Clinical Microbiology for Diagnostic Laboratory Scientists (eBook)

Sarah J. Pitt (Autor)

eBook Download: EPUB

2017
John Wiley & Sons (Verlag)
978-1-118-74582-3 (ISBN)

Infos

A modern, evaluative, and integrative approach to diagnostic microbiology encouraging problem-solving in the clinical laboratory context through the use of examples to illustrate clinical and diagnostic issues

Clinical Microbiology for Diagnostic Laboratory Scientists is designed to encourage readers to develop a way of thinking that can be applied to any diagnostic scenario in microbiology. Through consideration of a selected range of infections caused by pathogenic bacteria, viruses, fungi, protozoa, and helminths, the book encourages readers to explore connections between the available information about clinical symptoms, pathogenesis of infections, and the approaches used in laboratory diagnosis, in order to develop new insights.

The book begins with an introductory chapter that outlines the scope of clinical diagnostic microbiology and the key areas for the laboratory scientist to be aware of. The subsequent six chapters review a type of infection in depth, using particular pathogenic microorganisms to illustrate salient points. At the end of each chapter there are three exercises related to management of a diagnostic service and assessing the suitability of test methods to specific contexts. There are no right or wrong answers to these, but the reader can discuss them with their laboratory colleagues or university tutor. 

• Makes extensive use of published research in the form of journal articles, publically available epidemiological data, professional guidelines, and specialist websites
• Stimulates the reader in critical appraisal of published evidence and encourages problem-solving in the laboratory
• Outlines the scope of clinical diagnostic microbiology and the key areas for the laboratory scientist to be aware of
• Considers topics relevant to professional scientists working in the area of diagnostic microbiology

Clinical Microbiology for Diagnostic Laboratory Scientists is ideal for post graduate scientists intending to pursue careers in diagnostic clinical microbiology and for biomedical scientists, clinical scientists, and full time students studying for upper level qualifications in biomedical science, microbiology, or virology.

