Note: e9780123977632v1 -- Front Cover -- Molecular Medical Microbiology, Volume 1 -- Copyright Page -- Contents -- List of Contributors -- Preface -- Preface to the First Edition -- 1 Molecular Medical Microbiology - The Expanding Concept -- A Brief History -- Molecular Medical Microbiology -- References -- 1 Bacterial Structure -- 2 Bacterial Ultrastructure -- General Morphology -- Surface Appendages -- Flagella -- Pili and Fimbriae -- Glycocalyx -- Capsules -- S-layers -- Cell Wall -- Gram-Negative Cell Walls -- Outer Membrane -- Periplasm and Peptidoglycan Gel -- Gram-Positive Cell Walls -- Peptidoglycan Layer and Periplasmic Gel -- Cell Wall Growth -- Cytoplasmic Membrane -- Nucleoid -- Cytoplasmic Inclusions -- Non-Membrane Inclusions -- Volutin Granules -- Polysaccharide Granules -- Non-Unit Membrane Inclusions -- Carboxysomes -- Lipid Bodies -- Gas Vesicles -- Photosynthetic Systems -- Cell Division -- Bacterial Conjugation -- Bacterial Sporulation -- Bacterial Germination -- Bacterial Biofilms -- Microscopy and Microbiology -- Acknowledgements -- References -- 3 Bacterial Capsules -- Introduction -- Chemistry of Capsules -- Primary Structures -- Secondary Structures -- Other Properties of CPSs -- Genetics of Capsular Biosynthesis -- Gram-Negative Bacteria -- Gram-Positive Bacteria -- Biosynthesis of Capsules -- Wzy-Dependent Polymerization -- ABC Transporter-Dependent Polymerization -- Synthase-Dependent Polymerization -- Attachment of Bacterial Capsules to the Cell Surface -- Regulation of Capsular Synthesis -- Modulation at the DNA Level -- Modulation at the Transcriptional Level -- Biological Functions of Capsules -- Capsules as a Virulence Factor -- Capsules as an Immune Evasion Factor -- Immunogenicity of CPSs as Vaccine Antigens -- Acknowledgements -- References -- 4 Genetics and Biosynthesis of Lipopolysaccharide -- Overview. , Classical Pathway of Lipid A-Kdo2 Biosynthesis -- Biosynthesis of Lipid IVA -- LpxA -- LpxC -- LpxD -- LpxBH -- LpxK -- Incorporation of Kdo Residues -- Late Acyltransferases -- Biosynthesis and Assembly of the Core Oligosaccharide -- Kdo and Ko -- Heptoses -- Isomerization -- Phosphorylation -- Phosphatase Reaction -- Synthesis of Nucleotide-Activated Heptose -- ADP-L-glycero-D-manno-Heptose-6-Epimerase -- Glycosyltransferases -- Enzymes Involved in the Completion of the Inner Core -- Assembly of the Outer Core -- Remodelling of the Lipid A-Inner Core Oligosaccharide -- Modification of the Lipid A Phosphate Groups -- Removal of Phosphate Groups -- Covalent Modifications of Phosphates -- Modification of Lipid A Acyl Chains -- Kdo Modifications -- Heptose Modifications -- Biosynthesis and Assembly of OAg -- Initiation -- Polyisoprenyl-Phosphate N-Acetylaminosugar-1-Phosphate Transferases -- Polyisoprenyl-Phosphate Hexose-1-Phosphate Transferases -- Assembly of OAg -- Wzy-Dependent O Antigen Assembly Pathway -- Und-PP-O Antigen Translocation -- Polymerization and Chain Length Regulation -- ABC Transporter-Dependent Pathway -- Synthase-Mediated Pathway -- O Antigen Ligation -- Synthesis and Recycling of Und-PP -- Export of LPS to the Outer Membrane -- Lipid A-Core Export Across the Inner Membrane -- Transport of LPS Across the Periplasm to the Cell Surface -- Acknowledgements -- References -- 5 Teichoic Acids, Lipoteichoic Acids and Other Secondary Cell Wall and Membrane Polysaccharides of Gram-Positive Bacteria -- Structure of Wall Teichoic Acids and their Attachment to the Cell Wall -- Structure and Properties of Lipoteichoic Acids -- The Cellular Roles of Teichoic Acids -- The Biological Activities of Wall Teichoic Acids -- Biological Activities of Lipoteichoic Acids -- Adhesion -- Cytokine Induction -- Nitric Oxide Induction. , Soluble Teichoic Acids In Vivo -- Genetics and Regulation of Anionic Polymer Synthesis -- Acknowledgement -- References -- 6 Peptidoglycan -- Introduction -- The Basic Chemical Structure of Peptidoglycan -- The Glycan Strands in Peptidoglycan -- The Stem Peptides in Peptidoglycan -- Peptide Cross-Links -- Variation of the Fine Structure -- Biophysical Properties of Peptidoglycan -- Thickness of Peptidoglycan -- Elasticity of Sacculi -- Pores in the Sacculus -- Architecture of Peptidoglycan -- Peptidoglycan Biosynthesis and Modifications -- Cytoplasmic Steps to UDP-MurNAc Pentapeptide -- Synthesis of the Lipid-Linked Precursor -- Variation in Lipid II Structure -- Peptidoglycan Synthases -- Peptidoglycan Hydrolases -- Secondary Modifications in the Peptidoglycan Structure -- Covalent Attachment of Secondary Cell Wall Polymers to Peptidoglycan -- Covalent Attachment of Proteins to Peptidoglycan -- Peptidoglycan Synthesis During the Cell Cycle -- Peptidoglycan