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Half Title

Title Page

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Contents

Contributors

Preface

I. Bacterial Infections

1. Impact Of Genome Plasticity On Adaption Of

REDUCTIVE EVOLUTION OF E. COLI: ASYMPTOMATIC BACTERIURIA AS AN EXAMPLE OF BACTERIAL ADAPTATION TO PROLONGED IN VIVO GROWTH IN THE URINARY TRACT

IMPACT OF GENOMIC CHANGES ON BACTERIUM-HOST INTERACTION AND FITNESS

INTRAVESICLE GROWTH AFFECTS THE MOTILITY OF E. COLI

INTRAVESICLE GROWTH AFFECTS BACTERIAL GROWTH CHARACTERISTICS AND METABOLISM OF E. COLI

ANALYSIS OF HOST FACTORS AND THEIR IMPACT ON ADAPTATION OF E. COLI

CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

2. Genotypic Changes In Enterohemorrhagic Escherichia coli During Human Infection

EHEC: OVERVIEW OF EPIDEMIOLOGY AND CLINICAL PATHOGENESIS

GENOMES OF EHEC

IDENTIFICATION OF GENETIC CHANGES DURING EHEC INFECTIONS

INTERSEROTYPE DIFFERENCES IN CONVERSION OF EHEC TO EHEC-LST

CONSEQUENCES OF IN VIVO GENETIC CHANGES IN EHEC

DOES stx LOSS MITIGATE CLINICAL OUTCOME?

