Download or read book Studying Risk Factors for Antibiotic Resistance from Population scale Microbiome Data and Machine Learning written by Scott Eckert and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Host-microbiome interactions, as observed through host genotype and various microbiome metrics serve an important function in human disease and general health. Prior research has identified connections between the LCT locus and Bifidobacterium, but lacks statistical power to discover interactions with smaller effect sizes. We proposed and tested the ability to generate additional host genotypes with the goal of increasing the number of samples and cohorts to assess host-microbiome interactions and allow for meta-analysis. The additional power could provide the opportunity to identify novel host genome-microbiome association. Antibiotic resistance is a major growing international concern for the healthcare field. Numbers of cases are rising, while the development of novel treatments is slow. Therefore, it is important to understand both the mechanisms underlying antibiotic resistance as well as recording observable patterns in infection. This will allow a more optimized use of the resources currently available to treat bacterial infection. We sought to study patterns in antibiotic resistance using next-generation sequencing, bioinformatics, and machine learning. Machine learning (ML) models were trained in antibiogram data, where bacterial isolates with well-described antibiotic resistance phenotypes had been sequenced. The random forest models trained on antibiogram data were able to successfully predict (median F1 = 0.905) antibiotic resistance based off of called antimicrobial resistance-associated variants in a validation dataset. These models were broadly applicable enough to be applied to 9 publicly available microbiome-related studies, totaling 6,367 samples. Using these data, we were able to identify novel trends in multi-drug resistance and heteroresistance as well as recover known relationships between antibiotics. We also used genomic tools and novel analyses to identify a SFTPA2 variant that could be the cause of idiopathic pulmonary fibrosis in a multigenerational Pennsylvania family. All projects shared some bioinformatics tools and approaches, showing the strength of these methods.
Download or read book Mechanisms of antibiotic resistance written by Jun Lin and published by Frontiers Media SA. This book was released on 2015-06-01 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antibiotics represent one of the most successful forms of therapy in medicine. But the efficiency of antibiotics is compromised by the growing number of antibiotic-resistant pathogens. Antibiotic resistance, which is implicated in elevated morbidity and mortality rates as well as in the increased treatment costs, is considered to be one of the major global public health threats (www.who.int/drugresistance/en/) and the magnitude of the problem recently prompted a number of international and national bodies to take actions to protect the public (http://ec.europa.eu/dgs/health_consumer/docs/road-map-amr_en.pdf: http://www.who.int/drugresistance/amr_global_action_plan/en/; http://www.whitehouse.gov/sites/default/files/docs/carb_national_strategy.pdf). Understanding the mechanisms by which bacteria successfully defend themselves against the antibiotic assault represent the main theme of this eBook published as a Research Topic in Frontiers in Microbiology, section of Antimicrobials, Resistance, and Chemotherapy. The articles in the eBook update the reader on various aspects and mechanisms of antibiotic resistance. A better understanding of these mechanisms should facilitate the development of means to potentiate the efficacy and increase the lifespan of antibiotics while minimizing the emergence of antibiotic resistance among pathogens.
Download or read book Treating Infectious Diseases in a Microbial World written by National Research Council and published by National Academies Press. This book was released on 2006-01-03 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: Humans coexist with millions of harmless microorganisms, but emerging diseases, resistance to antibiotics, and the threat of bioterrorism are forcing scientists to look for new ways to confront the microbes that do pose a danger. This report identifies innovative approaches to the development of antimicrobial drugs and vaccines based on a greater understanding of how the human immune system interacts with both good and bad microbes. The report concludes that the development of a single superdrug to fight all infectious agents is unrealistic.
Download or read book Disease Control Priorities Third Edition Volume 6 written by King K. Holmes and published by World Bank Publications. This book was released on 2017-11-06 with total page 1027 pages. Available in PDF, EPUB and Kindle. Book excerpt: Infectious diseases are the leading cause of death globally, particularly among children and young adults. The spread of new pathogens and the threat of antimicrobial resistance pose particular challenges in combating these diseases. Major Infectious Diseases identifies feasible, cost-effective packages of interventions and strategies across delivery platforms to prevent and treat HIV/AIDS, other sexually transmitted infections, tuberculosis, malaria, adult febrile illness, viral hepatitis, and neglected tropical diseases. The volume emphasizes the need to effectively address emerging antimicrobial resistance, strengthen health systems, and increase access to care. The attainable goals are to reduce incidence, develop innovative approaches, and optimize existing tools in resource-constrained settings.
Download or read book Environmental Chemicals the Human Microbiome and Health Risk written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2018-03-01 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: A great number of diverse microorganisms inhabit the human body and are collectively referred to as the human microbiome. Until recently, the role of the human microbiome in maintaining human health was not fully appreciated. Today, however, research is beginning to elucidate associations between perturbations in the human microbiome and human disease and the factors that might be responsible for the perturbations. Studies have indicated that the human microbiome could be affected by environmental chemicals or could modulate exposure to environmental chemicals. Environmental Chemicals, the Human Microbiome, and Health Risk presents a research strategy to improve our understanding of the interactions between environmental chemicals and the human microbiome and the implications of those interactions for human health risk. This report identifies barriers to such research and opportunities for collaboration, highlights key aspects of the human microbiome and its relation to health, describes potential interactions between environmental chemicals and the human microbiome, reviews the risk-assessment framework and reasons for incorporating chemicalâ€"microbiome interactions.
