E-Book, Englisch, Band Volume 34-2, 265 Seiten
E-Book, Englisch, Band Volume 34-2, 265 Seiten
Reihe: The Clinics: Internal Medicine
ISBN: 978-0-323-29942-8
Verlag: Elsevier Health Care - Lehrbücher
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)
Autoren/Hrsg.
Weitere Infos & Material
1;Front Cover;1
2;Respiratory Infections;2
3;copyright
;3
4;Contributors;4
5;Contents;6
6;Clinics In Laboratory Medicine
;10
7;Preface
;12
8;Infections in Patients with Cystic Fibrosis;14
8.1;Key points;14
8.2;Introduction, epidemiology, and clinical presentation;14
8.3;Microbiology, diagnostic considerations, and susceptibility testing of agents of chronic infection;16
8.4;Staphylococcus aureus;16
8.5;Pseudomonas aeruginosa;20
8.6;Burkholderia cepacia complex and related organisms;22
8.7;Stenotrophomonas and Achromobacter;24
8.8;Mycobacterium;25
8.9;Fungi;26
8.10;Respiratory viruses;27
8.11;Microbiome considerations;27
8.12;References;28
9;Urine Antigen Tests for the Diagnosis of Respiratory Infections;36
9.1;Key points;36
9.2;Introduction;36
9.3;Microbiology;37
9.3.1;Legionella;37
9.3.2;Pneumococcus;37
9.3.3;Histoplasma;37
9.4;Epidemiology, disease presentation, and pathogenesis;38
9.4.1;Legionella;38
9.4.2;Pneumococcus;38
9.4.3;Histoplasma;39
9.5;Diagnosis;39
9.5.1;Legionella Urinary Antigen Testing;40
9.5.1.1;ELISA;40
9.5.1.2;LFA;40
9.5.2;Pneumococcal Urinary Antigen Test;42
9.5.2.1;Effects of study design on the sensitivity of the pUAT;42
9.5.2.2;Colonization and the pUAT;44
9.5.3;Histoplasma Antigen Testing;44
9.5.3.1;Miravista Diagnostics enzyme immunoassay;44
9.5.3.1.1;Second generation;44
9.5.3.1.2;Third generation;45
9.5.3.2;Immuno-Mycologics EIA;45
9.6;Treatment;46
9.6.1;Empiric Therapy for LD/Pneumococcal Pneumonia;46
9.6.2;Targeted Therapy for LD/Pneumococcal Pneumonia;46
9.6.3;Treatment of Histoplasma;46
9.7;Summary and discussion;47
9.8;References;47
10;Pertussis;54
10.1;Key points;54
10.2;Introduction;54
10.3;Microbiology;55
10.4;Epidemiology;55
10.5;Clinical presentations;57
10.6;Pathogenesis, immunity, and vaccination;57
10.7;Diagnosis;59
10.8;Case definitions;59
10.9;Laboratory testing;60
10.9.1;Specimens;60
10.9.2;Test Methods;60
10.9.2.1;Direct fluorescent antibody;62
10.9.2.2;Culture;62
10.9.2.3;Nucleic acid amplification tests;62
10.9.2.4;Pretreatment and extraction;62
10.9.2.5;Targets for PCR;63
10.9.2.6;Low copy number and high CT values;64
10.9.2.7;NAATs other than PCR;64
10.9.2.8;Contamination;65
10.9.2.9;Interpretation;65
10.9.2.10;Serology;65
10.10;Treatment;66
10.11;Summary/discussion;66
10.12;References;67
11;Antibiotic Resistance in Nosocomial Respiratory Infections;74
11.1;Key points;74
11.2;Introduction;74
11.3;Etiology;75
11.4;Epidemiology;76
11.5;Clinical presentation;77
11.6;Pathogenesis;77
11.7;Diagnosis;78
11.8;Treatment;83
11.9;Summary;84
11.10;References;84
12;Nontuberculous Mycobacteria in Respiratory Infections;88
12.1;Key points;88
12.2;Microbiology;89
12.3;Epidemiology;89
12.4;Pathogenesis and clinical significance;92
12.5;Diagnosis;94
12.6;Specimen processing;95
12.7;Acid-fast microscopy;96
12.8;Direct NAA assays;97
12.9;Growth detection;97
12.10;Identification;99
12.10.1;Nucleic Acid Hybridization Methods;99
12.10.2;PCR and Restriction Fragment Length Polymorphism Analysis;100
12.10.3;Line Probe Assays;101
12.10.4;DNA Sequencing;101
12.10.5;MALDI-TOF MS;102
12.11;Genotyping;103
12.12;Antimicrobial susceptibility testing;103
12.13;Identified focus areas in NTM research;105
12.14;References;106
13;Molecular Diagnosis of Tuberculosis and Drug Resistance;114
13.1;Key points;114
13.2;Introduction;114
13.3;Microbiology;115
13.4;Epidemiology;115
13.5;Clinical presentation;115
13.6;Pathogenesis of pulmonary tuberculosis;116
13.7;Molecular diagnosis;116
13.7.1;Genes Associated with Drug Resistance;116
13.7.1.1;Isoniazid;118
13.7.1.2;Rifampin and rifabutin;119
13.7.1.3;Ethambutol;120
13.7.1.4;Pyrazinamide;120
13.7.1.5;Fluoroquinolones;120
13.7.1.6;Injectable drugs;121
