Download or read book The use of next generation sequencing in fighting antimicrobial resistant pathogens written by Ibrahim Bitar and published by Frontiers Media SA. This book was released on 2023-03-07 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Application of Next Generation Sequencing NGS in Infection Prevention written by Michael Kemp and published by Frontiers Media SA. This book was released on 2022-07-04 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Next generation sequencing NGS and annotation of three Staphyloccocus aureus strains written by Theodore Ngwana and published by GRIN Verlag. This book was released on 2018-02-05 with total page 29 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific Essay from the year 2018 in the subject Medicine - Diagnostics, University of Salford (College of Science and Technology), course: Msc Biomedical Science, language: English, abstract: Next Generation Sequencing, one of the applications of genomics, employs bioinformatics tools and other molecular biology techniques such as the Polymerase Chain Reaction (PCR) and electrophoresis to diagnose diseases. Once sequenced, our assembled genome sequenced can be annotated to identify target genes and compared to a reference genome for similarities such as the case of BLAST, which is used to establish evolutionary relationships between species. The sequences can also be compared for variants. In this report Illumina-based next generation sequencing was used to sequence the genomes of three Staphylococcus aureus strains which are the methicillin resistant strain (MRSA), methicillin sensitive strain (MSSA) and an unknown strain of S. aureus (U). This involved an array of techniques, from the extraction of genomic DNA by way of the QIAGEN DNeasy DNA extraction kit, to quality control of our purified DNA by 1% agarose gel electrophoresis, Nanodrop and Qubit. It then moved on to preparation of DNA libraries from our genomic DNA extract, with the QIAGEN® QIAseq FX DNA Library Kit, from where the libraries went through an Illumina MiSeq sequencer. Raw sequence data was then assembled and analysed with genome annotation tools such as Atermis, Artemis Comparison Tool, WGSA and Abricate. Annotation of our S. aureus species revealed antimicrobial resistance genes. Abricate produced 10 antimicrobial genes for MRSA, 5 for MSSA and 6 for U. Meanwhile Artemis annotation gave 16 antimicrobial resistance genes for MRSA, 13 for MSSA and 14 for U. Information on antibiotic susceptibility of the three bacterial species can then be used to determine the best possible treatment for individuals with S. aureus infections, thus proving that next generation sequencing and genome annotation can serve as an alternative for routine disc antimicrobial susceptibility techniques to diagnose and treat infectious diseases.
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 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 Game Changer Next Generation Sequencing and Its Impact on Food Microbiology written by Jennifer Ronholm and published by Frontiers Media SA. This book was released on 2018-04-26 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in next-generation sequencing technologies (NGS) are revolutionizing the field of food microbiology. Microbial whole genome sequencing (WGS) can provide identification, characterization, and subtyping of pathogens for epidemiological investigations at a level of precision previously not possible. This allows for connections and source attribution to be inferred between related isolates that may be overlooked by traditional techniques. The archiving and global sharing of genome sequences allow for retrospective analysis of virulence genes, antimicrobial resistance markers, mobile genetic elements and other novel genes. The advent of high-throughput 16S rRNA amplicon sequencing, in combination with the advantages offered by massively parallel second-generation sequencing for metagenomics, enable intensive studies on the microbiomes of food products and the impact of foods on the human microbiome. These studies may one day lead to the development of reliable culture-independent methods for food monitoring and surveillance. Similarly, RNA-seq has provided insights into the transcriptomes and hence the behaviour of bacterial pathogens in food, food processing environments, and in interaction with the host at a resolution previously not achieved through the use of microarrays and/or RT-PCR. The vast un-tapped potential applications of NGS along with its rapidly declining costs, give this technology the ability to contribute significantly to consumer protection, global trade facilitation, and increased food safety and security. Despite the rapid advances, challenges remain. How will NGS data be incorporated into our existing global food safety infrastructure? How will massive NGS data be stored and shared globally? What bioinformatics solutions will be used to analyse and optimise these large data sets? This Research Topic discusses recent advances in the field of food microbiology made possible through the use of NGS.