Autor

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

Inhalt

Preface xiii

Acknowledgements xv

1 Overview of Clinical Diagnostic Microbiology 1

1.1 Introduction 1

1.2 Organisation and Management of Diagnostic Microbiology Services 2

1.3 Techniques 2

1.4 Point?]of?]Care Testing (POCT) 3

1.5 Antimicrobials 8

1.5.1 Antibacterial Agents (Antibiotics) 8

1.5.2 Antiviral Agents 8

1.5.3 Antifungal Agents 9

1.5.4 Antiparasitic Agents 12

1.5.5 Antimicrobial Sensitivity Testing 14

1.6 Selection and Evaluation of Diagnostic Tests 15

1.7 Quality Management 18

1.8 Infection Control, Monitoring and Surveillance 18

1.9 Exercises 21

References 21

2 Infections of the Blood 25

2.1 Introduction 25

2.2 Blood Stream Infections (Bacteraemia/Fungaemia) 26

2.2.1 Sepsis 27

2.2.1.1 Pathology 27

2.2.1.2 Epidemiology 28

2.2.1.3 Diagnostic Considerations 28

2.2.1.4 Treatment 31

2.2.2 Infective Endocarditis 31

2.2.2.1 Pathology 31

2.2.2.2 Epidemiology 32

2.2.2.3 Treatment 34

2.2.3 Laboratory Diagnosis of Blood Stream Infections 34

2.3 Blood?]Borne Infections 35

2.3.1 Human Immunodeficiency Virus 36

2.3.1.1 Epidemiology 37

2.3.1.2 Pathogenesis 38

2.3.1.3 Clinical Aspects 39

2.3.1.4 Laboratory Diagnosis 42

2.3.2 Human T?]Cell Lymphoma Viruses 43

2.3.3 Trypanosoma cruzi 44

2.3.4 Creutzfeldt?]Jakob Disease 44

2.3.5 West Nile Virus 45

2.3.6 Blood?]Borne Herpes Viruses 46

2.4 Exercises 47

2.5 Case Studies 48

References 49

3 Respiratory Tract Infections 55

3.1 Introduction 55

3.1.1 Upper Respiratory Tract Infections 57

3.1.2 Lower Respiratory Tract Infections 58

3.1.3 Respiratory Pathogens 60

3.2 Respiratory Syncytial Virus 60

3.2.1 Introduction 60

3.2.2 Pathogenesis and Clinical Symptoms 61

3.2.3 Epidemiology 63

3.2.4 Laboratory Diagnosis 63

3.2.5 Management and Treatment 65

3.3 Streptococcus pyogenes and Streptococcus pneumoniae 66

3.3.1 Introduction 66

3.3.2 Pathogenesis and Clinical Symptoms 66

3.3.2.1 Pathogenesis of Streptococcus pyogenes Infection 66

3.3.2.2 Pathogenesis of Streptococcus pneumoniae Infection 69

3.3.3 Epidemiology 70

3.3.4 Laboratory Diagnosis 71

3.3.5 Management and Treatment 73

3.4 Mycobacterium tuberculosis 74

3.4.1 Introduction 75

3.4.2 Pathogenesis and Clinical Symptoms 75

3.4.3 Epidemiology 77

3.4.4 Laboratory Diagnosis 77

3.4.5 Control, Treatment and Management 79

3.5 Pneumocystis jirovecii 81

3.5.1 Introduction 81

3.5.2 Pathogenesis and Clinical Symptoms 82

3.5.3 Epidemiology 82

3.5.4 Laboratory Diagnosis 83

3.5.5 Management and Treatment 84

3.6 Paragonimus westermani 84

3.6.1 Introduction 84

3.6.2 Pathogenesis and Clinical Symptoms 85

3.6.3 Epidemiology 86

3.6.4 Laboratory Diagnosis 86

3.6.5 Management and Treatment 86

3.7 Exercises 87

3.8 Case Studies 87

References 88

4 Gastrointestinal Infections 95

4.1 Introduction 95

4.1.1 Normal Gut Flora 95

4.1.2 Diarrhoea 96

4.1.3 Gastrointestinal Pathogens 98

4.2 Campylobacter 98

4.2.1 Introduction 98

4.2.2 Pathogenesis and Clinical Symptoms 98

4.2.3 Epidemiology 99

4.2.4 Laboratory Diagnosis 100

4.2.5 Treatment and Control 102

4.3 Clostridium difficle 103

4.3.1 Introduction 103

4.3.2 Pathogenesis and Clinical Symptoms 103

4.3.3 Epidemiology 104

4.3.4 Laboratory Diagnosis 105

4.3.5 Management, Treatment and Control 106

4.4 Cryptosporidium 108

4.4.1 Introduction 108

4.4.2 Pathogenesis and Clinical Symptoms 108

4.4.3 Epidemiology 109

4.4.4 Laboratory Diagnosis 110

4.4.5 Treatment and Control 111

4.5 Norovirus 112

4.5.1 Introduction 112

4.5.2 Pathogenesis and Clinical Symptoms 112

4.5.3 Epidemiology 113

4.5.4 Laboratory Diagnosis 115

4.6 Helicobacter pylori 118

4.6.1 Introduction 118

4.6.2 Pathogenesis and Clinical Symptoms 119

4.6.3 Epidemiology 120

4.6.4 Laboratory Diagnosis 121

4.6.5 Treatment and Management 124

4.7 Liver Infections 124

4.7.1 Hepatitis Viruses 125

4.7.1.1 Hepatitis A Virus 125

4.7.1.2 Hepatitis B Virus 127

4.7.1.3 Hepatitis C Virus 132

4.7.1.4 Hepatitis D (Delta) Virus 134

4.7.1.5 Hepatitis E Virus 134

4.7.1.6 Hepatitis G Virus (GB?]Virus C) 136

4.7.2 Liver Coinfections 136

4.8 Exercises 137

4.9 Case Studies 138

References 139

5 Congenital, Perinatal and Neonatal Infections 149

5.1 Introduction 149

