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...
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F1000 Research Ltd
2018
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| _version_ | 1796961636886511616 |
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| 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 |
| author_facet | 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 |
| author_sort | Angers-Loustau, Alexandre |
| collection | UM |
| description | 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. |
| first_indexed | 2024-03-06T05:57:04Z |
| format | Article |
| id | um.eprints-22472 |
| institution | Universiti Malaya |
| last_indexed | 2024-03-06T05:57:04Z |
| publishDate | 2018 |
| publisher | F1000 Research Ltd |
| record_format | dspace |
| spelling | um.eprints-224722019-09-20T04:00:49Z http://eprints.um.edu.my/22472/ 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 Q Science (General) QH Natural history 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. F1000 Research Ltd 2018 Article PeerReviewed Angers-Loustau, Alexandre and Petrillo, Mauro and Bengtsson-Palme, Johan and Berendonk, Thomas and Blais, Burton and Chan, Kok Gan and Coque, Teresa M. and Hammer, Paul and Heß, Stefanie and Kagkli, Dafni M. and Krumbiegel, Carsten and Lanza, Val F. and Madec, Jean-Yves and Naas, Thierry and O'Grady, Justin and Paracchini, Valentina and Rossen, John W.A. and Ruppé, Etienne and Vamathevan, Jessica and Venturi, Vittorio and Van den Eede, Guy (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. p. 459. ISSN 2046-1402, DOI https://doi.org/10.12688/f1000research.14509.2 <https://doi.org/10.12688/f1000research.14509.2>. https://doi.org/10.12688/f1000research.14509.2 doi:10.12688/f1000research.14509.2 |
| spellingShingle | Q Science (General) QH Natural history 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 |
| title | The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies |
| title_full | The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies |
| title_fullStr | The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies |
| title_full_unstemmed | The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies |
| title_short | The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies |
| title_sort | challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies |
| topic | Q Science (General) QH Natural history |
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