Download or read book WHO guidelines on use of medically important antimicrobials in food producing animals written by World Health Organization and published by World Health Organization. This book was released on 2017-11-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: WHO has launched new guidelines on use of medically important antimicrobials in food-producing animals, recommending that farmers and the food industry stop using antibiotics routinely to promote growth and prevent disease in healthy animals. These guidelines aim to help preserve the effectiveness of antibiotics that are important for human medicine by reducing their use in animals.
Download or read book The Evolving Threat of Antimicrobial Resistance written by World Health Organization and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antibiotic resistance development is a natural process of adaption leading to a limited lifespan of antibiotics. Unnecessary and inappropriate use of antibiotics favours the emergence and spread of resistant bacteria. A crisis has been building up over decades, so that today common and life-threatening infections are becoming difficult or even impossible to treat. It is time to take much stronger action worldwide to avert an ever increasing health and economic burden. A new WHO publication "The evolving threat of antimicrobial resistance--Options for action" describes examples of policy activities that have addressed AMR in different parts of the world. The aim is to raise awareness and to stimulate further coordinated efforts.
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 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 Game Changer Next Generation Sequencing and Its Impact on Food Microbiology written by and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in next-generation sequencing technologies (NGS) are revolutionizing the field of food microbiology. Microbial whole genome sequencing (WGS) can provide identification, characterization, and subtyping of pathogens for epidemiological investigations at a level of precision previously not possible. This allows for connections and source attribution to be inferred between related isolates that may be overlooked by traditional techniques. The archiving and global sharing of genome sequences allow for retrospective analysis of virulence genes, antimicrobial resistance markers, mobile genetic elements and other novel genes. The advent of high-throughput 16S rRNA amplicon sequencing, in combination with the advantages offered by massively parallel second-generation sequencing for metagenomics, enable intensive studies on the microbiomes of food products and the impact of foods on the human microbiome. These studies may one day lead to the development of reliable culture-independent methods for food monitoring and surveillance. Similarly, RNA-seq has provided insights into the transcriptomes and hence the behaviour of bacterial pathogens in food, food processing environments, and in interaction with the host at a resolution previously not achieved through the use of microarrays and/or RT-PCR. The vast un-tapped potential applications of NGS along with its rapidly declining costs, give this technology the ability to contribute significantly to consumer protection, global trade facilitation, and increased food safety and security. Despite the rapid advances, challenges remain. How will NGS data be incorporated into our existing global food safety infrastructure? How will massive NGS data be stored and shared globally? What bioinformatics solutions will be used to analyse and optimise these large data sets? This Research Topic discusses recent advances in the field of food microbiology made possible through the use of NGS.
Download or read book The Role of Next Generation Sequencing in Clinical Microbiology Diagnostics written by Victoria A. Janes and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Next Generation Sequencing (NGS) techniques are extensively used in research but application to clinical microbiology is still in its infancy. Because of the complexity of sequencing, some intrinsic to the technology and analysis, and some to the clinical interpretation of microbiology results, translation to clinical practice is challenging. This PhD-thesis examines the role of NGS in clinical microbiology diagnostics. Part one focusses on Whole Genome Sequencing (WGS) and describes how WGS was superior in differentiating outbreak from non-outbreak isolates compared to Amplified Fragment Length Polymorphism during a hospital outbreak with vancomycin resistant enterococci. Part two focusses on metagenomics for semi-quantitative pathogen detection from urine. A pilot study compared urine culture to urine metagenomics and investigated which metagenomic test characteristics were most comparable to culture outcomes. We developed an internal technical process control for clinical metagenomics in the form of DNA from the extremophile Thermus thermophilus. Next, we applied the hypotheses generated in the pilot study to a large prospective laboratory-based cohort of 529 urine samples and compared the metagenomics results to the results of semi-quantitative urine culture. We also explored antimicrobial drug resistance prediction from metagenomics and compared the results to phenotypic antimicrobial susceptibility testing. We also assessed the value of metagenomics in patients with a clinical syndrome in keeping with febrile UTI, in whom the diagnosis was only supported by a positive blood culture but in whom urine culture had remained negative. Finally, a summarising discussion and future directives are provided."--
