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Genome-Based Characterization of Yersinia Enterocolitica: Patho-Evolution and Adaptation of a Versatile Bacterium

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Genome-Based Characterization of Yersinia Enterocolitica: Patho-Evolution and Adaptation of a Versatile Bacterium Aus dem Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie Lehrstuhl: Bakteriologie der Ludwig-Maximilians-Universität München komm. Vorstand: Prof. Dr. Rainer Haas Genome-based characterization of Yersinia enterocolitica : patho-evolution and adaptation of a versatile bacterium Dissertation zum Erwerb des Doktorgrades der Naturwissenschaften an der Medizinischen Fakultät der Ludwig-Maximilians-Universität München vorgelegt von Debora Garzetti aus Treviglio/Italien 2014 ii Gedruckt mit Genehmigung der Medizinischen Fakultät der Ludwig-Maximilians-Universität München Betreuer: Prof. Dr. Dr. Jürgen Heesemann Zweigutachter: Priv. Doz. Dr. Ralf Heermann Dekan: Prof. Dr. med. Dr. h.c. Maximilian Reiser, FACR, FRCR Tag der mündlichen Prüfung: 21.01.2015 iii Eidesstattliche Erklärung Ich erkläre hiermit an Eides statt, dass ich die vorliegende Dissertation mit dem Thema “Genome-based characterization of Yersinia enterocolitica : patho-evolution and adaptation of a versatile bacterium” selbständig verfasst, mich außer der angegebenen keiner weiteren Hilfsmittel bedient und alle Erkenntnisse, die aus dem Schrifttum ganz oder annähernd übernommen sind, als solche kenntlich gemacht und nach ihrer Herkunft unter Bezeichnung der Fundstelle einzeln nachgewiesen habe. Ich erkläre des Weiteren, dass die hier vorgelegte Dissertation nicht in gleicher oder in ähnlicher Form bei einer anderen Stelle zur Erlangung eines akademischen Grades eingereicht wurde. München, den 19.08.2014 _______________________ Debora Garzetti iv “The important thing is not to stop questioning. Curiosity has its own reason for existing. One cannot help but be in awe when he contemplates the mysteries of eternity, of life, of the marvelous structure of reality. It is enough if one tries merely to comprehend a little of this mystery every day. Never lose a healthy curiosity.” Albert Einstein To my little sister v Table of Contents Table of Contents ........................................................................................................................ v List of Figures ............................................................................................................................. ix List of Tables .............................................................................................................................. xi Abbreviations ............................................................................................................................ xiii Summary .................................................................................................................................. xiv Zusammenfassung ................................................................................................................... xvi 1. Introduction .......................................................................................................................... 1 1.1. Yersinia enterocolitica taxonomy, classification and ecology ..................................... 1 1.1.1. Y. enterocolitica O-antigens and serotypes ............................................................ 2 1.2. Pathogenesis of Yersinia enterocolitica ..................................................................... 4 1.2.1. Pathogenesis model and clinical manifestations .................................................... 4 1.2.2. Plasmid-encoded virulence factors ........................................................................ 5 1.2.3. Chromosome-encoded virulence factors ................................................................ 6 1.3. Isolation and diagnosis of Yersinia enterocolitica .................................................... 12 1.3.1. Culture-based methods and serotyping ............................................................... 12 1.3.2. Molecular methods for Y. enterocolitica detection ................................................ 14 1.4. Epidemiology of Yersinia enterocolitica ................................................................... 14 1.4.1. Molecular subtyping of Yersinia enterocolitica ..................................................... 16 1.4.2. Yersinia enterocolitica bioserotype 4/O:3 ............................................................. 21 1.5. Yersinia enterocolitica genomes .............................................................................. 22 2. Aims of the study ............................................................................................................... 25 3. Materials and Methods ....................................................................................................... 26 3.1. Instruments and consumables ................................................................................. 26 3.2. Chemicals, kits and reagents .................................................................................. 27 3.3. Microbiological methods .......................................................................................... 28 3.3.1. Bacterial strains and plasmids ............................................................................. 28 3.3.2. Culture media ...................................................................................................... 33 vi 3.3.3. Bacterial growth and conservation ....................................................................... 34 3.3.4. Determining bacterial growth curves .................................................................... 34 3.3.5. Antibiotics and antimicrobial susceptibility test ..................................................... 34 3.3.6. Electrocompetent cells and transformation .......................................................... 35 3.3.7. Isolation of released proteins from Y. enterocolitica ............................................. 35 3.4. Molecular biology methods ...................................................................................... 35 3.4.1. Isolation of nucleic acids ...................................................................................... 35 3.4.2. Agarose gel electrophoresis ................................................................................ 36 3.4.3. Oligonucleotides .................................................................................................. 36 3.4.4. Polymerase chain reaction ................................................................................... 37 3.4.5. Patho-serotyping PCR ......................................................................................... 39 3.4.6. Synthesis of digoxigenin-labeled probes .............................................................. 39 3.4.7. Protein expression library generation ................................................................... 40 3.5. Biochemical and analytical methods ........................................................................ 41 3.5.1. SDS-PAGE .......................................................................................................... 41 3.5.2. Western Blot ........................................................................................................ 41 3.5.3. Quantification of proteins ..................................................................................... 42 3.5.4. Colony hybridization ............................................................................................ 42 3.5.5. Serum selection and adsorption........................................................................... 44 3.5.6. Screening of expression library ............................................................................ 46 3.6. Mouse experiments ................................................................................................. 47 3.6.1. Preparation of microorganisms ............................................................................ 47 3.6.2. Infection of animals .............................................................................................. 47 3.6.3. Recovery of bacteria from mouse organs ............................................................ 47 3.7. Bioinformatics ......................................................................................................... 48 3.7.1. Bioinformatics tools.............................................................................................. 48 3.7.2. General sequence analysis .................................................................................. 49 3.7.3. Sequencing of bacterial DNA and read quality control ......................................... 49 3.7.4. Read mapping and alignment post-processing .................................................... 50 3.7.5. Variant calling and filtering ................................................................................... 51 3.7.6. Genome annotation ............................................................................................. 51 vii 3.7.7. Whole genome comparison ................................................................................. 52 3.7.8. Functional annotation and comparative functionome analysis ............................. 52 3.7.9. Phylogenetic analyses ......................................................................................... 53 3.8. Statistics.................................................................................................................. 53 4. Results .............................................................................................................................. 54 4.1. Highly-virulent Y.
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