5.2 Antenatal Screening 149

5.3 Infections Which Adversely Affect the Mother During Pregnancy 150

5.3.1 Malaria 152

5.3.1.1 Pathogenesis and Clinical Symptoms 152

5.3.1.2 Laboratory Diagnosis 153

5.3.1.3 Management and Treatment 154

5.3.2 Influenza A 154

5.3.2.1 Pathogenesis and Clinical Symptoms 154

5.3.2.2 Laboratory Diagnosis 155

5.3.2.3 Management and Treatment 155

5.3.3 Chlamydia 156

5.3.3.1 Pathogenesis and Clinical Symptoms 156

5.3.3.2 Epidemiology 157

5.3.3.3 Laboratory Diagnosis 158

5.3.3.4 Treatment and Management 159

5.4 Congenital Infections 159

5.4.1 Treponema pallidum 160

5.4.1.1 Syphilis Infection 160

5.4.1.2 Pathogenesis and Clinical Symptoms of Congenital Syphilis 161

5.4.1.3 Laboratory Diagnosis 162

5.4.1.4 Management and Treatment 164

5.4.1.5 Epidemiology 164

5.4.2 Rubella 165

5.4.2.1 Rubella Infection 165

5.4.2.2 Pathogenesis and Clinical Symptoms of Congenital Rubella 165

5.4.2.3 Laboratory Diagnosis 166

5.4.2.4 Management 168

5.4.2.5 Epidemiology 168

5.4.3 Toxoplasma gondii 170

5.4.3.1 Toxoplasmosis Infection 170

5.4.3.2 Pathogenesis and Clinical Symptoms of Congenital Toxoplasmosis 171

5.4.3.3 Laboratory Diagnosis 172

5.4.3.4 Management and Treatment 173

5.4.3.5 Epidemiology 174

5.5 Perinatal Infections 175

5.5.1 Hepatitis B Virus 175

5.5.2 Human Immunodeficiency Virus 177

5.5.3 Neonatal Conjunctivitis (Ophthalmia Neonatorum) 178

5.6 Neonatal Infections 179

5.6.1 Neonatal Sepsis 179

5.6.2 Neonatal Meningitis 179

5.6.2.1 Laboratory Diagnosis 180

5.6.3 Group B Streptococcus spp. Infection 180

5.6.4 Neonatal Herpes Simplex 181

5.7 Exercises 183

5.8 Case Studies 183

References 184

6 Sexually Transmitted Infections 193

6.1 Introduction 193

6.2 Herpes Simplex Virus 195

6.2.1 Introduction 197

6.2.2 Pathogenesis and Clinical Symptoms 197

6.2.3 Epidemiology 198

6.2.4 Laboratory Diagnosis 199

6.2.5 Treatment and Management 200

6.3 Neisseria gonorrhoeae 201

6.3.1 Introduction 201

6.3.2 Clinical Symptoms and Pathogenesis 201

6.3.3 Epidemiology 203

6.3.4 Laboratory Diagnosis 204

6.3.5 Treatment 205

6.4 Human Papilloma Virus 206

6.4.1 Introduction 206

6.4.2 Clinical Symptoms and Pathogenesis 206

6.4.3 Epidemiology 208

6.4.4 Laboratory Diagnosis 208

6.4.5 Treatment 211

6.4.6 Vaccination 211

6.5 Trichomomas vaginalis 212

6.5.1 Introduction 213

6.5.2 Pathogenesis and Clinical Symptoms 213

6.5.3 Epidemiology 213

6.5.4 Laboratory Diagnosis 214

6.5.5 Treatment and Management 215

6.6 Exercises 215

6.7 Case Studies 215

References 216

7 Infections in Immunocompromised Patients 223

7.1 Introduction 223

7.2 Congenital Genetic Immunological Disorders 224

7.3 Blood Cell and Bone Marrow Disorders 226

7.4 HIV/AIDS 228

7.5 Cytomegalovirus 229

7.5.1 Introduction 229

7.5.2 Pathogenesis and Clinical Symptoms 229

7.5.3 Epidemiology 231

7.5.4 Laboratory Diagnosis 232

7.5.5 Treatment and Control 233

7.6 Staphylococcus spp. 234

7.6.1 Introduction 234

7.6.2 Pathogenesis and Clinical Symptoms 235

7.6.3 Epidemiology 236

7.6.4 Laboratory Diagnosis 237

7.6.5 Treatment and Management 241

7.7 Aspergillus spp. 241

7.7.1 Introduction 242

7.7.2 Pathogenesis and Clinical Symptoms 242

7.7.3 Epidemiology 243

7.7.4 Laboratory Diagnosis 244

7.7.5 Treatment and Management 246

7.8 Cryptococcus spp. 246

7.8.1 Introduction 247

7.8.2 Pathogenesis and Clinical Symptoms 247

7.8.3 Epidemiology 248

7.8.4 Laboratory Diagnosis 250

7.8.5 Treatment 251

7.9 Exercises 251

7.10 Case Studies 252

References 253

Appendix 261

Index 267

Textauszug

1
Overview of Clinical Diagnostic Microbiology

1.1 Introduction

The scope of diagnostic microbiology has developed along with technological advances in laboratory science. In the nineteenth century, detection of organisms relied on light microscopy and a limited range of in vitro culture methods. Some of these techniques are still used to detect and identify bacteria and parasites, in some cases with little or no modification (e.g., Gram’s stain). The discovery of proteins and then later nucleic acids during the twentieth century, along with the advent of the electron microscope, opened up the microbial world. The ability to determine and characterise the exact cause of an infectious disease, and thus to devise control measures, treatments, and prophylaxes has reduced morbidity and premature mortality throughout the world. Indeed, some diseases – smallpox in humans and rinderpest in cattle – have been eliminated altogether.

