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 Proposal – Rapid Detection of Microbial
 Contamination of Water: Application of
 Molecular Technologies to Source and
 Potable Water Monitoring

Note: EPA no longer updates this information, but it may be useful as a reference or resource.


Environmental Problem Statement


Team Members

Progress Report (PDF) (3 pp, 26 KB) September 2006

Approaches and Milestones (PDF) (2 pp, 160 KB)

Microbial pathogens continue to contaminate drinking water supplies and cause waterborne disease outbreaks (WBDOs) despite current regulations designed to prevent and control the spread of microbial pathogens in public and individual water systems. In the United States, from 1991 to 2000, 173 waterborne outbreaks and 432,733 cases of illness were reported. In 1993, an estimated 400,000 people became ill in Milwaukee, Wisconsin, after drinking water contaminated with Cryptosporidium parvum, a waterborne pathogen that had contaminated the drinking water supply. The Centers for Disease Control and Prevention estimate that pathogen-contaminated drinking water annually results in about a million new cases of illness and about a thousand deaths. Most cases, however, are not reported to health care providers.

EPA currently regulates two indicators of microbiological drinking water quality: total coliform and turbidity. Because of the great diversity of microbial pathogens, current indicators of water quality may not detect all types of microbial contamination. For example, some pathogens do not co-occur with indicators of fecal pollution. In addition, bacterial indicators have greater sensitivity to disinfection, relative to that of viruses and protozoan cysts, which resist disinfection. This sensitivity results in a lack of consistent correlations between indicator absence and the absence of pathogens. Quantitative methods that can detect a broad array of microorganisms are needed.

Another problem with using coliform indicator bacteria as a public health monitoring tool is the relative long time—18 hours to several days—for results to be final. This lag time is a concern for water utility operators who want to respond quickly to a contamination event. Consumers may be adversely affected before existing methods can detect the contamination. Rapid or near real-time analytical methods, which can give results in one to eight hours, not days, are needed.

Definition of the Technology Challenge

Development of Molecular Detection Technology for Monitoring Water
Molecular detection technologies can detect multiple pathogens in a single analysis to make highly specific identifications and to rapidly detect very low numbers of target organisms. Over the last decade, numerous molecular and genetic-based technologies have been developed to detect microorganisms such as flow cytometry, magnetic separation techniques, fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), reverse transcriptase-PCR (RT-PCR), and microarrays.

Although a considerable amount of work has been done to develop rapid, sensitive, and quantitative molecular methods, several challenges remain that must be resolved before EPA will approve these methods to be used to routinely monitor environmental waters. Prior to water analysis, steps involved in concentrating a sample must be developed for the needed sensitivity to detect the low number of pathogens that may be present in water samples. In addition, water samples must be free of interfering substances.

Comparison of Molecular Detection Technologies to Existing Methods
Existing methods are based on the detection of culturable indicator organisms. Results from molecular methods must be related to the existing methods for detection of viable organisms. In addition, molecular methods must have equal or greater detection sensitivity to indicator bacteria methods (1 per 100 milliliter). Molecular methods must detect specific pathogens (a characteristic that existing methods lack), including nonculturable pathogens. Eventually, molecular methods must match the cost of culture-based indicator methods and ease of use.

Acceptance of Molecular Methods
The water industry has used existing indicator bacteria methods for about 100 years. To gain acceptance, molecular methods must satisfactorily demonstrate that they provide useful data on pathogens; these data must have the same or greater predictive value as that of methods for indicator organisms. Current indicator bacteria methods perform satisfactorily in many instances. Molecular methods must not only meet these same requirements, but must demonstrate additional capabilities. Regulators must be satisfied.

Other Guiding Principles

The Government Performance and Results Act (GPRA) requires agencies to report to Congress each year on progress toward their strategic goals. Under GPRA, agencies set annual performance goals and establish measures to determine how well they are achieving those goals. To that end, EPA’s Goal #2: Clean and Safe Water guides this Action Team.

Milestones, Actions, and Due Dates

No. Milestone Due Date
1 Identification of innovative technologies (from EPA-convened workshops and literature reviews) that demonstrate the greatest potential for environmental application  
2 Identification of research gaps for consideration by EPA’s research program, including the Science to Achieve Results and Small Business Innovation Research extramural programs, and the American Water Works Association Research Foundation  
3 Technical support for the expansion of methods  
Quantification of economic and environmental benefits for the use of these methods  

See Also

Government Performance and Results Act


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