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Environmental Sampling and Analytical Methods (ESAM) Program

2020 Pathogen Methods Query

Please note: The web page you are viewing requires JavaScript. This web page is an enhancement to provide users of the Selected Analytical Methods for Environmental Remediation and Recovery (SAM) - 2017 document with the ability to search the analytical methods it contains. If you are unable to use the query, the methods may also be found in the PDF version of the document. In addition, due to the complexity of some tables and graphics, some of our products are not amenable to a screen reader. 

If you have trouble accessing information contact Kathleen Nickel ( and alternative accommodations will be made.

See: Selected Analytical Methods for Environmental Remediation and Recovery (SAM) - 2017.

Following a microbial contamination incident, it is assumed that identification, confirmation and strain-level characterization of the pathogen have been completed before the U.S. Environmental Protection Agency’s (EPA) remediation actions begin. The first phase of EPA’s actions includes site characterization, to determine the extent and magnitude of contamination and to guide remediation planning. Based on the results of site characterization, EPA will determine the approach for decontamination. During the post decontamination (clearance) phase of remediation, samples are collected and analyzed to determine the efficacy of the decontamination treatment. SAM provides guidance in determining the appropriate methods for each of these remedial phases, with emphasis given to the following environmental sample types: aerosols, particulates (wipes or swabs), soils, drinking water and post decontamination waste water.

Selection of analytical methods should be based on specific data and information needs, including consideration of the remediation phase and whether there is a need to determine either the presence of a pathogen, the viability of a pathogen or both. The fitness of a method for an intended use is related to site-specific data quality objectives (DQOs) for a particular remediation activity. The pathogen methods selected for SAM have been assigned tiers (below) to indicate a level of method usability for the specific analyte and sample type. The assigned tiers pertain only to technical aspects of method usability, and do not pertain to aspects such as cost, equipment availability and sample throughput.

Method-specific usability tiers are provided in SAM Appendix C. See SAM 2017 Appendix C: Selected Pathogen Methods.

Any questions regarding this information should be addressed to the appropriate contact(s). See SAM Technical Contacts.

Tier I: The method was developed for the pathogen and sample type. The method has been evaluated by multiple laboratories, a detailed protocol has been developed, and suitable QC measures and checks are provided. (Examples: EPA Method 1623.1 [Cryptosporidium in drinking water]; Standard Methods 9260 E [Shigella culture method].)

Tier II: The pathogen is the target of the method, and the method has been evaluated by one or more laboratories. The available data and/or information indicate that additional testing and/or modifications will likely be needed. (Example: Cunningham et al. 2010 [Shigella molecular method].)

Tier III: The pathogen is not the target of the method but the method is for the specific sample type and the pathogen is similar to the target of the method (i.e., vegetative bacteria, spore-forming bacteria, virus or protozoan). Data and expert opinion suggest, however, that the method(s) may be applicable with modifications. (Example: EPA Yersinia pestis protocol for Salmonella enterica serovar Typhi (S. Typhi) in post decontamination waste water.)

Note: Please see SAM Updates for important information about updates to SAM methods that may supercede methods listed in the SAM document and the results of this query.

Step 1. Select a Pathogen

Step 2. Sample Type(s)

Step 3. Phase(s)

Step 4. Retrieve Results