The ever‐expanding range of known microorganisms has led to the separation of diagnostic microbiology into distinct specialist areas – bacteriology, virology, mycology and parasitology. The diversity of microorganisms necessitates the training of individuals to be experts in one particular type of organism and they are often considered separately during study. It is important to remember that microorganisms do not operate in isolation and that a patient can be infected with more than one pathogen simultaneously. Advances in technology, in particular automation, make it possible to test for markers across pathology disciplines (not just within microbiology) on one single specimen in relatively short turnaround times. This means that the diagnostic microbiologist must be aware of the implications of an eclectic mixture of results and should certainly be able to solve problems and make decisions about patients with a wide range of infections.

N.B: This book assumes microbiological knowledge to at least graduate level. There are some very good general textbooks available for those who would like to revise any areas. For example, Greenwood et al. (2012) provides a brief overview of a comprehensive range of organisms, while clinical features are addressed clearly and simply in Murray et al. (2013) and Goering et al. (2013). Laboratory aspects are covered by Ford et al. (2014) and Wilkinson (2011), which were both written by practising diagnostic microbiologists.

Point to consider 1.1: What do you think is the most important scientific discovery in microbiology during the last 100 years and why?

1.2 Organisation and Management of Diagnostic Microbiology Services

The configuration of pathology services seems to be constantly changing in response to management trends, as well as financial constraints. Technological advances mean that it is easier to identify microorganisms to the level of a strain within a species, in a much shorter amount of time than it was 30 years ago. The techniques available have also been developed such that many aspects of the laboratory work can be done in automated systems (e.g., Fournier et al., 2013). The graduate and postgraduate microbiology scientist must therefore be able to interpret ever more complicated data, while retaining a working knowledge of the principles behind the tests used to generate that information. As laboratory microbiologists develop expertise and are given more responsibility, they sometimes find themselves working in larger teams, while at other times they are concentrating on a specialised area with a small number of colleagues. Cooperation with staff across pathology and in other departments in the hospital and primary care is becoming increasingly important in the daily running of the diagnostic microbiology service. Also, responding to the requirements of external bodies such as those involved in public health surveillance, quality assessment and service monitoring can create enough work for a full‐time post. Employing organisations can come and go, while the people who staff the laboratories often stay the same. This can be disconcerting, but it is important to keep sight of the facts. Firstly, each sample received in the laboratory has been collected from a patient with a clinical problem which needs addressing such as, ‘Has there been an adequate immunological response to this course of a vaccine?’, ‘What is causing this rash?’ and ‘Why does this antimicrobial treatment appear to be ineffective?’ Secondly, microbiology is endlessly fascinating; organisms can change very quickly – rendering diagnostic methods and treatments out of date – and infectious diseases are always in the news!

Point to consider 1.2: How many news stories involving microorganisms have you noticed during the last seven days? Find one article and think carefully about how well it was reported. Which points of information do you think were communicated well? Where there were inaccuracies, can you think of reason for the misunderstandings?

