Microbial Pathogenomics

'Microbial Pathogenomics' contains a unique collection of reviews demonstrating how genomics has revolutionized our understanding of virulence, host-adaptation strategies and the evolution of bacterial pathogens. Current technologies - computational tools and functional approaches to genome analysis - are carefully documented and clearly illustrated. These include visualization tools for genome comparison, databases, in silico metabolic reconstructions and function prediction as well as interactomics for the study of protein-protein interactions. The concepts of pan-genomics and reverse vaccinology are introduced as strategies when addressing the challenge presented by bacterial diversity in the prevention and treatment of infectious diseases. The authors explore individual bacterial pathogens and discuss the mechanisms that have contributed to their evolutionary success. Special cases of host adaptation, for example, are illustrated by Helicobacter pylori and 'Mycobacterium tuberculosis' which are human-specific and highly persistent; further bacteria discussed include 'Escherichia coli, Campylobacter, Pseudomonas, Legionella, Bartonella, Burkholderia' and 'Staphylococcus'.'Microbial Pathogenomics' provides the reader with a global view of key aspects and future trends in bacterial pathogenomics and evaluates their impact on the understanding and treatment of infectious diseases. Well illustrated and accessible to both specialists and nonspecialists, it is recommended not only for researchers in microbiology, genomics and biotechnology, but also for lecturers and teachers.

The first book on this young, highly dynamic, and expanding field. This comprehensive, interdisciplinary text focuses on those pathogenic bacteria that are of high scientific and public health interest, yet which also display great potential for the development of new diagnostic, prophylactic and therapeutic procedures. The authors cover all aspects of pathogenomics, including methods, genomics and applications. In addition, the ongoing development of genome, transcriptome, proteome and bioinformatic analyses of pathogenic microorganisms and their host interactions makes for a comprehensive introduction to the field of modern genomic analysis. This result is invaluable to researchers and students wishing to gain a general overview of microbial functional genome analysis and pathogenesis, while also representing a good starting point for those new to the area.

This landmark volume details progress in the fast-changing world of bacterial genomics and it includes contributions from a team of over forty world-renowned authors.

Generally, in accordance with anatomical characteristics, urinary tract infections (UTIs) and in particular recurrent UTIs occur in women; in contrast, UTIs normally occur in men with different predisposing factors. There are several types of UTIs, including asymptomatic and symptomatic, complicated and uncomplicated, acute and chronic with a diversity of microbial pathogens. In pathogens, virulence factors and genes determine the type and severity of the UTIs. Obviously, UTIs are a huge problem in global public healthcare systems with a wide range of predisposing factors, including gender, microbial agent, the host's immune deficiencies, genetic diseases, catheterization, etc. The recent items determine the microbiology of UTIs. Accurate diagnosis and definitive treatment are the key to UTI reduction.

Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.

This book discusses microbial diversity in various habitats and environments, its role in ecosystem maintenance, and its potential applications (e.g. biofertilizers, biocatalysts, antibiotics, other bioactive compounds, exopolysaccharides etc.). The respective chapters, all contributed by renowned experts, offer cutting-edge information in the fields of microbial ecology and biogeography. The book explains the reasons behind the occurrence of various biogeographies and highlights recent tools (e.g. metagenomics) that can aid in biogeography studies by providing information on nucleic acid sequence data, thereby directly identifying microorganisms in various habitats and environments. In turn, the book describes how human intervention results in depletion of biodiversity, and how numerous hotspots are now losing their endemic biodiversity, resulting in the loss of many ecologically important microorganisms. In closing, the book underscores the importance of microbial diversity for sustainable ecosystems.

Microbial transmission, the processes by which microbes transit to new environments, is a significant and broad-reaching concept with applications throughout the biological sciences. This collection of reviews, edited by an international team of experts studying and working across a range of disciplines, explores transmission not just as an idea in disease but as a fundamental biological process that acts in all domains of nature and exerts its force on disparate size scales, from the micro to the macro, and across units of time as divergent as a single bacterial replication cycle and the entire course of evolution. In five sections, this overview Defines the concept of transmission and covers basic processes of transmission, including causality, control strategies, fitness costs, virulence, and selection Presents numerous combinations of transmission scenarios across the bacterial, animal, and human interface Examines transmission as the defining characteristic of infectious disease Presents methods for experimentally verifying and quantifying transmission episodes Concludes with important theoretical and modeling approaches Anyone studying or working in microbial colonization, evolution, pathogenicity, antimicrobial resistance, or public health will benefit from a deeper understanding of Microbial Transmission.

Omic technologies, including genomics, proteomics and metabolomics, are used to study pathogen behavior at the molecular level and develop improved pathogen detection and typing systems. Omic technologies analyze complete or nearly complete expressions of cell functions. DNA sequencing has resulted in complete genomes of foodborne pathogens. Omic-based technologies explore biological processes in a quantitative and integrative manner. They facilitate identification of genes and proteins that contribute to survival and persistence in food and other environments, that play a role in pathogenesis and that are targets for detection methods and control strategies. Challenges that remain are performing genomic and proteomic studies in food and other complex matrices and interpreting and analyzing the data produced from these investigations to enhance food safety.