ArticleFrontiers in microbiology2025
Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings.
Article in Frontiers in microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Comparative performance of portable DNA extraction protocols and bioinformatics workflows for rapid detection of gram-negative bacteria and antimicrobial resistance using Oxford Nanopore sequencing.Microbiology spectrum · 2026Article
- Nanopore sequencing in suitcase lab enables improved detection ofFrontiers in microbiology · 2026Article
- Precision antimicrobials: the next paradigm shift after broad-spectrum therapy.Frontiers in microbiology · 2026Article
- Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.Frontiers in public health · 2026Article
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Authors and funding
10 authors.
Funding
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Abstract
Introduction: 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. Methods: 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, hand-on time, and equipment requirements were also assessed. Results: 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. Discussion: These findings support the integration of optimized DNA extraction workflows into public health surveillance systems. The DNeasy Blood & Tissue kit offers a reliable and scalable solution for real-time genomic monitoring of antimicrobial resistance in resource-limited settings.
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