) and two groups of a random sample of ELISA negatives (n = 137) were then tested with RT-rPCR, and ELISA testing was repeated. ELISA testing of broodstock provided the best diagnostic sensitivity (DSe; less chance of false-negative results). The use of joint RT-rPCR and ELISA testing improved DSe over that from each test alone, if a sample was considered positive when either test result was positive. Using these testing schemes in combination with management practices can decrease the likelihood of vertical transmission from subclinically infected broodstock.
Collapse
Affiliation(s)
- Emilie Laurin
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Diane Morrison
- Marine Harvest Canada, Campbell River, British Columbia, Canada
| | - Ian A Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ahmed Siah
- British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada
| | - James F F Powell
- British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada
| | | |
Collapse
|
13
|
Gardner IA, Colling A, Greiner M. Design, statistical analysis and reporting standards for test accuracy studies for infectious diseases in animals: Progress, challenges and recommendations. Prev Vet Med 2018; 162:46-55. [PMID: 30621898 DOI: 10.1016/j.prevetmed.2018.10.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/13/2018] [Accepted: 10/28/2018] [Indexed: 02/04/2023]
Abstract
The quality of diagnostic accuracy studies (DAS) for infectious diseases of animals has improved over the last 20 years because of international educational efforts, use of design and reporting standards to guide researchers and test developers, and acceptance of the use of latent class models to account for imperfect reference tests. In this review, we focus on measurement of diagnostic sensitivity and specificity as a measure of clinical validity, describe the leadership role of the World Organisation of Animal Health (OIE) in setting standards for test validation in the context of fitness-for-purpose, and describe how design and reporting quality have facilitated the increased use of systematic reviews and meta-analysis of DAS. Ongoing challenges for design, conduct, analysis and reporting of DAS are identified; and we make recommendations for improvements in these areas for OIE-listed and non-listed infectious diseases.
Collapse
Affiliation(s)
- Ian A Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, C1A 4P3, Canada.
| | - Axel Colling
- CSIRO Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC, 3220, Australia.
| | - Matthias Greiner
- Federal Institute for Risk Assessment, Department of Exposure, Berlin and University of Veterinary Medicine Hannover, Foundation, Germany.
| |
Collapse
|
14
|
Assis GBN, de Oliveira TF, Gardner IA, Figueiredo HCP, Leal CAG. Sensitivity and specificity of real-time PCR and bacteriological culture for francisellosis in farm-raised Nile tilapia (Oreochromis niloticus L.). JOURNAL OF FISH DISEASES 2017; 40:785-795. [PMID: 27670740 DOI: 10.1111/jfd.12559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Despite the worldwide occurrence of Francisella noatunensis subsp. orientalis (Fno) infection in farmed tilapia, sensitivity and specificity estimates of commonly used diagnostic tests have not been reported. This study aimed to estimate the sensitivity and specificity of bacteriological culture and qPCR to detect Fno infection. We tested 559 fish, sampled from four farms with different epidemiological scenarios: (i) healthy fish in a hatchery free of Fno; (ii) targeted sampling of diseased fish with suggestive external clinical signs of francisellosis during an outbreak; (iii) convenience sampling of diseased and clinically healthy fish during an outbreak; and (iv) sampling of healthy fish in a cage farm without a history of outbreaks, but with francisellosis reported in other farms in the same reservoir. The qPCR had higher median sensitivity (range, 48.8-99.5%) than culture (range, 1.6-74.4%). Culture had a substantially lower median sensitivity (1.6%) than qPCR (48.8%) to detect Fno in carrier tilapia (farm 4). Median specificity estimates for both tests were >99.2%. The qPCR is the superior test for use in surveillance and monitoring programmes for francisellosis in farmed Nile tilapia, but both tests have high sensitivity and specificity which make them fit for use in the diagnosis of Fno outbreaks.
