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Foodborne Pathogen Persistence in the Food Processing Environment

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FOODBORNE PATHOGEN PERSISTENCE IN THE FOOD PROCESSING ENVIRONMENT by Alex L. Brandt, M.S. A Dissertation In ANIMAL SCIENCE Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Approved Kendra K. Nightingale, Ph.D. Chair of Committee Mindy M. Brashears, Ph.D. J. Chance Brooks, Ph.D. Margarget D. Hardin, Ph.D. Haley F. Oliver, Ph.D. Mark Sheridan, Ph.D. Dean of the Graduate School May, 2014 Copyright 2014, Alex Brandt Texas Tech University, Alex Brandt, May 2014 ACKNOWLEDGEMENTS There are countless people who have been supportive of me in my endeavor to obtain my Ph.D., and I owe them all a great deal of gratitude. Mentioning all of them here would make up an entire dissertation in itself, so even though all are not mentioned by name, they still hold a special place in my heart. First and foremost, I thank my parents, who have always been by my side in both times of joyous accomplishment and in times when I was down and desperately needed someone to talk to. The love that constantly flows from their open hearts, and the concern that is constantly in their open ears, are gifts that I can only hope to give to others in my life. Also, the lessons they taught me about working hard, and carrying on in the midst of life’s trials, are something I will always carry in my heart and mind. My extended family, including all of my grandparents, aunts, uncles, and cousins have also been supportive of all my aspirations, and I also will be forever grateful to them for all the unwavering support and encouragement they have always given me. I also thank my dear girlfriend Samantha whose prayers, understanding, and love were sometimes the only things keeping me afloat through this process. I could not have carried on if not for her encouragement, love, and willingness to be there for me. I also have been blessed with many mentors who have helped me through this journey to whom I owe much gratitude. Dr. Kendra Nightingale, my Ph.D. advisor, is at the top of this list. She has been a caring mentor and wonderful teacher to me, and I thank her immensely for giving me this opportunity to grow professionally and to acquire at least a small portion of her wealth of knowledge. I also thank my committee members Dr. Margaret Hardin, Dr. Haley Oliver, Dr. Mindy Brashears, and Dr. Chance Brooks for all of their mentorship, intellectual input, and moral support over the past several years. I would also be remiss if I did not thank my past advisors, teachers, and colleagues Dr. Matthew Taylor, Mrs. Liz Treptow, Mrs. Nancy Jurecka, Dr. Jenna Anding, and Dr. Jay Neal for always believing in me and for aiding in my educational and professional formation. I also thank Drs. Dale Woerner, Martin Wiedmann, and Guy Loneragan for all of their help enrolling facilities, providing project guidance, and answering the occasional methodological and statistical questions that arose. ii Texas Tech University, Alex Brandt, May 2014 I also would be remiss if I did not thank all of my colleagues, friends, and labmates who were always willing to jump in and lend a helping hand. I especially thank Anna Van Stelten, Eva Borjas, Chip Manuel, Jessica Chen, Alex Tudor, Alma Perez- Mendez, Ashleigh Willems, Jake Elder, Gina Geornaras, Curtis Pittman, Tanya Jackson, Logan Jackson, Kathy Fermin, Miles Harris, Samantha Stewart, Peter Cook, Jessica Heiden, Sarah Navratil, Sara Gragg, Amy Parks, Jessie Vipham, Byron Chaves, Diana Ayala, Lacey Guillen, Marie Bugarel, Josh and Sarah Ison, Devin Hanson, Hattie Webb, Katelyn Malin, and Jennifer Martin for their constant support, willingness to help, and uplifting and stimulating discussions throughout the completion of my degree. Also, thanks to all the other unnamed graduate students, undergraduate students, and laboratory staff who always found time to be there when I needed it. I also thank all the facility managers and employees for their cooperation to accomplish this study. It literally could have not have been done without their willingness to participate, their flexibility, and heed of our thoughts, concerns, and suggestions. I forged relationships with them that helped me grow extensively from a professional standpoint, and I have no doubt that those relationships will last a lifetime. I also thank the United States Department of Agriculture National Institute of Food and Agriculture for providing the funding for this important study. I also thank all those at Cornell University who were so willing to help with subtyping, analysis, and interpretation of results. Sherry Roof, Emily Wright, Laura Strawn, Lorraine Rodriguez-Rivera, Tom Malley, and Matthew Stasiewicz were always willing to go the extra mile, and I am truly grateful for all of their support. Lastly, and most importantly, I thank God for His constant love and the blessings He has bestowed on me, which I am most unworthy of. I am so thankful for where He has taken me in my life. Though I count my blessings every day, I still cannot ever give Him all the gratitude He deserves. Without His comforting hand, I would not have made it through some of the trials I faced over the past few years. Thus, I am forever indebted to Him. Ad Majorem Dei Gloriam. iii Texas Tech University, Alex Brandt, May 2014 TABLE OF CONTENTS ACKNOWLEDGEMENTS ....................................................................................ii ABSTRACT ..............................................................................................................viii LIST OF TABLES ...................................................................................................xi LIST OF FIGURES .................................................................................................xiii I. REVIEW OF THE LITERATURE ....................................................................1 Foodborne Illness .................................................................................................1 Listeria monocytogenes .......................................................................................3 Salmonella enterica .............................................................................................9 Escherichia coli O157:H7....................................................................................15 Bacterial Subtyping ..............................................................................................20 Molecular Ecology and Persistence of Foodborne Pathogens .............................24 References ............................................................................................................42 II. INTEGRATING LONGITUDINAL SAMPLING, MOLECULAR SUBTYPING, AND STATISTICAL ANALYSIS TO INVESTIGATE PERSISTENCE OF LISTERIA MONOCYTOGENES, SALMONELLA ENTERICA, AND ESCHERICHIA COLI O157:H7 IN MEAT PROCESSING FACILITY ENVIRONMENTS .............................................92 Introduction ..........................................................................................................92 Materials and Methods .........................................................................................93 Results ..................................................................................................................103 Discussion ............................................................................................................110 Conclusions ..........................................................................................................117 References ............................................................................................................118 III. ASSESSING FOODBORNE PATHOGEN PERSISTENCE MITIGATION IN MEAT PROCESSING ESTABLISHMENTS FOLLOWING ENACTMENT OF PHYSICAL AND PERSONNEL-BASED CONTROL MEASURES ..........................................155 Introduction ..........................................................................................................155 Materials and Methods .........................................................................................156 Results ..................................................................................................................162 Discussion ............................................................................................................171 Conclusions ..........................................................................................................178 iv Texas Tech University, Alex Brandt, May 2014 References ............................................................................................................180 IV. CHARACTERIZING THE COMPOSITION OF BACTERIAL POPULATIONS AT SITES OF RECURRENT LISTERIA CONTAMINATION IN MEAT PROCESSING FACILITIES USING 16S RRNA GENE SEQUENCING .....................................................217 Introduction ..........................................................................................................217 Materials and Methods .........................................................................................218 Results ..................................................................................................................220 Discussion ............................................................................................................222 Conclusions ..........................................................................................................224 References ............................................................................................................225
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