Sequencing Technologies in Microbial Food Safety and Quality

Molecular landscape for food safety analysis is rapidly revolutionizing because of high resolution and value added resulting analysis ofnext-generation sequencing (NGS)approaches. These modern sequencing technologies drive worldwide advancements in food safety and quality. Sequencing Technologies in Microbial Food Safety and Quality reviews several practices in that NGS contributes to foodborne pathogens functional characterization, management and control. This book focuses on potential uses of sequencing technologies in microbial food safety and quality and highlights present challenges in the food industry. Key Features: Application of whole genome sequencing technologies in disease diagnostics, surveillance, transmission, and outbreak investigation in food sector Impact of sequencing tools in the area of food microbiology Recent advances in genomic DNA sequencing of microbial species from single cells Microbial bioinformatics resources for food microbiology High-throughput insertion tracking by deep sequencing for the analysis of food pathogens This book includes contributions from experts who have manipulated sequencing tools in relation to microbial food safety and quality. Presenting comprehensive details about NGS approaches in food science, this book is an updated and reliable reference for food scientists, nutritionists, food product investigators to study and implement the sequencing technologies fordeveloping quality and safe food. This book would also serve as informative resource for food industry officials, government researchers, food science or food nutrition students who seek comprehensive knowledge about the role of emerging sequencing technologies in revolutionizing the food industry.

Series Preface Preface Editors Contributors PART I Introduction, Genomics, Proteomics, and Bioinformatics Chapter 1 Food Quality and Food Safety: An Introduction Umar Farooq, Afshan Shafi, Muhammad Shahbaz, Muhammad Zaki Khan, Khizar Hayat, Muhammad Baqir, and Mariam Iqbal Chapter 2 Foodborne Pathogens and Food-Related Microorganisms Mary Theresa, Aparna Sankaran Unni, Amala Geevarghese, Sebastain Korattiparambil Sebastian, Sunil Pareek, and Radhakrishnan Edayileveettil Krishnankutty Chapter 3 Molecular Epidemiology of Foodborne Diseases Afshan Shafi, Umar Farooq, Kashif Akram, Muhammad Zaki Khan, Zafar Hayat, and Khizar Hayat Chapter 4 Nucleic Acid-Based Molecular Techniques in Microbial Food Safety Benssan K. Varghese, V.J. Rejish Kumar, and Radhakrishnan Preetha Chapter 5 Exploring the Landscape of the Genome and Transcriptome in Microbial Food Safety Adil Hussain and Amjad Iqbal Chapter 6 Proteomics Applications in Postharvest and Food Science S. Prasanna Raghavender, C. Anoint Yochabedh, and Radhakrishnan Preetha Chapter 7 Impact of Sequencing and Bioinformatics Tools in Food Microbiology Ramachandran Chelliah, Eric Banan-Mwine Daliri, Fazle Elahi, Imran Khan, Shuai Wei, Su-Jung Yeon, Kandasamy Saravanakumar, Inamul Hasan Madar, Sumaira Miskeen, Ghazala Sultan, Marie Arockianathan, Shanmugarathinam Alagarsamy, Thirumalai Vasan, Myeong-Hyeon Wang, Usha Antony, Devarajan Thangadurai, and Deog Hwan Oh PART II Generation of Sequencing Technologies Chapter 8 Evaluation of Sequencing Technologies in Food Science Jorianne Thyeska Castro Alves, Mônica Silva de Oliveira, Gislenne Moia, Rosyely da Silva Oliveira, Ronilson Santos dos Santos, Pablo Henrique Caracciolo Gomes de Sá, and Adonney Allan de Oliveira Veras Chapter 9 First Generation–The Sanger Shotgun Approach Muhsin Jamal, Sana Raza, Sayed Muhammad Ata Ullah Shah Bukhari, Saadia