Download or read book Human Microbiome written by Mohsin Khurshid and published by Springer Nature. This book was released on with total page 721 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book When Antibiotics Fail written by The Expert Panel on the Potential Socio-Economic Impacts of Antimicrobial Resistance in Canada and published by Council of Canadian Academies. This book was released on 2019-11-12 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: When Antibiotics Fail examines the current impacts of AMR on our healthcare system, projects the future impact on Canada’s GDP, and looks at how widespread resistance will influence the day-to-day lives of Canadians. The report examines these issues through a One Health lens, recognizing the interconnected nature of AMR, from healthcare settings to the environment to the agriculture sector. It is the most comprehensive report to date on the economic impact of AMR in Canada.
Download or read book The Social Biology of Microbial Communities written by Institute of Medicine and published by National Academies Press. This book was released on 2013-01-10 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.
Download or read book Microbiome and Machine Learning written by Isabel Moreno Indias and published by Frontiers Media SA. This book was released on 2022-08-02 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Antibiotic Resistome written by Gerry Wright and published by Wiley. This book was released on 2016-08-22 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Antimicrobial Resistance in the Environment written by Patricia L. Keen and published by John Wiley & Sons. This book was released on 2012-01-24 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: Examines effects of the environmental distribution of antimicrobial resistance genes on human health and the ecosystem Resistance genes are everywhere in nature—in pathogens, commensals, and environmental microorganisms. This contributed work shows how the environment plays a pivotal role in the development of antimicrobial resistance traits in bacteria and the distribution of resistant microbial species, resistant genetic material, and antibiotic compounds. Readers will discover the impact of the distribution in the environment of antimicrobial resistance genes and antibiotics on both the ecosystem and human and animal health. Antimicrobial Resistance in the Environment is divided into four parts: Part I, Sources, including ecological and clinical consequences of antibiotic resistance by environmental microbes Part II, Fate, including strategies to assess and minimize the biological risk of antibiotic resistance in the environment Part III, Antimicrobial Substances and Resistance, including antibiotics in the aquatic environment Part IV, Effects and Risks, including the effect of antimicrobials used for non-human purposes on human health Recognizing the intricate links among overlapping complex systems, this book examines antimicrobial resistance using a comprehensive ecosystem approach. Moreover, the book's multidisciplinary framework applies principles of microbiology, environmental toxicology, and chemistry to assess the human and ecological risks associated with exposure to antibiotics or antibiotic resistance genes that are environmental contaminants. Each chapter has been written by one or more leading researchers in such fields as microbiology, environmental science, ecology, and toxicology. Comprehensive reference lists at the end of all chapters serve as a gateway to the primary research in the field. Presenting and analyzing the latest findings in a field of growing importance to human and environmental health, this text offers readers new insights into the role of the environment in antimicrobial resistance development, the dissemination of antimicrobial resistant genetic elements, and the transport of antibiotic resistance genes and antibiotics.
Download or read book Peptide and Protein Engineering written by Olga Iranzo and published by Humana. This book was released on 2021-07-23 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough book aims to present the methods that have enabled the success of peptides and proteins in a wide variety of applications. It opens with a section on chemical tools applied to the production or engineering of peptides and proteins, and concludes with a collection of chapters on biological approaches used to engineer structure and function in peptides and proteins. As a book in the Springer Protocols Handbooks series, chapters include the kind of detailed descriptions and tips necessary for successful results in practice. Authoritative and practical, Peptide and Protein Engineering: From Concepts to Biotechnological Applications will be of great use to scientists in academia and industry seeking a better understanding of the emerging principles and methodologies in peptide and protein engineering.