13.8;Molecular assays;121
13.8.1;Molecular Beacon Assays;121
13.8.2;Line-Probe Assays;124
13.8.3;Sanger Sequencing;124
13.8.4;Pyrosequencing;124
13.8.5;Next-Generation Sequencing;125
13.9;Practical use of molecular diagnostic assays;125
13.10;Impact on patient management, TB control, and infection control;125
13.11;Summary;126
13.12;References;127
14;Nonmolecular Methods for the Diagnosis of Respiratory Fungal Infections;132
14.1;Key points;132
14.2;Introduction;132
14.3;Microbiology/Epidemiology;133
14.4;Clinical presentation;134
14.5;Pathogenesis;135
14.6;Diagnosis;135
14.6.1;Invasive Aspergillosis (IA);136
14.6.1.1;GM assay;136
14.6.1.2;BG assay;139
14.6.1.3;Aspergillus lateral-flow devices;140
14.6.1.4;Anti-Aspergillus antibodies;140
14.6.2;Chronic Pulmonary Aspergillosis;141
14.6.3;Pneumonia Caused by Non-Aspergillus Molds;141
14.6.4;Pneumocystis jirovecii Pneumonia;141
14.6.5;Pulmonary Cryptococcosis;142
14.7;Treatment;143
14.8;Discussion/Summary;143
14.9;References;145
15;Interferon-Gamma Release Assays;154
15.1;Key points;154
15.2;Introduction;154
15.3;Microbiology;155
15.4;Epidemiology;155
15.5;Clinical presentation;156
15.6;Pathogenesis;157
15.7;Diagnosis;158
15.7.1;Interferon-Gamma Release Assays;158
15.7.2;Test Performance of IGRAs;159
15.7.3;IGRAs in Targeted Populations;160
15.8;Treatment;162
15.9;Summary/Discussion;162
15.10;References;163
16;Respiratory Fungal Infections;168
16.1;Key points;168
16.2;Introduction;168
16.3;Aspergillosis;170
16.3.1;Diagnosis;170
16.3.2;Combination Testing;171
16.3.3;The Need for Prospective Clinical Trials;172
16.4;Pneumocystis jirovecii pneumonia;173
16.4.1;Introduction;173
16.4.2;Microbiology;173
16.4.3;Epidemiology;173
16.4.4;Clinical Presentation;174
16.4.5;Pathogenesis;174
16.4.6;Laboratory Diagnosis;174
16.4.7;PCR or Antigen Tests;176
16.4.8;Treatment;176
16.5;Summary;176
16.6;References;177
17;Rapid Diagnosis of Influenza;182
17.1;Key points;182
17.2;Influenza viruses;182
17.2.1;Pathogenesis;183
17.2.2;Clinical Presentation;183
17.2.3;Treatment;183
17.3;General principles of laboratory diagnosis of influenza infection;184
17.4;Sample collection and transport;186
17.5;Diagnostic methods;187
17.5.1;Viral Culture;187
17.5.2;Viral Antigen Detection;187
17.5.2.1;Immunofluorescence;187
17.5.2.2;Lateral flow IC;188
17.5.2.3;Performance of RIDTs;188
17.5.3;Nucleic Acid Detection;190
17.5.3.1;Conventional PCR;190
17.5.3.2;Real-time PCR;191
17.5.3.3;Multiplex methods;192
17.6;Rapid NAAT for the detection of influenza viruses;192
17.6.1;Description of the Systems;193
17.6.2;Assay Performance;195
17.6.3;Limitations and Future Developments;196
17.7;Factors to consider;196
17.8;Summary;198
17.9;References;198
18;Antiviral Resistance in Influenza Viruses;204
18.1;Key points;204
18.2;Introduction;204
18.3;Microbiology;205
18.4;Epidemiology and transmission;206
18.5;Pathogenesis;206
18.6;Clinical presentation;206
18.7;Pharmacologic agents;207
18.7.1;Adamantanes;207
18.7.2;NA Inhibitors;207
18.7.3;Other Antiviral Targets and Drugs;208
18.8;Resistance genetics;210
18.9;Influenza diagnosis;211
18.10;Antiviral drug susceptibility testing;212
18.10.1;Genotypic Methods;212
18.10.2;Phenotypic Methods;214
18.10.3;Patient Testing and Surveillance Programs;215
18.11;Treatment and prognosis;216
18.12;Summary;217
18.13;Acknowledgments;217
18.14;References;217
19;Emerging Respiratory Viruses Other than Influenza;226
19.1;Key points;226
19.2;Introduction;226
19.3;Microbiology;227
19.3.1;MERS-CoV;227
19.3.2;Ad14;228
19.3.3;RV-C;229
19.3.4;HBoV1;229
19.4;Epidemiology;230
19.4.1;MERS-CoV;230
19.4.2;Ad14;230
19.4.3;RV-C;231
19.4.4;HBoV1;232
19.5;Clinical presentation;232
19.5.1;MERS-CoV;232
19.5.2;Ad14;232
19.5.3;RV-C;233
19.5.4;HBoV1;233
19.6;Pathogenesis;234
19.6.1;MERS-CoV;234
19.6.2;Ad14;234
19.6.3;RV-C;234
19.6.4;HBoV1;236
19.7;Diagnosis;237
19.8;Treatment and prognosis;238
19.9;Summary;239
19.10;References;240
20;Index;248
Infections in Patients with Cystic Fibrosis
Diagnostic Microbiology Update
