{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T23:39:39Z","timestamp":1787787579827,"version":"build-2784847793"},"reference-count":102,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T00:00:00Z","timestamp":1781222400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Rapid and accurate detection of pathogenic microorganisms is the key to clinical diagnosis and treatment as well as public health prevention and control. As a representative of the third-generation sequencing technologies, nanopore sequencing technology has brought revolutionary potential to the field of pathogen detection by virtue of its unique advantages such as long read length, real-time sequencing and portable instruments. This paper aims to review the current application status of this technology and prospect its future development. Firstly, the basic principles and the development of mainstream platforms of nanopore sequencing are outlined. Subsequently, its specific applications in the detection of various pathogens including bacteria, viruses, fungi and parasites are systematically elaborated, with a focus on analyzing the practice and remarkable advantages of this technology in scenarios such as direct metagenomic detection without culture, rapid identification of drug resistance and virulence factors, and point-of-care rapid diagnosis. Meanwhile, this paper also objectively discusses the main technical challenges faced in the current application, including the raw read accuracy, the complexity of bioinformatics analysis and the balance between cost and benefit. Finally, the future technological optimization, standardization of data analysis workflows and the expansion of broader clinical application scenarios are prospected. Importantly, this review aims to equip clinical laboratory professionals with a balanced, evidence-based framework to evaluate the readiness, utility, and implementation pathway of nanopore sequencing for specific diagnostic use-cases (e.g., urgent meningitis\/endophthalmitis, culture-negative infections, resistance gene detection) within the constraints of a clinical lab, such as cost, turnaround time, and staff expertise, in order to provide new technical perspectives and theoretical support for the precise diagnosis and active surveillance of infectious diseases.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1843102","type":"journal-article","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T05:46:14Z","timestamp":1781243174000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms"],"prefix":"10.3389","volume":"17","author":[{"given":"Guo Run","family":"Zi","sequence":"first","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Kunming Medical University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Da-jiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Kunming Medical University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Lin","family":"He","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Kunming Medical University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Shu","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Kunming Medical University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yitian","family":"Ou","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Kunming Medical University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang-xing","family":"Ke","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Affiliated Hospital of Kunming Medical University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"001372","DOI":"10.1099\/mgen.0.001372","article-title":"High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy","volume":"11","author":"Abdel-Glil","year":"2025","journal-title":"Microb. Genom."},{"key":"B2","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1007\/s11259-025-10718-8","article-title":"Detection and genomic characterization of foot and mouth disease virus SAT2 XIV topotype using amplicon-based nanopore sequencing","volume":"49","author":"Abualghusein","year":"2025","journal-title":"Vet. Res. Commun."},{"key":"B3","doi-asserted-by":"publisher","first-page":"6534","DOI":"10.1038\/s41598-024-55635-z","article-title":"Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing","volume":"14","author":"Ali","year":"2024","journal-title":"Sci. Rep."},{"key":"B4","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.tibtech.2018.07.013","article-title":"Single-molecule sequencing: towards clinical applications","volume":"37","author":"Ameur","year":"2019","journal-title":"Trends Biotechnol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"001020","DOI":"10.1099\/acmi.0.001020.v3","article-title":"Utilization of Oxford nanopore technology for human infectious disease detection and surveillance in Africa: a scoping review","volume":"7","author":"Bastug","year":"2025","journal-title":"Access Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41467-025-66865-8","article-title":"Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours","volume":"17","author":"Bellankimath","year":"2025","journal-title":"Nat. Commun."