Leman: Swine pathogens in groundwater
Pathogens on the landscape from swine manure can contaminate wells
16 March 2026
2 minute read
By: [Excerpts of a presentation by Gabrielle E. Doughan, Iowa State University, USA and colleagues at Iowa State University, United States Geologic Survey, and USDA Agricultural Research Service, during the 2025 Leman Swine Conference]
Groundwater from private wells is a poorly understood biosecurity risk for pathogen transmission on swine farms. Water is one of the largest daily inputs on swine farms by volume and is not routinely tested or disinfected before consumption by animals. However, pathogens on the landscape, such as bacteria, viruses, and protozoa from swine manure, can reach groundwater and contaminate wells, presenting a potential route for disease transmission and increased biosecurity risks.
In laboratory studies, porcine reproductive and respiratory syndrome virus (PRRSV) has been demonstrated to percolate and be successfully recovered via virus isolation from Minnesota soils, as well as to survive up to 11 days in various water sources.
Porcine circovirus 2 (PCV2) has been detected in groundwater, and tile drains. Swine fecal indicator bacteria have also been identified in groundwater sources, demonstrating that a potential manure-to-groundwater pathway exists.
This study surveyed private wells supplying Iowa swine farms to detect endemic swine pathogens and swine manure markers. Private wells supplying 40 unique commercial swine farms in Iowa were sampled in the spring (n=20) and fall (n=20) of 2024. Enrolled farms included growing pig operations (n=36), breeding farms (n=3), and one nursery. Farm inventories ranged from 1200 to 5900 head with an average of 3200 head. Negative control samples were collected in the field for each field sample, which were tested for all organisms if the corresponding field sample tested positive for any organism. Samples were analyzed for 10 microbial gene targets using quantitative PCR.
Organisms were sampled for PRRSV-2, porcine epidemic diarrhea virus (PEDV), PCV2, rotavirus C, swine influenza A virus (IAV-S), Cryptosporidium spp., Salmonella spp., enteropathogenic E. coli, and two swine manure markers (pig Bacteroides).
Endemic swine pathogens and manure markers were detected in spring (7 of 20 samples) and fall (3 of 20 samples). Swine manure markers were detected most frequently (7 of 40 samples). Other detections included Cryptosporidium spp. and PCV2 (3 or fewer samples each); five samples contained two or more detected organisms. Tested control samples were negative for all organisms, except for one control sample that tested positive for PCV2 but no other organisms were detected.
Results demonstrate that manure-borne microorganisms, including swine pathogens, can contaminate private well water used for pig production. Findings indicate that groundwater may be a potential biosecurity risk for swine farms.
