Tuesday, January 17, 2017

Advanced Techniques in Diagnostic Microbiology

In the United States, hospitals annually report over 5 million cases of infectious-disease-related illnesses: clinical microbiology laboratories in these hospitals are engaged in detecting and identifying the pathogenic microorganisms in clinical specimens collected from these patients with suspected infections. Clearly, the timely and accurate detection/identification of these microbial pathogens is critical for patient treatment decisions and outcomes for millions of patients each year. Despite an appreciation that the outcome of an infectious-disease-related illness is directly related to the time required to detect and identify a microbial pathogen, clinical microbiology laboratories in the United States as well as worldwide have long been hampered by traditional culture-based assays, which may require prolonged incubation time for slowly growing microorganisms such as Mycobacterium tuberculosis. Moreover, traditional culture-based assays often require multiple steps with additional time needed for discernment of species and/or detection of antimicrobial resistance. Finally, these traditional, slow multistep culture-based assays are labor-intensive and required skilled clinical microbiologists at the bench.
Over the past several decades, advanced molecular techniques in diagnostic microbiology quietly have been revolutionizing the practice of clinical microbiology in the hospital setting. Indeed, molecular diagnostic testing in general and nucleic-acid-based amplification methods in particular have been heralded as diagnostic tools for the new millennium. There is no question that the development of rapid molecular techniques for nucleic acid amplification/characterization combined with automation and user-friendly software has greatly broadened the diagnostic capabilities of the clinical microbiology laboratory. These technical advances in molecular microbiology over the first decade of the 21st Century have profoundly influenced the physical structure of clinical microbiology laboratories as well as their staffing patterns, workflow, and turnaround time. These molecular microbiology advances have also resulted in the need for a revised and updated second edition of Advanced Techniques in Diagnostic Microbiology. This second edition again provides an updated and comprehensive description of the ongoing evolution of molecular methods for the diagnosis of infectious diseases. In addition, many new chapters have been added, including a chapter on the clinical interpretation and relevance of advanced technique results. The second edition, like the first edition, includes both a “techniques” section describing the latest molecular techniques and an “applications” section describing how these advanced molecular techniques are being used in the clinical setting. Finally, the second edition, like the first edition, utilizes a diverse team of authors who have compiled chapters that provide the reader with comprehensive and useable information on advanced molecular microbiology techniques.
Table of contents : 
Front Matter....Pages i-x
Front Matter....Pages 1-1
Automated Blood Cultures....Pages 3-12
Breath Tests for Detection of Helicobacter pylori and Aspergillus fumigatus ....Pages 13-30
Rapid Antigen Tests....Pages 31-51
Antibody Detection: Principles and Applications....Pages 53-73
Cytometry-Based Antimicrobial Resistance Techniques....Pages 75-85
Biochemical Profile-Based Microbial Identification Systems....Pages 87-121
Infectious Disease Biomarkers: Non-Antibody-Based Host Responses....Pages 123-149
Functional Assessment of Microbial and Viral Infections by Real-Time Cellular Analysis System....Pages 151-175
Cellular Fatty Acid-Based Microbial Identification and Antimicrobial Susceptibility Testing....Pages 177-185
MALDI-TOF Mass Spectrometry-Based Microbial Identification....Pages 187-207
Nucleic Acid Extraction Techniques....Pages 209-225
Nonamplified Probe-Based Microbial Detection and Identification....Pages 227-237
Molecular Typing Techniques: State of the Art....Pages 239-261
An Introduction to In Vitro Nucleic Acid Amplification Techniques....Pages 263-271
PCR and Its Variations....Pages 273-291
Non-PCR Target Amplification Techniques....Pages 293-306
Probe Amplification Technologies....Pages 307-325
Signal Amplification Technologies....Pages 327-344
Real-Time Nucleic Acid Quantification....Pages 345-353
An Introduction to Amplification–Production–Detection Techniques....Pages 355-365
Front Matter....Pages 1-1
Gel Electrophoresis, Southern Blot, and Colorimetric Microwell Plate-Based System....Pages 367-381
Direct Nucleotide Sequencing for Amplification Product Identification....Pages 383-395
Microarray-Based Amplification Product Detection and Identification....Pages 397-412
Real-Time Detection of Amplification Products Through Fluorescence Quenching or Energy Transfer....Pages 413-440
Microbial Identification by PCR/Electrospray Ionization-Mass Spectrometry....Pages 441-465
Amplification Product Inactivation....Pages 467-479
Front Matter....Pages 481-481
Bacterial Identification Based on Universal Gene Amplification and Sequencing....Pages 483-509
Molecular Techniques for Blood and Blood Product Screening....Pages 511-533
Molecular Diagnostics of Sexually Transmitted Diseases....Pages 535-556
Advances in the Diagnosis of Mycobacterium tuberculosis and Detection of Drug Resistance....Pages 557-586
Rapid Screening and Identification of Methicillin-Resistant Staphylococcus aureus ....Pages 587-603
Advanced Methods for Detection of Foodborne Pathogens....Pages 605-618
Technical and Clinical Niches for Point of Care Molecular Devices....Pages 619-626
Multiplex PCR in Molecular Differential Diagnosis of Microbial Infections: Methods, Utility, and Platforms....Pages 627-646
Technical Advances in Veterinary Diagnostic Microbiology....Pages 647-659
Recent Advances in Veterinary Diagnostic Virology: Report from a Collaborating Centre of the World Organization for Animal Health (OIE)....Pages 661-678
Deep Sequencing: Technical Advances and Clinical Microbiology Applications....Pages 679-692
Detection of Viral RNA Splicing in Diagnostic Virology....Pages 693-748
Application of Microarrays for Laboratory Detection and Identification of Medically Important Fungi....Pages 749-767
Laboratory Technical Advances in the Diagnosis of Clostridium difficile ....Pages 769-783
Front Matter....Pages 481-481
Molecular Diagnosis of HIV-1 Infections: Current State of the Art....Pages 785-812
Bead-Based Suspension Arrays for the Detection and Identification of Respiratory Viruses....Pages 813-833
Molecular Diagnosis and Monitoring of Human Papillomavirus Infections....Pages 835-844
Molecular Niches for the Laboratory Diagnosis of Sepsis....Pages 845-871
Advanced Pathology Techniques for Detecting Emerging Infectious Disease Pathogens....Pages 873-890
Diagnosis and Assessment of Microbial Infections with Host and Microbial microRNA Profiles....Pages 891-909
Interpretation and Relevance of Advanced Technique Results....Pages 911-936
Back Matter....Pages 937-957