title: Comparison of bacterial culture and real-time PCR for the detection of Salmonella in grow-finish pigs in Western Canada using a Bayesian approach.
abstract: The study objective was to evaluate the accuracy of a real-time polymerase chain reaction (RT-PCR) and a culture protocol used to detect Salmonella in the faeces of grow-finish pigs using a Bayesian approach. The RT-PCR was invA-gene-based assay, while the culture protocol included pre-enrichment in buffered peptone water, selective enrichment in tetrathionate and Rappaport-Vassiliadis broths, and isolation on semi-solid (modified semi-solid RV) or solid (XLT4, Rambach) agar plates. Bayesian analysis was performed using a two-test, two-population model with dependence between culture and RT-PCR and compared to a second model with conditional independence between these two tests. Two hundred and ninety three individual faecal and 294 pooled pen samples from grow-finish pig collected from 10 farms were tested and results were divided into two groups according to herd size (five herds <250 sows, five herds with >400 sows). In the dependence model, RT-PCR sensitivity (Se) and specificity (Sp) were estimated to be 90% (95% probability interval 74, 97) and 99% (98, 99), respectively. Culture Se was 92% (75, 99), while culture Sp was considered 100% as all culture-positive samples were confirmed by serotyping. In the conditional independence model, RT-PCR Se and Sp, and culture Se, were 96% (93, 98), 99% (98, 100) and 97% (94, 100), respectively. The dependence model resulted in posterior estimates of Se that were lower and with broader probability intervals than the independence model, indicating that when RT-PCR and culture are evaluated relative to each other, the correlation between these tests is an important source of bias and should be adjusted for during analysis. The RT-PCR evaluated in this study performed almost comparably to culture; given the cost savings associated with using this test and more timely results, the RT-PCR may be a useful alternative to culture for screening large numbers of samples, particularly when Salmonella prevalence is low.
authors.affiliation: Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, SK, Canada. wendy.wilkins@usask.ca
authors.forename: W
authors.initials: W
authors.lastname: Wilkins
authors.forename: C
authors.initials: C
authors.lastname: Waldner
authors.forename: A
authors.initials: A
authors.lastname: Rajić
authors.forename: M
authors.initials: M
authors.lastname: McFall
authors.forename: A
authors.initials: A
authors.lastname: Muckle
authors.forename: R C
authors.initials: RC
authors.lastname: Mainar-Jaime
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002170:Canada; D017046:Cost Savings; D005243:Feces / Q000382:microbiology*; D005516:Food Microbiology; D016133:Polymerase Chain Reaction / Q000191:economics / Q000379:methods / Q000662:veterinary*; D012475:Salmonella / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D012481:Salmonella Infections, Animal / Q000175:diagnosis* / Q000382:microbiology; D012680:Sensitivity and Specificity; D012703:Serotyping / Q000379:methods; D013552:Swine / Q000382:microbiology; D013553:Swine Diseases / Q000175:diagnosis* / Q000382:microbiology