biostudies-literatureChakrawarti ANational Institute of Food and Agriculture000766.v3https://www.ebi.ac.uk/biostudies/studies/S-EPMC11077346biostudies-literatureUnknown6(3)Antimicrobial resistance (AMR) in <i>Staphylococcus aureus</i> is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of <i>S. aureus</i>, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline. Our analyses showcased the hybrid-assembled genome's superior completeness compared to Oxford Nanopore (R9.4.1)Access microbiologyHybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies.PMC11077346VT-AH02703VT-2023-AH01VT-H02413MSChakrawarti AEckstrom KBarlow JWLaaguiby PfalseHybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies.Antimicrobial resistance (AMR) in <i>Staphylococcus aureus</i> is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of <i>S. aureus</i>, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline. Our analyses showcased the hybrid-assembled genome's superior completeness compared to Oxford Nanopore (R9.4.1)2024-01-01T00:00:00Z20242026-05-27T12:18:46.886Z2026-05-27T03:08:14.806ZS-EPMC110773463872558910.1099/acmi.0.000766.v3