MALDI-TOF mass spectrometry for microorganism identification
Publication date: Available online 9 October 2015 Source:Methods in Microbiology 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 availabl...
Source: Methods in Microbiology - October 9, 2015 Category: Microbiology Source Type: research
Virology: The next generation from digital PCR to single virion genomics
Publication date: Available online 1 October 2015 Source:Methods in Microbiology Author(s): Richard Allen White, Jessica N. Brazelton de Cárdenas, Randall T. Hayden In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. U...
Source: Methods in Microbiology - October 2, 2015 Category: Microbiology Source Type: research
Technical and software advances in bacterial pathogen typing
Publication date: Available online 13 August 2015 Source:Methods in Microbiology 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...
Source: Methods in Microbiology - August 14, 2015 Category: Microbiology Source Type: research
Molecular strain typing and characterisation of toxigenic Clostridium difficile
Publication date: Available online 12 August 2015 Source:Methods in Microbiology 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 polyme...
Source: Methods in Microbiology - August 13, 2015 Category: Microbiology Source Type: research
Low-density TaqMan® array cards for the detection of pathogens
Publication date: Available online 3 August 2015 Source:Methods in Microbiology 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....
Source: Methods in Microbiology - August 4, 2015 Category: Microbiology Source Type: research
Next-generation sequencing for pathogen detection and identification
Publication date: Available online 31 July 2015 Source:Methods in Microbiology Author(s): Kenneth G. Frey, Kimberly A. Bishop-Lilly Over the past decade, the field of genomics has seen such drastic improvements in sequencing chemistries that high-throughput sequencing, or next-generation sequencing (NGS), is being applied to generate data across many disciplines. NGS instruments are becoming less expensive, faster, and smaller, and therefore are being adopted in an increasing number of laboratories, including clinical laboratories. Thus far, clinical use of NGS has been mostly focused on the human genome, for purpo...
Source: Methods in Microbiology - August 2, 2015 Category: Microbiology Source Type: research
Chapter 3 Proteomics
Publication date: 2012 Source:Methods in Microbiology, Volume 39 Author(s): Andreas Otto, Jörg Bernhardt, Michael Hecker, Uwe Völker, Dörte Becher Within the concert of OMICs technologies proteomics is particularly important for systems biology approaches because it provides large-scale, quantitative information on the effectors of cellular processes inside living organisms. For a comprehensive analysis of the proteome 2D-gel- based and gel-free, mass spectrometry-driven methods are available relying on different workflows for identification of proteins and time-resolved analysis of changes in their abunda...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Chapter 6 Noise and Stochasticity in Gene Expression
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Mikkel Girke Jørgensen, Renske van Raaphorst, Jan-Willem Veening Not all cells in a bacterial population exhibit exactly the same phenotype, even though they grow in the same environment and are genetically identical. This phenomenon is known as phenotypic variation. The major source of phenotypic variation is noise or stochasticity in gene expression networks, which can directly promote the formation of population heterogeneity. Bistability, or the existence of two stable subpopulations, is a direct outcome of gene expression noise. In ...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Chapter 4 Bacillus subtilis
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Colin R. Harwood, Susanne Pohl, Wendy Smith, Anil Wipat The accumulation, over more than half a century, of detailed knowledge of the biochemistry, genetics and physiology of Bacillus subtilis, enhanced in recent years by a number of systematic ‘omics’ studies, has resulted in the recognition of this bacterium as a highly amenable chassis for synthetic biology. This chapter describes the features of this bacterium that support this recognition. Although the genome of B. subtilis was first published more that 15 years ago, recent gen...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Chapter 11 Multi-locus Sequence Analysis
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): Xiaoying Rong, Ying Huang Multi-locus sequence analysis (MLSA) is now established as a powerful phylogenetic approach for defining the taxonomic structure and evolutionary history of diverse bacteria, and for exploring population parameters that shape speciation. In this chapter, the emphasis is on practical procedures, notably MLSA schemes designed to clarify relationships within specific genera. MLSA uses data retrieved from fragmented nucleotide sequences of housekeeping genes (normally five to seven) spread across the chromosome, thereb...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Chapter 6 Whole-Genome Analyses
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): David R. Arahal Average nucleotide identity (ANI) was proposed almost 10 years ago as a means to compare genetic relatedness among prokaryotic strains. It was found that values around 95% corresponded to the 70% DNA–DNA hybridization cut-off value that is widely used to delineate archaeal and bacterial species. ANI calculations are one of the many aspects and approaches that can be derived from comparative genomic data and used for taxonomic purposes. Here, an overview about the impact and current usage of ANI values is given together with ...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Chapter 1 The Need for Change
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): William B. Whitman With the development of Next-Generation Sequencing techniques, genomic sequencing of prokaryotes has become inexpensive enough to become a routine tool in the research laboratory. For systematics, genome sequences will provide valuable insights into the phylogeny of prokaryotes and a wealth of information about their genealogy. By providing more reliable and complete data, it will allow the formation of more accurate groupings of taxa. As important, it will provide new understandings of the evolutionary processes within pro...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Host-based diagnostics for detection and prognosis of infectious diseases
Publication date: Available online 17 July 2015 Source:Methods in Microbiology 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 bioma...
Source: Methods in Microbiology - July 17, 2015 Category: Microbiology Source Type: research
Molecular diagnostics in the diagnosis of parasitic infection
Publication date: Available online 9 July 2015 Source:Methods in Microbiology 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 f...
Source: Methods in Microbiology - July 10, 2015 Category: Microbiology Source Type: research
Invasive fungal infections and approaches to their diagnosis
Publication date: Available online 9 July 2015 Source:Methods in Microbiology 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....
Source: Methods in Microbiology - July 10, 2015 Category: Microbiology Source Type: research
