Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2019 Novel approaches to the low-cost, portable and rapid detection of bacterial pathogens in foods and food-processing environments Stephanie Adeline Hice Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Food Science Commons Recommended Citation Hice, Stephanie Adeline, "Novel approaches to the low-cost, portable and rapid detection of bacterial pathogens in foods and food- processing environments" (2019). Graduate Theses and Dissertations. 17025. https://lib.dr.iastate.edu/etd/17025 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Novel approaches to the low-cost, portable and rapid detection of bacterial pathogens in foods and food-processing environments by Stephanie A. Hice A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Food Science and Technology Program of Study Committee: Byron F. Brehm-Stecher, Major Professor Carmen L. Gomes Aubrey F. Mendonça Gregory J. Phillips Joey N. Talbert The student author and the program of study committee are solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2019 Copyright © Stephanie A. Hice, 2019. All rights reserved. ii DEDICATION This dissertation is dedicated to my parents, Keith and Denise Hice, for their encouragement and words of wisdom during the completion of my PhD. I also dedicate this dissertation to Elliot Bauman, for his continued love and support during our extended time apart. iii TABLE OF CONTENTS ACKNOWLEDGMENTS ........................................................................................ v ABSTRACT………………………………. ............................................................. vi CHAPTER 1 A SURVEY OF RAPID METHODS OF DETECTION OF FOODBORNE PATHOGENS IN DAIRY PRODUCTS AND PROCESSING ENVIRONMENTS ............................................................................................. 1 1.1 Introduction ................................................................................................... 1 1.2 Detection of Foodborne Pathogens Using Paper-Based Analytical Devices 9 1.3 Detection of Foodborne Pathogens Using Bacteriophages ........................... 13 1.4 Multiplex Detection of Foodborne Pathogens by Real-Time PCR ............. 18 1.5 Multiplex Detection of Foodborne Pathogens by RPA ............................... 22 1.6 Automated Point-of-Care (POC) Testing of Foodborne Pathogens by RPA 26 1.7 Novel Sample Preparation Techniques Using Magnetic Ionic Liquids ........ 29 1.8 Conclusions ................................................................................................... 31 1.9 Organization of the Dissertation ................................................................... 33 1.10 References ................................................................................................... 34 CHAPTER 2 DISTINGUISHING BETWEEN METABOLICALLY ACTIVE AND DORMANT BACTERIA ON PAPER ..................................................... 43 Abstract ........................................................................................................ 43 2.1 Introduction ................................................................................................... 44 2.2 Materials and Methods .................................................................................. 46 2.3 Results and Discussion ................................................................................ 48 2.4 Conclusions .................................................................................................. 58 Acknowledgements ............................................................................................. 59 References ........................................................................................................ 59 CHAPTER 3 CAPTURE, CONCENTRATION AND DETECTION OF SALMONELLA IN FOODS USING MAGNETIC IONIC LIQUIDS AND RECOMBINASE POLYMERASE AMPLIFICATION .................................... 64 Abstract ........................................................................................................ 64 3.1 Introduction ................................................................................................... 65 3.2 Materials and Methods .................................................................................. 69 3.3 Results and Discussion ................................................................................ 73 3.4 Conclusions .................................................................................................. 84 Acknowledgements ............................................................................................. 86 References ........................................................................................................ 86 iv CHAPTER 4 MAGNETIC IONIC LIQUID-BACTERIA INTERACTIONS: CAPTURE AND RECOVERY OF SALMONELLA SPP. AND ESCHERICHIA COLI O157:H7 ......................................................................... 90 Abstract ........................................................................................................ 90 4.1 Introduction ................................................................................................... 90 4.2 Materials and Methods .................................................................................. 94 4.3 Results and Discussion ................................................................................ 98 4.4 Conclusions .................................................................................................. 109 Acknowledgements ............................................................................................. 110 References ........................................................................................................ 110 CHAPTER 5 GENERAL CONCLUSIONS ........................................................ 113 APPENDIX A SUPPORTING INFORMATION ACCOMPANYING CHAPTER 2 ................................................................................................... 116 APPENDIX B SUPPORTING INFORMATION ACCOMPANYING CHAPTER 3 .................................................................................................... 121 v ACKNOWLEDGMENTS I would like to thank my advisor Dr. Byron Brehm-Stecher for his input, guidance and advice during the completion of my PhD. The recommendations received from Dr. Brehm-Stecher will be invaluable during my career as a professional scientist. His commitment to research, coupled with his impressive attention to detail, inspires me to continue my pursuit of knowledge and to become the best scientist that I can be. While unconventional, my time as a PhD student was immensely rewarding. Thank you to Dr. Jared Anderson for allowing me to be a part of your research group through collaboration. My introduction to novel sample preparation and extraction technologies was exciting, and I am thrilled to have had the opportunity to learn from, and work with your research group. I believe that collaborative efforts in science are crucial, and welcomed the chance to further hone my skills as a researcher through cooperative learning. Our collaboration was hugely rewarding, and our successes motivate me to dream big. I would also like to thank my peers for their friendship, generosity and encouragement during the completion of my PhD: Allison Brost, Kelsey Harmon, Joshua Nazareth, Bridget Perry, Will Rock and Marcelino Varona—a special thanks to Kevin Clark, who provided irreplaceable wisdom during our collaboration, and challenged me to be a better scientist. Additionally, I would like to thank the departmental faculty for making my experience at Iowa State University a memorable one. Finally, thank you again to my family for their unconditional love and support. This is for, and because of, you. Thank you! vi ABSTRACT Continued outbreaks of foodborne illness involving dairy products in the United States stress the importance for rapid methods of detection of pathogenic microorganisms in food processing environments. Pathogenic microorganisms, such as Salmonella are widespread, and can be found in a variety of foods, ingredients and in industrial environments. The presence of pathogens in dairy products constitutes great risk for increased exposure, illness and reduces overall quality of the foodstream. As a result, emphasis has been placed on adapting or developing sensitive techniques to rapidly detect notable pathogens, such as Salmonella, Listeria monocytogenes and Escherichia coli O157:H7 in both contaminated foods and industrial environments. Common assays employed in the detection of pathogenic microorganisms, though effective in identification, are time consuming and may require several days for processing. The necessity to quickly screen food products and industrial environments has led to an emphasis to develop rapid, sensitive, automated techniques in food processing operations. Numerous