Author's personal copy Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems5

The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to themicrobial biota and ecological structure of both the pig andwastemanure lagoonwastewater.While someof these changesmaynot benegative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swinesow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits onmost farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future “downstream” implications from both an environmental and public health perspective. Published by Elsevier Ltd. 5 United States Department of Agriculture, Agricultural Research Service, Genetics and Precision Agriculture Research Unit, Post Office Box 5367, Mississippi State, MS 39762. Approved for publication as Journal Article No. Je12413 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University. Mention of a trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion of other products that may be suitable. This work was prepared by employees of the U.S. Government as part of their official duties and is in the public domain and may be used without further permission. * Corresponding author. Tel.: þ1 662 320 7411. E-mail address: [email protected] (J.P. Brooks). Available online at www.sciencedirect.com