},{"key":"B7","doi-asserted-by":"publisher","first-page":"2177","DOI":"10.1007\/s10096-024-04929-1","article-title":"Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine","volume":"43","author":"Bellankimath","year":"2024","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B8","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s12985-023-02059-2","article-title":"Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing","volume":"20","author":"Bosmeny","year":"2023","journal-title":"Virol. J."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1907","DOI":"10.1007\/s10096-025-05158-w","article-title":"Nationwide multicentre study of nanopore long-read sequencing for 16S rRNA-species identification","volume":"44","author":"Brunet","year":"2025","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B10","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1186\/s13073-024-01380-x","article-title":"Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses","volume":"16","author":"Buddle","year":"2024","journal-title":"Genome Med."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1517208","DOI":"10.3389\/fcimb.2025.1517208","article-title":"Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections","volume":"15","author":"Butler","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"811","DOI":"10.13345\/j.cjb.190368","volume":"36","author":"Cao","year":"2020","journal-title":"Sheng wu gong cheng xue bao = Chin. J. Biotechnol"},{"key":"B13","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1515\/jpm-2022-0504","article-title":"Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing","volume":"51","author":"Chaemsaithong","year":"2023","journal-title":"J. Perinat. Med."},{"key":"B14","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/s13000-020-00960-w","article-title":"Potential utility of targeted nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection","volume":"15","author":"Chan","year":"2020","journal-title":"Diagn. Pathol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1701570","DOI":"10.3389\/fcimb.2025.1701570","article-title":"Nanopore sequencing in veterinary medicine: from concepts to clinical applications","volume":"15","author":"Chaves","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1007\/s40291-023-00669-8","article-title":"Application of nanopore sequencing in the diagnosis and treatment of pulmonary infections","volume":"27","author":"Chen","year":"2023","journal-title":"Mol. Diagn. Ther."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1043967","DOI":"10.3389\/fmicb.2023.1043967","article-title":"Portable nanopore-sequencing technology: trends in development and applications","volume":"14","author":"Chen","year":"2023","journal-title":"Front. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"531","DOI":"10.3760\/cma.j.cn121430-20200228-00095","article-title":"Expert consensus for the application of metagenomic next generation sequencing in the pathogen diagnosis in clinical moderate and severe infections (first edition)","volume":"32","year":"2020","journal-title":"Zhonghua Wei Zhong Bing Ji Jiu Yi Xue."},{"key":"B19","doi-asserted-by":"publisher","first-page":"001657","DOI":"10.1099\/mgen.0.001657","article-title":"Nanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens","volume":"12","author":"Cottingham","year":"2026","journal-title":"Microb. Genom."},{"key":"B20","doi-asserted-by":"publisher","first-page":"e13613","DOI":"10.1002\/adma.202513613","article-title":"Nanopore-based label-free and single-molecule sequencing toward precision diagnosis","volume":"38","author":"Cui","year":"2025","journal-title":"Adv. Mater (Deerfield Beach, Fla.)"},{"key":"B21","doi-asserted-by":"publisher","first-page":"e0062824","DOI":"10.1128\/jcm.00628-24","article-title":"A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens","volume":"62","author":"Dabernig-Heinz","year":"2024","journal-title":"J. Clin. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"943859","DOI":"10.3389\/fcimb.2022.943859","article-title":"Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections","volume":"12","author":"Deng","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"5208","DOI":"10.12998\/wjcc.v12.i22.5208","article-title":"Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: three case reports","volume":"12","author":"Deng","year":"2024","journal-title":"World J Clin Cases"},{"key":"B24","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1167\/tvst.14.4.19","article-title":"A tear-based approach for rapid identification of bacterial pathogens in corneal ulcers using nanopore sequencing","volume":"14","author":"Dibbs","year":"2025","journal-title":"Transl. Vis. Sci. Technol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1991","DOI":"10.3390\/diagnostics15161991","article-title":"Metagenomic next-generation sequencing in infectious diseases: clinical applications, translational challenges, and future directions","volume":"15","author":"Elbehiry","year":"2025","journal-title":"Diagnostics (Basel)"},{"key":"B26","doi-asserted-by":"publisher","first-page":"2944","DOI":"10.3390\/diagnostics15232944","article-title":"Next-generation sequencing for bloodstream infections: shaping the future of rapid diagnostics and precision medicine","volume":"15","author":"Elbehiry","year":"2025","journal-title":"Diagnostics (Basel)"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1177651","DOI":"10.3389\/fmicb.2023.1177651","article-title":"Impact of nanopore-based metagenome sequencing on tick-borne virus detection","volume":"14","author":"Ergunay","year":"2023","journal-title":"Front. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/s41522-024-00634-1","article-title":"Saliva microbiome profiling by full-gene 16S rRNA Oxford nanopore technology versus illumina MiSeq sequencing","volume":"10","author":"Esberg","year":"2024","journal-title":"NPJ Biofilms Microbiomes"},{"key":"B29","doi-asserted-by":"publisher","first-page":"435","DOI":"10.16781\/j.CN31-2187\/R.20250888","article-title":"Expert consensus on innovation and standardized application of nanopore sequencing technology","volume":"47","year":"2026","journal-title":"Acad J Sec Mil Med Univ."},{"key":"B30","doi-asserted-by":"publisher","first-page":"ofaf183","DOI":"10.1093\/ofid\/ofaf183","article-title":"Influence of sequencing technology on pangenome-level analysis and detection of antimicrobial resistance genes in ESKAPE pathogens","volume":"12","author":"Frias-De-Diego","year":"2025","journal-title":"Open Forum Infect. Dis"},{"key":"B31","doi-asserted-by":"publisher","first-page":"e0027022","DOI":"10.1128\/spectrum.00270-22","article-title":"Clinical performance of nanopore targeted sequencing for diagnosing infectious diseases","volume":"10","author":"Fu","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"B32","doi-asserted-by":"publisher","first-page":"e0108024","DOI":"10.1128\/msystems.01080-24","article-title":"NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from nanopore and illumina data","volume":"9","author":"Fuchs","year":"2024","journal-title":"mSystems"},{"key":"B33","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu. Rev. Pathol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"106166","DOI":"10.1016\/j.jinf.2024.106166","article-title":"Molecular rapid diagnostic testing for bloodstream infections: nanopore targeted sequencing with pathogen-specific primers","volume":"88","author":"Han","year":"2024","journal-title":"J. Infect."},{"key":"B35","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1097\/IAE.0000000000003719","article-title":"Identification of pathogens in the intraocular fluid samples of patients with endogenous endophthalmitis using rapid nanopore targeted sequencing","volume":"43","author":"Hao","year":"2023","journal-title":"Retina"},{"key":"B36","doi-asserted-by":"publisher","first-page":"e0285625","DOI":"10.1128\/spectrum.02856-25","article-title":"Oxford nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing","volume":"14","author":"Helsmoortel","year":"2026","journal-title":"Microbiol. Spectr."},{"key":"B37","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1186\/s13071-025-06917-6","article-title":"Characterizing the transmission dynamics of Trypanosoma cruzi in Triatoma sanguisuga collected from dog kennels in southern Texas","volume":"18","author":"Hernandez","year":"2025","journal-title":"Parasit. Vectors"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf1314","article-title":"Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications Nucleic Acids Res","author":"Hewel","year":"2025"},{"key":"B39","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.semcdb.2021.11.009","article-title":"Technical challenges in defining RNA modifications","volume":"127","author":"Huang","year":"2022","journal-title":"Semin. Cell Dev. Biol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1186\/s12866-025-04132-y","article-title":"Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis","volume":"25","author":"Jing","year":"2025","journal-title":"BMC Microbiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"3333","DOI":"10.3390\/ijms25063333","article-title":"Enhancing clinical utility: utilization of international standards and guidelines for metagenomic sequencing in infectious disease diagnosis","volume":"25","author":"Kan","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"B42","doi-asserted-by":"publisher","first-page":"151630","DOI":"10.1016\/j.ijmm.2024.151630","article-title":"Real-time application of ITS and D1-D3 nanopore amplicon metagenomic sequencing in fungal infections: enhancing fungal infection diagnostics","volume":"316","author":"Kim","year":"2024","journal-title":"Int. J. Med. Microbiol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"5445","DOI":"10.4103\/jfmpc.jfmpc_1672_20","article-title":"COVID-19 reinfection: linked possibilities and future outlook","volume":"9","author":"Krishna","year":"2020","journal-title":"J. Fam. Med. Prim. Care"},{"key":"B44","doi-asserted-by":"publisher","first-page":"e17439","DOI":"10.1016\/j.heliyon.2023.e17439","article-title":"Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: a case report","volume":"9","author":"Kumburu","year":"2023","journal-title":"Heliyon"},{"key":"B45","doi-asserted-by":"publisher","first-page":"9250","DOI":"10.1038\/s41598-024-59343-6","article-title":"Snapshot study of canine distemper virus in Bangladesh with on-site PCR detection and nanopore sequencing","volume":"14","author":"Lanszki","year":"2024","journal-title":"Sci. Rep."