Synthesis Complexes Active in Cell Elongation and Division -- Molecular Mechanism of Peptidoglycan Growth: The 3-for-1 Growth Model -- Regulation of Peptidoglycan Growth from the Inside and Outside -- Acknowledgements -- References -- 7 Flagella -- Flagellar Function -- Rate of Rotation -- Tumbling -- Energy Source -- Flagellar Structure -- Filament -- Flagellin (Hag or FliC) -- Phase Variation -- Filament Structure -- Filament Helicity -- Polymorphism -- Calladine Model -- Flagella Family -- Hook -- Universal Joint -- Hook Length Control -- Hook Protein -- Hook-Associated Proteins -- Basal Body -- The LP Ring Complex -- Rod -- The MS Ring Complex -- The C Ring -- C Rod -- Chaperones -- The Mot Proteins -- Assembly System of Flagella -- Morphogenesis -- Distal Growth -- Cap Proteins -- Export Apparatus -- Type III Secretion System -- Flil ATPase Activity -- Switching of the Export Gate. , Morphological Pathway -- In the Cytoplasm -- In the Periplasmic Space -- Outside the Cell -- Origin of Flagella -- Type III Secretion System -- F0F1-ATPase -- Conclusion -- Acknowledgement -- References -- 8 Pili and Fimbriae of Gram-Negative Bacteria -- Introduction -- Chaperone-Usher Pathway Pili -- CUP Pilus Architecture -- Subunit Structure -- Assembly Proteins and Mechanisms -- Periplasmic Chaperones -- The Chaperone Necessity -- Conserved Chaperone Surfaces and Donor Strand Complementation -- Donor Strand Exchange -- Ushers -- Functions of the Usher Domains in Pilus Assembly -- Usher Selectivity and Potential Binding Surfaces -- Current Model of Chaperone-Usher Pilus Biogenesis at the Usher -- Structural Insights into the Growing Pilus -- Pore-Gating Mechanisms of Usher -- Alternative Chaperone-Usher Pathways -- Diversity of CUP Systems in Disease -- Different Pilus Systems Involved in Adhesion and Disease -- Curli: Extracellular Nucleation/Precipitation Pathway -- Interfering With the Pilus -- References -- 9 Endospores, Sporulation and Germination -- Endospore Structure and Resistance -- Endospore Formation -- Endospore Germination -- Endospore Germination as a Therapeutic Target -- Endospore Detection -- Endospore-Based Technology -- Endospore-Borne Diseases -- Anthrax -- Bacillus cereus Syndromes -- Tetanus -- Botulism -- Clostridium sordellii and Toxic Shock Syndrome -- Clostridium difficile Infections (CDI) -- Clostridium perfringens Infections -- Opportunistic Infections -- Acknowledgements -- References -- 2 Bacterial Cell Function -- 10 Bacterial Growth, Culturability and Viability -- Introduction -- Bacterial Growth -- Patterns of Growth and Sources of Information -- Molecular Information Related to Bacterial Growth -- Ribosomal RNA -- Chromosome Replication -- Cell Division -- Global Regulatory Proteins -- Growth and Stasis. , Exponential Phase -- Exponential Phase Inocula: A Key Resource in Bacteriology -- Stress Responses -- Stationary Phase -- Dormancy and Sporulation -- Exit from Dormant or Stationary Cellular States and Re-entry into Growth -- Asymmetric Cell Division -- Culturability and Viability -- Culturability -- 'As Yet Uncultured' (AYU) Bacteria -- Cells of Culturable Organisms That Are Not Recovered in Culture -- Viability -- The VBNC Controversy -- Conclusions -- References -- 11 Bacterial Energy Metabolism -- Introduction to Energy Metabolism -- Scope of Chapter -- Chemiosmosis -- ATPase -- Na+-ATPase -- Fermentation -- Fermentations of Sugars and Polysaccharides -- Fermentation Pathways -- Ethanol Fermentations -- Lactate Fermentations -- Mixed Acid Fermentations -- Butyrate Metabolism in the Human Gut -- Utilization of Complex Carbohydrates -- Starch Utilization -- Xylan Utilization -- Cellulose Degradation -- Aerobic Respiration -- Components of Respiratory Chains -- Cytochrome Oxidases -- Cytochrome caa3 Oxidases -- Cytochrome cbb3 Oxidases -- Cytochrome bo3 Oxidase -- Cytochrome bd Oxidase -- Anaerobic Respiration -- Denitrification -- The Reductases Involved in Denitrification -- Nitrate Reductase Nar and Nitrate/Nitrite Transporter NarK -- Nitrite Reductases -- Nitric Oxide Reductases -- Nitrous Oxide Reductases -- Fumarate and Trimethylamine Oxide Reductases -- Regulation of Aerobic and Anaerobic Metabolism -- The Requirement for Regulation of Aerobic and Anaerobic Energy Metabolism -- Basic Principles of Regulatory Systems in Bacteria -- NarX-NarL Two-Component System -- Regulation at the Global Level by a Two-Component System: ArcB-ArcA -- Fnr - a One-Component System -- Diversity of Bacterial Energy Metabolism Regulators -- Regulatory Networks -- Energy Metabolism of Selected Bacterial Pathogens -- Campylobacter jejuni -- Helicobacter pylori. , Neisseria gonorrhoeae and Neisseria meningitidis.

