Using heterogeneity in the population structure of U.S. swine farms to compare transmission models for porcine epidemic diarrhoea.

In 2013, U.S. swine producers were confronted with the disruptive emergence of porcine epidemic diarrhoea (PED). Movement of animals among farms is hypothesised to have played a role in the spread of PED among farms. Via this or other mechanisms, the rate of spread may also depend on the geographic density of farms and climate. To evaluate such effects on a large scale, we analyse state-level counts of outbreaks with variables describing the distribution of farm sizes and types, aggregate flows of animals among farms, and an index of climate. Our first main finding is that it is possible for a correlation analysis to be sensitive to transmission model parameters. This finding is based on a global sensitivity analysis of correlations on simulated data that included a biased and noisy observation model based on the available PED data. Our second main finding is that flows are significantly associated with the reports of PED outbreaks. This finding is based on correlations of pairwise relationships and regression modeling of total and weekly outbreak counts. These findings illustrate how variation in population structure may be employed along with observational data to improve understanding of disease spread.

Use estimates of in-feed antimicrobials in swine production in the United States.

When considering the development of antimicrobial resistance in food animals, comparing gross use estimates of different antimicrobials is of little value due to differences in potencies, duration of activity, relative effect on target and commensal bacteria, and mechanisms of resistance. However, it may be valuable to understand quantities of different antimicrobials used in different ages of swine and for what applications. Therefore, the objective of this project was to construct an estimate of antimicrobial use through the feed in swine production in the United States. Estimates were based on data from the National Animal Health Monitoring System (NAHMS) Swine 2006 Study and from a 2009 survey of swine-exclusive practitioners. Inputs consisted of number of pigs in a production phase, feed intake per day, dose of the antimicrobial in the feed, and duration of administration. Calculations were performed for a total of 102 combinations of antimicrobials (n=17), production phases (n=2), and reasons for use (n=3). Calculations were first conducted on farm-level data, and then extrapolated to the U.S. swine population. Among the nursery phase estimates, chlortetracycline had the largest estimate of use, followed by oxytetracycline and tilmicosin. In the grower/finisher phase, chlortetracycline also had the largest use estimate, followed by tylosin and oxytetracycline. As an annual industry estimate for all phases, chlortetracycline had the highest estimated use at 533,973 kg. The second and third highest estimates were tylosin and oxytetracycline with estimated annual uses of 165,803 kg and 154,956 kg, respectively. The estimates presented here were constructed to accurately reflect available data related to production practices, and to provide an example of a scientific approach to estimating use of compounds in production animals.