Clinical Microbiology for Diagnostic Laboratory Scientists

SARAH J. PITT, School of Pharmacy and Biomolecular Sciences, University of Brighton, UK.

• Preface xiiiAcknowledgements xv1 Overview of Clinical Diagnostic Microbiology 11.1 Introduction 11.2 Organisation and Management of Diagnostic Microbiology Services 21.3 Techniques 21.4 Point]of]Care Testing (POCT) 31.5 Antimicrobials 81.5.1 Antibacterial Agents (Antibiotics) 81.5.2 Antiviral Agents 81.5.3 Antifungal Agents 91.5.4 Antiparasitic Agents 121.5.5 Antimicrobial Sensitivity Testing 141.6 Selection and Evaluation of Diagnostic Tests 151.7 Quality Management 181.8 Infection Control, Monitoring and Surveillance 181.9 Exercises 21References 212 Infections of the Blood 252.1 Introduction 252.2 Blood Stream Infections (Bacteraemia/Fungaemia) 262.2.1 Sepsis 272.2.1.1 Pathology 272.2.1.2 Epidemiology 282.2.1.3 Diagnostic Considerations 282.2.1.4 Treatment 312.2.2 Infective Endocarditis 312.2.2.1 Pathology 312.2.2.2 Epidemiology 322.2.2.3 Treatment 342.2.3 Laboratory Diagnosis of Blood Stream Infections 342.3 Blood]Borne Infections 352.3.1 Human Immunodeficiency Virus 362.3.1.1 Epidemiology 372.3.1.2 Pathogenesis 382.3.1.3 Clinical Aspects 392.3.1.4 Laboratory Diagnosis 422.3.2 Human T]Cell Lymphoma Viruses 432.3.3 Trypanosoma cruzi 442.3.4 Creutzfeldt]Jakob Disease 442.3.5 West Nile Virus 452.3.6 Blood]Borne Herpes Viruses 462.4 Exercises 472.5 Case Studies 48References 493 Respiratory Tract Infections 553.1 Introduction 553.1.1 Upper Respiratory Tract Infections 573.1.2 Lower Respiratory Tract Infections 583.1.3 Respiratory Pathogens 603.2 Respiratory Syncytial Virus 603.2.1 Introduction 603.2.2 Pathogenesis and Clinical Symptoms 613.2.3 Epidemiology 633.2.4 Laboratory Diagnosis 633.2.5 Management and Treatment 653.3 Streptococcus pyogenes and Streptococcus pneumoniae 663.3.1 Introduction 663.3.2 Pathogenesis and Clinical Symptoms 663.3.2.1 Pathogenesis of Streptococcus pyogenes Infection 663.3.2.2 Pathogenesis of Streptococcus pneumoniae Infection 693.3.3 Epidemiology 703.3.4 Laboratory Diagnosis 713.3.5 Management and Treatment 733.4 Mycobacterium tuberculosis 743.4.1 Introduction 753.4.2 Pathogenesis and Clinical Symptoms 753.4.3 Epidemiology 773.4.4 Laboratory Diagnosis 773.4.5 Control, Treatment and Management 793.5 Pneumocystis jirovecii 813.5.1 Introduction 813.5.2 Pathogenesis and Clinical Symptoms 823.5.3 Epidemiology 823.5.4 Laboratory Diagnosis 833.5.5 Management and Treatment 843.6 Paragonimus westermani 843.6.1 Introduction 843.6.2 Pathogenesis and Clinical Symptoms 853.6.3 Epidemiology 863.6.4 Laboratory Diagnosis 863.6.5 Management and Treatment 863.7 Exercises 873.8 Case Studies 87References 884 Gastrointestinal Infections 954.1 Introduction 954.1.1 Normal Gut Flora 954.1.2 Diarrhoea 964.1.3 Gastrointestinal Pathogens 984.2 Campylobacter 984.2.1 Introduction 984.2.2 Pathogenesis and Clinical Symptoms 984.2.3 Epidemiology 994.2.4 Laboratory Diagnosis 1004.2.5 Treatment and Control 1024.3 Clostridium difficle 1034.3.1 Introduction 1034.3.2 Pathogenesis and Clinical Symptoms 1034.3.3 Epidemiology 1044.3.4 Laboratory Diagnosis 1054.3.5 Management, Treatment and Control 1064.4 Cryptosporidium 1084.4.1 Introduction 1084.4.2 Pathogenesis and Clinical Symptoms 1084.4.3 Epidemiology 1094.4.4 Laboratory Diagnosis 1104.4.5 Treatment and Control 1114.5 Norovirus 1124.5.1 Introduction 1124.5.2 Pathogenesis and Clinical Symptoms 1124.5.3 Epidemiology 1134.5.4 Laboratory Diagnosis 1154.6 Helicobacter pylori 1184.6.1 Introduction 1184.6.2 Pathogenesis and Clinical Symptoms 1194.6.3 Epidemiology 1204.6.4 Laboratory Diagnosis 1214.6.5 Treatment and Management 1244.7 Liver Infections 1244.7.1 