Download or read book Combating Antimicrobial Resistance written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2018-01-08 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: As of 2017, the emergence and spread of antimicrobial resistance continues unabated around the world, leaving devastating health and economic outcomes in its wake. Those consequences will multiply if collaborative global action is not taken to address the spread of resistance. Major drivers of antimicrobial resistance in humans have been accelerated by inappropriate antimicrobial prescribing in health care practices; the inappropriate use of antimicrobials in livestock; and the promulgation of antibiotic resistance genes in the environment. To explore the issue of antimicrobial resistance, the Forum of Microbial Threats planned a public workshop. Participants explored issues of antimicrobial resistance through the lens of One Health, which is a collaborative approach of multiple disciplines - working locally, nationally, and globally - for strengthening systems to counter infectious diseases and related issues that threaten human, animal, and environmental health, with an end point of improving global health and achieving gains in development. They also discussed immediate and short-term actions and research needs that will have the greatest effect on reducing antimicrobial resistance, while taking into account the complexities of bridging different sectors and disciplines to address this global threat. This publication summarizes the presentations and discussions from the workshop.
Download or read book Global Antimicrobial Resistance Surveillance System written by World Health Organization and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "In May 2015, the Sixty-eighth World Health Assembly adopted the Global action plan on antimicrobial resistance, which reflects the global consensus that AMR poses a profound threat to human health. One of the five strategic objectives of the Global action plan is to strengthen the evidence base through enhanced global surveillance and research. The Global Antimicrobial Resistance Surveillance System (GLASS) has been developed to facilitate and encourage a standardized approach to AMR surveillance globally and in turn support the implementation of the Global action plan on antimicrobial resistance. This manual addresses the early phase of implementation of GLASS, focussing on surveillance of resistance in common human bacterial pathogens. The intended readership of this publication is public health professionals and health authorities responsible for national AMR surveillance. It outlines the GLASS standards and describes the road map for implementation of the system between 2015 and 2019. Further development of GLASS will be based on the lessons learnt during this period"--Publisher's description.
Download or read book Combating Antimicrobial Resistance and Protecting the Miracle of Modern Medicine written by National Academies Of Sciences Engineeri and published by National Academies Press. This book was released on 2022-07-20 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The National Strategy for Combating Antibiotic Resistant Bacteria, published in 2014, sets out a plan for government work to mitigate the emergence and spread of resistant bacteria. Direction on the implementation of this strategy is provided in five-year national action plans, the first covering 2015 to 2020, and the second covering 2020 to 2025. Combating Antimicrobial Resistance and Protecting the Miracle of Modern Medicine evaluates progress made against the national strategy. This report discusses ways to improve detection of resistant infections and estimate the risk to human health from environmental sources of resistance. In addition, the report considers the effect of agricultural practices on human and animal health and animal welfare and ways these practices could be improved, and advises on key drugs and diseases for which animal-specific test breakpoints are needed.
Download or read book Microbiology 2 0 Update for a Sustainable Future written by Juhi Gupta and published by Springer Nature. This book was released on with total page 493 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Antimicrobial Resistance written by Mihai Mares and published by BoD – Books on Demand. This book was released on 2021-03-03 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tackling the realities of the antimicrobial resistance (AMR) situation today is no longer uncommon. Many battles have been fought in the past since the discovery of antibiotics between man and microbes. In the tussle of new antibiotic modifications, the transmission of resistant genes, both vertically and horizontally unveils yet another resistant attribute for the microbe, for it only to be faced with a more powerful, wide spectrum antibiotic; the cycle continues-and the winner is yet to be known. This book aims to provide some insight into various molecular mechanisms, agricultural mitigation methods, and the One Health applications to maybe, just maybe, tip the scales towards us.
