Bayesian techniques for comparison of the test performance of PCR and culture for the identification of Campylobacter in enriched comminuted chicken samples

• Published in: Journal of applied microbiology 2016-05, Vol.120 (5), p.1418-1426
• Main Authors: Ebel, E.D., Williams, M.S., Golden, N.J., Tankson, J.
• Format: Article
• Language: English
• Subjects: Animals; BAX® system real‐time PCR assay for Campylobacter jejuni/coli/lari; Bayes Theorem; Bayesian; Bayesian analysis; Campylobacter; Campylobacter - genetics; Campylobacter - isolation & purification; Chickens - microbiology; False Negative Reactions; Food contamination & poisoning; Food Safety; Humans; Microbiology; Polymerase chain reaction; Poultry; prevalence; Real-Time Polymerase Chain Reaction - methods; sensitivity; Sensitivity and Specificity; specificity; United States
• ISSN: 1364-5072; 1365-2672
• DOI: 10.1111/jam.13098

Aims Using Bayesian methods that do not require the definition of a gold standard, the diagnostic sensitivity and specificity of a real‐time polymerase chain reaction (PCR) assay are compared to those of an enriched culture assay for detection of Campylobacter in enriched comminuted chicken samples. Methods and Results Food Safety and Inspection Service comminuted chicken samples were collected from production facilities across the United States. Enriched samples were examined using a commercial real‐time PCR kit and plated for culture. Allowing for conditional dependence between these approaches and defining relatively uninformed prior distributions, the ‘no gold standard’ Bayesian methods generated estimates of the means (95% credible interval) of the posterior distributions for sensitivity and specificity of the PCR as 93% (79, 100%) and 95% (87, 100%) respectively. The estimated sensitivity implies a mean false negative frequency of 7%. The estimated means of the posterior distributions for sensitivity and specificity of the culture assay were 91% (76, 100%) and 96% (88, 100%) respectively. In this case, the mean false negative frequency is 9%. Graphical comparisons of the posterior distributions with their corresponding prior distributions suggested only subtle differences in the sensitivities of both tests, but the posterior distributions for specificities are substantially more certain than the prior distributions. Conclusions The study suggests that the commercial real‐time PCR assay is a more sensitive screening test that would provide timelier negative test results. The modest 1% reduction in specificity of this PCR assay, as compared to an enriched culture assay, is less of a concern for regulatory testing programs if a culture‐based confirmatory assay is applied to all presumptive positive samples. Significance and Impact of the Study The sensitivity and specificity of a PCR assay and a culture assay for Campylobacter in comminuted poultry produced in the United States were estimated. The PCR assay was shown to be an appropriate alternative screening test.