טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentOhad Shoshanit
SubjectMicrobial Source Tracking
DepartmentDepartment of Biotechnology and Food Engineering
Supervisor Professor Yechezkel Kashi
Full Thesis textFull thesis text - English Version


Abstract

Standard monitoring of water quality relies on indicator bacteria to assess possible risks for public health. Indicator bacteria are tested using culture-based methods and their acceptable levels are specified in public health regulations, worldwide.  However, detection of indicator bacteria without pinpointing their specific host species limits the potential scope and efficacy of pollution elimination. To that end, selected advanced molecular tools known as Microbial Source Tracking (MST) were recruited to attribute water fecal contamination events to their respective host species, thereby improving analysis of fecal contamination in complex and constantly changing water environments.  

Our MST testing framework targeted human, ruminant, bovine, porcine, and waterfowl fecal associated DNA markers, and included the following aspects. 1)  Testing MST assay feasibility. 2) Developing a novel DNA sequence screening approach to design new avian qPCR fecal markers using an NGS platform. 3) Developing a methodological approach for analyzing qPCR data from water samples with low bacterial concentrations, to decrease detection thresholds. 4) MST monitoring implementation in environmental samples to decipher fecal contamination sources.

MST has been implemented on a monthly basis during an entire calendric year, to electively, proactively, and routinely monitor three water springs at the Galilee area. During a 2018 summer Leptospirosis outbreak, extensive epidemiologic water monitoring of streams at the Golan Heights was conducted. By implementing MST qPCR battery assays we were able to identify temporal changes in host species presence in select streams. Thus, information generated by the MST methodology supported comprehensive monitoring processes that enabled appropriate and prompt decision making, which directly affected the solution for an urgent public health related crisis.

This research included comprehensive studies involving various components, including the development of novel avian marker screening methods, the assembling of a species-wide marker battery, successfully testing its analysis in low bacterial concentrations, and finally, applying it in complementary water monitoring during a public-health related crisis