Andleeb, Muhammad Asif Nawaz, Sidra Pervez, Liloma Shah, and Redaina Chapter 10 Fourth Generation–In Situ Sequencing Sadhna Mishra, Arvind Kumar, Shikha Pandhi, and Dinesh Chandra Rai Chapter 11 Library Preparations and Sequencing Platform for Improving Food Safety Mahesh Pattabhiramaiah and Shanthala Mallikarjunaiah Chapter 12 Microbial Genomes: Potential Systems for WGS and NGS Debadarshee Das Mohapatra and Smaranika Pattnaik Chapter 13 Single Cell Sequencing of Microbial Species Charles Oluwaseun Adetunji, Wadzani Dauda Palnam, Juliana Bunmi Adetunji, Benjamin Ewa Ubi, Ayodele Eugene Ayeni, Devarajan Thangadurai, Muhammad Akram, Fahad Said Khan, Olugbenga Samuel Michael, Olugbemi Tope Olaniyan, Ajayi Kolawole Temidayo, Saher Islam, Arowora Kayode Adebisi, and Daniel Ingo Hefft PART III High-Throughput Sequencing Technology Applications for Food Safety and Quality Chapter 14 Current Trends in the Detection of Foodborne Pathogens and Maintenance of Microbial Food Safety and Quality Based on Ribosomal RNA Approaches Charles Oluwaseun Adetunji, Ayodele Eugene Ayeni, Olugbemi Tope Olaniyan, Muhammad Akram, Benjamin Ewa Ubi, Saher Islam, Umme Laila, Mehvish Ajaz, Wadzani Dauda Palnam, Devarajan Thangadurai, Olugbenga Samuel Michael, Juliana Bunmi Adetunji, Fahad Said Khan, and Daniel Ingo Hefft Chapter 15 Application of WGS Technologies in Disease Diagnostics, Surveillance, Transmission, and Outbreak Investigation in the Food Sector Nayana Aluparambil Radhakrishnan, Sreejith Sreekumaran, Akshaya Chekkara Thandayan Santhosh, Sunil Pareek, and Radhakrishnan Edayileveettil Krishnankutty Chapter 16 High-Throughput Sequencing for Detection of Foodborne Pathogens in Food Safety Mahesh Pattabhiramaiah and Shanthala Mallikarjunaiah Chapter 17 Examining Microbial Ecology of Food Using NGS Techniques Nayana Aluparambil Radhakrishnan, Amisha Mathew, Sunil Pareek, and Radhakrishnan Edayileveettil Krishnankutty Chapter 18 Application of Next-Generation Sequencing Techniques in Food-Related Microbiome Studies Ramachandran Chelliah, Eric Banan-Mwine Daliri, Fazle Elahi, Imran Khan, Shuai Wei, Su-Jung Yeon, Kandasamy Saravanakumar, Inamul Hasan Madar, Sumaira Miskeen, Ghazala Sultan, Marie Arockianathan, Shanmugarathinam Alagarsamy, Thirumalai Vasan, Myeong-Hyeon Wang, Usha Antony, Devarajan Thangadurai, and Deog Hwan Oh Index

Devarajan Thangadurai, PhD, is Assistant Professor at Karnatak University, Dharwad in India and did his postdoctoral research at the University of Madeira, Portugal, University of Delhi, India, and ICAR National Research Centre for Banana, India. He is the recipient of Best Young Scientist Award with Gold Medal from Acharya Nagarjuna University, India, and the VGST-SMYSR Young Scientist Award of the Government of Karnataka, India. He has keen interest and expertise in the fields of biodiversity and biotechnology, genetics and genomics of food crops and beneficial microbes for crop productivity and food safety towards sustainable agricultural development. He has authored and edited more than twenty books including Genetic Resources and Biotechnology (3 Vols.), Genes, Genomes and Genomics (2 Vols.), Genomics and Proteomics, and, Biotechnology of Microorganisms with international scientific publishers in USA, Canada and India. He has extensively travelled to many universities and institutes in Africa, Europe and Asia for academic works, scientific meetings, and international collaborations. He is also reviewer for several journals including Comprehensive Reviews in Food Science and Food Safety, Food Science and Technology International, Journal of Agricultural and Food Chemistry, Journal of Food Science, Journal