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Description: The present invention relates to methods for using a specific method of solution phase competitive DNA hybridization, referred to as "Genome Fragment Enrichment" to identify microbial DNA sequences for determination of different sources of fecalcontamination. The invention also relates to using this method for comparing bacterial genomes, and developing specific PCR primer sets to differentiate among bacterial species, strains, and sources of pollution.BACKGROUND OF THE INVENTION Poultry farming for meat production has significantly increased in the last few decades. For example, the per capita consumption of chicken in the United states was estimated to be over 74 pounds in 2004, which represents a 200% increase inless than 20 years, according to the U.S. Department of Agriculture. As a result of this increase in production, fecal matter has become a significant byproduct of the poultry industry. Fecal matter is often used as fertilizer in the form of raw orcomposted manure. A potential risk arising from the disposal of poultry waste is the spread of enteric pathogens, such as Escherichia coli O157:H7, Salmonella spp., and Campylobacter spp. These pathogens can reach watersheds after rainfall, and therebyincrease risks associated with recreational use of waterways. Furthermore, environmental concerns also include high nutrient loads, such as nitrate and phosphate, from runoff to streams, ponds, and ground water. Methods that can specifically detectpoultry fecal pollution are therefore needed to assist in the development and evaluation of adequate management practices targeting pollution control. Current regulatory methods used to assess microbial water quality rely on measuring the levels of culturable fecal indicator bacteria such as Enterococci and other fecal coliforms. However, the plate culture approach cannot discriminate amongdifferent among specific bacterial strains or animal sources of fecal contamination. A limited number of studies have repor