Sampling and analytical capabilities

Science Center Objects

Molecular and culture analysis methods are paired with sampling capabilities across environmental matrices to address a wide range of questions and problems. LIDE collects and analyzes samples from groundwater, surface water, runoff, wastewater, sediments, soil, manure, compost, digestate, and air.

Photo of glass-wool filters used to concentrate waterborne virus material

Photo of glass-wool filters used to concentrate waterborne virus material.

Sampling capabilities

To provide comprehensive monitoring and analysis, LIDE samples for pathogens in a variety of settings and uses large-volume filtration concentration techniques that allow detection of low pathogen levels. The LIDE Outbreak Rapid Response team is equipped to use current sampling methods on short notice.

  • Glass wool filtration and dead-end ultrafiltration are used to concentrate viral, bacterial, and protozoan pathogens in water samples
  • Button filters and Andersen impactors concentrate airborne pathogens
  • Sampling protocols available for groundwater, surface water, agricultural runoff, wastewater, aquatic sediments, soil, manure, compost, digesate, and air


Analytical capabilities

LIDE has capabilities to analyze a large number of samples (nearly 20,000 assays per year) using state-of-the-art analysis techniques. These include:
Molecular methods

              ‒    Two real-time qPCR machines and two robotic nucleic acid extractors allow high sample throughput
             ‒    qPCR inhibition is measured and attenuated for every sample
             ‒    Evaluation and optimization of additional qPCR assays as needed

  • Droplet digital PCR for absolute quantification
  • Nucleic acid sequencing and gene analysis for performing pathogen subtyping and molecular epidemiology 
  • Automated ribosomal intergenic spacer analysis (ARISA) to assess microbial community composition in soil and water

Culture and quantification methods

  • Cell culture and Integrated Cell Culture-qPCR for human and bovine viruses, Cryptosporidium spp., and avian influenza
  • Standard enrichment and plating methods for bacterial pathogens
  • Coliphage (somatic and F-specific): presence/absence (U.S. Environmental Protection Agency (EPA) Method 1601) and single-agar layer (EPA Method 1602)
  • Standard methods for total coliforms, E. coli, and Enterococci
  • Epifluorescent microscopy for Cyclospora cayetanensis, Toxoplasma gondii, microsporidium, Eimeria, Cryptosporidium, and Giardia

Data analytical methods


Other laboratory capabilities

  • LIDE is a Biosafety Level 2+ approved lab with extensive QA/QC protocols
  • Automated Laboratory Information Management System provides advanced data management services for all qPCR data management and quality assurance/quality control  (QA/QC) evaluations