Related Experiment Video
Updated: May 16, 2026
Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Comparison of Oxford Nanopore Technologies sequencing protocols using R9.4.1 and R10.4.1 flow cells under 20-hour and
Mário Sérgio Braga do Couto1, Karin Helmersen2,3, Aluisio Valerio Deola4
1Bacterial Molecular Genetics Laboratory (GeMBac), Department of Microbiology, Immunology, and Parasitology, Biological Sciences Center, Universidade Federal de Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, 88040-960, SC, Brazil.
Background:
Rapid and accurate whole-genome sequencing (WGS) is increasingly important for detecting antimicrobial resistance and virulence determinants in clinical microbiology. Although short-read platforms remain widely used, long-read sequencing technologies have gained relevance due to their ability to resolve complex genomic regions.
Methods And Results:
We analyzed 92 draft genomes generated from 23 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates to compare Oxford Nanopore Technologies sequencing protocols using R9.4.1 (Kit V10) and R10.4.1 (Kit V14) flow cells under 20-hour and 48-hour conditions. The 20-hour R10.4.1 protocol (ONT20h R10) showed the best overall performance, with improved detection of antimicrobial resistance genes, virulence factors, plasmids, and mobile genetic elements. This protocol achieved perfect agreement with phenotypic antimicrobial susceptibility testing (accuracy 100%, κ = 1.0), supporting its suitability for rapid genomic analysis. Highly repetitive mobile genetic elements remained challenging to fully resolve, reflecting the technical difficulty of assembling complex repeats.
Conclusion:
Overall, this study supports the use of rapid long-read sequencing as a complementary approach for clinical microbiology and genomic surveillance, particularly when timely genomic information is required.
