Preface -- Contents -- Authors Index -- Contributors Index -- 1. Choice of adequate sample material -- 1.1 Viruses -- 1.2 Bacteria -- 1.3 Fungi -- 1.4 Protozoa -- 2. Stability of the specimen during preanalytics -- 2.1 Sample integrity during collection -- 2.1.1 Blood -- 2.1.2 Urine -- 2.1.3 Stool -- 2.2 Degradation of DNA -- 2.3 Degradation of RNA -- 2.4 Inhibitors of PCR -- 2.5 How can contamination during specimen collection and in the laboratory be avoided? -- 2.6 How can the sample identity be ensured? -- 2.7 Transport of diagnostic material -- 2.7.1 Category A Infectious Substances -- 2.7.2 Category B Infectious Substances -- 2.7.3 Exempt patient specimens -- 2.8 Stability of nucleic acids of selected pathogens during preanalytics -- 2.8.1 Human immunodeficiency virus type 1 (HIV-1) RNA -- 2.8.2 Hepatitis B virus (HBV) DNA -- 2.8.3 Hepatitis C virus (HCV) RNA -- 2.8.4 Chlamydia trachomatis and Neisseria gonorrhoeae DNAs -- 2.8.5 Viral pathogens producing respiratory tract infections -- 2.8.6 Pathogens in stool specimens -- 2.9 Take home messages -- 2.10 Further reading -- 3. Quality assurance and quality control -- 3.1 Accreditation issues -- 3.2 Standardization of diagnostic tests or test systems -- 3.3 Validation and verification work -- 3.4 Components of validation work -- 3.4.1 Internal and external quality controls -- 3.4.2 Proficiency testing -- 3.4.3 Validation of employee competency -- 3.4.4 Instrument maintenance and calibration -- 3.4.5 Correlation with clinical findings -- 3.5 Components of verification work -- 3.5.1 Components of verification work for IVD/CE labeled and/or FDA-approved or -cleared tests or test systems -- 3.5.2 Components of verification work for laboratory-developed tests or test systems -- 3.6 Take home messages -- 3.7 Further reading -- 4. Extraction of nucleic acids.

4.1 Manual nucleic acid extraction protocols -- 4.2 Automated nucleic acid extraction platforms -- 4.2.1 Technology principle -- 4.2.2 Desirable features of automated platforms -- 4.3 Preparation of qPCR mixes and addition of eluates (qPCR assay setup) -- 4.4 Currently frequently used commercially available platforms -- 4.5 Take home messages -- 4.6 Further reading -- 5. Amplification and detection methods -- 5.1 Nucleic acid-based tests -- 5.2 Target amplification methods -- 5.2.1 Real-time polymerase chain reaction (qPCR) -- 5.2.2 Isothermal amplification techniques -- 5.2.3 Next generation sequencing (NGS) -- 5.3 Signal amplification methods -- 5.3.1 Branched DNA (bDNA) -- 5.3.2 Hybrid capture assay -- 5.4 What are the key challenges for the future? -- 5.5 Take-home messages -- 5.6 Further reading -- 6. Interpreting and reporting molecular diagnostic tests -- 6.1 Detection of viral infections -- 6.2 Detection of bacterial infections -- 6.3 Quantitative endpoint PCR -- 6.4 Real-time PCR (qPCR) -- 6.5 Reporting results -- 6.5.1 Genetic names -- 6.5.2 Recommendations for reporting results of molecular tests -- 6.5.3 Recommendations for the contents of the molecular test report -- 6.6 Interpretation -- 6.7 Important issues when clinically interpreting molecular diagnostic results -- 6.8 Take home messages -- 6.9 Further reading -- 7. Human immunodeficiency virus -- 7.1 Major symptoms -- 7.1.1 Untreated individuals -- 7.1.2 Treated individuals -- 7.2 Preanalytics -- 7.2.1 Specimen collection -- 7.2.2 Clinical circumstances for using NAT to diagnose HIV infection -- 7.2.3 Clinical circumstances for using NAT to monitor HIV infection -- 7.3 Analytics -- 7.3.1 Main technologies for NAT -- 7.3.2 HIV RNA assays -- 7.3.3 HIV DNA assays -- 7.3.4 HIV drug resistance assays -- 7.3.5 HIV tropism assays.

