Development of antibiotic regimens using graph based evolutionary algorithms.

This paper examines the use of evolutionary algorithms in the development of antibiotic regimens given to production animals. A model is constructed that combines the lifespan of the animal and the bacteria living in the animal's gastro-intestinal tract from the early finishing stage until the animal reaches market weight. This model is used as the fitness evaluation for a set of graph based evolutionary algorithms to assess the impact of diversity control on the evolving antibiotic regimens. The graph based evolutionary algorithms have two objectives: to find an antibiotic treatment regimen that maintains the weight gain and health benefits of antibiotic use and to reduce the risk of spreading antibiotic resistant bacteria. This study examines different regimens of tylosin phosphate use on bacteria populations divided into Gram positive and Gram negative types, with a focus on Campylobacter spp. Treatment regimens were found that provided decreased antibiotic resistance relative to conventional methods while providing nearly the same benefits as conventional antibiotic regimes. By using a graph to control the information flow in the evolutionary algorithm, a variety of solutions along the Pareto front can be found automatically for this and other multi-objective problems.

Risk-based analysis of the Danish pork Salmonella program: past and future.

The Danish pork Salmonella control program was initiated in 1993 in response to a prominent pork-related outbreak in Copenhagen. It involved improved efforts at slaughter hygiene (postharvest) and on-farm (preharvest) surveillance and control. After 10 years, 95 million Euros, significant reductions in seropositive herds, Salmonella positive carcasses, and pork-attributable human cases (PAHC), questions have arisen about how best to continue this program. The objective of this study was to provide some analysis and information to address these questions. The methods used include a computer simulation model constructed of a series of Excel workbooks, one for each simulated year and scenario (http://www.ifss.iastate/DanSalmRisk). Each workbook has three modules representing the key processes affecting risk: seropositive pigs leaving the farm (Production), carcass contamination after slaughter (Slaughter), and PAHC of Salmonella (Attribution). Parameter estimates are derived from an extensive farm-to-fork database collected by industry and government and managed by the Danish Zoonosis Centre (http://www.food.dtu.dk). Retrospective (1994-2003) and prospective (2004-2013) simulations were evaluated. The retrospective simulations showed that, except for the first few years (1994-1998), the on-farm program had minimal impact in reducing the number of positive carcasses and PAHC. Most of the reductions in PAHC up to 2003 were, according to this analysis, due to various improvements in abattoir processes. Prospective simulations showed that minimal reductions in human health risk (PAHC) could be achieved with on-farm programs alone. Carcass decontamination was shown as the most effective means of reducing human risk, reducing PAHC to about 10% of the simulated 2004 level.