Detection of Viable Foodborne Pathogens & Spoilage

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Detection of Viable Foodborne Pathogens & Spoilage Detection of Viable Foodborne Pathogens & Spoilage Microorganisms by Nucleic Acid Amplification Based Platforms Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Linlin Xiao, M.S. Graduate Program in Food Science & Nutrition The Ohio State University 2011 Dissertation Committee: Dr. Hua H. Wang, Advisor Dr. M. Monica Giusti, Co-advisor Dr. John Litchfield Dr. Zhongtang Yu Copyright by Linlin Xiao 2011 I Abstract Foodborne disease outbreaks and microbial spoilage threaten public health and cause major financial loss to the food industry and the society. Proper detection of concerned microorganisms in both raw materials and final food productes is a key to control the problems associated with microbial contamination. Several platforms were used to develop accurate, rapid, quantitative, specific and sensitive detection methods for targeted, viable cells, including RNA-based amplification platforms, such as nucleic acid sequence based amplification (NASBA) and reverse transcriptase PCR (RT-PCR), as well as DNA amplification coupled with sample treatment with DNA-intercalating dye propidium monoazide (PMA). In this study, a NASBA-molecular beacon assay targeting 18S ribosomal RNA has been established to investigate its potential to detect viable spoilage yeasts in juice products. Using the developed platform, less than 100 yeast cells per reaction was detected rapidly and specifically. In addition, significant decrease of amplification signals after lethal heat treatments indicated that this platform has the potential for rapid detection of viable spoilage yeasts if combined with quantitative analysis. Listeria monocytogenes contamination is a serious public health issue. The second part of my project compared the suitability of using 16S rRNA, inlA mRNA and rplD ii mRNA as indictors to detect viable L. monocytogenes cells via Taqman real-time RT- PCR assay. Under the conditions examined, the amplification signals by all three transcripts were reduced in dead cells, while the inlA and rplD mRNA signals decreased more dramatically than 16S rRNA. However, residue signals were still detected from dead cells even after extreme heat treatments. The ideal cell viability indictor should disappear rapidly and completely after cell inactivation. In the third part of my study, cDNA microarray analysis was conducted to select unstable mRNA targets. Using unstable transcript ornithine decarboxylase (ODC) mRNA screened by cDNA microarray assay, a Taqman real-time RT-PCR platform was established to detect viable and heat or disinfectant Pro-san® inactivated spoilage Pseudomonas. Under the experimental condition, ODC-specific RT-PCR signals were almost undectable after Pseudomonas cells were exposed to mild heat treatments. DNA-intercalating dye propidium monoazide (PMA) only can penetrate damaged cell membrane and form crosslinkage with DNA molecules, resulting in inhibition of amplification. PMA coupled Taqman real-time PCR was developed to examine viable Pseudomonas spp. PMA treatment successfully minimized false positive amplification signals by dead cells after heat, acid or disinfectant Pro-san® inactivation. Results from this study provided critical information regarding nucleic acid amplification-baed methods for viable foodborne microbial detection, and the new knowledge regarding overall RNA stability will have significant impact on data interpretation for transcriptome related studies. The rapid detection platforms developed have direct applications in both food industry and basic scientific research. iii Dedication Dedicated to my son Allen Xiong, my daughter Alivia Xiong, and my husband Qingming Xiong for their endless love and generous patience in my life Dedicated to my parents, Xingshu Xiao and Jiayu Fu, my grandparents, Mingzhen Wang and Mingquan Fu, for their deepest love and forever support iv Acknowledgements First and foremost, I am sincerely grateful to my adviser, Dr. Hua Wang, for her intellectual advice, encouragement and support throughout the four years of my study in OSU. I also would like to thank her for insightful discussion and tireless effort in preparing this dissertation. Without her generous help, I could not finish my Ph. D. degree as a young mother having two little kids. I would like to thank my committee members, Dr. John Litchfield, Dr. David Min, Dr. Zhongtang Yu, and Dr. M. Monica Giusti for providing assistance and inspiring comments. I wish to thank Xinhui Li, Dr. Wangyu Tong, Dr. Yingli Li, Andrew Wassinger, Hanna Cortado, Monchaya Rattanaprasert, Dan Kinkelaar, Xiaojing Li, and Ying Huang for their wonderful teamwork and friendship. I specially would like to thank Lu Zhang for his wonderful technical assistance. v Vita Jan. 14, 1978 ··························· Born, Yuan‟an, Hubei, China 2000 ········································ B.S. Animal Science, Yangtze University, Jingzhou, China 2003 ········································ M.S. Food Science and Technology, Nanjing Agricultural University, Nanjing, China 2007 ~ present ························ Graduate Research Associate, The Ohio State University vi Publications Presentations at national conferences: Xiao, L. and Wang, H. (2009) Critical issues in assessing live Listeria monocytogenes cells by real-time reverse transcription-PCR. Institute of Food Technologists (IFT) 2009 annual meeting book of abstract. Anaheim, CA. Xiao, L. and Wang, H. (2008) Development of a real-time, NASBA-molecular beacon assaysfor rapid and specific detection of live microbes in juice products. International Association for Food Protection (IAFP) 2008 annual meeting book of abstract, Columbus, OH. Fields of Study Major Field: Food Science and Nutrition Food microbiology vii Table of Contents Abstract ............................................................................................................................. ii Dedication ........................................................................................................................ iv Acknowledgements ........................................................................................................... v Vita ................................................................................................................................... vi Chapter 1 Introduction ...................................................................................................................... 1 Chapter 2 Literature Review ............................................................................................................. 6 2.1 Conventional culturing detection methods .......................................................................... 7 2.2 Biochemical identification methods ..................................................................................... 9 2.3 Immunoassay ......................................................................................................................... 10 2.4 Biosensors .............................................................................................................................. 13 2.5 Molecular detection methods ............................................................................................... 15 2.6 Main limitation of application of rapid methods for food microbial detection ............ 20 2.7 Food sample preparation ...................................................................................................... 21 2.8 Microbial cell viability indictors ......................................................................................... 23 2.9 Reverse transcriptase polymerase chain reaction (RT-PCR) .......................................... 25 2.10 Nucleic acid sequence based amplification (NASBA) .................................................. 26 viii 2.11 Selective detection of live microorganisms by ethidium monoazide (EMA)-PCR and propidium monoazide (PMA)-PCR .......................................................................... 27 2.12 Listeria monocytogenes and challenge to food safety ................................................... 28 2.13 Microbial spoilage of food products ................................................................................ 30 2.14 Yeasts and juice spoilage ................................................................................................... 31 2.15 Pseudomonas and food spoilage ....................................................................................... 33 References ........................................................................................................................ 35 Chapter 348 Development of a NASBA-Molecular Beacon System Targeting the 18S rRNA for Rapid and Specific Detection of Viable Spoilage Yeasts in Juice Products .............. 48 3.1 Abstract ................................................................................................................................... 48 3.2 Introduction ............................................................................................................................ 49 3.3 Materials and Methods ......................................................................................................... 53 3.4 Results ..................................................................................................................................... 59 3.5 Discussion and Conclusion ................................................................................................
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