Stephen H. Gillespie - Medical Microbiology and Infection at a Glance

1 Cover

2 Title Page

3 Copyright Page

4 Biographies

5 Preface to the fifth edition

6 About the companion website

7 Part 1: Concepts 1 Microbial pathogens, classification and concepts Characteristics of bacteria Bacterial structural components Bacterial classification Medically important groups of bacteria 2 Innate and acquired immunity Phagocytes Complement and other plasma proteins The adaptive (specific) immune response Damaging immunity 3 The ‘normal’ flora in health and disease Normal flora Physical and chemical barriers 4 Pathogenicity and pathogenesis of infectious disease Definitions Types of pathogen Mechanisms of pathogenicity Damaging the host 5 Making a microbiological diagnosis of infection Specimens Laboratory examination Culture Identification Susceptibility testing Serology Molecular techniques 6 Antimicrobial therapy – principals and concepts Adverse events Acute allergy and intolerance Targeting treatment Monitoring therapy 7 Antibacterial agents – pharmacology and modes of action Beta‐lactam antibiotics Penicillins Cephalosporins Monobactams Carbapenems Aminoglycosides Glycopeptides Daptomycin Quinolones Macrolides Streptogramins Oxazolidinones Metronidazole Tetracyclines Sulphonamides and trimethoprim 8 Antimicrobial use and stewardship A holistic approach in antibiotic therapy Antibiotic prescribing policies Choice of therapy Routes of administration Choosing an antibiotic 9 Emergence and detection of resistance Transmission of resistance determinants between bacteria Mechanisms of resistance 10 Sources and transmission of infection Sources of infection Survival and transmission 11 Principles of infection control Identifying an outbreak Infection control Isolation 12 Infection in the healthcare environment The environment The host Medical activities 13 Immunization Immunization Vaccine safety Vaccination schedules 14 Emerging infections New pathogens 15 High consequence infectious diseases and bioterrorism preparedness Identification of threat Assessing the threat Detecting new infections Integrated response by health protection bodies

8 Part 2: Bacteriology 16 Staphylococcus Staphylococcus aureus Staphylococcus epidermidis Staphylococcus haemolyticus Staphylococcus saprophyticus 17 Haemolytic streptococcal infections Microbiological summary Streptococcus pyogenes Streptococcus agalactiae Group C and G haemolytic streptococci 18 Other Gram‐positive cocci and the alpha‐haemolytic streptococci Spectrum of disease Other Gram‐positive cocci Enterococcus spp. 19 Streptococcus pneumoniae Streptococcus pneumoniae 20 Listeria, bacillus , non‐diphtheria corynebacterium Listeria Corynebacterium spp. Bacillus 21 Diphtheria, tetanus and pertussis Corynebacterium diphtheriae Tetanus Bordetella spp. 22 Mycobacterium tuberculosis Mycobacterium tuberculosis 23 Non‐tuberculous mycobacteria and leprosy Mycobacterium leprae Non‐tuberculous mycobacteria (NTM) 24 Clostridium Clostridium difficile Botulism Clostridium perfringens 25 Non‐sporing anaerobic infections Anaerobic sepsis Pathogens of anaerobic sepsis 26 Neisseria and Moraxella Neisseria gonorrhoeae Neisseria meningitidis Moraxella catarrhalis 27 Small Gram‐negative coccobacilli Haemophilus Brucella spp. Francisella tularensis Yersinia Bartonella spp. 28 Pathogenicity of enteric Gram‐negative bacteria Habitat and transmission Pathogenicity 29 Enterobacteriaceae clinical syndromes Salmonella Other infections 30 Vibrio, Campylobacter and Helicobacter Vibrio spp. Campylobacter spp. Helicobacter pylori 31 Environmental pathogens: Pseudomonas, Burkholderia, Legionella and Acinetobacter Pseudomonas spp. Burkholderia spp. Stenotrophomonas maltophilia and Acinetobacter spp. Legionella spp. 32 Chlamydia, Mycoplasma and Rickettsia Chlamydia Mycoplasma and Ureaplasma Rickettsia Coxiella burnetii 33 Spiral bacteria Leptospira Borrelia Treponema pallidum

