This Is AuburnElectronic Theses and Dissertations

Detection and monitoring of microbes of concern in animal production environment




Windham, Amanda

Type of Degree

Master's Thesis


Animal Sciences


An estimated 48 million Americans become ill, 128,000 are hospitalized, and 3,000 die of foodborne illnesses each year, and foodborne illness costs the United States $14.6-16.3 billion annually. Because foodborne illness continues to be costly, in terms of money and health, in the United States, new aspects of food protection are being evaluated including microbial contamination of the crop production environment. This study evaluated two separate aspects of environmental microbial contamination. The first portion of this study evaluated the presence and spread of Salmonella spp. in the environment surrounding the Auburn University Poultry Research Unit. Two Nalidixic acid resistant Salmonella strains were used for tracking the spreading of Salmonella spp. throughout the environment. Nalidixic acid resistant strains were isolated from environmental samples 0.44 km and 0.38 km away from the central location of the poultry farm. This signifies that environmental carriers/factors could contribute to the spreading of Salmonella spp. In addition, Salmonella serogroup B was isolated from 8 out 13 sampling locations throughout a 3-month time span. Serotyping of these isolates showed that they are Salmonella Saintpaul. Pulse Field Gel Electrophoresis (PFGE) was performed and showed that those isolates are genetically identical. The second portion of this study focused on the application of microbial water safety guidelines set forth by the 2016 Food Safety Modernization Act (FSMA): Produce Safety Rule. Six farms in the East Central Alabama area were selected, and water samples were collected once a month from October 13, 2015 to June 20, 2016 from five farms with ponds on them. Four out of the six farms have streams running through them. For these, surface water samples were collected at the site where the stream enters and exits the farm. Each point that was sampled was considered a site, and there were a total of thirteen sites. Following the U.S. Environmental Protection Agency (USEPA) method 1603, generic Escherichia coli were enumerated using modified mTEC agar. Geometric Mean (GM) and Statistical Threshold Value (STV) were calculated using Cornell University’s Produce Safety Alliance Excel tool. Although differences were seen in E. coli numbers from samples collected in different months, based on the calculations, water quality of five sites is in compliance with water quality microbial requirements. Eight sites had GM and/or STV values that did not comply with these standards. However, by using the Excel tool, a die-off period of one day is suggested for seven of them, and a two-day die-off period is suggested for one. For all four streams sampled, the outgoing stream sites did not consistently show higher generic E. coli concentrations than the incoming stream sites. No conclusion can be made at this point about whether animal agriculture has significant impact on microbial surface water quality. However, land use, geographical layout, weather variations, and even surrounding land factors can affect the microbial quality of surface water sources (Mallin, Johnson, & Ensign, 2008). For these reasons, it is important that each water source to be used for irrigation be monitored to prevent crop contamination.