Why Digital PCR for Pathogen Quantification?

Digital PCR partitions every sample into tens of thousands of independent reactions and counts positive partitions directly, yielding an absolute count of target copies per volume without reference to a standard curve. For pathogen quantification in environmental samples, this approach offers four meaningful advantages:

• Sensitivity at low pathogen concentrations typical of treated water, recycled water, and dilute environmental samples
• Inhibitor resistance in challenging matrices including wastewater, stormwater, sludge, and shellfish tissue
• Multiplexing of up to 6 targets per reaction, enabling efficient panel-based screening
• Reproducibility across operators, instruments, and laboratories, important for longitudinal monitoring and regulatory defensibility

Read more about digital PCR for environmental samples

Pathogen Panels

H₂O Molecular offers validated pathogen panels designed around specific monitoring use cases. All panels are run by dPCR, and individual targets can be ordered independently. Example panels, including but not limited to:

Respiratory Pathogen Panel

For wastewater-based epidemiology and respiratory disease surveillance:

• SARS-CoV-2
• Influenza A
• Influenza B
• Respiratory Syncytial Virus (RSV)
• Adenovirus (respiratory subtypes)

Enteric Pathogen Panel

Viral, bacterial, and protozoan enteric pathogens commonly monitored in water and shellfish:

• Viral: norovirus GI, norovirus GII, rotavirus, enterovirus, adenovirus, hepatitis A virus, hepatitis E virus
• Bacterial: Salmonella spp., E. coli O157:H7, Shigella spp., Campylobacter jejuni, Listeria monocytogenes
• Protozoan: Cryptosporidium parvum / hominis, Giardia lamblia

Vibrio Pathogen Panel

For coastal water, shellfish, and aquaculture applications:

• Vibrio parahaemolyticus
• Vibrio vulnificus
• Vibrio cholerae

Oyster Enteric Pathogen Panel

A specialized panel for shellfish tissue and growing-area surveillance, combining the highest-priority enteric viruses and bacterial pathogens of concern for shellfish sanitation programs.

Antimicrobial Resistance (AMR) Panels

Quantification of clinically important antimicrobial resistance genes in wastewater, surface water, and reuse applications:

• Beta-lactamase genes: blaCTX-M, blaKPC, blaNDM, blaOXA-48, blaTEM, blaSHV
• Colistin resistance: mcr-1, mcr-2, mcr-3
• Vancomycin resistance: vanA, vanB
• Sulfonamide / tetracycline resistance: sul1, sul2, tetA, tetW, tetM
• Integrase markers: intI1 (class 1 integron), a broad indicator of anthropogenic resistance burden

Legionella Panel

• Legionella pneumophila
• Legionella spp. (genus-level)

Individual Pathogen Assays

Beyond panels, individual targets can be ordered for focused investigations. Common requests include:

• Norovirus GI, Norovirus GII: outbreak investigation and recycled water monitoring
• Cryptosporidium and Giardia: source water and recreational water assessments
• Legionella pneumophila: premise plumbing and cooling tower investigations
• Naegleria fowleri: warm freshwater and treatment system monitoring
• Helicobacter pylori: drinking water investigations
• SARS-CoV-2: wastewater surveillance

See Resources for our full list of pathogen assays

Custom Assay Development

Our team has extensive experience designing and validating digital PCR assays for novel targets. If your project requires quantification of an organism, gene, or sequence not on our panel list, we offer end-to-end custom assay design, validation against performance criteria, and ongoing analytical service. [Talk to a Scientist]

Sample Types We Analyze

Wastewater (influent, effluent, sludge, biosolids) · Drinking water (raw and treated) · Recycled water · Stormwater · Surface water · Groundwater · Marine and coastal water · Shellfish tissue · Sediment · Premise plumbing · Cooling tower water

Who We Work With

Public health departments · Water and wastewater utilities · State and federal regulators · Recycled water program managers · Shellfish industry and growing-area managers · Aquaculture operations · Environmental consultants · Academic and clinical researchers