{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T23:39:37Z","timestamp":1787787577212,"version":"build-2784847793"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T00:00:00Z","timestamp":1778716800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T00:00:00Z","timestamp":1778716800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100007082","name":"Universidade Federal De Santa Catarina","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007082","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Biol Rep"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods and results<\/jats:title>\n                    <jats:p>\n                      We analyzed 92 draft genomes generated from 23 clinical methicillin-resistant\n                      <jats:italic>Staphylococcus aureus<\/jats:italic>\n                      (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%, \u03ba\u2009=\u20091.0), 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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s11033-026-11956-y","type":"journal-article","created":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T12:58:08Z","timestamp":1778763488000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Comparison of Oxford Nanopore Technologies sequencing protocols using R9.4.1 and R10.4.1 flow cells under 20-hour and 48-hour conditions for genotyping methicillin methicillin-resistant Staphylococcus aureus (MRSA)"],"prefix":"10.1007","volume":"53","author":[{"given":"M\u00e1rio S\u00e9rgio Braga","family":"do Couto","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karin","family":"Helmersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aluisio Valerio","family":"Deola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glauber","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hege Vangstein","family":"Aamot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6444-6007","authenticated-orcid":false,"given":"Fabienne Antunes","family":"Ferreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,14]]},"reference":[{"issue":"10","key":"11956_CR1","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1038\/s41579-024-01054-w","volume":"22","author":"WR Miller","year":"2024","unstructured":"Miller WR, Arias CA (2024) ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 22(10):598\u2013616. https:\/\/doi.org\/10.1038\/s41579-024-01054-w","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"11956_CR2","doi-asserted-by":"publisher","first-page":"e0108224","DOI":"10.1128\/aac.01082-24","volume":"69","author":"NL Sherry","year":"2025","unstructured":"Sherry NL, Lee JYH, Giulieri SG, Connor CH, Horan K, Lacey JA, Lane CR, Carter GP, Seemann T, Egli A, Stinear TP, Howden BP (2025) Genomics for antimicrobial resistance-progress and future directions. Antimicrob Agents Chemother 69(5):e0108224. https:\/\/doi.org\/10.1128\/aac.01082-24","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"11956_CR3","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1186\/s13073-024-01412-6","volume":"16","author":"F Landman","year":"2024","unstructured":"Landman F, Jamin C, de Haan A, Witteveen S, Bos J, van der Heide HGJ, Schouls LM, Hendrickx APA, Dutch, CPE\/MRSA surveillance study group (2024) Genomic surveillance of multidrug-resistant organisms based on long-read sequencing. Genome Med 16(1):137. https:\/\/doi.org\/10.1186\/s13073-024-01412-6","journal-title":"Genome Med"},{"issue":"7","key":"11956_CR4","doi-asserted-by":"publisher","first-page":"e0036925","DOI":"10.1128\/jcm.00369-25","volume":"63","author":"K Prior","year":"2025","unstructured":"Prior K, Becker K, Brandt C, Cabal Rosel A, Dabernig-Heinz J, Kohler C, Lohde M, Ruppitsch W, Schuler F, Wagner GE, Mellmann A (2025) Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data. J Clin Microbiol 63(7):e0036925. https:\/\/doi.org\/10.1128\/jcm.00369-25","journal-title":"J Clin Microbiol"},{"issue":"5","key":"11956_CR5","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1139\/cjm-2023-0175","volume":"70","author":"N Lerminiaux","year":"2024","unstructured":"Lerminiaux N, Fakharuddin K, Mulvey MR, Mataseje L (2024) Do we still need Illumina sequencing data? Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies. Can J Microbiol 70(5):178\u2013189. https:\/\/doi.org\/10.1139\/cjm-2023-0175","journal-title":"Can J Microbiol"},{"issue":"7","key":"11956_CR6","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/s41592-022-01539-7","volume":"19","author":"M Sereika","year":"2022","unstructured":"Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, S\u00f8rensen EA, Wollenberg RD, Albertsen M (2022) Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat Methods 19(7):823\u2013826. https:\/\/doi.org\/10.1038\/s41592-022-01539-7","journal-title":"Nat Methods"},{"issue":"3","key":"11956_CR7","doi-asserted-by":"publisher","first-page":"001990","DOI":"10.1099\/jmm.0.001990","volume":"74","author":"G Cipriani","year":"2025","unstructured":"Cipriani G, Helmersen K, Mazzon RR, Wagner G, Aamot HV, Ferreira FA (2025) Evaluation of whole-genome sequencing protocols for detection of antimicrobial resistance, virulence factors and mobile genetic elements in antimicrobial-resistant bacteria. J Med Microbiol 74(3):001990. https:\/\/doi.org\/10.1099\/jmm.0.001990","journal-title":"J Med Microbiol"},{"issue":"5","key":"11956_CR8","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA (2019) Assembly of long, error-prone reads using repeat graphs (. Nat Biotec 37(5):540\u2013546. https:\/\/doi.org\/10.1038\/s41587-019-0072-8","journal-title":"Nat Biotec"},{"issue":"13","key":"11956_CR9","doi-asserted-by":"publisher","first-page":"i142","DOI":"10.1093\/bioinformatics\/bty266","volume":"34","author":"A Mikheenko","year":"2018","unstructured":"Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A (2018) Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34(13):i142\u2013i150. https:\/\/doi.org\/10.1093\/bioinformatics\/bty266","journal-title":"Bioinformatics"},{"issue":"12","key":"11956_CR10","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nyk\u00e4senoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491\u20133500. https:\/\/doi.org\/10.1093\/jac\/dkaa345","journal-title":"J Antimicrob Chemother"},{"issue":"10","key":"11956_CR11","doi-asserted-by":"publisher","first-page":"e01269","DOI":"10.1128\/JCM.01269-20","volume":"58","author":"AM Malberg Tetzschner","year":"2020","unstructured":"Malberg Tetzschner AM, Johnson JR, Johnston BD, Lund O, Scheutz F (2020) In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. J Clin Microbiol 58(10):e01269\u2013e01220. https:\/\/doi.org\/10.1128\/JCM.01269-20","journal-title":"J Clin Microbiol"},{"issue":"7","key":"11956_CR12","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli A, Zankari E, Garc\u00eda-Fern\u00e1ndez A, Voldby Larsen M, Lund O, Villa L, M\u00f8ller Aarestrup F, Hasman H (2014) In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58(7):3895\u20133903. https:\/\/doi.org\/10.1128\/AAC.02412-14","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"11956_CR13","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/jac\/dkaa390","volume":"76","author":"MHK Johansson","year":"2021","unstructured":"Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN (2021) Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 76(1):101\u2013109. https:\/\/doi.org\/10.1093\/jac\/dkaa390","journal-title":"J Antimicrob Chemother"},{"key":"11956_CR14","doi-asserted-by":"publisher","first-page":"127666","DOI":"10.1016\/j.micres.2024.127666","volume":"283","author":"L Ye","year":"2024","unstructured":"Ye L, Liu X, Ni Y, Xu Y, Zheng Z, Chen K, Hu Q, Tan L, Guo Z, Wai CK, Chan EWC, Li R, Chen S (2024) Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing. Microbiol Res 283:127666. https:\/\/doi.org\/10.1016\/j.micres.2024.127666","journal-title":"Microbiol Res"},{"issue":"8","key":"11956_CR15","doi-asserted-by":"publisher","first-page":"e0330304","DOI":"10.1371\/journal.pone.0330304","volume":"20","author":"MHK Johansson","year":"2025","unstructured":"Johansson MHK, Petersen TN, Nag S, Lagermann TMR, Birkedahl LEK, Tafaj S, Bradbury S, Collignon P, Daley D, Dougnon V, Fabiyi K, Coulibaly B, Demb\u00e9l\u00e9 R, Magloire N, Ouindgueta IJ, Hossain ZZ, Begoum A, Donchev D, Diggle M, Turnbull L, L\u00e9vesque S, Berlinger L, S\u00f8gaard KK, Guevara PD, Duarte C, Maikanti P, Amlerova J, Drevinek P, Tkadlec J, Dilas M, Kaasch A, Westh HT, Bachtarzi MA, Amhis W, Salazar CES, Villacis JE, L\u00fazon MAD, Palau DB, Duployez C, Paluche M, Asante-Sefa S, M\u00f8ller M, Ip M, Marekovi\u0107 I, P\u00e1l-Sonnevend A, Cocuzza CE, Dambrauskiene A, Macanze A, Cossa A, Mandomando I, Nwajiobi-Princewill P, Okeke IN, Kehinde AO, Adebiyi I, Akintayo I, Popoola O, Onipede A, Blomfeldt A, Nyquist NE, Bocker K, Ussher J, Ali A, Ullah N, Khan H, Gustafson NW, Jarrar I, Al-Hamad A, Luvira V, Paveenkittiporn W, Baran I, Mwansa JCL, Sikakwa L, Yamba K, Aarestrup FM (2025) Investigation of mobile genetic elements and their association with antibiotic resistance genes in clinical pathogens worldwide. PLoS ONE 20(8):e0330304. https:\/\/doi.org\/10.1371\/journal.pone.0330304","journal-title":"PLoS ONE"},{"issue":"1","key":"11956_CR16","doi-asserted-by":"publisher","first-page":"mgen000910","DOI":"10.1099\/mgen.0.000910","volume":"9","author":"ND Sanderson","year":"2023","unstructured":"Sanderson ND, Kapel N, Rodger G, Webster H, Lipworth S, Street TL, Peto T, Crook D, Stoesser N (2023) Comparison of R9.4.1\/Kit10 and R10\/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction. Microb Genom 9(1):mgen000910. https:\/\/doi.org\/10.1099\/mgen.0.000910","journal-title":"Microb Genom"},{"issue":"5","key":"11956_CR17","doi-asserted-by":"publisher","first-page":"e00246","DOI":"10.1128\/jcm.00246-24","volume":"62","author":"HH Mostafa","year":"2024","unstructured":"Mostafa HH (2024) An evolution of Nanopore next-generation sequencing technology: implications for medical microbiology and public health. J Clin Microbiol 62(5):e00246\u2013e00224. https:\/\/doi.org\/10.1128\/jcm.00246-24","journal-title":"J Clin Microbiol"},{"issue":"4","key":"11956_CR18","doi-asserted-by":"publisher","first-page":"000557","DOI":"10.1099\/mgen.0.000557","volume":"7","author":"FA Ferreira","year":"2021","unstructured":"Ferreira FA, Helmersen K, Visnovska T, J\u00f8rgensen SB, Aamot HV (2021) Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation. Microb Genom 7(4):000557. https:\/\/doi.org\/10.1099\/mgen.0.000557","journal-title":"Microb Genom"}],"container-title":["Molecular Biology Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11033-026-11956-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11033-026-11956-y","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11033-026-11956-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T12:58:09Z","timestamp":1778763489000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11033-026-11956-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,14]]},"references-count":18,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["11956"],"URL":"https:\/\/doi.org\/10.1007\/s11033-026-11956-y","relation":{},"ISSN":["0301-4851","1573-4978"],"issn-type":[{"value":"0301-4851","type":"print"},{"value":"1573-4978","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,14]]},"assertion":[{"value":"17 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 May 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"The study was approved by the local Data Protection Official at Akershus University Hospital (2017_147).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}}],"article-number":"775"}}