Collapse
Affiliation(s)
- G B N Assis
- AQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - T F de Oliveira
- AQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - I A Gardner
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - H C P Figueiredo
- AQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - C A G Leal
- AQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| |
Collapse
|
15
|
Clouthier SC, McClure C, Schroeder T, Desai M, Hawley L, Khatkar S, Lindsay M, Lowe G, Richard J, Anderson ED. Diagnostic validation of three test methods for detection of cyprinid herpesvirus 3 (CyHV-3). DISEASES OF AQUATIC ORGANISMS 2017; 123:101-122. [PMID: 28262633 DOI: 10.3354/dao03093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of koi herpesvirus disease in koi and common carp. The disease is notifiable to the World Organisation for Animal Health. Three tests-quantitative polymerase chain reaction (qPCR), conventional PCR (cPCR) and virus isolation by cell culture (VI)-were validated to assess their fitness as diagnostic tools for detection of CyHV-3. Test performance metrics of diagnostic accuracy were sensitivity (DSe) and specificity (DSp). Repeatability and reproducibility were measured to assess diagnostic precision. Estimates of test accuracy, in the absence of a gold standard reference test, were generated using latent class models. Test samples originated from wild common carp naturally exposed to CyHV-3 or domesticated koi either virus free or experimentally infected with the virus. Three laboratories in Canada participated in the precision study. Moderate to high repeatability (81 to 99%) and reproducibility (72 to 97%) were observed for the qPCR and cPCR tests. The lack of agreement observed between some of the PCR test pair results was attributed to cross-contamination of samples with CyHV-3 nucleic acid. Accuracy estimates for the PCR tests were 99% for DSe and 93% for DSp. Poor precision was observed for the VI test (4 to 95%). Accuracy estimates for VI/qPCR were 90% for DSe and 88% for DSp. Collectively, the results show that the CyHV-3 qPCR test is a suitable tool for surveillance, presumptive diagnosis and certification of individuals or populations as CyHV-3 free.
Collapse
Affiliation(s)
- Sharon C Clouthier
- Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Jaramillo D, Peeler EJ, Laurin E, Gardner IA, Whittington RJ. Serology in Finfish for Diagnosis, Surveillance, and Research: A Systematic Review. JOURNAL OF AQUATIC ANIMAL HEALTH 2017; 29:1-14. [PMID: 28166451 DOI: 10.1080/08997659.2016.1244577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Historically, serological tests for finfish diseases have been underused when compared with their use in terrestrial animal health. For years the nonspecific immune response in fish was judged to make serology unreliable and inferior to the direct measurement of agent analytes. We conducted a systematic review of peer-reviewed publications that reported on the development, validation, or application of serological tests for finfish diseases. A total of 168 articles met the screening criteria; most of them were focused on salmonid pathogens (e.g., Aeromonas spp. and viral hemorrhagic septicemia virus). Before the 1980s, most publications reported the use of agglutination tests, but our review indicates that enzyme-linked immunosorbent assay (ELISA) has more recently become the dominant serological test. The main application of serological tests has been in the assessment of vaccine efficacy, with few applications for surveillance or demonstration of freedom from disease, despite the advantages of serological tests over direct detection at the population level. Nonlethal sampling, low cost, and postinfection persistence of antibodies make serological assays the test of choice in surveillance, especially of valuable broodstock. However, their adoption has been constrained by poor characterization and validation. The number of publications in our review reporting diagnostic sensitivity and specificity of serological tests in finfish was small (n = 7). Foreseeing a wider use of serological tests in the future for diagnostic end purposes, we offer recommendations for mitigating deficiencies in the development and evaluation of serological tests, including optimization, control of nonspecific reactions, informed cutoff points, diagnostic accuracy, and serological baseline studies. Achieving these goals will facilitate greater international recognition of serological testing in programs supporting aquatic animal health. Received March 21, 2016; accepted September 24, 2016.
Collapse
Affiliation(s)
- Diana Jaramillo
- a Atlantic Veterinary College , University of Prince Edward Island , 550 University Avenue, Charlottetown , Prince Edward Island C1A 4P3 , Canada
- b Faculty of Veterinary Science , The University of Sydney , 425 Werombi Road, Camden , New South Wales 2570 , Australia
| | - Edmund J Peeler
- c Centre for Environment , Fisheries and Aquaculture Science , Barrack Road, Weymouth DT4 8UB , UK
| | - Emilie Laurin
- a Atlantic Veterinary College , University of Prince Edward Island , 550 University Avenue, Charlottetown , Prince Edward Island C1A 4P3 , Canada
| | - Ian A Gardner
- a Atlantic Veterinary College , University of Prince Edward Island , 550 University Avenue, Charlottetown , Prince Edward Island C1A 4P3 , Canada
| | - Richard J Whittington
- b Faculty of Veterinary Science , The University of Sydney , 425 Werombi Road, Camden , New South Wales 2570 , Australia
| |
Collapse
|