Swine Microbial Source Tracking Case Studies

Detect Swine Fecal Load, Quantify % Swine Contamination, Multiple Samples Recommended

Swine MST Case Studies 2017-11-22T11:02:53+00:00

1. Northeast Cape Fear River Contaminated by Hog Waste

Hog waste contamination in the Northeast Cape Fear River was detected by investigators from the Water Resources Research Institute of the University of North Carolina in water samples they collected in 2010.

Researchers point out that pollution from concentrated animal feeding operations (CAFOs) during and after large storms has been well documented in North Carolina. Contributors to water quality degradation in North Carolina rivers, estuaries, and groundwater supplies include chronic runoff and subsurface movement from sprayfields. However, no definitive investigation has been conducted to identify swine manure contamination as a source of chronic microbial pollution in watersheds. This led investigators to initiate an examination of the levels of swine manure contamination in waterways of hog farm areas by detecting and quantifying the 16S rRNA genes of hog-specific Bacteroides-Prevotella.

In order to monitor hog-specific fecal contamination in the Cape Fear River watershed, two molecular techniques were employed: T-RFLP (Terminal Restriction Fragment Length Polymorphism) and qPCR (Quantitative Polymerase Chain Reaction) of 16S rRNA genes in Bacteroides-Prevotella. TRFLP is a DNA fingerprinting method, which is used to compare the structural similarities of Bacteroides-Prevotella communities in hog lagoon wastes and water samples collected from 9 stations in two watersheds; the Black River and the Northeast Cape Fear River. The qPCR technique is used to quantify the levels of hog manure contamination in each water sample based on the copy numbers of hog specific Bacteroides-Prevotella 16S rRNA genes. In addition, fecal coliform bacteria counts and nutrient analyses have been conducted along with the molecular analysis.

In their 2011 progress report, investigators disclosed they completed Quantitative PCR assays of water samples collected bi-monthly from 5 sites in the Black River watershed and 4 locations in the Northeast Cape Fear River watershed. Investigators conducted multiple correlation analyses between the Q-PCR data and the water quality parameters monitored at the sampling stations.

According to investigators, the hog waste contamination in the Northeast Cape Fear River seemed to depend primarily on proximity of the sampling site from upstream hog related facilities. Sites furthest away from hog farms had the least amount of contamination compared to those directly downstream from a hog facility. On a seasonal basis, all but one site had a spike in hog waste contamination during May 2010. This is most likely a result from run-off or leaching from seasonal spraying of fields with lagoon waste. In contrast, the contamination in the Black River appears to be more related to the sampling location on the river as well as rainfall events. One site had the highest overall contamination in the Black River watershed. Even though the sampling station is not located in immediate proximity from any CAFOs, there are numerous CAFOs in its watershed (153). The contamination levels were also significantly correlated to rain events on the day of sampling.

Researchers contend that estimating the scales of swine manure contamination in streams, rivers and groundwater will allow development of proper and effective efforts to manage and remediate water quality in North Carolina.

Click for a copy of the Report and the 2011 Progress Report.

2. French Researchers Develop Two New Pig Markers

Pig fecal contamination was not as frequent as human or bovine fecal contamination in the Daoulas estuary in Brittany, France, a 2009 study revealed.

French researchers designed a library-independent microbial source tracking method targeting Bacteroidales host-specific 16S rRNA gene markers by real-time PCR to discriminate pig fecal pollution from other pollution. Two pig-specific Bacteroidales markers (Pig-1-Bac and Pig-2-Bac) were developed by the team.

Samples collected around pig farms were positive of Pig-1-Bac and Pig-2-Bac. They were also detected in water samples collected downstream from pig farms but never detected near cattle farms. But these were in much lower concentrations than the human-specific and ruminant-specific markers.

The study concluded that among the two pig Bacteroidales markers designed, the Pig-2-Bac marker appears to be the most suitable, as it was detected more frequently in rivers. It also confirmed that fecal pollution in river waters often comes from multiple sources. Researchers suggested that additional sampling should be carried out during high-rainfall events within the pig slurry spreading period to determine whether the pig markers and thus pollution from pigs could be more prevalent then.

Researchers note that the Daoulas estuary has commercial and recreational shellfish harvesting areas and is potentially subject to fecal contamination. They believe these pig-specific Bacteroidales markers could represent an efficient tool in a microbial source tracking toolbox, to discriminate between fecal pollution from pigs and other fecal sources. “This tool will assist in the management of microbial water quality of bathing and shellfish farming areas.”

The study, “Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers,” was published in the March 2009 edition of the Applied and Environmental Microbiology journal. It was conducted by French researchers Sophie Mieszkin and Michele Gourmelon of Ifremer EMP, Laboratoire de Microbiologie; and Jean-Pierre Furet and Gerard Corthier of Unite d’Ecologie et de Physiologie du Systeme Digestif (UEPSD), INRA.