Peter H. Gilligan, PhD, DABMMgilliganncphd@gmail.com, Pathology-Laboratory Medicine and Microbiology-Immunology, Clinical Microbiology-Immunology Laboratories, UNC Health Care, UNC Hospitals, UNC School Medicine, Room 1035, CB 7600, Chapel Hill, NC 27516, USA Survival has improved in patients with cystic fibrosis (CF), in part because of aggressive antimicrobial management. Two multidrug-resistant environmental bacteria, the Burkholderia cepacia group and nontuberculous mycobacteria, have emerged. Improving genomic and proteomic technologies are allowing better identification of bacteria and fungi found in the CF lung and detection of viral agents that may be associated with pulmonary exacerbations. Anaerobic bacteria and Streptococcus angionsus group organisms may play a role in chronic CF lung infections. The diversity of organisms declines perhaps as a result of aggressive antimicrobial therapy, and an apex predator, Pseudomonas aeruginosa, may emerge in many patients with CF. Keywords Infection Cystic fibrosis Diagnostic microbiology Update Key points
• Cystic fibrosis is the most important genetic disease in Caucasians. Patients with this disease die prematurely primarily as a result of chronic lung infection. Staphylococcus aureus and mucoid Pseudomonas aeruginosa continue to be the key pulmonary pathogens. • Survival has improved in patients with CF in part because of aggressive antimicrobial management. An unintended consequence of this therapy has been the emergence of 2 multidrug-resistant environmental bacteria: the Burkholderia cepacia group and nontuberculous mycobacteria. • Burkholderia cenocepacia, a species within the Burkholderia cepacia complex, is associated with high mortality and is a contraindication for lung transplantation. The key nontuberculous mycobacterial pathogen, Mycobacterium abscessus, is not so virulent and is not a lung transplantation contraindication. Both present an infection control challenge, because they can be spread from person to person. • Improving genomic and proteomic technologies are allowing better identification of bacteria and fungi found in the CF lung and to detect viral agents that may be associated with pulmonary exacerbations. Chronic rhinovirus infections are of particular interest. • Microbiome studies have identified 2 groups of bacteria that may play a role in chronic CF lung infections: anaerobic bacteria and Streptococcus angionsus group organisms. Microbiome studies also show that as the diversity of organisms decline, perhaps as a result of aggressive antimicrobial therapy, an apex predator, etc., Pseudomonas aeruginosa, may emerge in many patients with CF. Introduction, epidemiology, and clinical presentation
Cystic fibrosis (CF) is the most common autosomal-recessive genetic disease that occurs in non-Hispanic Caucasians populations, although other racial groups may have this disease as well.1 Affected individuals have mutation in the CF transmembrane conductance gene (CFTR), a membrane protein involved in sodium and chloride transport in epithelial cells.2 The resulting dysregulation in electrolyte transport leads to depletion in airway surface liquid on bronchial epithelial cell surfaces. As a result, patients with CF have thick, dry, tenacious mucus, which impairs mucociliary clearance of particulates, especially bacteria and fungal conidia, from the airways. This environment is ideal for the growth of a limited number of organisms, primarily those that thrive in natural environments such as water. This thickened mucus provides an ideal niche for the establishment of chronic infection. It is this chronic infection that results in the premature death that in seen in CF.3 More than 1800 CFTR mutations have been associated with CF.4 The most common mutation is F508del, which is found in ~85% of people in the United States; approximately 47% are homozygous for this mutated gene.4 Further carrier rate for mutated CFTR genes is estimated