Hepatitis Viruses 1254.7.1.1 Hepatitis A Virus 1254.7.1.2 Hepatitis B Virus 1274.7.1.3 Hepatitis C Virus 1324.7.1.4 Hepatitis D (Delta) Virus 1344.7.1.5 Hepatitis E Virus 1344.7.1.6 Hepatitis G Virus (GB]Virus C) 1364.7.2 Liver Coinfections 1364.8 Exercises 1374.9 Case Studies 138References 1395 Congenital, Perinatal and Neonatal Infections 1495.1 Introduction 1495.2 Antenatal Screening 1495.3 Infections Which Adversely Affect the Mother During Pregnancy 1505.3.1 Malaria 1525.3.1.1 Pathogenesis and Clinical Symptoms 1525.3.1.2 Laboratory Diagnosis 1535.3.1.3 Management and Treatment 1545.3.2 Influenza A 1545.3.2.1 Pathogenesis and Clinical Symptoms 1545.3.2.2 Laboratory Diagnosis 1555.3.2.3 Management and Treatment 1555.3.3 Chlamydia 1565.3.3.1 Pathogenesis and Clinical Symptoms 1565.3.3.2 Epidemiology 1575.3.3.3 Laboratory Diagnosis 1585.3.3.4 Treatment and Management 1595.4 Congenital Infections 1595.4.1 Treponema pallidum 1605.4.1.1 Syphilis Infection 1605.4.1.2 Pathogenesis and Clinical Symptoms of Congenital Syphilis 1615.4.1.3 Laboratory Diagnosis 1625.4.1.4 Management and Treatment 1645.4.1.5 Epidemiology 1645.4.2 Rubella 1655.4.2.1 Rubella Infection 1655.4.2.2 Pathogenesis and Clinical Symptoms of Congenital Rubella 1655.4.2.3 Laboratory Diagnosis 1665.4.2.4 Management 1685.4.2.5 Epidemiology 1685.4.3 Toxoplasma gondii 1705.4.3.1 Toxoplasmosis Infection 1705.4.3.2 Pathogenesis and Clinical Symptoms of Congenital Toxoplasmosis 1715.4.3.3 Laboratory Diagnosis 1725.4.3.4 Management and Treatment 1735.4.3.5 Epidemiology 1745.5 Perinatal Infections 1755.5.1 Hepatitis B Virus 1755.5.2 Human Immunodeficiency Virus 1775.5.3 Neonatal Conjunctivitis (Ophthalmia Neonatorum) 1785.6 Neonatal Infections 1795.6.1 Neonatal Sepsis 1795.6.2 Neonatal Meningitis 1795.6.2.1 Laboratory Diagnosis 1805.6.3 Group B Streptococcus spp. Infection 1805.6.4 Neonatal Herpes Simplex 1815.7 Exercises 1835.8 Case Studies 183References 1846 Sexually Transmitted Infections 1936.1 Introduction 1936.2 Herpes Simplex Virus 1956.2.1 Introduction 1976.2.2 Pathogenesis and Clinical Symptoms 1976.2.3 Epidemiology 1986.2.4 Laboratory Diagnosis 1996.2.5 Treatment and Management 2006.3 Neisseria gonorrhoeae 2016.3.1 Introduction 2016.3.2 Clinical Symptoms and Pathogenesis 2016.3.3 Epidemiology 2036.3.4 Laboratory Diagnosis 2046.3.5 Treatment 2056.4 Human Papilloma Virus 2066.4.1 Introduction 2066.4.2 Clinical Symptoms and Pathogenesis 2066.4.3 Epidemiology 2086.4.4 Laboratory Diagnosis 2086.4.5 Treatment 2116.4.6 Vaccination 2116.5 Trichomomas vaginalis 2126.5.1 Introduction 2136.5.2 Pathogenesis and Clinical Symptoms 2136.5.3 Epidemiology 2136.5.4 Laboratory Diagnosis 2146.5.5 Treatment and Management 2156.6 Exercises 2156.7 Case Studies 215References 2167 Infections in Immunocompromised Patients 2237.1 Introduction 2237.2 Congenital Genetic Immunological Disorders 2247.3 Blood Cell and Bone Marrow Disorders 2267.4 HIV/AIDS 2287.5 Cytomegalovirus 2297.5.1 Introduction 2297.5.2 Pathogenesis and Clinical Symptoms 2297.5.3 Epidemiology 2317.5.4 Laboratory Diagnosis 2327.5.5 Treatment and Control 2337.6 Staphylococcus spp. 2347.6.1 Introduction 2347.6.2 Pathogenesis and Clinical Symptoms 2357.6.3 Epidemiology 2367.6.4 Laboratory Diagnosis 2377.6.5 Treatment and Management 2417.7 Aspergillus spp. 2417.7.1 Introduction 2427.7.2 Pathogenesis and Clinical Symptoms 2427.7.3 Epidemiology 2437.7.4 Laboratory Diagnosis 2447.7.5 Treatment and Management 2467.8 Cryptococcus spp. 2467.8.1 Introduction 2477.8.2 Pathogenesis and Clinical Symptoms 2477.8.3 Epidemiology 2487.8.4 Laboratory Diagnosis 2507.8.5 Treatment 2517.9 Exercises 2517.10 Case Studies 252References 253Appendix 261Index 267