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The Role of Genomic Versatility in Multi-Niche Preferences of Escherichia Coli Gitanjali Nandakafle South Dakota State University

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The Role of Genomic Versatility in Multi-Niche Preferences of Escherichia Coli Gitanjali Nandakafle South Dakota State University South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2018 The Role of Genomic Versatility in Multi-Niche Preferences of Escherichia Coli Gitanjali NandaKafle South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Biology Commons, and the Microbiology Commons Recommended Citation NandaKafle, Gitanjali, "The Role of Genomic Versatility in Multi-Niche Preferences of Escherichia Coli" (2018). Electronic Theses and Dissertations. 2463. https://openprairie.sdstate.edu/etd/2463 This Dissertation - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. THE ROLE OF GENOMIC VERSATILITY IN MULTI-NICHE PREFERENCES OF ESCHERICHIA COLI BY GITANJALI NANDAKAFLE A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy Major in Biological Sciences Specialization in Microbiology South Dakota State University 2018 iii ACKNOWLEDGEMENTS First and foremost, I would like to express my sincere gratitude and deep appreciation to my advisor Dr. Volker S. Brözel for his continuous support and guidance throughout my PhD study and research. I greatly appreciate the freedom he has given me to do my research and develop myself as researcher in the best possible way. I have been extremely lucky to have him as my supervisor, who cared so much about my research and, responded to my questions and queries promptly despite of his busy schedules. I could not have imagined having a better advisor and mentor for my PhD study. This dissertation would not have been possible without his guidance and persistent help. I would like to thank my committee members Dr. Radhey S. Kaushik, Dr. Ruanbo Zhou and Dr. Madhav Nepal for their assistance, insightful comments and encouragements while pursuing my research. My Sincere thanks goes to all faculties and staffs of Biology and Microbiology department who directly and indirectly help me to achieve this goal. I wish to thank our department secretaries Jan Matson, Karen Barthel, Sharon Ellens and Carol Doyle for helping the department to run smoothly and for assisting me in many different ways. I am thankful to my fellow lab mates Dakota York, Nabilah Alshibli, Amrit Koirala and Bikram Das for helping me various ways to accomplish my research. I will always remember those days we spent together in lab, all about exchange of views and about sharing joys, sorrows and lunches. Also, I would like to thank my undergrad interns Meghan Schenk, Taylor Haugen and Lane Blasius for their sincere hard work to generate iv good data. My special thank goes to Toby Flint (Department of Statistics and Mathematics), Alexander Wireko Kena (Department of Agronomy, Horticulture and Plant Science) for helping me to do the statistical analysis. Many thanks to our research collaborator Dr. Fanus Venter from University of Pretoria for his insightful feedback and updating my research knowledge time to time by sending research articles. I greatly appreciate Tarren Seale, Sarah Potgieter, and Emma Steenkamp for helping to analyze the genome data and population genetics. I owe a special thanks to my family, my parents, brother, sisters, and in-laws for believing in me and being there for practical support in all ups and downs in my life beyond doing a PhD. I greatly appreciate my two lovely children Himesh and Omnima for their support and patience during my PhD studies. At last, a big thank to my loving, supportive, encouraging and patient husband Arjun, who provide me the unending inspiration. Thanks for everything! v CONTENTS LIST OF ABBREVIATIONS ............................................................................................ xi LIST OF FIGURES ......................................................................................................... xiii LIST OF TABLES .......................................................................................................... xvii ABSTRACT ................................................................................................................... xviii Chapter 1: Literature Review .............................................................................................. 1 Diversity, Survival Potential and Virulence of Naturalized Escherichia coli .................... 1 1. Introduction ......................................................................................................................... 1 2. E. coli as an indicator organism ........................................................................................... 3 2.1. E. coli in its Primary Habitat......................................................................................... 6 2.1.1. Commensal E. coli .............................................................................................................. 6 2.1.2. Diarrheagenic E. coli ........................................................................................................... 7 2.1.2.1. Shiga toxin producing E.coli (STEC) .......................................................................... 8 2.1.2.2. Enterotoxigenic E. coli (ETEC) ................................................................................... 9 2.1.2.3. Enteropathogenic E. coli (EPEC) .............................................................................. 10 2.1.2.4. Enteroaggregative E. coli (EAEC)............................................................................. 11 2.1.2.5. Enteroinvasive E. coli (EIEC) ................................................................................... 12 2.1.2.6. Diffusely adherent E. coli (DAEC)............................................................................ 12 2.1.3. Extra Intestinal Pathogenic E. coli (ExPEC) ..................................................................... 13 2.2. Growth of E. coli in its primary habitat ...................................................................... 14 2.3. E. coli in its secondary habitat (in the environment outside of hosts) ........................ 16 2.3.1. E. coli associated with soil, sands, sediment and aquatic plants ....................................... 17 2.3.2. Response of E. coli to Environmental challenges ............................................................. 18 2.3.3. Availability of resources ................................................................................................... 19 2.3.4. Temperature ...................................................................................................................... 20 vi 2.3.5. Salinity / Osmolarity ......................................................................................................... 21 2.3.6. pH / acid stress .................................................................................................................. 22 2.3.7. Oxidative stress ................................................................................................................. 23 2.3.8. Solar Radiation .................................................................................................................. 23 2.3.9. Biotic Factors or other microbial communities ................................................................. 23 2.3.10. Ability to form Biofilm ................................................................................................... 24 2.4. E. coli Diversity and Population genetics ................................................................... 24 2.4.1. Tools for studying E. coli population genetics .................................................................. 26 2.4.1.1. Serotyping.................................................................................................................. 26 2.4.1.2. Multilocus Enzyme Electrophoresis-MLEE .............................................................. 27 2.4.1.3. Multi locus Sequence Typing –MLST....................................................................... 27 2.4.1.4. Phylogrouping Triplex PCR to multiplex PCR ......................................................... 28 2.4.1.5. Pulse Field Gel Electrophoresis (PFGE) ................................................................... 29 2.4.1.6. Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR ................................. 29 2.4.1.7. Repetitive Extragenic Palindromic (REP) PCR ......................................................... 30 2.4.1.8. Arbitrarily primed (AP) PCR or Random Amplified Polymorphic DNA Assay (RAPD) 30 2.4.1.9. Amplified Fragment Length Polymorphism (AFLP) ................................................ 30 3. Conclusions and Future Perspectives ................................................................................ 31 4. References ......................................................................................................................... 33 Chapter 2: Distribution of Diverse Escherichia coli between Cattle and Pasture ........... 45 1. Introduction ....................................................................................................................... 45
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