Skip to main content
U.S. flag

An official website of the United States government

Pathogen analyses support investigations of how disease-causing microbes affect the quality and availability of groundwater, rivers, and lakes for water consumption and recreation.

The Laboratory for Infectious Disease and the Environment (LIDE) analyzes human, livestock, and zoonotic pathogens, including viruses, bacteria, and protozoa.  The LIDE can help guide selection of the pathogen tests relevant to your project goals, and they offer support for study design, sample collection, data analysis, and interpretation of pathogen test results.

  • Pathogen analyses quantify microbial threats to human and animal health in drinking water, recreational water, groundwater, and other matrices.
  • Results can be used with quantitative microbial risk assessment to characterize health risks from exposure to pathogens via drinking water or water recreation.  For example, we used pathogen measurments to estimate the risk of illness from drinking public well water.
  • Microbial source tracking can be combined with pathogen analyses to identify potential sources of pathogen contamination, like wastewater and livestock manure.  For example, we identified human and livestock contamination of private wells in rural Wisconsin and related contamination sources to health risk in an agricultural region.
  • Genetic testing techniques allow specific identification of many pathogens, and microscopy and culture methods are also available for some pathogens.


Pathogen assays available for analysis by quantitative polymerase chain reaction (qPCR) at LIDE (additional qPCR assays are evaluated and optimized as needed):

Viral pathogens

Avian viruses

Human adenovirus groups A-F Avian influenza (H5 subtype)
Human enterovirus Avian influenza (H7 subtype)
Hepatitis A virus Poultry parvovirus
Human polyomavirus


Norovirus genogroup I

Bovine pathogens

Norovirus genogroup II Bovine adenovirus
Hepatitis E virus Bovine enterovirus
Influenza A (matrix gene) Bovine polyomavirus
Rotavirus group A (NSP3 gene) Bovine viral diarrhea virus type 1
Rotavirus group A (VP7 gene) Bovine viral diarrhea virus type 2
Rotavirus group C Bovine coronavirus
  Mycobacterium avium subsp. Paratuberculosis (MAP 251)

Bacterial pathogens

Mycobacterium avium subsp. Paratuberculosis (MAP 900)
Campylobacter jejuni


Enteropathogenic E. coli (eae gene)

Porcine pathogens

Legionella pneumophila (serogroup 1) Porcine adenovirus
Salmonella (invA gene) Porcine epidemic diarrhea virus
Salmonella (ttr gene) Swine influenza A (matrix gene)
Shiga toxin-producing bacteria (stx1, stx2) Swine influenza A (H1 subtype)
Staphylococcus spp.  
Streptococcus spp.  

Protozoan pathogens

Cryptosporidium spp.  
Cryptosporidium baileyi  
Cryptosporidium bovis  
Cryptosporidium galli  
Cryptosporidium hominis  
Cryptosporidium meleagridis  
Cryptosporidium parvum  
Cryptosporidium suis  
Cryptosporidium ubiquitum  
Giardia lamblia