},{"key":"B46","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1080\/09273948.2023.2173243","article-title":"Rapid pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing: a preliminary study","volume":"32","author":"Lee","year":"2024","journal-title":"Ocul. Immunol. Inflamm."},{"key":"B47","doi-asserted-by":"publisher","first-page":"1469440","DOI":"10.3389\/fcimb.2025.1469440","article-title":"Clinical utility of nanopore-targeted sequencing for diagnosing and treating pulmonary infectious diseases from bronchoalveolar lavage fluid","volume":"15","author":"Li","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"1554965","DOI":"10.3389\/fmicb.2025.1554965","article-title":"Applying nanopore sequencing in the etiological diagnosis of bloodstream infection","volume":"16","author":"Liao","year":"2025","journal-title":"Front. Microbiol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"214","DOI":"10.3390\/bios11070214","article-title":"Nanopore technology and its applications in gene sequencing","volume":"11","author":"Lin","year":"2021","journal-title":"Biosensors (Basel)"},{"key":"B50","doi-asserted-by":"publisher","first-page":"355","DOI":"10.16250\/j.32.1915.2025003","volume":"37","author":"Lin","year":"2025","journal-title":"Zhongguo xue xi chong bing fang zhi za zhi = Chin. J. Schistosomiasis Control"},{"key":"B51","doi-asserted-by":"publisher","first-page":"5238","DOI":"10.21037\/jtd-2025-1163","article-title":"Diagnostic performance of metagenomics sequencing for pulmonary fungal infections: a clinical evaluation using the nanopore platform","volume":"17","author":"Liu","year":"2025","journal-title":"J. Thorac. Dis."},{"key":"B52","doi-asserted-by":"publisher","first-page":"1610063","DOI":"10.3389\/fmed.2025.1610063","article-title":"Global trends in the application of nanopore sequencing technology in the detection of infectious disease pathogens: a bibliometric analysis from 2014 to 2024","volume":"12","author":"Long","year":"2025","journal-title":"Front. Med. (Lausanne)"},{"key":"B53","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/j.ajo.2022.05.022","article-title":"Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform","volume":"242","author":"Low","year":"2022","journal-title":"Am. J. Ophthalmol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"1230650","DOI":"10.3389\/fcimb.2024.1230650","article-title":"Illumina and nanopore sequencing in culture-negative samples from suspected lower respiratory tract infection patients","volume":"14","author":"Ma","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"459","DOI":"10.3390\/mi14020459","article-title":"An introduction to nanopore sequencing: past, present, and future considerations","volume":"14","author":"MacKenzie","year":"2023","journal-title":"Micromachines (Basel)"},{"key":"B56","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JCM.01972-20","article-title":"Nanopore sequencing of the fungal intergenic spacer sequence as a potential rapid diagnostic assay","volume":"58","author":"Morrison","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"21484","DOI":"10.1038\/s41598-021-01022-x","article-title":"Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom's first national lockdown","volume":"11","author":"Munis","year":"2021","journal-title":"Sci. Rep."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1911","DOI":"10.2147\/IDR.S357162","article-title":"Application value of metagenomic next-generation sequencing for bloodstream infections in pediatric patients under intensive care","volume":"15","author":"Nan","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"B59","doi-asserted-by":"publisher","first-page":"2352","DOI":"10.1016\/j.csbj.2023.03.038","article-title":"Benchmarking of nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing","volume":"21","author":"Ni","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"B60","doi-asserted-by":"publisher","first-page":"e0329524","DOI":"10.1128\/spectrum.03295-24","article-title":"Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study","volume":"13","author":"Nielsen","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"B61","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1007\/s40588-025-00247-y","article-title":"Long-read sequencing for the rapid response to infectious diseases outbreaks","volume":"12","author":"Oehler","year":"2025","journal-title":"Curr. Clin. Microbiol. Rep."},{"key":"B62","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s12941-022-00530-6","article-title":"Diagnosis of pathogens causing bacterial meningitis using nanopore sequencing in a resource-limited setting","volume":"21","author":"Pallerla","year":"2022","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"B63","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1007\/s00436-025-08516-x","article-title":"First complete mitochondrial genome of Armillifer moniliformis (Pentastomida: Porocephalida) isolated from a human case in Northern Thailand: comparative and phylogenetic analyses","volume":"124","author":"Pataradool","year":"2025","journal-title":"Parasitol. Res."