9 Part 3: Virology 34 Virus structure and classification Viral classification Viral diagnosis Viral pathogenesis 35 Antiviral therapy Antiviral therapy Reverse transcriptase inhibition Protease inhibitors Integrase inhibitors Fusion inhibitors HIV regimens Release inhibitors Immune modulators 36 Herpesviruses I Classification Cytomegalovirus Epstein–Barr virus Human herpesviruses 6 and 7 37 Herpesviruses II Herpes simplex Varicella zoster virus 38 DNA viruses: adenovirus, parvovirus and poxvirus Adenovirus Parvovirus Papillomavirus Poxvirus 39 Measles, mumps and rubella Measles Mumps Rubella Prevention of measles, mumps and rubella 40 Influenza viruses Influenza virus 41 Parainfluenza and other respiratory viruses Parainfluenza virus Respiratory syncytial virus Coronavirus Metapneumovirus 42 Enterovirus and viruses that infect the gastrointestinal tract Enterovirus Rhinovirus Rotavirus Norovirus and astrovirus 43 Hepatitis viruses Hepatitis A Hepatitis B Hepatitis D Hepatitis C Hepatitis E 44 Tropical, exotic or arbovirus infections Rabies Yellow fever Dengue Zika virus Japanese B encephalitis West Nile virus Lassa fever Ebola virus Hantavirus Nipah and Hendra virus

10 Part 4: Mycology 45 Yeast infections Candida spp. Cryptococcus neoformans Pityriasis versicolor Systemic yeast infections Antifungal compounds 46 Filamentous fungi Aspergillus spp. Other filamentous fungal infections Dermatophytes 47 Antifungal drugs and antifungal therapy Fungal cell targets Antifungal compounds Antifungal stewardship Prophylaxis Adjuvant therapy

11 Part 5: Parasitology 48 Intestinal protozoa Entamoeba histolytica Giardia lamblia Cryptosporidium Cyclospora cayetanensis Isospora belli Microsporidia 49 Malaria, leishmaniasis and trypanosomiasis Malaria Leishmaniasis Trypanosomiasis 50 Intestinal helminths Roundworms and hookworms Strongyloides stercoralis Tapeworms 51 Tissue helminths Schistosomiasis Filariasis Hydatid disease Clonorchis sinensis (Opisthorchis sinensis) Fasciola hepatica Paragonimus spp.

12 Part 6: Systemic infection 52 Congenital and perinatal infections Congenital rubella Cytomegalovirus Congenital and intrapartum herpes simplex infections Varicella Listeriosis Syphilis Toxoplasmosis Zika Parvovirus Vaccination 53 HIV infection and AIDS Human immunodeficiency virus 54 Pyrexia of unknown origin and puerperal sepsis Pyrexia of unknown origin Puerperal fever 55 Sepsis 56 Endocarditis, myocarditis and pericarditis Endocarditis Myocarditis Pericarditis 57 Infections of the central nervous system Bacterial meningitis Brain abscess Viral meningitis Viral encephalitis Postinfectious encephalitis Spongiform encephalopathies 58 Acute respiratory tract infections Upper respiratory tract infections Lower respiratory tract infections 59 Chronic infections of the lung and hospital acquired pneumonia Cystic fibrosis Bronchiectasis Chronic obstructive pulmonary disease Empyaema Hospital acquired pneumoniae (HAP) 60 Urinary and genital infections Urinary tract infection Genital infection Epididymo‐orchitis 61 Infections of the bones and joints Osteomyelitis Suppurative arthritis Prosthetic joint infections Reactive arthritis Viral arthritis Diabetic foot infections 62 Bacterial diarrhoeal disease Epidemiology Pathogenesis Clinical features Diagnosis Management Prevention 63 Zoonoses Viral zoonoses Rat‐bite fever Anthrax Plague Borreliosis Toxoplasmosis Dermatophytes Toxocariasis Cat‐scratch disease Hydatid disease 64 Infections in immunocompromised patients Neutropenia T‐cell deficiency Hypogammaglobulinaemia Complement deficiency Postsplenectomy infection Pneumocystis jiroveci Toxoplasma gondii 65 Ocular infections Bacterial conjunctivitis Bacterial keratitis Viral conjunctivitis Varicella zoster virus Herpes simplex Trachoma Endophthalmitis Ocular manifestations of HIV 66 Infections of the skin and soft tissue Bacterial Manifestations of systemic infections Warts