title: Evaluation of fecal culture and fecal RT-PCR to detect Mycobacterium avium ssp. paratuberculosis fecal shedding in dairy goats and dairy sheep using latent class Bayesian modeling.
abstract: BACKGROUND
  The study's objective was to evaluate the ability of fecal culture (FCUL) and fecal PCR (FPCR) to identify dairy goat and dairy sheep shedding Mycobacterium avium ssp. paratuberculosis. A cross-sectional study of the small ruminant populations was performed in Ontario, Canada between October 2010 and August 2011. Twenty-nine dairy goat herds and 21 dairy sheep flocks were visited, and 20 lactating females > two years of age were randomly selected from each farm resulting in 580 goats and 397 sheep participating in the study. Feces were collected per rectum and cultured using the BD BACTEC™ MGIT™ 960 system using a standard (49 days) and an extended (240 days) incubation time, and underwent RT-PCR based on the hsp-X gene (Tetracore®). Statistical analysis was performed using a 2-test latent class Bayesian hierarchical model for each species fitted in WinBUGS.
  
  
  RESULTS
  Extending the fecal culture incubation time statistically improved FCUL sensitivity from 23.1 % (95 % PI: 15.9-34.1) to 42.7 % (95 % PI: 33.0-54.5) in dairy goats and from 5.8 % (95 % PI: 2.3-12.4) to 19.0 % (95 % PI: 11.9-28.9) in dairy sheep. FPCR demonstrated statistically higher sensitivity than FCUL (49 day incubation) with a sensitivity of 31.9 % (95 % PI: 22.4-43.1) in goats and 42.6 % (95 % PI: 28.8-63.3) in sheep.
  
  
  CONCLUSIONS
  Fecal culture demonstrates such low sensitivity at the standard incubation time it cannot be recommended as a screening test to detect shedding of MAP in either goats or sheep. Extending the incubation time resulted in improved sensitivity; however, it is still disappointingly low for screening purposes. Fecal PCR should be the screening test of choice in both species; however, it is important to recognize that control programs should not be based on testing alone when they demonstrate such low sensitivity.
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. cbauman@uoguelph.ca.
authors.forename: Cathy A
authors.identifier: http://orcid.org/0000-0001-6706-5456
authors.initials: CA
authors.lastname: Bauman
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
authors.forename: Andria
authors.initials: A
authors.lastname: Jones-Bitton
authors.affiliation: Veterinary Science & Policy Unit, Animal Health and Welfare Branch, Ontario Ministry of Agriculture, Food & Rural Affairs, Elora, Ontario, N0B 1S0, Canada.
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Jansen
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Kelton
authors.affiliation: Department of Population Medicine, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
authors.forename: Paula
authors.initials: P
authors.lastname: Menzies
mesh_terms: D000818:Animals; D001431:Bacteriological Techniques; D001499:Bayes Theorem; D003430:Cross-Sectional Studies; D003612:Dairying; D005243:Feces / Q000382:microbiology*; D005260:Female; D015511:Goat Diseases / Q000382:microbiology*; D006041:Goats; D007774:Lactation; D016927:Mycobacterium avium subsp. paratuberculosis / Q000302:isolation & purification*; D009864:Ontario / Q000453:epidemiology; D010283:Paratuberculosis / Q000453:epidemiology / Q000382:microbiology*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000662:veterinary; D012756:Sheep; D012757:Sheep Diseases / Q000382:microbiology*
keywords: Dairy goats; Fecal PCR; Fecal culture; Paratuberculosis