Grantee Research Project Results
2020 Progress Report: A Field-Deployable Droplet Digital PCR System for the Rapid Detection of Waterborne Bacterial Pathogens
EPA Grant Number: SU839880Title: A Field-Deployable Droplet Digital PCR System for the Rapid Detection of Waterborne Bacterial Pathogens
Investigators: Li, Yiyan
Current Investigators: Li, Yiyan , Ferguson, James , Duran, Jesse , Theobald, Nic , Kukula, Kaitlyn
Institution: Fort Lewis College
EPA Project Officer: Callan, Richard
Phase: I
Project Period: October 1, 2019 through September 30, 2020 (Extended to September 30, 2021)
Project Period Covered by this Report: October 1, 2019 through September 30,2020
Project Amount: $24,824
RFA: P3 Awards: A National Student Design Competition Focusing on People, Prosperity and the Planet (2019) RFA Text | Recipients Lists
Research Category: P3 Awards , P3 Challenge Area - Safe and Sustainable Water Resources
Objective:
Conventional waterborne bacteria monitoring is carried out by traditional culturing methods which suffer from long turnaround time, inaccurate bacteria count, and unclear genotype characterizations. The main goals of this proposed project are: 1) Develop a field-deployable Droplet Digital Polymerase Chain Reaction (ddPCR) system that can rapidly detect pathogenic Escherichia coli (E. coli) in the field. 2) Use this proposed system to test the water samples of Animas River and the Bear Creek in Colorado. 3) Educate communities (including the Native American tribes) in the four-corner area on the importance of water resource protection and the technologies for environmental protection.
Progress Summary:
The main goal of this project is to develop a field-deployable Droplet Digital Polymerase Chain Reaction (ddPCR) system that can rapidly detect pathogenic Escherichia coli (E. coli) in the field. There are five objectives described in the original application to be progressively completed during the funding cycle. The tasks include the ddPCR assay development, microfluidic device design, and fabrication, design and test a customizable PCR thermocycler, system integration, and field tests. The team has received strong institutional and external support since this project was granted and by leveraging these supports the team expanded to 9 students and 3 faculty mentors (volunteers) during the first year of the funding cycle. Six of the students were from a senior design team and they have graduated in April 2020 from the college. While the senior design team helped with the microfabrication of the microfluidic chips and environmental E. coli collection, two engineering students were hired by this grant to work on the PCR machine development and the optics of the detection system. One biology student was recruited in the summer of 2020 to train our engineering students on genetic engineering and DNA sequencing for bacterial samples. In addition to the funding provided by this award, the team has raised an extra $6,000 for lab materials and supplies, $9,711 for a VWR -80 ℃ freezer to permanently store the environmental bacterial samples, and $23,999 for a Raman spectrometer. As a result of all the efforts and supports, the team has made significant progress toward the objectives of the proposal and contributed two peer-reviewed IEEE conference articles, two poster presentations, and two oral presentations. As all the students back to the lab after the winter break and the labs are re-opened for research, the team pledges to implement the verified PCR assays in single-cell droplets and run the field tests in the summer of 2021.
Future Activities:
We found that Elution fluid was found to be the most reliable and cost-effective method for concentering 100 mL of E. coli spiked water into volumes of approximately 0.1 mL. Our fabricated microfluidic device was able to create uniform droplets of the appropriate size (approximately 50 microns). However, we are still experiencing issues with premature wetting with the microfluidic chips. Our optical detection setup was able to detect fluorescence down to 1:100,000 concentrations. False readings were found occasionally from the DAQ. In the next phase of this project, the entire device will need to be tested and timed in series, eventually using raw water during testing. After these tests have been successfully completed, a field-deployable prototype will be fabricated.
Journal Articles:
No journal articles submitted with this report: View all 4 publications for this projectSupplemental Keywords:
Rapid, Bacteria Detection, ddPCR, Single CellProgress and Final Reports:
Original AbstractThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.