Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
- Author
- Bram Bloemen (UGent) , Mathieu Gand, Kevin Vanneste (UGent) , Kathleen Marchal (UGent) , Nancy H. C. Roosens and Sigrid C. J. De Keersmaecker
- Organization
- Abstract
- Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.
- Keywords
- HALOTOLERANS GEN. NOV.
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HKQ029D8DXEHCMT3HKBSSYYH
- MLA
- Bloemen, Bram, et al. “Development of a Portable On-Site Applicable Metagenomic Data Generation Workflow for Enhanced Pathogen and Antimicrobial Resistance Surveillance.” SCIENTIFIC REPORTS, vol. 13, no. 1, 2023, doi:10.1038/s41598-023-46771-z.
- APA
- Bloemen, B., Gand, M., Vanneste, K., Marchal, K., Roosens, N. H. C., & De Keersmaecker, S. C. J. (2023). Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance. SCIENTIFIC REPORTS, 13(1). https://doi.org/10.1038/s41598-023-46771-z
- Chicago author-date
- Bloemen, Bram, Mathieu Gand, Kevin Vanneste, Kathleen Marchal, Nancy H. C. Roosens, and Sigrid C. J. De Keersmaecker. 2023. “Development of a Portable On-Site Applicable Metagenomic Data Generation Workflow for Enhanced Pathogen and Antimicrobial Resistance Surveillance.” SCIENTIFIC REPORTS 13 (1). https://doi.org/10.1038/s41598-023-46771-z.
- Chicago author-date (all authors)
- Bloemen, Bram, Mathieu Gand, Kevin Vanneste, Kathleen Marchal, Nancy H. C. Roosens, and Sigrid C. J. De Keersmaecker. 2023. “Development of a Portable On-Site Applicable Metagenomic Data Generation Workflow for Enhanced Pathogen and Antimicrobial Resistance Surveillance.” SCIENTIFIC REPORTS 13 (1). doi:10.1038/s41598-023-46771-z.
- Vancouver
- 1.Bloemen B, Gand M, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance. SCIENTIFIC REPORTS. 2023;13(1).
- IEEE
- [1]B. Bloemen, M. Gand, K. Vanneste, K. Marchal, N. H. C. Roosens, and S. C. J. De Keersmaecker, “Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance,” SCIENTIFIC REPORTS, vol. 13, no. 1, 2023.
@article{01HKQ029D8DXEHCMT3HKBSSYYH,
abstract = {{Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.}},
articleno = {{19656}},
author = {{Bloemen, Bram and Gand, Mathieu and Vanneste, Kevin and Marchal, Kathleen and Roosens, Nancy H. C. and De Keersmaecker, Sigrid C. J.}},
issn = {{2045-2322}},
journal = {{SCIENTIFIC REPORTS}},
keywords = {{HALOTOLERANS GEN. NOV.}},
language = {{eng}},
number = {{1}},
pages = {{14}},
title = {{Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance}},
url = {{http://doi.org/10.1038/s41598-023-46771-z}},
volume = {{13}},
year = {{2023}},
}
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