Note: Front Cover -- MOLECULAR MEDICAL MICROBIOLOGY -- Copyright Page -- Content -- PART 12: RESPIRATORY INFECTIONS -- Chapter 74. Respiratory Tract Infections: A Clinical Overview -- Chapter 75. Bordetella pertussis -- Chapter 76. Streptococcus pneumoniae -- Chapter 77. Klebsiella pneumoniae -- Chapter 78. Moraxella (Branhamella) catarrhalis -- Chapter 79. Mycoplasma pneumoniae and other Mycoplasmas -- Chapter 80. Coxiella burnetii -- PART 13: MYCOBACTERIAL INFECTIONS -- Chapter 81. Mycobacterium tuberculosis -- Chapter 82. Mycobacterium leprae -- Chapter 83. The Mycobacterium avium- intracellulare Complex -- PART 14: SEXUALLY-TRANSMITTED INFECTIONS -- Chapter 84. Sexually Transmitted and Genital Infections: A Clinical Overview -- Chapter 85. Treponema pallidum -- Chapter 86. Haemophilus ducreyi -- Chapter 87. Chlamydia -- PART 15: ANAEROBIC INFECTIONS -- Chapter 88. Anaerobic Infections: A Clinical Overview -- Chapter 89. Clostridium perfringens: Wound Infections -- Chapter 90. Clostridium tetani -- Chapter 91. Bacteroides -- PART 16: CENTRAL NERVOUS SYSTEM INFECTIONS -- Chapter 92. Central Nervous System Infections: A Clinical Overview -- Chapter 93. Haemophilus influenzae -- PART 17: ANIMAL AND ECTOPARASITIC SOURCE INFECTIONS -- Chapter 94. Brucella -- Chapter 95. Bacillus anthracis and Other Bacillus species -- Chapter 96. Yersinia pestis -- Chapter 97. Borrelia burgdorferi -- Chapter 98. Relapsing Fever Borrelia -- Chapter 99. Bartonella -- Chapter 100. Leptospira -- Chapter 101. Francisella -- Chapter 102. Rickettsia and Orientia -- Chapter 103. Identification of Uncultured Pathogens -- Index -- Colour Plates.

Note: Intro -- Preface -- Contents -- Contributors -- Bacterial Identification Based on Universal Gene Amplification and Sequencing -- Introduction -- 16S rDNA Gene Sequencing for Bacterial Identification -- Routine Bacterial Identification in Clinical Laboratories -- Identification of Rare Bacteria and Bacteria with Unusual Phenotypic Profiles -- Identification of Slow-Growing and Uncultivable Bacteria -- Guidelines for Interpretation of 16S rDNA Gene Sequence Results -- Automation of 16S rDNA Gene Sequencing -- Other Gene Targets for Bacterial Identification -- Future Developments and New Technologies for Bacterial Identification -- References -- Molecular Techniques for Blood and Blood Product Screening -- Introduction -- Limitations for Current Technologies Used in Blood Safety -- Application of Advanced Molecular Techniques in Blood Safety Applications -- Major Different Generations of Nucleic Acid Detection Techniques -- Southern Blot Hybridization (1970s) -- Polymerase Chain Reaction (1980s) -- Microarrays (1990s) -- Screening of Donor Blood for Infectious Agents -- Confirmatory Testing of Donor Blood for Infectious Agents -- Application of Nucleic Acid Testing for Infectious Agents -- Hepatitis B Virus -- Hepatitis B Surface Antigen -- Antibodies to the Hepatitis B Core Antigen (Anti-HBc) -- Hepatitis C Virus -- Antibodies to the Hepatitis C Virus (Anti-HCV) -- HCV Confirmatory Tests -- Human Retroviruses -- Antibodies to Human Immunodeficiency Virus: Types 1 and 2 (Anti-HIV-1, -2) -- Antibodies to Human T-Lymphotropic Virus: Types I and II (Anti-HTLV-I, Anti-HTLV-I-II) -- West Nile Virus -- Syphilis -- Other Concerns -- Hepatitis Viruses -- Hepatitis Delta Virus -- TT Virus -- Cytomegalovirus -- Trypanosoma Cruzi -- Malaria -- Variant Creutzfeldt-Jakob Disease -- Dengue Viruses -- Babesia Species -- Chagas' Disease. , Severe Acute Respiratory Syndrome -- Ebola Virus -- Discovery of Unrecognized and Uncharacterized Viral Agents -- Conclusion -- References -- Molecular Diagnostics of Sexually Transmitted Diseases: Bacterial, Trichomonas, and Herpes Simplex Virus Infections -- Introduction -- Chlamydia trachomatis and Neisseria gonorrhoeae -- Signal Amplification -- Strand Displacement Amplification (SDA) -- Transcription-Mediated Amplification (TMA) -- Polymerase Chain Reaction (PCR) -- Treponema Pallidum -- Polymerase Chain Reaction (PCR) -- Haemophilus Ducreyi -- Nucleic Acid Hybridization -- Polymerase Chain Reaction (PCR) -- Mycoplasma and Ureaplasma -- Nucleic Acid Hybridization -- Transcription-Mediated Amplification (TMA) -- Polymerase Chain Reaction -- Trichomonas Vaginalis -- Nucleic Acid Hybridization -- Strand Displacement Amplification (SDA) -- Helicase-Dependent Amplification (HDA) -- Transcription-Mediated Amplification (TMA) -- Polymerase Chain Reaction (PCR) -- Herpes Simplex Virus -- Loop-Mediated Isothermal Amplification (LAMP) -- Strand Displacement Amplification (SDA) -- Polymerase Chain Reaction (PCR) -- Conclusion -- References -- Advances in the Diagnosis of Mycobacterium tuberculosis Infection -- Introduction -- Mechanism of Mycobacterium tuberculosis Infection -- Epidemiology of Tuberculosis -- Epidemiology of Drug-Resistant TB -- Epidemiology of Tuberculosis and HIV Coinfection -- New Compounds in Development -- Cell- and Culture-Based Methods of TB Diagnosis -- Bacilloscopy -- In Vitro Culturing -- BACTEC MGIT960 System -- Molecular Methods -- NAAT (Nucleic Acid Amplification Test) -- Xpert MTB/RIF -- Cobas TaqMan MTB Test -- Abbott RealTime MTB Automated Assay -- BD ProbeTec ET TB System -- Gen-Probe Amplified Mycobacterium tuberculosis Direct Test -- Multiplex Allele-Specific PCR (MAS-PCR) -- PCR-Reverse Blot Hybridization Assay (REBA). , Line Probe Assay -- Genotype MTBDRplus -- Nipro NTM + MDRTB Detection Kit 2 -- Genotype MTBDRsl® V 1.0 and V 2.0 -- GenoQuick® MTB VER 1.0 -- GenoType MTBC VER 1.X -- IS6110-Based Restriction Fragment Length Polymorphism (RFLP) -- Spacer Oligonucleotide Typing (Spoligotyping) -- Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) -- Loop-Mediated Isothermal Amplification PCR (LAMP) -- Next-Generation Sequencing -- Whole Genome Sequencing -- Immunological Methods -- Tuberculin Skin Test (TST) -- Interferon-Gamma Release Assay -- Urine Lipoarabinomannan Rapid Test -- Nanodisk-MS Platform -- Microscopy Methods -- Automated Microscopic System, TBDx -- Sputum Smear Light-Emitting Diode Fluorescent Microscopy (LED-FM) -- Concluding Remarks -- References -- Advanced Microbial Strain Subtyping Techniques for Molecular Epidemiology Investigations -- Introduction -- Definition of Molecular Epidemiology -- Genotyping Techniques Used to Conduct Epidemiologic Investigations -- Repetitive Element PCR Genotyping Tests -- Broad-Spectrum Repetitive Element PCR Genotyping Tests -- Limitations of Broad-Spectrum Rep-PCR Genotyping Tests -- Species-Specific Repetitive Element PCR Genotyping Tests -- Pulsed-Field Gel Electrophoresis (PFGE) -- Multilocus Sequence Typing (MLST) -- Whole-Genome Sequence (WGS)-Based Genotyping Tests -- Applications of Genotyping Tests in Epidemiologic Investigations -- Foodborne Diseases -- Tuberculosis -- Healthcare-Associated Infections -- Other Applications of NGS Technology in Epidemiologic Investigations -- Next-Generation Molecular Epidemiology -- References -- Molecular Detection and Characterization of Carbapenem-Resistant Enterobacteriaceae -- Introduction -- Rapid Nucleic Acid-Based Tests -- Conventional PCR Assays -- Real-Time PCR Assays -- In-house Real-Time PCR -- Commercial Real-Time PCRs. , FDA-Approved Real-Time PCR Assays -- Commercially Available Research Use-Only (RUO) Assays -- PCR/ESI-MS -- Loop-Mediated Isothermal Amplification -- Microarray -- Next-Generation Sequencing (NGS) -- Rapid Non-nucleic Acid-Based Tests: MALDI-TOF MS -- Conclusion -- References -- Advanced Methods for Screening and Identification of Methicillin-Resistant Staphylococcus aureus -- Clinical Relevance -- Molecular Epidemiology -- Culture-Based MRSA Detection -- Molecular Methods for MRSA Screening for Surveillance -- Molecular Methods for MRSA Diagnosis in Active Infection -- Detection of MRSA/MSSA in Positive Blood Cultures -- Detection of MRSA in Other Sites -- Direct Detection of MRSA in Blood -- Next-Generation Sequencing (NGS) for Rapid Detection of MRSA -- Conclusions -- References -- Advanced Techniques in Diagnostic Parasitology -- Introduction -- Advanced Technologies in Clinical Parasitology -- Mobile Phone Microscopy -- Digital Image Analysis -- Molecular Diagnostics -- Nucleic Acid Amplification Methods -- Sequencing-Based Approaches -- Proteomics -- Conclusions -- References -- Advanced Methods for Detection of Foodborne Pathogens -- Introduction -- Traditional Methods -- Serotyping -- Enzyme-Linked Immunosorbent Assay (ELISA) -- Bacteriophage -- Polymerase Chain Reaction (PCR), Real-Time PCR, and Reverse Transcriptase PCR -- Microarray -- PFGE -- Whole Genome Sequencing (WGS) -- Metagenomics -- Conclusions -- References -- Technical and Clinical Niches for Point-of-Care Molecular Devices -- Defining POCT: The Debate -- Why Point-of-Care for Clinical Microbiology? -- Technologies for POCT: The Right Technology for the Right Job -- Clinical Situations for Which POCT for Microbiology Are Used -- The Transition of POC to "On-Demand" Hospital Testing -- Infectious Syndromes and Syndromic POC Testing in Clinical Microbiology. , Limitations of Current POC Technologies -- References -- The Human Coronaviruses -- Introduction -- HCoV Genome Organization -- Clinical Symptoms -- Epidemiology -- Human Coronavirus 229E (Group 1/Alpha-Coronavirus) -- Human Coronavirus NL63 (Group 1/Alpha-Coronavirus) -- Human Coronavirus HKU1 (Group 2/Betacoronavirus, Lineage A) -- Human Coronavirus OC43 (Group 2/Betacoronavirus of Lineage A) -- SARS Coronavirus (Group 2 Coronavirus/Betacoronavirus of Lineage B) -- MERS Coronavirus (Group 2/Betacoronavirus, Lineage C) -- Virus Ecology of Human Coronaviruses -- Diagnostics -- Advanced Molecular Techniques Relevant to Human Coronaviruses -- Concluding Remarks -- References -- The Role of the Human Bocavirus (HBoV) in Respiratory Infections -- Introduction -- HBoV Biology -- Epidemiology -- Clinical Features -- Coinfections and Persistence -- Diagnostics -- Advanced Molecular Techniques in HBoV Research and Diagnostics -- Summary and Perspective -- References -- Technical Advances in Veterinary Diagnostic Microbiology -- Introduction -- Identification -- Typing -- Virulence Determination -- Antimicrobial Susceptibility Testing -- Conclusion -- References -- Recent Advances in Veterinary Diagnostic Virology -- Introduction -- Standardization of Diagnostic Assays -- Sample Collection, Transportation, Storage, Enrichment, and Nucleic Acid Preparation -- Sample Collection -- Transportation -- Sample Storage -- Sample Enrichment -- Nucleic Acid Preparation Processes -- Nucleic Acid Amplification-Based Assays -- Quantitative PCR Assays -- Multiplex PCR: Detection of Multiple Viruses, Variants of a Virus, Including Vaccine Strains -- Molecular Tests for the Improved Detection of Food and Waterborne Zoonotic Pathogens -- Proximity Ligation Assays -- Isothermal Nucleic Acid Amplification -- Digital PCR -- Genomic Sequencing and Viral Metagenomics. , xMAP Technology (Suspension Array Technology).