1.3 Techniques

Some techniques used to isolate and identify microorganisms have not changed substantially since they were first introduced – which in some cases is well over 100 years ago. This is usually because they are still useful and cost effective in helping to isolate and identify microorganisms from clinical samples. Others have been superseded by methods which give a more accurate or rapid result. It is therefore useful to critically evaluate techniques and to challenge assumptions about them. Does a traditional technique such as the Gram’s stain still have a place in twenty‐first century routine diagnostic microbiology? Why did virology services phase out virus isolation in monolayer cell culture? Is ‘PCR’ really the answer to every search for the optimal microbiology test?

The principles behind each technique will not be considered in any detail within this book. Readers are referred to laboratory protocols or standard operating procedures as appropriate, along with Wilkinson (2011) and Ford et al. (2014) for details.

Table 1.1 outlines some of the discussion points to consider about a selection of the techniques commonly used in diagnostic microbiology settings. The suite of tests used to investigate a particular clinical problem depends on a range of factors, which may include workload, available space, skill mix of workforce and service user requirements, as well as cost.

Table 1.1 Comparison of selected techniques used in diagnostic microbiology departments to isolate and characterise microorganisms.

Technique

Use in diagnostic microbiology

Advantages

Disadvantages

Light microscopy (with appropriate stains to aid visualisation)

Detection of bacteria, fungi and parasites

Low cost Sample preparation straightforward and relatively quick Equipment easy to obtain and maintain ‘Catch all’ technique

Relatively low sensitivity Limit of resolution around 0.2 μm Recognition of organisms requires training and skill Slides examined individually so labour‐intensive and time‐consuming Follow‐up tests usually necessary for full identification.

Light microscopy with fluorescent‐labelled antibodies and UV microscope

Detection of bacteria, fungi and parasites

Very specific due to immunological detection method Good sensitivity as fluorescence easy to detect.

Expensive compared to use of general stain Detects pre‐determined organisms only Slides examined individually so labour‐intensive and time‐consuming If no organism detected, further investigations may be indicated Requires ultraviolet (UV) microscope.

Culture on agar including selective, differential and chromogenic media

Isolation and initial identification of bacteria and fungi

‘Catch‐all’ technique Selective media or specialised culture conditions exclude all but organism of interest to grow Chromogenic media allow presumption identification on basis of colonial appearance and colour change Live viable organism obtained to do further investigations –e.g., antimicrobial sensitivities, analysis of strain variation

Preparation of media time‐consuming (most laboratories buy pre‐prepared plates) Follow‐up tests usually necessary for full identification.

Electron microscopy

Detection of viruses and small protozoa in clinical samples Detection/identification of viruses isolated in monolayer culture.

Limit of resolution is around 2 nm ‘Catch all’ technique Organisms identified due to morphological appearance.

Relatively low sensitivity Grids examined individually so labour‐intensive and time‐consuming Equipment very expensive to purchase and maintain Identification of structures requires specialised training and skill.

Monolayer cell culture

Detection of viruses (and some other obligate intracellular organisms) in clinical samples

‘Catch‐all’ technique Detects viable viruses Live organism obtained to do further investigations –e.g., antiviral sensitivities, analysis of strain variation....

Produkt-Details

• Erscheint lt. Verlag: 8.11.2017
• Sprache: englisch
• Themenwelt: Medizin / Pharmazie ► Gesundheitsfachberufe
• Themenwelt: Medizin / Pharmazie ► Medizinische Fachgebiete ► Mikrobiologie / Infektologie / Reisemedizin
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Schlagworte: Biomedical Science • Biowissenschaften • Cell & Molecular Biology • Cell Biology • clinical laboratory • clinical microbiology • Clinical Microbiology for Diagnostic Laboratory Scientists • clinical microbiology handbook • clinical science • diagnostic library • Diagnostic microbiology • Diagnostics • fungi infections • guide to clinical microbiology • helminthes • lab diagnostics • laboratory scientist • Life Sciences • Microbiology • Microbiology & Virology • microbiology text • Mikrobiologie u. Virologie • Molecular Biology • pathogenic bacteria • Pathology • protozoa infections • Virology • Viruses • Zell- u. Molekularbiologie
• ISBN-10: 1-118-74582-5 / 1118745825
• ISBN-13: 978-1-118-74582-3 / 9781118745823