EVOLUTIONARY ASPECTS AND ADAPTATION

CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCE

3. Genomic Fluidity Of The Human Gastric Pathogen Helicobacter pylori

THE HELICOBACTER GENOMES

GENETIC MECHANISMS UNDERLYING GENOME DIVERSITY IN H. PYLORI

GENOMIC ISLANDS OF H. PYLORI

FUNCTIONAL RELEVANCE OF THE PLASTIC GENOMES OF H. PYLORI

GENOMIC FLUIDITY OF H. PYLORI: CLINICAL IMPLICATIONS

PERSPECTIVES

REFERENCES

4. Genome Structure And Variability in Coagulase-Negative Staphylococci

FITNESS AND VIRULENCE-ASSOCIATED FACTORS OF CoNS

THE oriC ENVIRON OF CoNS GENOMES: A HOT SPOT FOR GENOME REARRANGEMENTS

CoNS HAVE AN UNBALANCED GENOME STRUCTURE

CoNS GENOMES AND MOBILE GENETIC ELEMENTS

EXTENSIVE HORIZONTAL GENE TRANSFER AMONG CoNS AND MECHANISMS OF ITS LIMITATION

BIOFILM FORMATION ON MEDICAL DEVICES AND EVASION OF HOST DEFENSES BY CoNS

PHENOTYPIC AND GENETIC INSTABILITY OF CoNS

CLINICAL IMPACT OF CoNS HETEROGENEOUS GENE EXPRESSION AND GENOME VARIABILITY

CONCLUSIONS

REFERENCES

5. Genome Plasticity In Legionella pneumophila And Legionella longbeachae: Impact On Host Cell Exploitation

GENERAL FEATURES OF THE L. PNEUMOPHILA AND L. LONGBEACHAE GENOMES

HOST-PATHOGEN INTERACTION: SPECIFICITIES AND COMMON FEATURES OF L. PNEUMOPHILA AND L. LONGBEACHAE

EVOLUTION OF EUKARYOTIC EFFECTORS: ACQUISITION BY HORIZONTAL GENE TRANSFER

CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

6. Genome Plasticity In Salmonella enterica And Its Relevance To Host-Pathogen Interactions

GENETIC MECHANISMS LEADING TO PLASTICITY AND HOST ADAPTATION IN SALMONELLA

GENOME ORGANIZATION IN SALMONELLA

SALMONELLA SEROVARS AND HOST ADAPTATION

CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

7. Mechanisms Of Genome Plasticity In Neisseria meningitidis: Fighting Change With Change

GENETIC VARIABILITY AT THE POPULATION LEVEL

GENOME PLASTICITY IN THE PREGENOMIC ERA

THE SEQUENCED GENOMES OF N. MENINGITIDIS: AN OVERVIEW

GENERATION OF GENOME VARIABILITY IN N. MENINGITIDIS

GENETIC BASIS OF VIRULENCE IN N. MENINGITIDIS

CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

8. Selfish Elements And Self-Defense In The Enterococci

EVIDENCE OF GENOME PLASTICITY

RELATIONSHIP OF GENOME PLASTICITY TO VIRULENCE

GENOME DEFENSE MECHANISMS IN THE ENTEROCOCCI

CRISPR

CONCLUSIONS AND FUTURE DIRECTIONS

REFERENCES

II. Viral Infections

9. Host-Driven Plasticity Of The Human Immunodeficiency Virus Genome

GENOMIC STRUCTURE AND LIFE CYCLE OF HIV

MECHANISMS OF GENOMIC VARIATION

ORIGIN OF HIV

GLOBAL VARIABILITY

EVOLUTION IN THE SINGLE INDIVIDUAL

FORCES DRIVING HIV EVOLUTION

EVOLUTION OF HIV WITHIN THE HUMAN POPULATION

ESCAPE FROM ANTIVIRAL DRUGS

CONCLUSIONS

REFERENCES

10. Genome Plasticity Of Influenza Viruses

VIRAL FACTORS

HOST FACTORS

PERSPECTIVES

REFERENCES

11. Plasticity Of The Hepatitis C Virus Genome

GENETIC DIVERSITY OF HCV: GENOTYPES AND SUBTYPES

ORGANIZATION OF THE HCV GENOME AND REPLICATION

MODEL SYSTEMS FOR HCV REPLICATION

THE QUASISPECIES NATURE OF HCV

THE TRANSMISSION EVENT

SEQUENCE DIFFERENCES BETWEEN HCV ISOLATES OF THE SAME SUBTYPE

LIMITATIONS TO HCV EVOLUTION: NEGATIVE SELECTION PRESSURE

REFERENCES

12. Genome Diversity And Host Interaction Of Noroviruses

GENETIC DIVERSITY AND CLASSIFICATION OF NOROVIRUSES

RECOMBINATION

PREVALENCE OF NV GENOTYPE GII.4 VARIANTS

NOROVIRUS-HOST INTERACTIONS

CONCLUSIONS AND PROSPECTS

REFERENCES

13. Genome Diversity And Evolution Of Rotaviruses