},{"key":"B64","doi-asserted-by":"publisher","first-page":"e155","DOI":"10.1101\/2021.02.09.430478","article-title":"High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples","volume":"8","author":"Pater","year":"2021","journal-title":"J. Biol. Methods"},{"key":"B65","doi-asserted-by":"publisher","first-page":"883921","DOI":"10.3389\/fmicb.2022.883921","article-title":"Systematic comparison of nanopore and illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approach","volume":"13","author":"Pecman","year":"2022","journal-title":"Front. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JCM.01315-19","article-title":"Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of nanopore sequencing","volume":"58","author":"Petersen","year":"2019","journal-title":"J. Clin. Microbiol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s12920-025-02305-2","article-title":"Benchmarking illumina and Oxford nanopore technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology","volume":"19","author":"Purushothaman","year":"2026","journal-title":"BMC Med. Genom"},{"key":"B68","doi-asserted-by":"publisher","first-page":"1057977","DOI":"10.21203\/rs.3.rs-1782867\/v1","article-title":"Diversity of RNA viruses of three dominant tick species in North China","volume":"9","author":"Qin","year":"2022","journal-title":"Front. Vet. Sci."},{"key":"B69","doi-asserted-by":"publisher","first-page":"275","DOI":"10.3390\/pathogens13040275","article-title":"Hybrid-capture target enrichment in human pathogens: identification, evolution, biosurveillance, and genomic epidemiology","volume":"13","author":"Quek","year":"2024","journal-title":"Pathogens"},{"key":"B70","doi-asserted-by":"publisher","first-page":"106971","DOI":"10.1016\/j.ijid.2024.02.014","article-title":"Real-time genomic epidemiologic investigation of a multispecies plasmid-associated hospital outbreak of NDM-5-producing Enterobacterales infections","volume":"142","author":"Raabe","year":"2024","journal-title":"Int. J. Infect. Dis."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1111\/trf.70051","article-title":"Unbiased metagenomic exploration of transfusion-transmitted infections with nanopore sequencing","author":"Ragupathy","year":"2025","journal-title":"Transfusion"},{"key":"B72","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1089\/ast.2020.2349","article-title":"Assessment of automated nucleic acid extraction systems in combination with MinION sequencing as potential tools for the detection of microbial biosignatures","volume":"22","author":"Raymond-Bouchard","year":"2022","journal-title":"Astrobiology"},{"key":"B73","doi-asserted-by":"publisher","first-page":"9831","DOI":"10.3390\/ijms26199831","article-title":"Viral metagenomic next-generation sequencing for one health discovery and surveillance of (re)emerging viruses: a deep review","volume":"26","author":"Russell","year":"2025","journal-title":"Int. J. Mol. Sci."},{"key":"B74","doi-asserted-by":"publisher","first-page":"001564","DOI":"10.1099\/mgen.0.001564","article-title":"Reproducibility and accuracy of bacterial methylome profiling using Oxford nanopore technologies nanopore sequencing platform","volume":"11","author":"Schababerle","year":"2025","journal-title":"Microb. Genom."},{"key":"B75","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1007\/s44197-025-00455-1","article-title":"Unveiling the future of infective endocarditis diagnosis: the transformative role of metagenomic next-generation sequencing in culture-negative cases","volume":"15","author":"Shinge","year":"2025","journal-title":"J. Epidemiol. Glob. Health"},{"key":"B76","doi-asserted-by":"publisher","first-page":"1667422","DOI":"10.3389\/fcimb.2025.1667422","article-title":"Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever","volume":"15","author":"Slune\u010dko","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"201","DOI":"10.2144\/btn-2022-0014","article-title":"Nanopore sequencing approach for variation detection of a live attenuated Newcastle disease virus vaccine","volume":"72","author":"Sun","year":"2022","journal-title":"BioTechniques"},{"key":"B78","doi-asserted-by":"publisher","first-page":"3493","DOI":"10.1038\/s41598-025-87858-z","article-title":"Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study","volume":"15","author":"Sung","year":"2025","journal-title":"Sci. Rep."},{"key":"B79","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.3390\/antibiotics14101001","article-title":"Rapid nanopore sequencing of positive blood cultures using automated benzyl-alcohol extraction improves time-critical sepsis management","volume":"14","author":"Tai","year":"2025","journal-title":"Antibiotics (Basel)"},{"key":"B80","doi-asserted-by":"publisher","first-page":"e13909","DOI":"10.1111\/1755-0998.13909","article-title":"In situ metagenomics: a platform for rapid sequencing and analysis of metagenomes in less than one day","volume":"24","author":"Tamames","year":"2024","journal-title":"Mol. Ecol. Resour."