The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms. In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed. NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced. Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process. This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017. Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a “One Health” approach.

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Beginner’s guide to next-generation sequencing

The Biochemist ◽

10.1042/bio_2021_135 ◽

2021 ◽

Author(s):

Louise Aigrain

Keyword(s):

Next Generation Sequencing ◽

Sample Preparation ◽

Third Generation ◽

Next Generation ◽

Sequencing Technologies ◽

Long Read ◽

Pros And Cons ◽

The Cost ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Since the publication of the first draft of the human genome 20 years ago, several novel sequencing technologies have emerged. Whilst some drive the cost of DNA sequencing down, others address the difficult parts of the genome which remained inaccessible so far. But the next-generation sequencing (NGS) landscape is a fast-changing environment and one can easily get lost between second- and third- generation sequencers, or the pros and cons of short- versus long-read technologies. In this beginner’s guide to NGS, we will review the main NGS technologies available in 2021. We will compare sample preparation protocols and sequencing methods, highlighting the requirements and advantages of each technology.

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NEXT GENERATION SEQUENCING TECHNOLOGIES TOWARDS EXPLORATION OF MEDICINAL PLANTS

Journal of Experimental Biology and Agricultural Sciences ◽

10.18006/2021.9(4).507.516 ◽

2021 ◽

Vol 9 (4) ◽

pp. 507-516

Author(s):

Sunanya Das ◽

◽

Rukmini Mishra ◽

Keyword(s):

Next Generation Sequencing ◽

Medicinal Plants ◽

Large Scale ◽

Plant Cover ◽

Next Generation ◽

Sequencing Technologies ◽

Medicinal Value ◽

Modern Biotechnology ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

With the ever-increasing population, the plant cover is decreasing at an alarming rate. The medicinal plants are most affected by this because they are present in the last tier of cultivation. Let it be pharmaceutical companies or people using it for herbalism, medicinal plants have been exploited without getting a chance to flourish in their natural environment. Modern biotechnology acts as a bridge between the cultivation and utilization of medicinal plants. Next Generation Sequencing (NGS) technology which is a decade old but emerging field helps to unveil the importance of medicinal plants. Thus, it paves the way for sustenance of medicinal plants by molecular breeding, micropropagation, large-scale tissue culture, and other methods to conserve the plants with great medicinal value. Various NGS technologies can be found in the market like Ilumina, PacBio, Ion Torrent, and others. The present review will summarize the NGS technologies and their potential use to study the genomes, transcriptome, epigenome, and interactome of medicinal plants towards the identification of bioactive compounds.

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Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

Bioinformatics and Biology Insights ◽

10.4137/bbi.s12462 ◽

2015 ◽

Vol 9 ◽

pp. BBI.S12462 ◽

Cited By ~ 180

Author(s):

Anastasis Oulas ◽

Christina Pavloudi ◽

Paraskevi Polymenakou ◽

Georgios A. Pavlopoulos ◽

Nikolas Papanikolaou ◽

...

Keyword(s):

Next Generation Sequencing ◽

Rapid Expansion ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Sequencing Technologies ◽

Multiple Datasets ◽

Dataset Analysis ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of “metagenomics”, often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.

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Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics

Microorganisms ◽

10.3390/microorganisms8020305 ◽

2020 ◽

Vol 8 (2) ◽

pp. 305 ◽

Cited By ~ 6

Author(s):

Molemi E. Rauwane ◽

Udoka V. Ogugua ◽

Chimdi M. Kalu ◽

Lesiba K. Ledwaba ◽

Adugna A. Woldesemayat ◽

...

Keyword(s):

Next Generation Sequencing ◽

Fusarium Graminearum ◽

Virulence Factors ◽

Next Generation ◽

Grain Crops ◽

Sequencing Technologies ◽

Current Review ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Made In

Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the discovery of a multitude of pathogenicity and virulence factors of F. graminearum. This current review aimed to trace progress made in discovering F. graminearum pathogenicity and virulence factors in general, as well as pathogenicity and virulence factors discovered using NGS, and to some extent, using proteomics. We present more than 100 discovered pathogenicity or virulence factors and conclude that although a multitude of pathogenicity and virulence factors have already been discovered, more work needs to be done to take advantage of NGS and its companion applications of proteomics.

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Clinical Integration of Next Generation Sequencing: A Policy Analysis

The Journal of Law Medicine & Ethics ◽

10.1111/jlme.12158 ◽

2014 ◽

Vol 42 (S1) ◽

pp. 5-8 ◽

Cited By ~ 4

Author(s):

David Kaufman ◽

Margaret Curnutte ◽

Amy L. McGuire

Keyword(s):

Next Generation Sequencing ◽

Human Genetics ◽

Rapid Evolution ◽

Fourth Generation ◽

Next Generation ◽

Genetic Sequencing ◽

Sequencing Technologies ◽

The Cost ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

In 1996, President Clinton offered a promissory vision for human genetics when he said: “I think it won't be too many years before parents will be able to go home from the hospital with their newborn babies with a genetic map in their hands that will tell them, here's what your child's future will likely be like.”The rapid evolution of genetic sequencing technologies has advanced that vision. In October 2006, the cost of sequencing an entire human genome was $10.4 million; by 2014 the cost had decreased a thousand fold. The term next generation sequencing (NGS) describes a variety of laboratory methods that allow efficient determination of the precise order of nucleotides in a DNA sequence. The papers in this issue of the Journal of Law, Medicine & Ethics focus on “clinical NGS,” which refers to rapid DNA sequencing using second-, third- and fourth-generation sequencing technologies to perform genome-wide sequencing of multiple genes or alleles for clinical prognostic, diagnostic, and therapeutic purposes.

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Next-generation sequencing technology in relation to our understanding and tackling of Antimicrobial Resistance [Tecnología de secuenciación de próxima generación en relación con nuestra comprensión y lucha contra la resistencia a los antimicrobianos]

Journal of Sciences and Engineering ◽

10.32829/sej.v3i1.99 ◽

2019 ◽

Vol 3 (1) ◽

pp. 1

Author(s):

Roxana Guillen

Keyword(s):

Next Generation Sequencing ◽

Antimicrobial Resistance ◽

Next Generation ◽

Sequencing Technology ◽

Antibiotic Resistant ◽

Next Generation Sequencing Technology ◽

Molecular Assays ◽

Sequencing Technologies ◽

Very High ◽

Generation Sequencing

Sequencing technologies have suffered over the last few years improvements in its performance, Next-generation Sequencing is being used more frequently to control infectious diseases, to know and anticipate antimicrobial resistance (AMR) and in surveillance controls against possible infectious outbreaks. Molecular assays used to detect pathogenic or antibiotic resistant agents take a lot of time and effort, and often enough information is not collected to make decisions. Next- generation sequencing appears to elucidate in the least time possible the whole DNA sequence and provide us with enough data to know resistance, virulence and typing that can be analyzed and a great help in research and decision making. NGS is a very promising technology, in order for it to be used extensively, requires the development of data analysis platforms and reduction of trials costs that still is very high for a massive use.

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