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
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 routi...
Published in: | Journal of Fish Diseases |
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crwiley:10.1111/jfd.13226 2024-06-09T07:44:47+00:00 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 Laurin, Emilie Gardner, Ian A. Peña, Andrea Rozas‐Serri, Marco Gayosa, Jorge Neumann Heise, Joaquin Mardones, Fernando O. SalmonChile and Sernapesca Canada Excellence Research Chair in Aquatic Epidemiology, University of Prince Edward Island 2020 http://dx.doi.org/10.1111/jfd.13226 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjfd.13226 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jfd.13226 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/jfd.13226 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Journal of Fish Diseases volume 43, issue 10, page 1167-1175 ISSN 0140-7775 1365-2761 journal-article 2020 crwiley https://doi.org/10.1111/jfd.13226 2024-05-16T14:27:54Z 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 . Article in Journal/Newspaper Atlantic salmon Salmo salar Wiley Online Library Journal of Fish Diseases 43 10 1167 1175 |
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Wiley Online Library |
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English |
description |
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 . |
author2 |
SalmonChile and Sernapesca Canada Excellence Research Chair in Aquatic Epidemiology, University of Prince Edward Island |
format |
Article in Journal/Newspaper |
author |
Laurin, Emilie Gardner, Ian A. Peña, Andrea Rozas‐Serri, Marco Gayosa, Jorge Neumann Heise, Joaquin Mardones, Fernando O. |
spellingShingle |
Laurin, Emilie Gardner, Ian A. Peña, Andrea Rozas‐Serri, Marco Gayosa, Jorge Neumann Heise, Joaquin Mardones, Fernando O. 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 |
author_facet |
Laurin, Emilie Gardner, Ian A. Peña, Andrea Rozas‐Serri, Marco Gayosa, Jorge Neumann Heise, Joaquin Mardones, Fernando O. |
author_sort |
Laurin, Emilie |
title |
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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
publisher |
Wiley |
publishDate |
2020 |
url |
http://dx.doi.org/10.1111/jfd.13226 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjfd.13226 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jfd.13226 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/jfd.13226 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Journal of Fish Diseases volume 43, issue 10, page 1167-1175 ISSN 0140-7775 1365-2761 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/jfd.13226 |
container_title |
Journal of Fish Diseases |
container_volume |
43 |
container_issue |
10 |
container_start_page |
1167 |
op_container_end_page |
1175 |
_version_ |
1801373601696317440 |