Bayesian estimation of diagnostic sensitivity and specificity of a qPCR and a bacteriological culture method forPiscirickettsia salmonisin farmed Atlantic salmon (Salmo salarL.) in Chile
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Date
2020
Journal Title
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Volume Title
Publisher
WILEY
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 forDSp(culture (beta(999,1); qPCR (beta(98,2)), and flat priors (beta 1,1) forDSeand prevalence. Models were run for liver and kidney tissues combined and separately, based on the presence of selected gross-pathological signs. Across all models, qPCRDSewas 5- to 30-fold greater than for culture. Combined-tissue qPCR medianDSewas highest in Farm 3 (sampled duringP. salmonisoutbreak (DSe = 97.6%)) versus Farm 1 (DSe = 85.6%) or Farm 2 (DSe = 83.5%), both sampled before clinical disease. MedianDSeof qPCR was similar for liver and kidney, but higher when gross-pathological signs were evident at necropsy. HighDSeandDSpand 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 enhanceDSe.
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Keywords
Bayesian latent class model, Piscirickettsia salmonis, piscirickettsiosis, qPCR, sensitivity, specificity, LATENT CLASS ANALYSIS, REAL-TIME PCR, PISCIRICKETTSIA-SALMONIS, INFECTIOUS-DISEASES, IMMUNE-RESPONSE, TISSUE-CULTURE, PATHOGEN, ACCURACY, FISH, STANDARDS