ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Antimicrobials, Resistance and Chemotherapy
This article is part of the Research TopicLeveraging Real-Time Genomic Surveillance to Combat Infectious Diseases and Antimicrobial ResistanceView all 14 articles
Evaluation of four DNA extraction kits for implementation of Nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings
Provisionally accepted
Natasia Rebekka Thornval1*
Niamh Lacy Roberts1
Pernille Nilsson1
Carmen Espinosa Gongora1Henrik Hasman2
Joana Mourão1
Astrid Rasmussen2
Ana Rita Rebelo1Christa Gibson1
Rene S. Hendriksen1- 1Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
- 2Statens Serum Institut Bakterier Parasitter & Svampe, Copenhagen, Denmark
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Whole genome sequencing (WGS) is a valuable tool in surveillance of antimicrobial resistance (AMR). However, the technology faces several implementation challenges in low-resource settings. While advances in Oxford Nanopore Technologies (ONT) field sequencing have enabled sequencing in low-resource settings, DNA extraction remains a critical barrier to implementation. In this study, we evaluated four commercially available DNA extraction kits: QIAGEN DNeasy Blood & Tissue, NEB Monarch® HMW, Thermo Fisher MagMAX™ Microbiome, and Thermo Fisher MagMax™ Viral/Pathogen, for their suitability in ONT-based AMR surveillance across Gram-positive and Gram-negative bacterial strains. Kits were evaluated for DNA purity, yield, and fragment length, as well as sequencing metrics including mean read quality, read N50, sequencing depth, multilocus sequence typing concordance, and AMR gene detection. Practical parameters such as cost, hands-on time, and equipment requirements were also assessed. The DNeasy Blood & Tissue kit consistently produced DNA of sufficient quality and quantity to enable high-sequencing depth ONT sequencing, enabling robust multi-locus sequence typing and AMR gene recovery, while remaining cost-effective and requiring minimal technical expertise. These findings support the integration of optimized DNA extraction workflows into public health surveillance systems to enhance real-time genomic monitoring of AMR in resource-limited settings.
Keywords: antimicrobial resistance, WGS, nanopore sequencing, Capacity Building, surveillance, pathogens, Glass, Low-resource settings
Received: 29 Sep 2025; Accepted: 27 Oct 2025.
Copyright: © 2025 Thornval, Roberts, Nilsson, Gongora, Hasman, Mourão, Rasmussen, Rebelo, Gibson and Hendriksen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Natasia Rebekka Thornval, nareth@food.dtu.dk
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.