Simulation modelling to estimate the herd-sensitivity of various pool sizes to test beef herds for Johne's disease in Australia.

Abstract Johne’s disease is a chronic intestinal disease affecting livestock. It leads to the shedding of Mycobacterium avium subspecies paratuberculosis (MAP) in the faeces, wasting and eventually death, with animal welfare, economic, and trade implications. The Johne’s Beef Assurance Scheme, used in Australia to determine the risk of Johne’s disease on beef properties and facilitate trade, is based on testing a subset of the herd with pooled faecal quantitative PCR. This study aimed to model the herd-sensitivity of pooled faecal testing under different Australian farming scenarios. Animals from simulated herds were randomly sampled and allocated into their respective pools. Each tested pool was provided a test outcome, with herd-sensitivity estimated as the probability of detecting a truly infected herd. The models simulated the test performance for the ‘Sample’ and ‘Check’ tests used in the assurance schemes (recommended sample sizes of 300 and 50, respectively) for a range of herd sizes, infection prevalence and MAP faecal shedding levels for the pool sizes of 5, 10, 15 and 20. Sensitivity and specificity input values of each pool size were obtained from a previous laboratory investigation. The herd-sensitivity estimate increased with herd size and infection prevalence levels, regardless of the pool size. Higher herd-sensitivity was also achieved for testing scenarios involving larger sampling sizes. A pool size of 10 achieved the highest herd-sensitivity for the majority of the Sample test (60% for a herd size of 1000 with 2% infection prevalence) and Check test, in comparison to the other pool sizes. This was particularly evident when pool-specificity was assumed to be perfect. However, the overall herd-sensitivity of the Check test was very low for all infection prevalence levels and pool sizes. Further simulations demonstrated that herd-sensitivity had more than doubled, when the sample size increased from 50 to 100 animals for the Check test (11% versus 26% for a herd size of 500 cattle with a 2% infection prevalence). The results show that the majority of beef producers participating in the assurance scheme can benefit from using a larger pool size for the pooled faecal quantitative PCR testing of their herd, in comparison to the pool size currently used.