Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure as influenced by three swine management systems

Authors: Brooks, John; Adeli, Ardeshir; McLaughlin, Michael

Submitted to: Water Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2014
Publication Date: 3/19/2014
Publication URL: https://handle.nal.usda.gov/10113/59340
Citation: Brooks, J.P., Adeli, A., McLaughlin, M.R. 2014. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure as influenced by three swine management systems. Water Research. 57:96-103.

Interpretive Summary: Changes to swine farm management systems due to economic pressures have far reaching influences on the microbial environment of not only the pigs, but on the manure lagoons as well. The microbial population of the manure lagoon effluent can affect the soil as well as nearby ground and surface water if not properly managed. The manure lagoon environment can select for bacterial pathogens, antibiotic resistance, and other members of the microbial community which can affect the nutrient quality of the effluent and hence the value to those that rely on it for fertilizer. In this study, 37 farms were visited comprised of three farm types, including: sow, nursery, and finisher farms. The presence of younger pigs in the sow and nursery farms selected for more antibiotic resistance genes, while some pathogens were selected for in the finisher farms. The microbial ecology of all three manure lagoon types were significantly different; however, it appears that sow and nursery farms were more similar to one another than finisher farms were to the other farm types. Changes in these populations have future “downstream” implications from both an environmental and public health perspective.

Technical Abstract: The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vastly different microbial constituents in both the pig and the manure lagoons used to treat the fecal waste of the operation. While some of these changes may not be negative, it is possible that the CAFO can positively enrich antibiotic resistant bacteria or pathogens. The purpose of this study was to measure the microbial constituents of swine sow, nursery, and finisher farm manure lagoons 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. Additionally, 16S rRNA sequence profiles were created from unique farm profiles and compiled to create individual libraries for each farm type. 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, except for mecA, which was only detected in sow and nursery farms. The influence of individual pressures associated with each farm type influences the bacterial populations of the lagoon effluent. Finisher farms have fewer antibiotic inputs, in general, and as such demonstrate fewer antibiotic resistance genes. Likewise, the stabilization of the gut microflora induced a less diverse 16S rRNA distribution. Additionally, Campylobacter and Salmonella culture most probable number (MPN) data (from a previous study) was compiled and compared to genomic values to determine a potential genomic unit to MPN ratio. Ratios ranged from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria are selected for, given the farm type pressures. Changes in these populations have future “downstream” implications from both an environmental and public health perspective.