Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Genetic and phenotypic characterization of livestock associated methicillin resistant Staphylococcus aureus sequence type (ST) 5 in comparison with clinical ST5 isolates from humans Samantha Jean Hau Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons Recommended Citation Hau, Samantha Jean, "Genetic and phenotypic characterization of livestock associated methicillin resistant Staphylococcus aureus sequence type (ST) 5 in comparison with clinical ST5 isolates from humans" (2017). Graduate Theses and Dissertations. 16143. https://lib.dr.iastate.edu/etd/16143 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]. Genetic and phenotypic characterization of livestock associated methicillin resistant Staphylococcus aureus sequence type (ST) 5 in comparison with clinical ST5 isolates from humans by Samantha Jean Hau A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Veterinary Microbiology Program of Study Committee: Qijing Zhang, Co-Major Professor Timothy S. Frana, Co-Major Professor Steve A. Carlson Ganwu Li Tracy L. Nicholson The student author and the program of study committee are solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2017 Copyright © Samantha Jean Hau, 2017. All rights reserved. ii DEDICATION For L.B. Your enthusiasm and sense of adventure make life more interesting. iii TABLE OF CONTENTS LIST OF FIGURES ....................................................................................................... viii LIST OF TABLES ........................................................................................................... ix NOMENCLATURE ...........................................................................................................x ACKNOWLEDGMENTS ............................................................................................. xiii ABSTRACT .................................................................................................................... xiv CHAPTER 1. GENERAL INTRODUCTION AND LITERATURE REVIEW .........1 General Biology of Staphylococcus aureus ...................................................................1 S. aureus Classification and Genetics ...........................................................................2 S. aureus Colonization and Disease ..............................................................................5 S. aureus Virulence Factors and Pathogenesis ............................................................7 Adhesion to host tissues ...............................................................................................7 Biofilm formation ......................................................................................................10 Nutrient acquisition ....................................................................................................10 Invasion and tissue destruction ..................................................................................10 Toxin mediated disease ..............................................................................................11 Immune evasion .........................................................................................................14 Drug Resistance in S. aureus .......................................................................................16 Methicillin Resistance ..................................................................................................23 MRSA Epidemiology ...................................................................................................27 LA-MRSA Characteristics ..........................................................................................32 Aims and Significance of Research ............................................................................36 Organization of Dissertation .......................................................................................38 CHAPTER 2. SINGLE NUCLEOTIDE POLYMORPHISM ANALYSIS INDICATES GENETIC DISTINCTION AND REDUCED DIVERSITY OF AGRICULTURAL METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS (MRSA) ST5 ISOLATES AS COMPARED TO CLINICAL MRSA ST5 ISOLATES ................................................................................................................39 Abstract .........................................................................................................................40 Introduction ..................................................................................................................40 Methods .........................................................................................................................43 Isolate Acquisition .....................................................................................................43 Whole Genome Sequencing .......................................................................................43 iv Core Genome SNP Discovery ...................................................................................44 Mobile genetic element analysis ................................................................................46 Results ...........................................................................................................................47 Isolate provenance and sequence information ...........................................................47 Single nucleotide polymorphism typing ....................................................................47 Phylogenetic analysis .................................................................................................49 Mobile genetic element analysis ................................................................................52 Discussion......................................................................................................................54 Acknowledgements ......................................................................................................56 CHAPTER 3. COMPARATIVE PREVALENCE OF IMMUNE EVASION COMPLEX GENES ASSOCIATED WITH BETA-HEMOLYSIN CONVERTING BACTERIOPHAGES IN MRSA ST5 ISOLATES FROM SWINE, SWINE FACILITIES, HUMANS WITH SWINE CONTACT, AND HUMANS WITH NO SWINE CONTACT ...................................................................57 Abstract .........................................................................................................................57 Introduction ..................................................................................................................59 Methods .........................................................................................................................63 Strain acquisition .......................................................................................................63 DNA isolation ............................................................................................................63 PCR reactions.............................................................................................................64 Southern blotting ........................................................................................................66 Phage typing...............................................................................................................66 Statistical analysis ......................................................................................................67 Results ...........................................................................................................................67 IEC gene prevalence ..................................................................................................67 β-hemolysin converting bacteriophage prevalence via integrase gene screening .....69 β-hemolysin gene analysis .........................................................................................70 Phage typing...............................................................................................................72 Discussion......................................................................................................................73 Acknowledgments ........................................................................................................77 CHAPTER 4. ZINC RESISTANCE WITHIN SWINE-ASSOCIATED METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS ISOLATES IN THE UNITED STATES IS ASSOCIATED WITH MULTILOCUS SEQUENCE TYPE LINEAGE .............................................................................................................78 Abstract .........................................................................................................................78 Importance....................................................................................................................79 v Introduction ..................................................................................................................80