ReviewF1000Research2018
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies.
Review in F1000Research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Wastewater Metagenomics for Antimicrobial Resistance and Pathogen Surveillance: A Bibliometric Analysis.Microorganisms · 2026Review
- A Novel Bioinformatics Pipeline and a Machine-Learning Approach for Antimicrobial Resistance Phenotypic Prediction.Bioinformatics and biology insights · 2026Article
- Genomics for antimicrobial resistance-progress and future directions.Antimicrobial agents and chemotherapy · 2025Review
- The role of artificial intelligence and machine learning in predicting and combating antimicrobial resistance.Computational and structural biotechnology journal · 2025Review
- Advancing One Health implementation and technological innovation in China: a technology assessment approach.Science in One Health · 2025Review
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria.Frontiers in molecular biosciences · 2024Article
- Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria.Diagnostics (Basel, Switzerland) · 2023Review
- Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae.Scientific reports · 2023Article
- Article
- Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes.Microorganisms · 2023Article
- An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance.Nature communications · 2023Article
- LMAS: evaluating metagenomic short de novo assembly methods through defined communities.GigaScience · 2022Article
- Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance.Scientific reports · 2022Article
- Timing RNA polymerase pausing with TV-PRO-seq.Cell reports methods · 2021Article
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.Nature methods · 2021Review
- Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in CommensalMicroorganisms · 2021Article
- A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing.F1000Research · 2021Article
- Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS.Infection and drug resistance · 2021Article
- Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales.Frontiers in medicine · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.