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Microbial Source Tracking

Microbial Source Tracking (MST) is a genetic testing tool that identifies sources of fecal contamination in surface water, stormwater, and groundwater. 

Gene-Trac MST

Gene-Trac MST uses microbial genetic markers associated with specific microbial hosts (often humans, animals, or agricultural sources) to help our clients better understand and manage fecal pollution in surface water, groundwater, wastewater, and stormwater systems.  

 

Gene-Trac MST is a powerful tool to help pinpoint likely sources, assess risk, plan remediation, and support regulatory decision-making.

Gene-Trac MST Provides Actionable Data for Risk Assessment, Source Identification, and Remedial Action Assessment

SiREM’s quantitative PCR (qPCR) assays target host-associated microbial genetic markers and general microbial populations as follows: 

  • HF183, Human-Associated Bacteroides: Detects human sewage impacts according the USEPA method

  • Ruminant–Associated Bacteroidales: Identifies fecal contributions associated with cattle

  • Canine-Associated Bacteroides: Detects urban dog waste sources

  • Wild–Bird–Associated Helicobacter: Quantifies fecal contamination associated with seagulls

  • Universal Microbial Profiles: Comprehensive microbial population profiles for pathogen screening and high-resolution source identification using Gene-Trac next generation sequencing (NGS) 

Gene-Trac MST supports multiple stages of source identification and remediation: 

  • Identify contamination from agricultural, urban, and wildlife sources.

  • Differentiate between human and animal fecal contamination.

  • Prioritize remediation actions and infrastructure improvements.

  • Make watershed management decisions (e.g., Total Maximum Daily Load calculations).

  • Support regulatory compliance.

  • Track changes in contamination sources over time and following corrective actions.

Contact Us

Please contact our technical team for more information on Gene-Trac MST or to obtain a cost quotation. 

Documentation

MST Cut Sheet

 

Accreditation and Data Quality Assurance

Gene-Trac MST standard operating procedures adhere to the highest quality standards to provide data suitable for regulatory and compliance applications:

  • SiREM’s qPCR testing is accredited to the ISO/IEC 17025:2017 quality system standard, including documented training and competency programs, method verification and validation protocols, and regular intra- and inter-laboratory proficiency testing.

  • All tests include robust data quality assurance procedures, including positive, negative, and inhibition controls, with full and transparent data reporting for all controls.

  • Full traceability for test procedures with Level IV reporting are available upon request.

Custom Target Development and Regional Adaptation

Veterans in qPCR assay development and implementation, SiREM offers custom MST assay development and adaptation to support site-specific and regulatory needs:

  • Develop custom host-associated markers for specific regions or species.

  • Optimize assays for matrix-specific performance and sensitivity requirements.

  • Perform assays for direct detection of viral or microbial pathogens.