Bacterial genome plasticity and its role for adaptation and evolution of asymptomatic bacteriuria (ABU) Escherichia coli strains [Elektronische Ressource] = (Über die Bedeutung der bakteriellen Genomplastizität für die Adaptation und Evolution asymptomatischer Bakteriurie (ABU) Escherichia coli Isolate) / submitted by Jarosław Maciej Zdziarski

Zdzierak

Sujets

• Biologie

Informations

• Publié par: julius-maximilians-universitat_wurzburg
• Publié le: 01 janvier 2008
• Nombre de lectures: 11
• Langue: English
• Poids de l'ouvrage: 9 Mo

Extrait

Bacterial Genome Plasticity and its Role for Adaptation
and Evolution of Asymptomatic Bacteriuria (ABU)
Escherichia coli Strains


(Über die Bedeutung der bakteriellen Genomplastizität
für die Adaptation und Evolution asymptomatischer
Bakteriurie (ABU) Escherichia coli Isolate)






Doctoral thesis for submission to a doctoral degree
at the Graduate School of Life Sciences,
Julius Maximilian University Würzburg,
Section: Infection and Immunity


submitted by




Jarosław Maciej Zdziarski


from

Góra, Poland





Würzburg, 2008
 


























Submitted on: …………………………………………………………….
office stamp


Members of the Promotionskomitee:

Chairperson: ………………………………………………………………
to be completed by the office

Primary Supervisor: Prof. Dr. Dr. h. c. mult. Jörg Hacker

Supervisor (second): Prof. Catharina Svanborg

Supervisor (third): PD Dr.rer.nat. Ulrich Dobrindt


Day of Rigorosum: ……………………………………………………….



Certificates were handed out on: ……………………………………..


Erklärung
Gemäß § 4 Abs. 3 Ziff. 3, 5 und 8 der Promotionsordnung der Fakultät für Biologie der
Bayerischen Julius-Maximilians-Universität Würzburg.









Ich versichere hiermit, dass ich die vorliegende Arbeit selbständig und nur unter Verwendung
der angegebenen Quellen und Hilfsmittel verfasst habe.
Weiterhin versichere ich, dass die Dissertation bisher nicht in gleicher oder ähnlicher Form in
einem anderen Prüfungsverfahren vorgelegen hat und ich bisher keine akademischen Grade
erworben oder zu erwerben versucht habe.




Würzburg, im Juli 2008


(Jaroslaw Zdziarski) Acknowledgement
This study was carried out at the Institute of Molecular Biology of Infectious Diseases at the
th stUniversity of Würzburg, Germany from September 15 , 2004 until May 31 , 2008. In this
time period, many people helped me to accomplish my PhD dissertation.

First of all I am grateful to Prof. Jörg Hacker, who gave me the opportunity to join his group
and for the whole support that allowed me to complete my PhD.
Secondly, I am very happy that Prof. Catharina Svanborg (Institute of Laboratory Medicine,
Department of Microbiology, Immunology and Glycobiology, Lund University, Sweden)
gave me the opportunity to stay in her laboratory and learn more about asymptomatic
bacteriuria. By her extraordinary scientific input she made my work very interesting and
‘colourful’.
I kindly thank Prof. Björn Wullt (Department of Urology, Lund University Hospital, Sweden)
for providing with consecutive re-isolates of strain 83972 and the corresponding patient data.
Every scientific and non-scientific discussion, we had together, was just fantastic.
I would love to express my deepest gratitude to Dr. Ulrich Dobrindt who is a great supervisor.
In the time of my PhD, he has helped me to develop scientific ideas and together we drilled
into the depths of science. Despite his very tight schedule, we could go through all crazy
things....and that he polished his polish...
Many thanks to all ‘Colis’ and ‘Staphis’, especially to Barbara Plaschke, whose experience
and engagement significantly contributed to my work.
Torben – thanks for the “Zusammenfassung” and all that happy times.
In addition, to all ‘Lunds’ friends, especially Mattias Gustafsson, Bryndis Ragnarsdottir and
Eva Ljunggren - thank you very much.
Special thanks to Hilde Merkert for many helpful advices and solving ‘unsolvable’ problems.
The German bureaucracy would be far more difficult without Elke Stahl, Claudia Borde and
Wilma Samfass. Jozef handyman and his tools were also often needed in laboratory – thanks.
Lissi and Gabi from ‘die Kuche’ – thank you very much and sorry for that ‘difficult material’
to be sometimes autoclaved.
Importantly, special thanks to my parents who gave me the opportunity to study and for the
whole help – DZIEKUJE RODZICE!
And finally, thank you Kerstin for being there for me, and all support and love I have got
from you!
– Danke schön – Thank you – Dzi ękuj ę – Content
 
TABLE OF CONTENT 
1.  SUMMARY ........................................................................................................................................... 12 
1.  ZUSAMMENFASSUNG .......................................................................................................................... 14 
2.  INTRODUCTION.................................................................................................................................... 16 
2.1. EPIDEMIOLOGY OF URINARY TRACT INFECTION ....................................................................................................... 16 
2.2. ESCHERICHIA COLI AS A PATHOGEN ...................................................................................................................... 18 
2.2.1. Virulence factors of uropathogenic E. coli ........................................................................................... 20 
Adhesins ....................................... 20 
Flagella ......................................... 21 
Toxins ........................................... 21 
Iron acquisition systems ............... 22 
O‐, K‐antigens and serum resistance ........................................................................................................................... 23 
2.3. ASYMPTOMATIC BACTERIURIA (ABU) .................................................................................................................. 24 
2.3.1. UTI versus ABU .................................................................................................................................... 24 
2.3.2. Escherichia coli strain 83972: a model ABU E. coli isolate .................................................................. 24 
2.4. MECHANISMS OF PATHOGEN RECOGNITION .......................................................................................................... 26 
2.5. NITRIC OXIDE ‐ A HOST DEFENCE MECHANISM ....................................................................................................... 27 
2.6. GENOME PLASTICITY AND BACTERIAL EVOLUTION ................................................................................................... 28 
2.7. BACTERIAL POPULATION DYNAMICS ..................................................................................................................... 30 
2.8. AIMS OF THIS WORK .......... 32 
3.  MATERIAL ............. 33 
3.1.  STRAINS .................... 33 
3.2.  PLASMIDS .................. 34 
3.3.  OLIGONUCLEOTIDES ..... 34 
3.4.  CHEMICALS AND ENZYMES ........................................................................................................................... 36 
3.5.  MEDIA, AGAR PLATES AND ANTIBIOTICS .......................................................................................................... 37 
3.5.1. Media .................................................................................................................................................. 37 
3.5.2. Agar plates ........... 38 
3.5.3. Antibiotics............................................................................................................................................ 38 
3.5.4. DNA Markers ........ 39 
3.6.  TECHNICAL EQUIPMENT .............................................................................................................................. 39 
4.  METHODS ............. 42 
4.1.  WORKING WITH DNA .. 42 
4.1.1. Isolation of chromosomal DNA ........................................................................................................... 42 
4.1.2. Precipitation of DNA with alcohol ....................................................................................................... 42 
4.1.3. Determination of nucleic acid co