of the Science of Food and Agriculture, and, International Journal of Plant Production. Leo M. L. Nollet earned an MS (1973) and PhD (1978) in biology from the Katholieke Universiteit Leuven, Belgium. He is an editor and associate editor of numerous books. He edited for M. Dekker, New York—now CRC Press of Taylor & Francis Publishing Group—the first, second, and third editions of Food Analysis by HPLC and Handbook of Food Analysis. The last edition is a two-volume book. Dr. Nollet also edited the Handbook of Water Analysis (first, second, and third editions) and Chromatographic Analysis of the Environment, third and fourth editions (CRC Press). With F. Toldrá, he coedited two books published in 2006, 2007, and 2017: Advanced Technologies for Meat Processing (CRC Press) and Advances in Food Diagnostics (Blackwell Publishing—now Wiley). With M. Poschl, he coedited the book Radionuclide Concentrations in Foods and the Environment, also published in 2006 (CRC Press). Dr. Nollet has also coedited with Y. H. Hui and other colleagues on several books: Handbook of Food Product Manufacturing (Wiley, 2007), Handbook of Food Science, Technology, and Engineering (CRC Press, 2005), Food Biochemistry and Food Processing (first and second editions; Blackwell Publishing—now Wiley—2006 and 2012), and the Handbook of Fruits and Vegetable Flavors (Wiley, 2010). In addition, he edited the Handbook of Meat, Poultry, and Seafood Quality, first and second editions (Blackwell Publishing—now Wiley—2007 and 2012). From 2008 to 2011, he published five volumes on animal product-related books with F. Toldrá: Handbook of Muscle Foods Analysis, Handbook of Processed Meats and Poultry Analysis, Handbook of Seafood and Seafood Products Analysis, Handbook of Dairy Foods Analysis, and Handbook of Analysis of Edible Animal By-Products. Also, in 2011, with F. Toldrá, he coedited two volumes for CRC Press: Safety Analysis of Foods of Animal Origin and Sensory Analysis of Foods of Animal Origin. In 2012, they published the Handbook of Analysis of Active Compounds in Functional Foods. In a coedition with Hamir Rathore, Handbook of Pesticides: Methods of Pesticides Residues Analysis was marketed in 2009; Pesticides: Evaluation of Environmental Pollution in 2012; Biopesticides Handbook in 2015; and Green Pesticides Handbook: Essential Oils for Pest Control in 2017. Other finished book projects include Food Allergens: Analysis, Instrumentation, and Methods (with A. van Hengel; CRC Press, 2011) and Analysis of Endocrine Compounds in Food (Wiley-Blackwell, 2011). Dr. Nollet’s recent projects include Proteomics in Foods with F. Toldrá (Springer, 2013) and Transformation Products of Emerging Contaminants in the Environment: Analysis, Processes, Occurrence, Effects, and Risks with D. Lambropoulou (Wiley, 2014). In the series Food Analysis & Properties, he edited (with C. Ruiz-Capillas) Flow Injection Analysis of Food Additives (CRC Press, 2015) and Marine Microorganisms: Extraction and Analysis of Bioactive Compounds (CRC Press, 2016). With A.S. Franca, he coedited Spectroscopic Methods in Food Analysis (CRC Press, 2017), and with Horacio Heinzen and Amadeo R. Fernandez-Alba he coedited Multiresidue Methods for the Analysis of Pesticide Residues in Food (CRC Press, 2017). Saher Islam, PhD, is an HEC Scholar (Higher Education Commission) of the Islamic Republic of Pakistan at the University of Veterinary and Animal Sciences, Lahore, where she received her BS, MPhil and PhD in Molecular Biology, Biotechnology and Bioinformatics. She was an IRSIP Scholar at Cornell University, New York and Visiting Scholar at West Virginia State University, Wes