Download or read book Microbiome and Cancer written by Erle S. Robertson and published by Springer. This book was released on 2019-02-20 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book ventures into a new and exciting area of discovery that directly ties our current knowledge of cancer to the discovery of microorganisms associated with different types of cancers. Recent studies demonstrate that microorganisms are directly linked to the establishment of cancers and that they can also contribute to the initiation, as well as persistence of, the cancers. Microbiome and Cancer covers the current knowledge of microbiome and its association with human cancers. It provides important reading for novices, senior undergraduates in cancer and microbiology, graduate students, junior investigators, residents, fellows and established investigators in the fields of cancer and microbiology. We cover areas related to known, broad concepts in microbiology and how they can relate to the ongoing discoveries of the micro-environment and the changes in the metabolic and physiologic states in that micro-environment, which are important for the ongoing nurturing and survival of the poly-microbial content that dictates activities in that micro-environment. We cover the interactions of microorganisms associated with gastric carcinomas, which are important for driving this particular cancer. Additional areas include oral cancers, skin cancers, ovarian cancers, breast cancers, nasopharyngeal cancers, lung cancers, mesotheliomas, Hodgkin’s and non-Hodgkin’s lymphomas, glioblastoma multiforme, hepatocellular carcinomas, as well as the inflammatory response related to the infectious agents in cancers. This book covers the metabolic changes that occur because of infection and their support for development of cancers, chronic infection and development of therapeutic strategies for detection and control of the infection. The field of microbiome research has exploded over the last five years, and we are now understanding more and more about the context in which microorganisms can contribute to the onset of cancers in humans. The field of microbiome research has demonstrated that the human body has specific biomes for tissues and that changes in these biomes at the specific organ sites can result in disease. These changes can result in dramatic differences in metabolic shifts that, together with genetic mutations, will produce the perfect niche for establishment of the particular infection programmes in that organ site. We are just beginning to understand what those changes are and how they influence the disease state. Overall, we hope to bring together the varying degrees of fluctuations in the microbiome at the major organ sites and how these changes affect the normal cellular processes because of dysregulation, leading to proliferation of the associated tissues.
Download or read book Novel Approaches in Microbiome Analyses and Data Visualization written by Jessica Galloway-Peña and published by Frontiers Media SA. This book was released on 2019-02-06 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput sequencing technologies are widely used to study microbial ecology across species and habitats in order to understand the impacts of microbial communities on host health, metabolism, and the environment. Due to the dynamic nature of microbial communities, longitudinal microbiome analyses play an essential role in these types of investigations. Key questions in microbiome studies aim at identifying specific microbial taxa, enterotypes, genes, or metabolites associated with specific outcomes, as well as potential factors that influence microbial communities. However, the characteristics of microbiome data, such as sparsity and skewedness, combined with the nature of data collection, reflected often as uneven sampling or missing data, make commonly employed statistical approaches to handle repeated measures in longitudinal studies inadequate. Therefore, many researchers have begun to investigate methods that could improve incorporating these features when studying clinical, host, metabolic, or environmental associations with longitudinal microbiome data. In addition to the inferential aspect, it is also becoming apparent that visualization of high dimensional data in a way which is both intelligible and comprehensive is another difficult challenge that microbiome researchers face. Visualization is crucial in both the analysis and understanding of metagenomic data. Researchers must create clear graphic representations that give biological insight without being overly complicated. Thus, this Research Topic seeks to both review and provide novels approaches that are being developed to integrate microbiome data and complex metadata into meaningful mathematical, statistical and computational models. We believe this topic is fundamental to understanding the importance of microbial communities and provides a useful reference for other investigators approaching the field.
Download or read book Infections in Surgery written by Massimo Sartelli and published by Springer Nature. This book was released on 2021-01-29 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although most clinicians are aware of the problem of antimicrobial resistance, most also underestimate its significance in their own hospital. The incorrect and inappropriate use of antibiotics and other antimicrobials, as well as poor prevention and poor control of infections, are contributing to the development of such resistance. Appropriate use of antibiotics and compliance with infection prevention and control measures should be integral aspects of good clinical practice and standards of care. However, these activities are often inadequate among clinicians, and there is a considerable gap between the best evidence and actual clinical practice. In hospitals, cultural determinants influence clinical practice, and improving behaviour in terms of infection prevention and antibiotics-prescribing practice remains a challenge. Despite evidence supporting the effectiveness of best practices, many clinicians fail to implement them, and evidence-based processes and practices that are known to optimize both the prevention and the treatment of infections tend to be underused. Addressing precisely this problem, this volume offers an essential toolkit for all surgeons and intensivists interested in improving their clinical practices.
Download or read book Natural Language Processing with Python written by Steven Bird and published by "O'Reilly Media, Inc.". This book was released on 2009-06-12 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a highly accessible introduction to natural language processing, the field that supports a variety of language technologies, from predictive text and email filtering to automatic summarization and translation. With it, you'll learn how to write Python programs that work with large collections of unstructured text. You'll access richly annotated datasets using a comprehensive range of linguistic data structures, and you'll understand the main algorithms for analyzing the content and structure of written communication. Packed with examples and exercises, Natural Language Processing with Python will help you: Extract information from unstructured text, either to guess the topic or identify "named entities" Analyze linguistic structure in text, including parsing and semantic analysis Access popular linguistic databases, including WordNet and treebanks Integrate techniques drawn from fields as diverse as linguistics and artificial intelligence This book will help you gain practical skills in natural language processing using the Python programming language and the Natural Language Toolkit (NLTK) open source library. If you're interested in developing web applications, analyzing multilingual news sources, or documenting endangered languages -- or if you're simply curious to have a programmer's perspective on how human language works -- you'll find Natural Language Processing with Python both fascinating and immensely useful.
Download or read book Analysis of Biological Networks written by Björn H. Junker and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.