Note: 9780323899925v1_WEB -- Front Cover -- Molecular Medical Microbiology -- Copyright Page -- Contents -- List of contributors -- About the editors -- Preface -- 1 Molecular medical microbiology-from bench to bedside -- 1.1 The concept -- 1.2 The evolving concept -- 1.3 From bench to bedside -- References -- 1 Bacterial structure -- 2 Classification of medically important bacteria -- 2.1 Introduction -- 2.2 Basics of bacterial taxonomy -- 2.3 Gram-negative bacteria -- 2.3.1 Enterobacterales -- 2.3.1.1 Enterobacter spp -- 2.3.1.2 Klebsiella spp -- 2.3.1.3 Citrobacter spp -- 2.3.1.4 Escherichia and Shigella -- 2.3.1.5 Pseudomonas spp -- 2.3.1.6 Other glucose nonfermenting gram-negative bacilli -- 2.3.1.7 Acinetobacter spp -- 2.3.1.8 Burkholderia spp -- 2.4 Gram-positive bacteria -- 2.4.1 Mycobacterium -- 2.4.1.1 Staphylococci -- 2.4.1.2 Viridans group streptococci -- 2.5 Conclusion and summary -- References -- 3 Bacterial ultrastructure -- 3.1 Introduction -- 3.2 Overview of bacterial ultrastructures -- 3.3 Surface appendages -- 3.4 Flagella -- 3.5 Pili and fimbriae -- 3.6 Capsules and S-layers -- 3.7 Membrane vesicles -- 3.8 Bacterial cell walls -- 3.9 Gram-negative bacterial cell wall -- 3.10 Gram-positive bacterial cell walls -- 3.11 Mycobacteria -- 3.12 Cell wall-deficient bacteria -- 3.13 Cell walls of Archea and surface appendages -- 3.14 Cytoplasmic membrane -- 3.15 Nucleoid -- 3.16 Bacterial cell division -- 3.17 Cytoplasmic inclusions -- 3.18 Outlook -- References -- 4 Bacterial cell walls: peptidoglycan -- 4.1 Introduction -- 4.2 The basic chemical structure of peptidoglycan -- 4.2.1 The glycan strands in peptidoglycan -- 4.2.2 The stem peptides in peptidoglycan -- 4.2.3 Peptide cross-links -- 4.2.4 Variation of the fine structure -- 4.3 Biophysical properties of peptidoglycan -- 4.3.1 Thickness of peptidoglycan -- 4.3.2 Elasticity of sacculi. , 4.3.3 Pores in the sacculus -- 4.4 Architecture of peptidoglycan -- 4.5 Peptidoglycan biosynthesis and modifications -- 4.5.1 Cytoplasmic steps to UDP-MurNAc pentapeptide -- 4.5.2 Synthesis of the lipid-linked precursor -- 4.5.3 Variation in the lipid II structure -- 4.5.4 Peptidoglycan synthases -- 4.5.5 Peptidoglycan hydrolases -- 4.5.6 Secondary modifications in the peptidoglycan structure -- 4.6 Covalent attachment of secondary cell wall polymers to peptidoglycan -- 4.7 Covalent attachment of proteins to peptidoglycan -- 4.8 Peptidoglycan synthesis during the cell cycle -- 4.8.1 Peptidoglycan synthesis complexes active in cell elongation and division -- 4.8.2 Molecular mechanism of peptidoglycan growth: the 3-for-1 growth model -- 4.8.3 Regulation of peptidoglycan growth from the inside and outside -- Acknowledgments -- References -- 5 Bacterial capsules -- 5.1 Introduction -- 5.2 Chemical and structural properties of the capsules -- 5.2.1 Primary structures -- 5.2.2 Secondary structures -- 5.2.3 Other properties of capsular polysaccharides -- 5.3 Genetics of capsule biosynthesis -- 5.3.1 Gram-negative bacteria -- 5.3.2 Gram-positive bacteria -- 5.4 Biosynthesis of the capsules -- 5.4.1 Wzy-dependent polymerization -- 5.4.2 ABC transporter-dependent polymerization -- 5.4.3 Synthase-dependent polymerization -- 5.4.4 Attachment of bacterial capsules to the cell surface -- 5.5 Regulation of capsule production -- 5.5.1 Modulation at the DNA level -- 5.5.2 Modulation at the transcriptional level -- 5.5.3 Posttranscriptional regulation -- 5.5.4 Metabolic regulation -- 5.6 Biological functions of the capsules -- 5.6.1 Capsules as a virulence factors -- 5.6.2 Capsules as an immune evasion factor -- 5.6.3 Other functions of capsules -- 5.7 The capsules as targets for host immunity and therapeutics. , 5.7.1 Molecular recognition of bacterial capsules by host immune systems -- 5.7.2 Capsules as vaccine antigens -- 5.7.3 Capsules as therapeutic targets -- 5.8 Conclusion and prospect -- Acknowledgments -- References -- 6 Flagella -- 6.1 Flagellar function -- 6.1.1 Estimation of torque -- 6.1.2 Tumbling -- 6.1.3 Energy source -- 6.2 Flagellar structure -- 6.2.1 Filament -- 6.2.1.1 Flagellin (Hag or FliC) -- 6.3 Phase variation -- 6.4 Filament structure -- 6.5 Filament helicity -- 6.5.1 Polymorphism -- 6.6 Calladine model -- 6.6.1 Flagella family -- 6.7 Hook -- 6.7.1 Hook protein -- 6.7.2 Universal joint -- 6.7.3 Hook length control -- 6.8 Hook-associated proteins -- 6.8.1 Basal body -- 6.9 Rod -- 6.10 The LP ring complex -- 6.10.1 The MS ring complex -- 6.11 The cytoplasmic ring -- 6.12 Flagellar protein export apparatus -- 6.13 Chaperones -- 6.14 The Mot proteins -- 6.15 Assembly system of flagella -- 6.15.1 Morphogenesis -- 6.15.2 Distal