to range from 1/25 for non-Hispanic Caucasians to 1/61 for African Americans to 1/94 for Asian Americans.1 CF is seen most frequently in North America, Northern Europe, Australia, New Zealand, Brazil, and Argentina. It is estimated that 1 in 3500 live births result in clinical disease.4 Currently life expectancy in US patients with CF is approximately 38 years, significantly less than that of the general population.4 Cardiopulmonary failure secondary to chronic lung disease is responsible for 85% of premature deaths in CF. The airways of patients with CF become infected in infancy. This situation begins periods of chronic infection and lung inflammation with accompanying cough, which is a lifelong reality in patients with CF. A hallmark of chronic infection and airway inflammation is periods of pulmonary exacerbations. Pulmonary exacerbations are characterized by worsening symptoms, including increased cough and sputum production, hemoptysis, shortness of breath, increased respiratory rate, loss of appetite, weight loss, increased neutrophil counts, and declining pulmonary function.5 The events that trigger these pulmonary exacerbations are not clearly understood, although viral infections and perhaps changes in the microbiome may be important.6,7 Exacerbations are characterized by the recruitment of neutrophils, cytokine release, and high level of neutrophil-derived elastases in the bronchi and bronchioles, causing significant lung disease.8 Antimicrobial therapy has been shown to be effective in treating exacerbations symptomatically.9 However, over time, lung function deteriorates and becomes so low, that it is no longer compatible with life (Fig. 1). Only lung transplantation can successfully reverse this disease course.8
Fig. 1 Lung function by age group, 2011. FEV1, forced expiratory volume in 1 second. (From Cystic Fibrosis Foundation. Cystic Fibrosis Foundation patient registry 2011 annual data report. 2012.) Microbiology, diagnostic considerations, and susceptibility testing of agents of chronic infection
Over the past 4 decades, our understanding of the complex nature of chronic lung infections has greatly expanded. Over the past 3 decades, there has been more than a doubling in life expectancy in the population with CF.4 Three factors have been central to this improvement: a. More effective antimicrobial therapy and treatment strategies, with early eradication of Pseudomonas aeruginosa being a key strategy b. Improvement in airway clearance techniques c. Improvements in infection control techniques to prevent the spread of organisms highly virulent to patients with CF, especially Burkholderia cenocepacia2,9 With the use of broader-spectrum antimicrobials, we are seeing a plethora of emerging highly resistant bacteria and fungi in the CF airways. Our understanding of the role of these organisms in chronic infection and inflammation is poorly delineated (Box 1). Over the past decades, new technologies (Fig. 2) have been developed and applied to this understanding. These technologies include nucleic acid amplification techniques (NAATs) for direct organism detection, including multiplex NAAT for viruses; the use of DNA sequence analysis for organism identification; molecularly based epidemiologic techniques, including pulsed field gel electrophoresis (PFGE), multilocus sequence type, whole genome sequencing; and matrix-assisted laser desorption ionization–time of flight mass spectroscopy (MALDI-TOF MS). Box 1 Pathogenic potential of commonly recovered organisms from chronic CF airway infections or pulmonary exacerbations • Known Pseudomonas aeruginosa Staphylococcus aureus Methicillin resistant Small colony variant Burkholderia multivorans Burkholderia cenocepacia Burkholderia dolosa Aspergillus spp Scedosporium spp Mycobacterium abscessus Influenza virus Respiratory syncytial virus • Possible/likely Haemophilus influenzae Mycobacterium avium complex Anaerobic bacteria especially Prevotella...
