Clinical microbiology

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Preface
About the author
Disclaimer
Acknowledgements
Abbreviations
Chapter 1: Introduction to Clinical Microbiology
	Introduction
	Bacteria
		Cell wall
		Bacterial physiology
		Synthesis of DNA, RNA and proteins
		Protein synthesis
		Cytoplasmic membrane and some of its functions
		Capsules
		Sporulation
		Genetic exchange in bacteria
	Viruses
		The replication of viruses
	Fungi
		Diseases caused by fungi
	Parasites
		The life cycle of malaria
		The life cycle of Schistosoma haematobium
Chapter 2: How Bacteria Cause Disease
	Introduction
	Non-specific defences
	Active defences
	The acute reaction to infection
		Markers of the cytokine response
		Acute phase proteins
	Complement
	Pathogenic properties of bacteria
		Structural features
		Adhesion
		Secreted proteins
		Endotoxin
	Superantigens
	Immune-mediated diseases
Chapter 3: Epidemiology and Assessment
	Introduction
	Epidemiology
		World-wide
		Regional
		Local
	The incubation period
	The HIV test
	The steps in management of the patient
		MEWS and the ‘Sepsis Six’
		Which organisms and which antibiotics?
		Antibiotic treatment in the septic patient with an unknown source
	Fever of unknown origin
	Infection control
	Public health
	Laboratory tests
Chapter 4: Anti-Infective Agents
	Introduction
	Antibacterial agents
		The β-lactam antibiotics
		Antibiotic resistance in bacteria
	The antifungals
		Resistance to antifungals
	The antivirals
		Influenza virus
		The herpesviruses
		Hepatitis B virus and hepatitis C virus
		HIV
		Resistance to antiviral agents
	Antimalarial agents
		Artesunate
		4-aminoquinoline
		8-aminoquinolines
		Tetracyclines
	The science of antibiotic use
		Minimum inhibitory concentration
		Minimum bactericidal concentration
		Antibiotic kinetics
		The distribution of antibiotics in the body
		Importance of estimating renal function
		Antibiotic assays
	Antibiotic guidelines
	Prudent antibiotic prescribing
	Prophylactic antibiotics
		The role of antibiotic prophylaxis
		The contamination classification of surgical procedures
		Which prophylactic antibiotic to use
	Allergy to penicillins
		The nature of the immunological reaction to penicillin
		The types of drug reactions to consider
		Cross-reaction between the β-lactams in the setting of the non-immediate allergic reaction
		Obtaining the history
	Vaccination
		Active immunity
		Passive immunity
		Vaccination of patients in ‘at risk’ groups
Chapter 5: The Microbiology Laboratory
	Introduction
	The laboratory
	Bacteriology laboratory tests
		Basic processing of a specimen
		The time scale of events in the laboratory
		How bacteria are identified
		Speciation of bacteria and fungi
		Antibiotic susceptibility testing
	The Virology laboratory (serology and molecular testing)
		Serological tests
		Molecular tests
		Nucleic acid sequencing
Chapter 6: Infection Control
	Introduction
	Occupational health compliance
	Dress code and personal protective equipment
	Hand washing
	The 5 moments of hand hygiene
	The ward layout and environment
		Negative-pressure ventilation single rooms
	The source of organisms and how they are spread
		Air-borne
		Faecal-oral
		Direct contact
		Indirect contact
		Blood-borne
		Water-borne
		Reusable surgical equipment
	Venous access lines
	Screening for infection control ‘alert’ organisms
Chapter 7: Infections of the Blood
	Introduction
	Organisms
	Pathogenesis
		Infective endocarditis
		Infections of implantable cardiac electronic devices
	Diagnosis and management
		Blood cultures
		Infective endocarditis
		Infections of implantable cardiac electronic devices
		Other ways of making the diagnosis
	The identification of Staphylococcus aureus in blood culture
Chapter 8: Infections of the Respiratory Tract
	Introduction
	Organisms
	Pathogenesis
		Otitis media, mastoiditis and sinusitis
		Pharyngitis
		Pneumonia
		Lung abscess
	Diagnosis and management
		Lung abscess
	Infection from hospital water systems
