Clinical Bacteriology

Preface 6(1) Abbreviations 7(1) Normal Ranges and Conversion of Units 8(1) UK and US Drug Names 8(1) 1 Structure and Function of Bacteria 9(10) Introduction 9(1) Cell wall 10(2) Bacterial physiology 12(1) Synthesis of DNA, RNA and proteins 13(1) Protein synthesis 14(1) Cytoplasmic membrane and some of its functions 14(2) Protein synthesis 16(1) Adhesin proteins 16(1) Flagellum 16(1) Capsules 16(1) Sporulation 17(1) Genetic exchange in bacteria 17(1) Comment 18(1) 2 How Bacteria Cause Disease 19(13) Introduction 19(1) Defences of the body 19(3) Non-specific defences 20(1) Active defences 20(2) Acute reaction to infection 22(4) Markers of the cytokine response 24(1) Acute phase proteins 24(1) Complement 25(1) Pathogenic properties of bacteria 26(2) Structural features 26(2) Adhesion 27(1) Secreted proteins 28(2) Endotoxin 28(2) Superantigens 30(1) Immune-mediated diseases 30(1) Comment 30(2) 3 Characterization of Bacteria from Clinical Specimens 32(17) Introduction 33(2) Processing of a specimen 35(2) Identification of gram-positive bacteria 37(3) Differentiation of streptococci and staphylococci 37(1) Differentiation of staphylococci 38(1) Coagulase test 38(1) DNase test 38(1) Identification of streptococci 39(1) α- and β-haemolysis 39(1) Optochin test 39(1) Lancefield grouping of the 3-haemolytic streptococci 40(1) Identification of gram-negative bacteria 40(4) Oxidase test 40(1) X and V test 40(2) Enterobacteriaceae 42(8) Biochemical tests 42(2) Serological tests 44(1) Anaerobic bacteria 44(1) Bacteriophage typing 44(1) Enzyme immunoassay 44(2) Complement fixation test 46(1) Polymerase chain reaction 46(2) Comment 48(1) 4 Use of Antibiotics 49(17) Introduction 49(1) Antibiotic susceptibility tests 50(3) Minimum inhibitory concentration 50(1) Minimum bactericidal concentration 51(1) Disc susceptibility test 52(1) Etest™ 53(1) Antibiotic kinetics 53(3) Pharmacokinetics of the f3-lactams 54(1) Pharmacokinetics of the aminoglycosides 54(2) Importance of estimating renal function 56(1) Antibiotics assays 56(1) Commonly used antibiotics, their range of action and bacterial resistance mechanisms 56(8) Benzylpenicillin, ampicillin/amoxycillin, co-amoxiclav, piperacillin/tazobactam and flucloxacillin 56(4) Methicillin resistant Staphylococcus aureus (MRSA) 58(1) Penicillin resistant pneumococci 58(2) Cephalosporins 60(1) Carbapenems 60(1) Glycopeptides vancomycin and teicoplanin 61(1) Aminoglycosides 62(1) Metronidazole 62(1) The fluorinated quinolones 62(1) Macrolides 62(2) Clindamycin 64(1) Rifampicin 64(1) Chloramphenicol 64(1) Tetracyclines 64(1) β-lactamase test 64(1) Allergies to antibiotics 64(1) Comment 65(1) 5 Infections of the Blood: Bacteraemia and Endocarditis 66(14) Introduction 66(1) Organisms 67(1) Pathogenesis 68(2) Bacterial endocarditis 68(2) Native valve endocarditis 68(1) Prosthetic valve endocarditis 69(1) Diagnosis 70(4) Bacterial endocarditis 72(1) Culture-positive endocarditis 72(1) Culture-negative endocarditis 73(1) Molecular diagnostic methods: the polymerase chain reaction 73(1) Treatment 74(2) Treatment of endocarditis 74(2) Response to treatment 76(1) Septic shock 76(1) Prevention, prophylaxis and public health issues 76(2) Prevention 76(1) Public health issues 76(2) Antibiotic prophylaxis to prevent endocarditis 78(1) Comment 78(2) 6 Infections of the Alimentary Canal 80(13) Introduction 80(2) Organisms 82(1) Pathogenesis 83(5) Dental infections 83(1) Infections of the upper gastrointestinal tract 84(1) Endogenous organisms 84(1) Exogenous organisms 84(1) Infections of the lower gastrointestinal tract 85(9) Exogenous organisms 85(1) Endogenous organisms 86(1) Peritonitis 87(1) Diagnosis 88(2) Treatment 90(1) Public health issues 90(1) Comment 91(2) 