Sampling and analytical capabilities
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.
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.
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Glass wool filtration and dead-end ultrafiltration are used to concentrate viral, bacterial, and protozoan pathogens in water samples
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Button filters and Andersen impactors concentrate airborne pathogens
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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
- Real-time quantitative polymerase chain reaction (qPCR) assays for over 30 pathogens, fecal indicators, and antibiotic resistance genes
‒ 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
- Quantitative microbial risk assessment (QMRA) for characterizing human health risk
- Analysis of molecular data by phylogenetic approaches (e.g., similarity coefficients, dendrograms)
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