		Legionella pneumophila
		Pseudomonas aeruginosa
Chapter 9: Tuberculosis
	Introduction
	Organisms
	Pathogenesis
	Diagnosis and management
		Molecular testing
		The histopathology specimen
		Treatment
		Infection control
	Public health issues
Chapter 10: Infections of the Urinary Tract
	Introduction
	Organisms
	Pathogenesis
		Uncomplicated and complicated UTI
	Diagnosis and management
		Examination of the specimen; the urine dipstick
		The laboratory report
	The catheterized patient
	Sterile pyuria
	Relapsing UTI
Chapter 11: Infections of the Alimentary Canal
	Introduction
	Organisms
	Pathogenesis
		Dental infections
		Infections of the upper alimentary canal
		Infections of the lower alimentary canal
	Diagnosis and management
	Clostridium difficile
Chapter 12: Infections of the Liver, Biliary Tract and Pancreas
	Introduction
	Organisms
	Pathogenesis
		Via the hepatic artery to the liver
		Via the portal vein to the liver
		Via the biliary system from the duodenum
	Diagnosis and management
	Hepatitis viruses
		HAV
		HBV
		HCV
		HEV
	An outline of the treatment of chronic HBV and HCV infection
		HBV
		HCV
Chapter 13: Infections of the Skin, Soft Tissues, Joints and Bone
	Introduction
	Organisms
	Pathogenesis
		Infections of the skin and soft tissue
		Fasciitis and myositis
		Septic arthritis
		Osteomyelitis
		Diabetic foot infections
	Diagnosis and management
Chapter 14: Infections of the Central Nervous System
	Introduction
	Organisms
	Pathogenesis
		Meningitis
		Brain abscess
		Subdural and extradural infections
		Ventriculoperitoneal shunt and external ventricular drain infections
		Toxin-mediated diseases
	Diagnosis and management
		Laboratory diagnosis
		Treatment
Chapter 15: Infections of the Eye
	Introduction
	Organisms
	Pathogenesis
	Diagnosis and management
		Treatment
Chapter 16: Infections of the Genital Systems
	Introduction
	Organisms
	Pathogenesis
		Gonorrhoea
		Chlamydia trachomatis
		Pelvic inflammatory disease
		Vaginitis
		Postpartum infections, septic abortions and gynaecological infections
	Diagnosis and management
		The patient with a vaginal discharge where a STI is unlikely
		Sexually transmitted diseases: gonorrhoea and chlamydia
		Streptococcus pyogenes in female and male genital infection
		Pelvic inflammatory disease
	Infections in pregnancy, the fetus, newborn and neonate
		The role of antenatal screening
		Other infections that pose a risk to the mother and fetus
Chapter 17: Infections in a Modern Society
	Introduction
	The immunosuppressed patient
		The patient infected with HIV
		The haematology and oncology patient
		The solid organ transplant patient
	The renal patient
		Haemodialysis
		Chronic ambulatory peritoneal dialysis peritonitis
	The injecting drug user
	The intensive care unit patient
	The elderly patient
	The patient with an absent or dysfunctional spleen
Index
Infection Control Scenarios
	Introduction
	Management of an Infection Control Situation, Such as A HAI
	The Consequences of A HAI
	The Scenario Ward
		How Ward Areas are Cleaned and Decontaminated
	Scenario I Hospital-Acquired Streptococcus Pyogenes (GAS) Scalp Wound Incident and Subsequent Identification of an Outbreak
		Day 0; 0600 Hours
		Day 0; 1700 Hours
		Infection Control Action Required
		Day 0; 2000
		Day 1; 0900
		Day 2; 0900
		Discussion
	Scenario II A Hospital-Acquired Outbreak of Clostridium Difficile Antibiotic-Associated Diarrhoea
		Day 0; 0600
		Infection Control Action Required
		Day 0; 1600 Hours
		Infection Control Action Required
		Day 1; 1600 Hours
		Discussion
	III A Norovirus Outbreak Involving Patients and Staff During the ‘Norovirus Season’
		Day 0; 0600 Hours
		Infection Control Action Required
		Day 0; 0830 Hours
		Infection Control Action Required
		Day 0; 1630 Hours
		Discussion
	IV A Case of Influenza A on the Ward
		Day 0; 0600 Hours
		Infection Control Action Required
		Day 0; 1600
		Discussion
	V A Case of Open Pulmonary Tuberculosis in a Health Care Professional
		Infection Control Action Required
		Discussion