7 Infections of the Respiratory Tract 93(11) Introduction 93(1) Organisms 94(1) Pathogenesis 94(4) Otitis media, mastoiditis and sinusitis 94(2) Pharyngitis 96(1) Pneumonia 96(1) Lung abscess 97(1) Cystic fibrosis 98(1) Diagnosis 98(2) Treatment 100(2) Hospital-acquired pneumonia 101(1) Lung abscess 101(1) Cystic fibrosis 102(1) Public health issues 102(1) Comment 102(2) 8 Tuberculosis 104(11) Introduction 104(1) Organisms 104(2) Pathogenesis 106(3) Diagnosis 109(2) Treatment 111(1) Public health issues 112(2) Comment 114(1) 9 Infections of the Central Nervous System 115(14) Introduction 115(3) Organisms 118(1) Pathogenesis 119(5) Meningitis 119(1) Brain abscess 120(2) Subdural and extradural infections 122(1) Ventriculo-peritoneal shunt infections 122(1) Tetanus 122(2) Botulism 124(1) Guillain-Barré syndrome 124(1) Diagnosis 124(2) Laboratory diagnosis 124(2) Treatment 126(2) Public health issues 128(1) Comment 128(1) 10 Infections of the Eye 129(6) Introduction 129(1) Organisms 130(1) Pathogenesis 130(2) Diagnosis 132(1) Treatment 133(1) Conjunctivitis 133(1) Keratitis 134(1) Endophthalmitis 134(1) Orbital cellulitis and cavernous sinus thrombosis 134(1) Dacrocystitis and canaliculitis 134(1) Public health issues 134(1) Comment 134(1) 11 Infections of the Urinary Tract 135(8) Introduction 135(1) Organisms 136(1) Pathogenesis 136(3) Diagnosis 139(2) Treatment 141(1) Public health issues 142(1) Comment 142(1) 12 Infections of the Genital Systems 143(11) Introduction 143(1) Organisms 144(1) Pathogenesis 144(4) Sexually transmitted diseases: gonorrhoea and chlamydia 144(2) Gonorrhoea 144(2) Chlamydia trachomatis 146(1) Pelvic inflammatory disease 146(1) Vaginitis 147(1) Congenital infections 147(1) Rubella 147(1) Syphilis 147(1) Perinatal infections 147(1) Hepatitis B virus 147(1) Human immunodeficiency virus 147(1) Group B streptococcus 148(1) Listeria monocytogenes 148(1) Post-partum infections, septic abortions and gynaecological infections 148(1) Diagnosis 148(4) Sexually transmitted diseases: gonorrhoea and chlamydia 148(2) Vaginitis 150(1) Pelvic inflammatory disease 150(1) Congenital infections 150(6) Rubella 150(1) Syphilis 151(1) Hepatitis B virus 151(1) Human immunodeficiency virus 151(1) Group B streptococcus and listeria 152(1) Treatment 152(1) Public health issues 152(1) Comment 153(1) 13 Infections of the Skin, Soft Tissues, Joints, and Bone 154(9) Introduction 154(2) Organisms 156(1) Pathogenesis 156(4) Infections of the skin 156(1) Fasciitis and myositis 157(1) Septic arthritis 158(2) Osteomyelitis 160(1) Diagnosis 160(1) Treatment 160(1) Public health issues 160(1) Comment 161(2) 14 Infections in a Modern Society 163(10) Introduction 163(1) Intravenous drug user 164(1) Intensive care patient 164(2) Immunocompromised patient 166(4) Splenectomized patient 166(1) Renal dialysis patient 166(1) Haemodialysis 166(1) Chronic ambulatory peritoneal dialysis peritonitis 166(1) Solid organ transplant patient 166(3) Haematology and oncology patient 169(1) Biological warfare and bioterrorism 170(1) Bacillus anthracia 171(1) Botulism 171(1) Smallpox (variola) 171(1) Discussion 171(1) Comment 171(2) 15 Control of Infection in the Hospital and the Community 173(16) Introduction 173(1) Antibiotic guidelines 173(2) Prophylactic antibiotics 175(2) Infection control in the hospital 177(5) Blood-borne viruses 178(1) Infection control committee 178(1) Universal precautions 178(2) Risk assessment in infection control 180(2) Infection control in the community 182(4) Outbreaks at the local and national level 182(2) National reporting 184(1) Notification of infectious diseases 184(2) International travel 186(1) Vaccination 186(2) Passive immunity 186(1) Active immunity 186(2) Comment 188(1) Index 189