growth -- 6.15.3 Cap proteins -- 6.16 Protein export apparatus -- 6.16.1 Type 3 secretion system -- 6.16.2 Substrate specificity switching -- 6.17 Morphological pathway -- 6.18 In the cytoplasm -- 6.19 In the periplasmic space -- 6.20 Outside the cell -- 6.21 Origin of flagella -- 6.21.1 Type 3 secretion system -- 6.21.2 FOF1-ATPase -- 6.22 Conclusion -- Acknowledgment -- References -- 7 Bacterial pili and fimbriae -- 7.1 Introduction -- 7.2 Chaperone-usher pathway pilus represented by type I fimbriae and P pilus of Escherichia coli -- 7.2.1 Structure of type I fimbriae and pili -- 7.2.2 Biogenesis model of type I fimbriae and P pili -- 7.2.3 Alternative chaperone/usher pathways -- 7.2.4 Regulation of type I fimbriae and P pili -- 7.2.5 Function of type I fimbriae and pili -- 7.3 Type IV fimbriae and P pilus -- 7.3.1 Structure and biogenesis of type IV fimbriae and pili. , 7.3.2 Regulation of type IV fimbriae and pili -- 7.3.3 Function of type IV fimbriae and pili -- 7.3.4 Type V pilus -- 7.3.5 Structure of type V fimbriae and pili -- 7.3.6 Biogenesis model of type V fimbriae and pili -- 7.3.7 Regulation of type V fimbriae and pili -- 7.3.8 Function of type V fimbriae and pili -- 7.4 Development of novel therapeutics via targeting the pilus biogenesis -- 7.5 Emerging themes and future directions -- Acknowledgment -- References -- 8 Endospores, sporulation, and germination -- 8.1 Introduction -- 8.2 Sporulation as a survival strategy -- 8.3 The endospore structure and resistance -- 8.4 Endospore formation -- 8.5 Spore awakening: germination -- 8.6 Endospore formers pathogens -- 8.7 Pathogenic spore formers control -- 8.8 Endospore detection -- 8.9 Endospore-based technology -- 8.9.1 Probiotics -- 8.9.2 Biocides -- 8.9.3 Biofuels and organic compounds -- 8.9.4 Bioparticles -- References -- 2 Bacterial cell function -- 9 Bacterial growth and cultivation -- 9.1 Introduction -- 9.2 Bacterial growth -- 9.2.1 Patterns of growth and sources of information -- 9.2.2 Molecular information related to bacterial growth -- 9.2.2.1 Ribosomal RNA -- 9.2.2.2 Chromosome replication -- 9.2.2.3 Cell division -- 9.2.2.4 Global regulatory proteins -- 9.2.3 Growth and stasis -- 9.2.3.1 Lag phase -- 9.2.3.2 Exponential phase -- 9.2.3.3 Stationary phase -- 9.2.3.4 Death phase -- 9.2.3.5 Exit from dormant or stationary cellular states and re-entry into growth -- 9.2.4 The Environmental factors that affect bacterial growth -- 9.2.4.1 Temperature -- 9.2.4.2 Oxygen -- 9.2.4.3 pH -- 9.2.4.4 Osmotic pressure -- 9.2.5 Unique growth forms: spores, biofilms, and persisters -- 9.3 Bacterial growth and antibiotics treatment -- 9.4 Bacterial cultivations -- 9.4.1 Historic perspective of cultivation -- 9.4.2 "As-yet-unculturable" bacteria. , 9.4.3 The renaissance of bacterial cultivation -- 9.4.3.1 Cocultivation -- 9.4.3.2 Community cultivation -- 9.4.3.3 In situ cultivation -- 9.4.3.4 Single-cell isolation and cultivation -- 9.4.3.5 High-throughput cultivation -- 9.4.3.6 Culturomics -- 9.5 Final remarks -- Acknowledgments -- References -- 10 Bacterial energy metabolism -- 10.1 Introduction -- 10.1.1 Scope of chapter -- 10.2 Fermentation -- 10.2.1 Bacterial fermentation of sugars -- 10.2.2 Bacterial ethanol fermentation -- 10.2.3 Bacterial lactate fermentation -- 10.2.4 Propionate fermentation -- 10.2.5 Bacterial organic acid fermentation -- 10.2.6 Bacterial biogas fermentation -- 10.2.7 Its role in human health -- 10.2.8 Industrial bacterial fermentation -- 10.2.8.1 Chemiosmosis -- 10.2.9 Complete steps of chemiosmosis and adenosine triphosphate synthesis -- 10.2.10 Adenosine triphosphate synthase -- 10.2.11 Evolutionary significance -- 10.2.11.1 Aerobic respiration -- 10.2.12 Glycolysis -- 10.2.13 Formation of acetyl-CoA -- 10.2.14 Tricarboxylic acid cycle -- 10.2.15 Pyruvate dehydrogenase complex -- 10.2.16 Citrate synthase -- 10.2.17 Isocitrate dehydrogenase -- 10.2.18 α-Ketoglutarate dehydrogenase complex -- 10.2.18.1 Anaerobic respiration -- 10.2.19 Nitrate respiration -- 10.2.20 Denitrification -- 10.2.21 Applications of denitrification -- 10.2.22 Sulfate respiration -- 10.2.23 Fumaric acid respiration -- 10.2.23.1 Metabolism of complex carbohydrates -- 10.2.24 Starch metabolism -- 10.2.25 Cellulose degradation -- 10.2.26 Lignin degradation -- 10.2.27 Xylan degradation -- 10.2.27.1 Energy metabolism in selected bacteria -- 10.2.28 Obligate aerobes -- 10.2.29 Obligate anaerobes -- 10.2.30 Facultative anaerobes -- 10.2.31 Microaerophile -- References -- 11 Biofilms, quorum sensing, and crosstalk -- 11.1 Communal behavior of bacteria -- 11.2 A conceptual overview of quorum sensing. , 11.3 Quorum signals and circuits.

