HomePublications

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

Research output: Contribution to journalReview article

Standard

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. / Angers-Loustau, Alexandre; Petrillo, Mauro; Bengtsson-Palme, Johan; Berendonk, Thomas; Blais, Burton; Chan, Kok-Gan; Coque, Teresa M; Hammer, Paul; Heß, Stefanie; Kagkli, Dafni M; Krumbiegel, Carsten; Lanza, Val F; Madec, Jean-Yves; Naas, Thierry; O'Grady, Justin; Paracchini, Valentina; Rossen, John W A; Ruppé, Etienne; Vamathevan, Jessica; Venturi, Vittorio; Van den Eede, Guy.

In: F1000Research, Vol. 7, 2018.

Research output: Contribution to journalReview article

Harvard

Angers-Loustau, A, Petrillo, M, Bengtsson-Palme, J, Berendonk, T, Blais, B, Chan, K-G, Coque, TM, Hammer, P, Heß, S, Kagkli, DM, Krumbiegel, C, Lanza, VF, Madec, J-Y, Naas, T, O'Grady, J, Paracchini, V, Rossen, JWA, Ruppé, E, Vamathevan, J, Venturi, V & Van den Eede, G 2018, 'The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies', F1000Research, vol. 7. https://doi.org/10.12688/f1000research.14509.2

APA

Angers-Loustau, A., Petrillo, M., Bengtsson-Palme, J., Berendonk, T., Blais, B., Chan, K-G., Coque, T. M., Hammer, P., Heß, S., Kagkli, D. M., Krumbiegel, C., Lanza, V. F., Madec, J-Y., Naas, T., O'Grady, J., Paracchini, V., Rossen, J. W. A., Ruppé, E., Vamathevan, J., ... Van den Eede, G. (2018). The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7. https://doi.org/10.12688/f1000research.14509.2

Vancouver

Author

Angers-Loustau, Alexandre ; Petrillo, Mauro ; Bengtsson-Palme, Johan ; Berendonk, Thomas ; Blais, Burton ; Chan, Kok-Gan ; Coque, Teresa M ; Hammer, Paul ; Heß, Stefanie ; Kagkli, Dafni M ; Krumbiegel, Carsten ; Lanza, Val F ; Madec, Jean-Yves ; Naas, Thierry ; O'Grady, Justin ; Paracchini, Valentina ; Rossen, John W A ; Ruppé, Etienne ; Vamathevan, Jessica ; Venturi, Vittorio ; Van den Eede, Guy. / The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. In: F1000Research. 2018 ; Vol. 7.

Bibtex- Download

@article{3a81da0affa84a3da07afaf1f2ebda65,
title = "The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies",
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.",
keywords = "Anti-Bacterial Agents/pharmacology, Benchmarking, Computational Biology/methods, Drug Resistance, Bacterial/genetics, High-Throughput Nucleotide Sequencing",
author = "Alexandre Angers-Loustau and Mauro Petrillo and Johan Bengtsson-Palme and Thomas Berendonk and Burton Blais and Kok-Gan Chan and Coque, {Teresa M} and Paul Hammer and Stefanie He{\ss} and Kagkli, {Dafni M} and Carsten Krumbiegel and Lanza, {Val F} and Jean-Yves Madec and Thierry Naas and Justin O'Grady and Valentina Paracchini and Rossen, {John W A} and Etienne Rupp{\'e} and Jessica Vamathevan and Vittorio Venturi and {Van den Eede}, Guy",
year = "2018",
doi = "10.12688/f1000research.14509.2",
language = "English",
volume = "7",
journal = "F1000Research",
issn = "2046-1402",
publisher = "F1000 Research Ltd.",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

AU - Angers-Loustau, Alexandre

AU - Petrillo, Mauro

AU - Bengtsson-Palme, Johan

AU - Berendonk, Thomas

AU - Blais, Burton

AU - Chan, Kok-Gan

AU - Coque, Teresa M

AU - Hammer, Paul

AU - Heß, Stefanie

AU - Kagkli, Dafni M

AU - Krumbiegel, Carsten

AU - Lanza, Val F

AU - Madec, Jean-Yves

AU - Naas, Thierry

AU - O'Grady, Justin

AU - Paracchini, Valentina

AU - Rossen, John W A

AU - Ruppé, Etienne

AU - Vamathevan, Jessica

AU - Venturi, Vittorio

AU - Van den Eede, Guy

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - Anti-Bacterial Agents/pharmacology

KW - Benchmarking

KW - Computational Biology/methods

KW - Drug Resistance, Bacterial/genetics

KW - High-Throughput Nucleotide Sequencing

U2 - 10.12688/f1000research.14509.2

DO - 10.12688/f1000research.14509.2

M3 - Review article

C2 - 30026930

VL - 7

JO - F1000Research

JF - F1000Research

SN - 2046-1402

ER -

ID: 181765639