GENOME, GENE PROTEIN ASSIGNMENTS, AND VIRUS PARTICLE STRUCTURE

REPLICATION

REVERSE GENETICS

CLASSIFICATION

EPIDEMIOLOGY OF RVS

GENETIC MECHANISMS OF RV EVOLUTION

FURTHER UNDERSTANDING OF RV EVOLUTION ENABLED BY WHOLE-GENOME SEQUENCING

GROUP A RVs

NON-GROUP A RVs

RV VACCINATION AND GENOTYPE DISTRIBUTION OF WILD-TYPE RVs

REFERENCES

14. Genome Plasticity Of Papillomaviruses

GENETIC FEATURES OF PAPILLOMAVIRUSES

TAXONOMY, BIOLOGY, AND PATHOGENICITY OF PAPILLOMAVIRUSES

GENOMIC STABILITY OF PAPILLOMAVIRUSES IN LABORATORY SETTINGS

DIVERSIFICATION OF PAPILLOMAVIRUSES IN HUMANS SINCE THE EMERGENCE OF HOMO SAPIENS

ANCIENT DIVERSITY OF PAPILLOMAVIRUSES IN HUMANS

THE TAXONOMIC DIVERSITY OF PAPILLOMAVIRUSES IS SHAPED BY LINKED EVOLUTION OF THE VIRUS WITH THE HOST SPECIES

OVERALL STABILITY OF THE ORGANIZATION OF PAPILLOMAVIRUS GENOMES

MEDICAL CONSIDERATIONS EMERGING FROM THE LOW PLASTICITY OF PAPILLOMAVIRUS GENOMES

REFERENCES

15. Genome Plasticity Of Herpesviruses: Conservative Yet Flexible

AN INTRODUCTION TO HERPESVIRUSES AND THEIR LIFESTYLE

PRODUCTIVE VERSUS LATENT HERPESVIRUS INFECTION

GENETIC FEATURES CONTRIBUTING TO THE PLASTICITY OF HERPESVIRUS GENOMES

IMPLICATIONS OF HERPESVIRUS PLASTICITY FOR CURRENT RESEARCH

HOMOLOGOUS RECOMBINATION UPON COINFECTION

INTRASPECIES CONSERVATION VERSUS VARIATION OF HERPESVIRUS GENOMES

ADAPTIVE MUTATIONS IN HERPESVIRUSES AND MAINTENANCE OF VIRAL FITNESS IN VIVO

REFERENCES

III. Parasitic And Fungal Infections

16. Genome Diversity, Population Genetics, And Evolution Of Malaria Parasites

MALARIA AND MALARIA PARASITES

MALARIA GENOMES

THE HIGHLY DIVERSE GENOME OF THE P. FALCIPARUM PARASITE

HIGH RECOMBINATION RATE AND GENOME DIVERSITY

GENOTYPING AND MEASUREMENT OF GENOME DIVERSITY

GENOME DIVERSITY AND ESTIMATES OF THE AGE AND CLONALITY OF P. FALCIPARUM

GENOME DIVERSITY AND P. FALCIPARUM POPULATION STRUCTURE

GENETIC MAPPING

GENOME DIVERSITY, VACCINE DEVELOPMENT, AND DRUG RESISTANCE

GENOME DIVERSITY AND POPULATION STRUCTURE OF P. VIVAX

SUMMARY

ACKNOWLEDGMENTS

REFERENCES

17. The Fundamental Contribution Of Genome Hypervariability To The Success Of A Eukaryotic Pathogen, Trypanosoma brucei

WHAT IS ANTIGENIC VARIATION?

CONTRIBUTION OF THE GENOME TO ANTIGENIC VARIATION

VSG Switching

VSG EVOLUTION

CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

18. Genome Plasticity In Candida albicans

PLOIDY LEVEL

RETROTRANSPOSONS IN C. ALBICANS

MATING AND RECOMBINATION

CHROMOSOME POLYMORPHISMS

HETEROZYGOSITY AND LOSS OF HETEROZYGOSITY IN C. ALBICANS

GENOME PLASTICITY AND LABORATORY STRAINS

CONCLUSIONS

REFERENCES

19. Genome Plasticity Of Aspergillus Species

THE GENUS ASPERGILLUS

COMPARISON OF ASPERGILLUS GENOMES

SECONDARY METABOLITES IN A. FUMIGATUS

TRANSPOSABLE ELEMENTS IN ASPERGILLI

INTRAGENIC TANDEM REPEATS

REFERENCES

IV. Host Susceptibility

20. Dna Polymorphisms And Their Relevance For Infections With Human Cytomegalovirus And Aspergillus fumigatus

SINGLE-NUCLEOTIDE POLYMORPHISMS

CLINICAL RELEVANCE AND PATHOBIOLOGY OF A. FUMIGATUS

SNPs ASSOCIATED WITH A. FUMIGATUS INFECTIONS

CLINICAL RELEVANCE AND PATHOBIOLOGY OF HCMV

SNPs INFLUENCING SUSCEPTIBILITY TO HCMV

CONCLUSIONS

REFERENCES

21. Host Genetic Variation, Innate Immunity, And Susceptibility To Urinary Tract Infection

HUMAN GENETICS AND UTI SUSCEPTIBILITY

TLR4 AND ADAPTOR PROTEIN SIGNALING

CHEMOKINE RECEPTOR POLYMORPHISMS AND UTI SUSCEPTIBILITY

SUMMARY AND CONCLUSIONS

REFERENCES

Index