Note: Intro -- Advanced Techniquesin Diagnostic Microbiology -- Preface -- Contents -- Contributors -- Part I: Methods -- Chapter 1: Automated Blood Cultures -- Introduction -- Principles -- Automated Culturing Systems -- Blood Culture and CMBCS for Mycobacteria -- Concluding Remarks -- References -- Chapter 2: Breath Tests for Detection of Helicobacter pylori and Aspergillus fumigatus -- Introduction -- Helicobacter pylori -- Aspergillus spp. -- Conventional Diagnostic Tests -- Detection of H. pylori -- Detection of Aspergillus spp. -- Breath Tests -- Introduction -- Sample Collection -- Urea Breath Test for H. pylori -- Breath Test for Aspergillosis -- Conclusions -- References -- Chapter 3: Rapid Antigen Tests -- Introduction -- Principles of the Techniques -- Agglutination -- Immuno uorescence -- Enzyme Immunoassay -- Chemiluminescent Methods -- Lateral Flow Immunochromatography and Fluoroimmunoassay -- Characteristics of the Techniques -- Applications of the Techniques -- Bacteria -- Fungi -- Parasites -- Viruses -- References -- Chapter 4: Antibody Detection: Principles and Applications -- Introduction -- Principles and Characteristics of Techniques -- Colorimetric or Chromogenic Substrate -- Radioimmunoassay -- Chemiluminescence-Immunoassay -- Electrochemiluminescent -- Fluorescent Immunoassays -- Multi-Analyte Pro le Technology -- Contrast of These Techniques -- Application of the Techniques in the Diagnostic Microbiology -- Clinical Applications -- Automation -- Summary -- References -- Chapter 5: Cytometry-Based Antimicrobial Resistance Techniques -- Introduction -- Flow Cytometry Setup -- Antimicrobial Resistance Measurements -- Assay Turnaround Time -- Comparator Methods -- Flow Cytometry Challenges -- Conclusions and Future Prospects -- References -- Chapter 6: Biochemical Pro le-Based Microbial Identi cation Systems. , Introduction -- Conventional Microbial Identi cation Systems -- Single Enzyme Rapid Tests -- Catalase Test -- Oxidase Test -- Spot Indole Test -- Slide Coagulase Test -- Microdase -- Bile Solubility Test -- PYR -- Leucine Aminopeptidase Test -- MUG Test -- Indoxyl Butyrate Disk -- Chromogenic Enzyme Substrate Test -- Gonocheck II -- Bacticard Neisseria -- Hippurate -- Lysostaphin -- CLO Test -- Overnight Biochemical Tests -- Tube Coagulase Test -- DNA Hydrolysis -- Vancomycin Disk Test -- Bacitracin Inhibition Test (Taxo A Disk) -- Bacitracin and STX Susceptibility Test -- Taxo P Disks (Optochin) -- CAMP Test -- Reverse CAMP Test -- Bile Esculin Agar Slant -- 6.5 % Salt Broth -- Indole Test -- Nitrite Test -- ALA ( Haemophilus in uenzae Porphyrin Test) -- Motility Indole Lysine Sul de (MILS) Medium -- O -Nitrophenyl-b- d -Galactopyranoside Test -- Methyl Red Test -- Voges-Proskauer Test -- Pseudosel Agar Slant -- Urea Agar Slant -- Citrate Agar Slant -- Cetrimide Agar -- Gelatin -- Acetate Utilization -- Lead Acetate for Hydrogen Sul de Detection -- Lysine Iron Agar -- Triple Sugar Iron Agar Slant -- Phenylalanine Deaminase -- Decarboxylase (Moeller's Method) -- OF Glucose Medium -- OF Sugars -- Commercial Microbial Identi cation System -- API Identi cation System -- API Gram-Negative Identi cation -- API Gram-Positive Identi cation -- API Anaerobe Identi cation -- BBL™ Crystal™ Identi cation System -- BBL Phoenix Identi cation and Susceptibility System -- VITEK and VITEK 2 Identi cation System -- MicroScan WalkAway -- Sensititre ® Microbiology Systems -- MIDI Sherlock -- BioLog ID System -- References -- Chapter 7: Infectious Disease Biomarkers: Non-Antibody-Based Host Responses -- Introduction -- Procalcitonin -- The Roles of PCT and Other Biomarkers in Sepsis -- The Roles of PCT in Sepsis -- The Roles of CRP in Sepsis. , The Roles of CRP and PCT in Infectious States Other than Sepsis -- The Roles of Miscellaneous and Novel Biomarkers in Infectious States -- Serum Amyloid A -- Lipopolysaccharide-Binding Protein -- Coagulation Markers -- Angiopoietins -- Neopterin -- Toll-Like Receptor-2 -- Triggering Receptor Expressed on Myeloid Cells-1 -- Soluble Urokinase-Type Plasminogen Activator Receptor -- Soluble Receptor for Advanced Glycation End Products -- CD64 -- HLA-DR -- Presepsin -- Cytokines -- Proadrenomedullin -- Alpha-1 Antitrypsin and Other Hepatitis Biomarkers -- Gelsolin -- Interferon-Gamma-Inducible Protein-10 -- Neutrophil Distribution Width -- Regulatory T Lymphocytes (Treg) -- Summary of Miscellaneous Biomarkers -- Newer Platforms for Measurement of Biomarkers -- Conclusions and Future Directions -- References -- Chapter 8: Functional Assessment of Microbial and Viral Infections by Real-Time Cellular Analysis System -- Introduction -- RTCA and Its Principle of Detection Using Impedance Microelectrode Sensor Arrays -- Analysis of Host Cell Responses to Bacterial Infections on RTCA System -- Detection of Clostridium dif cile Toxin -- Detection of Clostridium botulinum Toxin -- Detection of Meningococcal Infection -- Virus-Induced CPE and Neutralizing Antibody Detection on RTCA System -- West Nile Virus and St. Louis Encephalitis Virus CEP and Neutralizing Antibody Detection -- In uenza Virus and Neutralizing Antibody Detection -- Hand-Foot-Mouth Virus Detection -- Helminth Motility and Egg Hatching Activity on RTCA System -- Host Immune Function Assessment on RTCA: Nature Killer Cells and T Cells -- Natural Killer Cell Function Assessment -- T Cell Surface Receptor Detection -- Perspectives -- References -- Chapter 9: Cellular Fatty Acid-Based Microbial Identi cation and Antimicrobial Susceptibility Testing -- Introduction. , General Principles and Methods of Cellular Fatty Acid Analysis -- CFA Testing Platforms for Bacterial Identi cation -- Library Expansion and Fatty Acid Polymorphisms -- Identi cation of Agents of Bioterrorism and Other Select Agents -- Mycolic Acid Analysis for Identi cation of Mycobacteria -- HPLC and Susceptibility Testing -- Advantages and Disadvantages of Fatty Acid-Based Identi cation Methods -- References -- Chapter 10: MALDI-TOF Mass Spectrometry-Based Microbial Identi cation -- Introduction -- General Remarks on Mass Spectrometry -- MALDI and ESI MS -- Species Identi cation Using MALDI-TOF MS -- Limitations and Shortcomings of MALDI-TOF MS -- Further Challenges Approaching MALDI-TOF MS for Species Diagnosis -- Conclusion -- References -- Chapter 11: Nucleic Acid Extraction Techniques -- Introduction -- Nucleic Acid Extraction Techniques -- Cesium Chloride/Ethidium Bromide Density Gradient Centrifugation -- Phenol-Chloroform Extraction -- Solid-Phase Extraction -- Magnetic Bead Method -- Applications to Clinical Specimens -- Cellular Component -- Serum, Plasma, and Whole Blood -- In uence of Speci c Pathogen -- PCR Inhibitors -- Measurement of DNA Quality -- Comparison of Nucleic Acid Extraction Methods -- Manual Method -- Automatic Methods -- Conclusion -- References -- Chapter 12: Nonampli ed Probe-Based Microbial Detection and Identi cation -- Introduction -- Probe-Based Assay Design -- Target Selection -- Probe Selection -- Nucleic Acid Hybridization Formats -- Clinical Application of Nonampli ed Probe-Based Assays -- Gen-Probe Nucleic Acid Detection Methods -- Hybrid Capture Assay -- Af rm DNA Assay -- Line Probe Assay -- In Situ Hybridization Assays -- Peptide Nucleic Acid FISH Assays -- Future Considerations -- References -- Chapter 13: Molecular Typing Techniques: State of the Art -- Introduction. , What Does "State of the Art" Mean? -- The Ultimate Foundation for Epidemiological Comparison: The Bacterial Genome -- Methods with Electrophoretic Output -- Pulsed-Field Gel Electrophoresis -- Optical Mapping -- PCR-Based -- Repetitive Sequence-Based PCR -- PCR Ribotyping -- Staphylococcal Cassette Chromosome mec Typing -- Multiple-Locus VNTR Analysis -- DNA Sequence-Based Methods -- Single-Locus Sequence Typing -- S. aureus Protein A Typing -- Strepcococcus pyogenes M Protein ( emm) Typing -- mec -Associated Direct Repeat Unit Typing -- Multi-Locus Sequence Typing -- Other Multi-Locus Approaches: Hybridization-Based Typing -- Whole Genome Sequence Typing -- Non-Sequence-Based Whole Cell Typing -- Strain Typing in the Context of the Epidemiological Window -- References -- Chapter 14: An Introduction to In Vitro Nucleic Acid Ampli cation Techniques -- Target Ampli cation Systems -- Probe Ampli cation Systems -- Signal Ampli cation Systems -- References -- Chapter 15: PCR and Its Variations -- PCR: The Quintessential Nucleic Acid Ampli cation Method -- Principles of PCR -- Enzymatic Ampli cation of DNA: Components of the PCR -- The PCR Cycle -- Denaturation -- Annealing -- Extension -- Detection and Analysis of the PCR Product -- Conventional PCR -- Real-Time PCR -- PCR Variations -- Allele-Speci c PCR -- Hot-Start PCR -- Touchdown PCR -- Degenerate PCR -- Nested and Heminested PCR -- Multiplex PCR -- Reverse Transcription-PCR -- Quantitative PCR -- Real-Time PCR -- PCR-Based Strain Typing Techniques -- Arbitrarily Primed-PCR and Random Ampli ed Polymorphic DNA -- Ampli ed Fragment-Length Polymorphism -- ERIC-, Rep-, BOX-, IS-, and VNTR-PCR -- Appendix -- Primer Design Resources -- References -- Chapter 16: Non-PCR Target Ampli cation Techniques -- Introduction -- Isothermal Transcription-Based Ampli cation. , Strand Displacement Ampli cation.