Assessing the Effect of Interventions on Pathogens and The Microbial Ecology of the Poultry Processing Chain by Microbial Profiling and the Phenotypic and Genotypic Characterization of Antimicrobial Resistance by Alejandra Ramirez-Hernandez, 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 Marcos X. Sanchez-Plata, Ph.D. Chair of Committee Mindy M. Brashears, Ph.D. Co-chair of Committee Kendra Nightingale, Ph.D. Alejandro Echeverry, Ph.D. Michael San Francisco, Ph.D. Mark Sheridan Dean of the Graduate School May, 2019 Copyright 2019, Alejandra Ramirez-Hernandez Texas Tech University, Alejandra Ramirez-Hernandez, May 2019 ACKNOWLEDGMENTS I would like to express my most sincere thanks to the following: First and foremost, to my advisors, Dr. Mindy Brashears and Dr. Marcos Sanchez-Plata, thank you for believing in me and for all the opportunities received during the past years. I am beyond grateful for your valuable support, guidance, and encourage to become a stronger scientist and better student. To Drs. Kendra Nightingale, Alejandro Echeverry, and Michael San Francisco thank you for serving on my advisory committee. I thank each of you for your time, support, and intellectual input during my Ph.D. program. Thank you to Dr. Marie Bugarel, for her kind support with the whole genome analysis, and help with molecular methods. I also want to thank Dr. Kameswara Rao Kottapalli for assisting me with microbiome analysis; and a special thanks to Dr. John Rupnow for his unconditional support, valuable advice and for belief in my abilities to succeed as a young scientist. To my fellow graduate students, student assistants, and co-workers in our research group thank you for your help and time during my projects. I have special gratitude to Brenda Inestroza, Diana Ayala, Ilan Arvelo, Kathy Fermin, Andrea English and David Campos for their unconditional support, and friendship through this enjoyable experience. I am also grateful to my dear friends in Lubbock, thank you to David F. D'Croz-Baron and Diana Vargas for all the fun and unconditional friendship. ii Texas Tech University, Alejandra Ramirez-Hernandez, May 2019 I thank you to Andrea Varon, Ana Karina Carrascal, Iliana Chamorro, and Francisco Garces for all their help, hard work, and assistance to conduct the research projects in Colombia. Last but not least, thank you to my parents, Fernando and Luz Marina for their endless love, support, and encouragement through this journey far from home. Thank you to my sister and brother-in-law, Natalia and Fredy, for encouraging to dream big. I also thank to Emilia for the blessings and happiness she has brought to my family. iii Texas Tech University, Alejandra Ramirez-Hernandez, May 2019 TABLE OF CONTENTS ACKNOWLEDGMENTS .................................................................................... ii ABSTRACT ......................................................................................................... vii LIST OF TABLES ............................................................................................. viii LIST OF FIGURES .............................................................................................. x LIST OF ABBREVIATIONS ........................................................................... xiii I. REVIEW OF LITERATURE ........................................................................... 1 Salmonella ......................................................................................................... 1 Campylobacter .................................................................................................. 4 Poultry-associated pathogens ............................................................................ 6 Salmonella in poultry .................................................................................. 7 Campylobacter in poultry ........................................................................... 8 Poultry processing operations ......................................................................... 10 Farming growing ....................................................................................... 12 Transportation ........................................................................................... 15 Slaughtering .............................................................................................. 15 Scalding ..................................................................................................... 16 Defeathering .............................................................................................. 17 Evisceration ............................................................................................... 18 Chilling ...................................................................................................... 19 Cut-up ........................................................................................................ 21 Products ..................................................................................................... 21 Pathogen performance standards in poultry processing operations. ............... 22 Antimicrobial interventions to reduce and control Salmonella and Campylobacter in the poultry industry ........................................................... 26 Chlorine ..................................................................................................... 26 Lactic acid ................................................................................................. 27 Acidified sodium chlorite .......................................................................... 28 Peroxyacetic acid ...................................................................................... 29 Poultry processing interventions and formation of semicarbazide ........... 30 Antimicrobial agents ....................................................................................... 31 Antimicrobial resistance in bacteria. ............................................................... 33 Antimicrobial resistance in poultry-associated pathogens .............................. 36 Antimicrobial resistant of Salmonella ....................................................... 37 iv Texas Tech University, Alejandra Ramirez-Hernandez, May 2019 Antimicrobial resistant of Campylobacter ................................................ 39 Chicken Microbiome ....................................................................................... 40 References ....................................................................................................... 42 II. EFFICACY OF LACTIC ACID, LACTIC ACID-CITRIC-ACID BLENDS, AND PERACETIC ACID TO REDUCE SALMONELLA ON CHICKEN PARTS UNDER SIMULATED COMMERCIAL PROCESSING CONDITIONS .......................................................................... 56 Summary ......................................................................................................... 56 Introduction ..................................................................................................... 57 Materials and Methods .................................................................................... 59 Results ............................................................................................................. 64 Discussion ....................................................................................................... 65 Acknowledgments ........................................................................................... 69 Tables and Figures .......................................................................................... 70 References ....................................................................................................... 77 III. MICROBIOME ANALYSIS, ANTIMICROBIAL RESISTANT PROFILES AND WHOLE GENOME SEQUENCING ANALYSIS OF PATHOGENS ISOLATED FROM CHICKEN CARCASSES RINSATE SAMPLES COLLECTED AT DIFFERENT STAGES DURING PROCESSING ................................................................................... 80 Summary ......................................................................................................... 80 Introduction ..................................................................................................... 81 Materials and Methods .................................................................................... 86 Results ............................................................................................................. 94 Discussion ..................................................................................................... 104 Acknowledgments ......................................................................................... 111 Tables and Figures ........................................................................................ 112 References ..................................................................................................... 128 IV. MICROBIOLOGICAL PROFILE OF THREE COMMERCIAL POULTRY PROCESSING PLANTS IN COLOMBIA ................................ 135 Summary ....................................................................................................... 135 Introduction ................................................................................................... 136 Materials and Methods .................................................................................