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.
Animals
Aquaculture
Bacteriological Techniques
Bayes Theorem
Chile
Fish Diseases
/ diagnosis
Latent Class Analysis
Piscirickettsia
/ growth & development
Piscirickettsiaceae Infections
/ diagnosis
Real-Time Polymerase Chain Reaction
/ veterinary
Salmo salar
/ microbiology
Sensitivity and Specificity
Piscirickettsia salmonis
Bayesian latent class model
piscirickettsiosis
qPCR
sensitivity
specificity
Journal
Journal of fish diseases
ISSN: 1365-2761
Titre abrégé: J Fish Dis
Pays: England
ID NLM: 9881188
Informations de publication
Date de publication:
Oct 2020
Oct 2020
Historique:
received:
04
05
2020
revised:
30
06
2020
accepted:
02
07
2020
pubmed:
28
7
2020
medline:
20
2
2021
entrez:
28
7
2020
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1167-1175Subventions
Organisme : SalmonChile and Sernapesca
ID : EPIVET project 201707240090
Organisme : SalmonChile and Sernapesca
ID : Fondo Inversion Estrategica (FIE-2015-V014
Organisme : Canada Excellence Research Chair in Aquatic Epidemiology, University of Prince Edward Island
Informations de copyright
© 2020 John Wiley & Sons Ltd.
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