Chapter 13 Host-Based Diagnostics for Detection and Prognosis of Infectious Diseases
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): William E. Yang, Christopher W. Woods, Ephraim L. Tsalik The field of infectious diseases is witnessing the rapid evolution of molecular diagnostics, mostly focused on pathogen detection. However, targeting the host response for diagnostic and prognostic purposes has been described as a paradigm shift (Ramilo & Mejias, 2009). The concept of host response is not new. The erythrocyte sedimentation rate described in 1917 and C-reactive protein in 1930 are still used today albeit with limitations. More contemporary biomarkers based on...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 12 Gene Amplification and Sequencing for Bacterial Identification
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Susanna K.P. Lau, Jade L.L. Teng, Chi-Chun Ho, Patrick C.Y. Woo The most important task of the clinical microbiology laboratory is to accurately identify the responsible pathogens to species level. Phenotypic methods for bacterial identification are associated with many problems, such as strains with unusual biochemical profiles and slowly growing bacterial species. In the past few decades, gene sequencing has evolved to be an objective method for bacterial identification. Among the various gene targets, the 16S rRNA gene is the most co...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 11 Solid and Suspension Microarrays for Microbial Diagnostics
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Steve Miller, Ulas Karaoz, Eoin Brodie, Sherry Dunbar Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarr...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 10 Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Hannes Pouseele, Philip Supply Efficient molecular-guided epidemiological control of tuberculosis is especially important, because of the complex epidemiology, the insidious transmission and the specific biological features of its etiologic agent Mycobacterium tuberculosis. The most used typing system for epidemiological tracing of the pathogen is MIRU-VNTR typing, which has been internationally standardised under two formats (standard 24-locus based and 4 hypervariable locus based), optionally combined with spoligotyping. This generalised ...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 9 Molecular Strain Typing and Characterisation of Toxigenic Clostridium difficile
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Tanis C. Dingle, Duncan R. MacCannell At the turn of the century, a shift in incidence of Clostridium difficile infection occurred with the emergence of a novel, more virulent strain of C. difficile. It became apparent that strain typing was critical to our understanding of the epidemiology and transmission of the disease. Over the past 25 years, C. difficile strain typing methods have developed from phenotypic to genotypic techniques, each with their own advantages and disadvantages. Unfortunately, with the advent of polymerase chain react...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 8 Technical and Software Advances in Bacterial Pathogen Typing
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Linda Chui, Vincent Li Bacterial typing is an integral part of many public health systems and is a crucial tool for pathogen surveillance and outbreak detection. Choosing an appropriate typing method depends on many factors including cost, time, discriminatory power, reproducibility, ease of result interpretation, and the availability of materials and technical expertise. In recent years, advancements have been made in laboratory techniques and computer hardware and software, significantly changing the landscape of bacterial typing. Classic...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 7 Invasive Fungal Infections and Approaches to Their Diagnosis
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Michael A. Pfaller Invasive fungal infections have become a major source of morbidity and mortality over the past three decades. The use of aggressive chemotherapy, organ transplantation, and the availability and widespread use of immunosuppressive treatments for many medical ailments has resulted in large populations at risk for fungal disease. Early diagnosis and prompt therapy are instrumental to successful treatment of these infections. Unfortunately, conventional methods for diagnosing fungal disease are slow and insensitive. Important a...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 6 Low-Density TaqMan® Array Cards for the Detection of Pathogens
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Jude Heaney, Kathryn Rolfe, Nicholas S. Gleadall, Jane S. Greatorex, Martin D. Curran Real-time PCR assays have revolutionised diagnostic microbiology over the past 15 years or more. Adaptations and improvements over that time frame have led to the development of multiplex assays. However, limitations in terms of available fluorophores has meant the number of assays which can be combined has remained in single figures. This latter limitation has led to the focus tending to be on individual pathogens and their detection. This chapter d...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Julia Engstrom-Melnyk, Pedro L. Rodriguez, Olivier Peraud, Raymond C. Hein Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adopti...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 4 Molecular Diagnostics in the Diagnosis of Parasitic Infection
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Bobbi S. Pritt Molecular testing is increasingly used to supplement or replace conventional microscopy-based methods of parasite identification. Potential benefits of molecular methods such as nucleic acid amplification tests include increased sensitivity, ability to differentiate morphologically similar organisms and lack of reliance on subjective microscopic features. However, several challenges exist for widespread implementation of molecular diagnostics, including the expense of reagents and equipment, need for sophisticated facilities an...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 3 POC Tests in Microbial Diagnostics
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Luc Bissonnette, Michel G. Bergeron In January 2015, the Alere™ i Influenza A & B test became the first molecular test to receive a CLIA waiver, thereby leading the way to the detection of nucleic acids at point of care (POC). For the diagnosis and management of infectious diseases, there is an urgent need of such devices for controlling the morbidity and mortality of infections, and the evolution and progression of antimicrobial resistance. This chapter provides a snapshot of CLIA-waived tests marketed for the diagnosis of infect...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 2 MALDI-TOF Mass Spectrometry for Microorganism Identification
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Lori Bourassa, Susan M. Butler-Wu Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate and high-throughput method for microorganism identification. MALDI-TOF MS identification of microorganisms has revolutionised the clinical microbiology laboratory offering species-level identifications in minutes with accuracy that matches and often exceeds that of conventional identification systems. This chapter summarises the performance characteristics of commercially available MALDI-TOF MS s...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 1 Total Laboratory Automation in Clinical Bacteriology
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Susan M. Novak-Weekley, Elizabeth M. Marlowe In today's clinical microbiology laboratory, automation is being introduced that will change the nature of how clinical specimens are processed and analysed. Over the last several years, many microbiology laboratories have implemented automation to process liquid specimens which have historically been inoculated to media manually. In some institutions, this automation has been able to free up staff to concentrate on other tasks and has resulted in increased efficiency in the laboratory setting. I...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
POC tests in microbial diagnostics: current status
Publication date: Available online 20 October 2015 Source:Methods in Microbiology Author(s): Luc Bissonnette, Michel G. Bergeron In January 2015, the Alere™ i Influenza A & B test became the first molecular test to receive a CLIA waiver, thereby leading the way to the detection of nucleic acids at point of care (POC). For the diagnosis and management of infectious diseases, there is an urgent need of such devices for controlling the morbidity and mortality of infections, and the evolution and progression of antimicrobial resistance. This chapter provides a snapshot of CLIA-waived tests marketed for the di...
Source: Methods in Microbiology - November 6, 2015 Category: Microbiology Source Type: research
Total laboratory automation in clinical bacteriology
Publication date: Available online 21 October 2015 Source:Methods in Microbiology Author(s): Susan M. Novak-Weekley, Elizabeth M. Marlowe In today's clinical microbiology laboratory, automation is being introduced that will change the nature of how clinical specimens are processed and analysed. Over the last several years, many microbiology laboratories have implemented automation to process liquid specimens which have historically been inoculated to media manually. In some institutions, this automation has been able to free up staff to concentrate on other tasks and has resulted in increased efficiency in the labo...
Source: Methods in Microbiology - November 6, 2015 Category: Microbiology Source Type: research
