Journal: Frontiers in Microbiology

Article Title: Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings

doi: 10.3389/fmicb.2025.1715467

Figure Lengend Snippet: Workflow for evaluation of four commercial DNA extraction kits for Nanopore WGS on Gram-positive and Gram-negative bacteria. (1) Pure cultures of four bacterial strains: Escherichia coli , Campylobacter coli , Enterococcus faecalis , and Staphylococcus hominis . (2) gDNA from all four strains was extracted in triplicates to a total of 12 reactions with DNeasy Blood & Tissue spin-columns (DBT), MagMAX™ Microbiome Ultra Nucleic Acid Isolation kit (MMM), MagMAX™ Viral/Pathogen Ultra Nucleic Acid Isolation kit (MMV), and Monarch® HMW DNA Extraction kit for Tissue (MCB) according to manufacturer’s protocol. (3) DNA extraction kits were scored according to ease of use, time per sample, cost, DNA concentration, and DNA purity. (4) During library preparation, triplicate extractions per strain were pooled, combining DBT with MMV and MCB with MMM. Libraries were prepared in duplicate using Rapid Barcoding Kit V14 and sequenced on R10.4.1 Flow Cells (Oxford Nanopore Technologies). Created in https://BioRender.com .

Article Snippet: Genomic DNA (gDNA) was extracted in triplicate for each bacterial strain using four different commercially available DNA extraction kits: DNeasy Blood &Tissue spin-columns (DBT) (Qiagen, Germany), MagMAXTM Microbiome Ultra Nucleic Acid Isolation kit (MMM) (Thermo Fisher Scientific, USA), MagMAXTM Viral/Pathogen Ultra Nucleic Acid Isolation kit (MMV) (Thermo Fisher Scientific, USA), and Monarch® HMW DNA Extraction kit for Cells & Blood (MCB) (New England Biolabs, USA).

Techniques: DNA Extraction, Bacteria, Isolation, Concentration Assay

Journal: Frontiers in Microbiology

Article Title: Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings

doi: 10.3389/fmicb.2025.1715467

Figure Lengend Snippet: Effect of DNA extraction methods. (a) DNA concentration (ng/μl), DNA purity measured by (b) A 260/280 ratio and (c) A 260/230 ratio of the four bacterial species. The bar charts show mean across replications ± SD of three replications. Dotted line indicates (a) the DNA concentration required to provide 200 ng gDNA for the current Nanopore library preparation protocol for the Rapid Barcoding kit (RBK_9176_v114_revR_04Jun2025) and (b,c) the recommended purity measurements from Nanopore. DNeasy Blood & Tissue spin-columns (DBT, dark blue), Monarch® HMW DNA Extraction kit for Tissue (MCB, yellow) MagMAX™ Microbiome Ultra Nucleic Acid Isolation kit (MMM, light blue), and MagMAX™ Viral/Pathogen Ultra Nucleic Acid Isolation kit (MMV, purple).

Article Snippet: Genomic DNA (gDNA) was extracted in triplicate for each bacterial strain using four different commercially available DNA extraction kits: DNeasy Blood &Tissue spin-columns (DBT) (Qiagen, Germany), MagMAXTM Microbiome Ultra Nucleic Acid Isolation kit (MMM) (Thermo Fisher Scientific, USA), MagMAXTM Viral/Pathogen Ultra Nucleic Acid Isolation kit (MMV) (Thermo Fisher Scientific, USA), and Monarch® HMW DNA Extraction kit for Cells & Blood (MCB) (New England Biolabs, USA).

Techniques: DNA Extraction, Concentration Assay, Isolation

Journal: Frontiers in Microbiology

Article Title: Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings

doi: 10.3389/fmicb.2025.1715467

Figure Lengend Snippet: Effect of DNA extraction methods. (a) Mean quad quality (Q-score), (b) number of base pairs (bp), (c) estimated N50 (kb), (d) mean sequencing depth, and (e) number of fragments in assembly of four bacterial species sequenced on the Nanopore sequencing platform. The bar charts show mean across replications ± SD of three independent replication that was sequenced in duplicates ( n = 6). (a) Dotted line indicates the min. Read quality filtered for and (d) indicates minimum mean sequencing depth defined as adequate, and in this study. (e) Dotted line indicates the number of fragments (chromosome and plasmids) for each isolate according to closed reference genome. DNeasy Blood & Tissue spin-columns (DBT, dark blue), Monarch® HMW DNA Extraction kit for Tissue (MCB, yellow) MagMAX™ Microbiome Ultra Nucleic Acid Isolation kit (MMM, light blue), and MagMAX™ Viral/Pathogen Ultra Nucleic Acid Isolation kit (MMV, purple).

Article Snippet: Genomic DNA (gDNA) was extracted in triplicate for each bacterial strain using four different commercially available DNA extraction kits: DNeasy Blood &Tissue spin-columns (DBT) (Qiagen, Germany), MagMAXTM Microbiome Ultra Nucleic Acid Isolation kit (MMM) (Thermo Fisher Scientific, USA), MagMAXTM Viral/Pathogen Ultra Nucleic Acid Isolation kit (MMV) (Thermo Fisher Scientific, USA), and Monarch® HMW DNA Extraction kit for Cells & Blood (MCB) (New England Biolabs, USA).

Techniques: DNA Extraction, Sequencing, Nanopore Sequencing, Isolation