Source Molecular: Only Commercial Lab Offering Digital PCR for Environmental Water Testing

Source Molecular Corporation is the only commercial laboratory in the United States providing Droplet Digital Polymerase Chain Reaction (ddPCR or Digital PCR) service in the field of environmental water testing. It is also the world’s only ISO-accredited microbial source tracking (MST) laboratory.

Routine water quality monitoring tests for fecal indicator bacteria such as enterococci, which may or may not be from human sources. Since exposure to human fecal bacteria are more likely to make people sick, researchers developed the use of genetic markers (MST markers) to differentiate FIB from animals and humans through quantitative PCR (qPCR).

Digital PCR is the next generation PCR-based quantification technology. As with qPCR, when combined with MST markers, digital PCR can tell water managers the source of fecal pollution and the extent of fecal pollution is in the water. Moreover, digital PCR addresses certain limitations of qPCR and it is particularly suited for testing difficult environmental water samples.

Dr. Yiping Cao, Source Molecular’s Vice-President of Technology, pioneered the applications of the ddPCR technology in environmental water testing. When she was senior microbiologist at the Southern California Coastal Water Research Project (SCCWRP), Dr. Cao and her colleagues developed and validated a suite of digital PCR assays and subsequently conducted an inter-laboratory comparison study on the use of Digital PCR to monitor environmental contaminants in water. Source Molecular was one of the laboratories that supported the study.

Droplet Digital PCR

Dr. Cao’s work has garnered the attention of Front Line Genomics, a London-based online and print magazine focusing on genomics. In an interview, Dr. Cao explained that the ddPCR method utilizes a water-oil emulsion droplet system. A twenty-microliter sample reagent mixture would be partitioned into nanoliter water-in-oil droplets. This creates tens of thousands of miniature reactions. Then binary positive or negative results for each droplet are recorded. The percentage of negative droplets is used to calculate original sample concentration based on Poisson statistics. In qPCR, tests can underestimate pollution because environmental water often has compounds that interfere with and slow down the PCR process. However, the binary nature of digital PCR quantification greatly reduces impact of interfering compound. This makes digital PCR highly suitable for complex environmental samples such as storm water or those contain high concentration of interference compounds.

In addition, the huge amount of sample partitioning allows ddPCR to measure multiple targets at the same time. “Because we partition the entire sample into droplets, each droplet only has one target. In this way, you are essentially able to quantify both targets at the same time, at sample level,” Dr. Cao told Front Line Genomics.

Dr. Cao and her colleagues developed and validated a duplex digital PCR assay (EntHF183 dPCR) for simultaneous quantification of Enterococcus spp. and the human fecal-associated HF183 marker. Water Research, a leading international journal, published the ddPCR assay. Researchers found that ddPCR provides consistent quantification of Enterococcus and HF183 whether quantified individually or simultaneously in the same reaction. The ddPCR assay is also able to tolerate PCR inhibitor concentrations that are one to two orders of magnitude higher than those tolerated by qPCR.

Since then, Dr. Cao and her colleagues have developed a suite of ddPCR assays for various FIB, MST marker, and pathogens. They published a book chapter on the topic of using digital PCR for ambient water monitoring. Many high-profile epidemiology, risk assessment and microbial source tracking studies in southern California have used these digital PCR assays. The National Association of Clean Water Agencies recently recognized an MST project in Boston that used Digital PCR. The association found it to be an effective and innovative project. More water managers are now using ddPCR in their bacteria source tracking projects.

World’s Only ISO-Accredited MST Lab

Source Molecular is also the world’s only ISO/IEC 17025:2005 microbial source tracking (MST) laboratory. The ISO-accreditation is a recognition of the laboratory’s management system for quality.

The American Association for Laboratory Accreditation (A2LA) found Source Molecular competent to perform tests on water, filters, and DNA samples for Human, Cow, Dog, Ruminant, Beaver, Pig, Bird, Gull, Poultry Litter and Goose. A2LA is an independent and internationally-recognized accreditation body in the U.S. It offers comprehensive laboratory and laboratory-related accreditation services and training.

Hundreds of water managers have worked with Source Molecular on bacteria source tracking projects around the world. To discuss how its genetic tests would help resolve issues in the watershed, just select a convenient time.