7.3.6 Assays for minority HIV variants -- 7.4 Postanalytics -- 7.4.1 Molecular diagnosis of HIV infection -- 7.4.2 Monitoring HIV infection -- 7.5 Take-home messages -- 7.6 Further reading -- 8. Hepatitis viruses -- 8.1 Major symptoms -- 8.2 Preanalytics -- 8.3 Analytics -- 8.3.1 Adenoviruses -- 8.3.2 HAV -- 8.3.3 HBV -- 8.3.4 HCV -- 8.3.5 HDV -- 8.3.6 HEV -- 8.3.7 Herpes viruses -- 8.3.8 Yellow fever virus and hemorrhagic fever viruses -- 8.4 Postanalytics - interpretation of results -- 8.4.1 HAV/HEV -- 8.4.2 HBV -- 8.4.3 HDV -- 8.4.4 HCV -- 8.5 Take-home messages -- 8.6 Further reading -- 9. Pathogens relevant in transplantation medicine -- 9.1 Clinical manifestations -- 9.2 Preanalytics -- 9.2.1 Adenoviruses -- 9.2.2 CMV -- 9.2.3 EBV -- 9.2.4 HHV-6 -- 9.2.5 HHV-8 -- 9.2.6 VZV -- 9.2.7 BKPyV -- 9.2.8 JCPyV -- 9.3 Analytics -- 9.3.1 Sample preparation -- 9.3.2 Nucleic acids amplification and detection -- 9.4 Postanalytics - interpretation of results -- 9.4.1 Adenoviruses -- 9.4.2 CMV -- 9.4.3 EBV -- 9.4.4 HHV-6 -- 9.4.5 HHV-8 -- 9.4.6 VZV -- 9.4.7 BKPyV -- 9.4.8 JCPyV -- 9.5 Take-home messages -- 9.6 Further reading -- 10. Pathogens in lower respiratory tract infections -- 10.1 Clinical importance of different etiologic agents -- 10.2 Specimen collection -- 10.2.1 S. pneumoniae -- 10.2.2 M. pneumoniae, L. pneumophila, and C. pneumoniae -- 10.2.3 B. pertussis -- 10.2.4 Respiratory viruses -- 10.3 Diagnostic procedures -- 10.3.1 Sample preparation and nucleic acid extraction -- 10.3.2 Amplification and detection methods for individual agents -- 10.3.3 Multiplex NAATs -- 10.4 External quality control -- 10.5 The clinical usefulness and implementation of NAATs -- 10.6 Concluding remarks -- 10.7 Further reading -- 11. Molecular diagnosis of gastrointestinal pathogens -- 11.1 Clinical manifestations -- 11.2 Preanalytics.

11.3 Analytics -- 11.4 Postanalytics -- 11.4.1 Clinical sensitivity and diagnostic specificity -- 11.4.2 Interpretation of results -- 11.5 Further reading -- 12. Pathogens relevant in the central nervous system -- 12.1 Clinical manifestations -- 12.1.1 Viral meningitis -- 12.1.2 Acute community-acquired bacterial meningitis -- 12.1.3 Mycobacterium tuberculosis -- 12.1.4 Encephalitis -- 12.2 Preanalytics -- 12.2.1 Goals of etiological investigations -- 12.2.2 Specimens and handling -- 12.2.3 Time of lumbar puncture during the course of illness and quantity of CSF required -- 12.2.4 Transport and storage of specimens -- 12.3 Analytics -- 12.3.1 Sample preparation -- 12.3.2 Nucleic acid amplification and detection -- 12.4 Postanalytics -- 12.4.1 Workflow and testing schedules for molecular tests -- 12.4.2 Limitations of molecular tests -- 12.4.3 Viral CNS infections -- 12.4.4 Bacterial CNS infections -- 12.4.5 Which pathogens should we look for? -- 12.5 Conclusion -- 12.6 Take-home messages -- 12.7 Acknowledgment -- 12.8 Further reading -- 13. Pathogens relevant in sexually transmitted infections -- 13.1 Symptoms and clinical manifestations -- 13.2 Preanalytics -- 13.3 Analytics -- 13.4 Postanalytics -- 13.5 Further reading -- Index.