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Genomic Epidemiology and Characterization of Neonatal Meningitis Escherichia Coli and Their Virulence Plasmids Bryon Alex Nicholson Iowa State University

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Genomic Epidemiology and Characterization of Neonatal Meningitis Escherichia Coli and Their Virulence Plasmids Bryon Alex Nicholson Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2015 Genomic epidemiology and characterization of neonatal meningitis Escherichia coli and their virulence plasmids Bryon Alex Nicholson Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Bioinformatics Commons, and the Microbiology Commons Recommended Citation Nicholson, Bryon Alex, "Genomic epidemiology and characterization of neonatal meningitis Escherichia coli and their virulence plasmids" (2015). Graduate Theses and Dissertations. 14936. https://lib.dr.iastate.edu/etd/14936 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. 1 Genomic epidemiology and characterization of Neonatal Meningitis Escherichia coli and their virulence plasmids by Bryon Alex Nicholson A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Microbiology Program of Study Committee: Ganwu Li, Co-Major Professor Lisa K Nolan, Co-Major Professor Qijing Zhang F. Chris Minion Gwyn Beattie Iowa State University Ames, Iowa 2015 Copyright © Bryon Alex Nicholson, 2015 All rights reserved ii TABLE OF CONTENTS NOMENCLATURE .................................................................................................. iii ACKNOWLEDGMENTS ......................................................................................... iv ABSTRACT ............................................................................................................... v CHAPTER 1 INTRODUCTION ......................................................................... 1 General biology of Escherichia coli .................................................................... 1 Genetic diversity of E. coli .................................................................................. 3 Intestinal pathogenic E. coli ................................................................................. 7 Extra intestinal pathogenic E. coli ....................................................................... 7 Virulence plasmids of extra intestinal pathogenic E. coli .................................... 18 Neonatal bacterial meningitis .............................................................................. 22 Pathogenesis of neonatal meningitis E. coli ........................................................ 24 Role of adhesion and invasion in Neonatal Meningitis E. coli ............................ 26 Immunomodulation by Neonatal Meningitis E. coli ............................................ 28 Aims and significance of this research ................................................................ 31 Organization of this dissertation .......................................................................... 33 References ......................................................................................................... 33 CHAPTER 2 EPIDEMIOLOGICAL ANALYSIS OF NEONATAL MENINGITIS ESCHERICHIA COLI : GENETIC DISTRIBUTION, VARIANCE, AND RELATION TO OTHER EXTRA-INTESTINAL PATHOGENIC E. COLI ........................................................................................... 47 Introduction ......................................................................................................... 48 Materials and Methods ......................................................................................... 51 Results ......................................................................................................... 58 Discussion ......................................................................................................... 73 Acknowledgements .............................................................................................. 84 References ......................................................................................................... 84 CHAPTER 3 LARGE VIRULENCE PLASMIDS IN NEONATAL MENINGITIS ESCHERICHIA COLI : PHYLOGENETIC RELATIONSHIPS AND CORE AND PAN-GENOME .......................................... 92 Abstract ......................................................................................................... 93 Importance ......................................................................................................... 94 Introduction ......................................................................................................... 94 Materials and Methods ......................................................................................... 96 Results ......................................................................................................... 101 Discussion ......................................................................................................... 112 Acknowledgements .............................................................................................. 117 References ......................................................................................................... 117 iii CHAPTER 4 COMPLETE GENOME SEQUENCE OF THE NEONATAL MENINGITIS ESCHERICHIA COLI STRAIN, NMEC O18 ......................................................................................................... 121 Abstract ......................................................................................................... 122 Genome Announcement....................................................................................... 122 References ......................................................................................................... 124 CHAPTER 5 COMPLETE GENOME SEQUENCE OF THE AVIAN PATHOGENIC ESCHERICHIA COLI STRAIN, APEC O18 ................... 125 Abstract ......................................................................................................... 126 Genome Announcement....................................................................................... 126 References ......................................................................................................... 127 CHAPTER 6 CONCLUSION AND DISCUSSION ............................................ 128 iv NOMENCLATURE ETEC Enterotoxigenic E. coli EPEC Enteropathogenic E. coli EHEC Enterohaemorrhagic E. coli EAEC Enteroaggregative E. coli DAEC Diffusely Adherent E. coli EIEC Enteroinvasive E. coli AIEC Adherent Invasive E. coli ExPEC Extra intestinal Pathogenic E. coli NMEC Neonatal Meningitis E. coli APEC Avian Pathogenic E. coli UPEC Urinary Pathogenic E. coli NBM Neonatal Bacterial Meningitis BBB Blood-Brain Barrier CNS Central Nervous System CSF Cerebrospinal Fluid FimH Fimbrial protein H OmpA Outer Membrane Protein A NF-κB Nuclear Factor Kappa-light-chain-enhancer of activated B cells HBMEC Human Brain Microvascular Endothelial Cells PMN Polymorphonuclear v ACKNOWLEDGMENTS First and foremost, I would like to thank my major professors, Dr. Ganwu Li and Dr. Lisa K. Nolan, for allowing me the opportunity to work and learn with them. A special thanks to Yvonne Wannemuehler, who provided me with my initial laboratory training and constant support throughout my research. I would also like to Dr. Catherine Logue for her tireless efforts in teaching me experimental methods and providing editorial input, and Dr. Nicolle Barbieri for generously assisting me in performing cell culture and animal assays and being a constant source for thought-provoking discussion and ideas. I would also like to thank my committee members: Drs. Chris Minion, Qijing Zhang, and Gwyn Beattie for contributing their time, knowledge, expertise, and support. Finally, I would like to thank my wife, Jennifer, my parents, and the rest of my friends and family for their encouragement and support. vi ABSTRACT Neonatal meningitis Eschericha coli (NMEC), a sub-pathotype of extra intestinal E. coli (ExPEC) , is one of the most common causative agents of neonatal bacterial meningitis (NBM). NBM is a devastating disease affecting neonates less than four weeks old, causing acute onset of sepsis and invasion of the central nervous system. Without treatment, NBM is almost certainly fatal, but early intervention and empiric treatment, as well as new broad spectrum antibiotics, have reduced the mortality rates from 32% in 1975 to as low as 8.5% in the United States. Recent studies have greatly improved knowledge of NMEC pathogenic mechanisms by characterizing multiple NMEC virulence factors; however, nearly all experiments were performed using a single NMEC strain, RS218, and its derivative mutants. Broader studies examining larger populations of NMEC have begun to show that some of the virulence factors critical for NMEC RS218 pathogenesis are uncommon in other NMEC, while other virulence factors identified using NMEC RS218 are present in multiple E. coli sub-pathotypes and even non-pathogenic E. coli. Such findings beg the questions, what genes define the NMEC sub-pathotype? How diverse are members of the NMEC sub-pathotype? And can another NMEC strain, other than NMEC RS218, serve as a more representative prototype of the NMEC group? Additionally, other studies have found that some Avian Pathogenic E. coli (APEC) strains can cause NBM in the rat model of human disease, while some NMEC are able to cause
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