},{"key":"B81","doi-asserted-by":"publisher","first-page":"e0116323","DOI":"10.1128\/msystems.01163-23","article-title":"Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications","volume":"9","author":"Tan","year":"2024","journal-title":"mSystems"},{"key":"B82","doi-asserted-by":"publisher","first-page":"7622","DOI":"10.1038\/s41598-020-64616-x","article-title":"Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing","volume":"10","author":"Taxt","year":"2020","journal-title":"Sci. Rep."},{"key":"B83","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/s41579-025-01223-5","article-title":"Clinical metagenomics for diagnosis and surveillance of viral pathogens","volume":"24","author":"Torres Montaguth","year":"2026","journal-title":"Nat. Rev. Microbiol."},{"key":"B84","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"B85","doi-asserted-by":"publisher","first-page":"e70482","DOI":"10.1002\/ctm2.70482","article-title":"CRISPR-driven diagnostics: molecular mechanisms, clinical efficacy and translational challenges","volume":"15","author":"Wang","year":"2025","journal-title":"Clin. Transl. Med."},{"key":"B86","doi-asserted-by":"publisher","first-page":"18732","DOI":"10.1039\/D4NR01325E","article-title":"Nanopore-based sensors for DNA sequencing: a review","volume":"16","author":"Wei","year":"2024","journal-title":"Nanoscale"},{"key":"B87","doi-asserted-by":"publisher","first-page":"1037134","DOI":"10.3389\/fgene.2022.1037134","article-title":"Modification mapping by nanopore sequencing","volume":"13","author":"White","year":"2022","journal-title":"Front. Genet."},{"key":"B88","doi-asserted-by":"publisher","first-page":"114798","DOI":"10.1016\/j.celrep.2024.114798","article-title":"Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing","volume":"43","author":"Xu","year":"2024","journal-title":"Cell Rep."},{"key":"B89","doi-asserted-by":"publisher","first-page":"e0143325","DOI":"10.1128\/jcm.01433-25","article-title":"Accuracy of nanopore-based targeted next-generation sequencing assay for detection of Mycobacterium tuberculosis and drug resistance from non-sputum specimens: a multicenter prospective study in China","volume":"64","author":"Yang","year":"2026","journal-title":"J. Clin. Microbiol."},{"key":"B90","doi-asserted-by":"publisher","first-page":"127666","DOI":"10.1016\/j.micres.2024.127666","article-title":"Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing","volume":"283","author":"Ye","year":"2024","journal-title":"Microbiol. Res."},{"key":"B91","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1038\/s41565-022-01193-2","article-title":"Nanopore-based technologies beyond DNA sequencing","volume":"17","author":"Ying","year":"2022","journal-title":"Nat. Nanotechnol."},{"key":"B92","doi-asserted-by":"publisher","first-page":"e05978","DOI":"10.1002\/advs.202505978","article-title":"CLAE: a high-fidelity nanopore sequencing strategy for read-level viral variant detection and environmental RNA virus discovery","volume":"12","author":"Yu","year":"2025","journal-title":"Adv. Sci. (Weinh)"},{"key":"B93","doi-asserted-by":"publisher","first-page":"858777","DOI":"10.3389\/fmicb.2022.858777","article-title":"Rapid detection of bacterial pathogens and antimicrobial resistance genes in clinical urine samples with urinary tract infection by metagenomic nanopore sequencing","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Microbiol."},{"key":"B94","first-page":"381","article-title":"Application of nanopore sequencing technology in the clinical diagnosis of infectious diseases","volume":"35","author":"Zhang","year":"2022","journal-title":"Biomed. Environ. Sci."},{"key":"B95","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1016\/j.jgg.2024.09.007","article-title":"Nanopore sequencing: flourishing in its teenage years","volume":"51","author":"Zhang","year":"2024","journal-title":"J. Genet. Genom."},{"key":"B96","doi-asserted-by":"publisher","first-page":"3659","DOI":"10.2147\/IDR.S475861","article-title":"Nanopore sequencing technology: a reliable method for pathogen diagnosis in elderly patients with community-acquired pneumonia","volume":"17","author":"Zhang","year":"2024","journal-title":"Infect. Drug Resist."},{"key":"B97","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1186\/s12981-025-00801-0","article-title":"Metagenomic next-generation sequencing for pathogen detection of pulmonary infections in persons living with HIV","volume":"22","author":"Zhang","year":"2025","journal-title":"AIDS Res. Ther."},{"key":"B98","doi-asserted-by":"publisher","first-page":"1330788","DOI":"10.3389\/fcimb.2024.1330788","article-title":"Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario","volume":"14","author":"Zhao","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B99","doi-asserted-by":"publisher","first-page":"e316","DOI":"10.1002\/mco2.316","article-title":"Nanopore sequencing technology and its applications","volume":"4","author":"Zheng","year":"2023","journal-title":"MedComm (2020)"},{"key":"B100","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.3390\/nano12091534","article-title":"Application of nanopore sequencing in the detection of foodborne microorganisms","volume":"12","author":"Zhou","year":"2022","journal-title":"Nanomaterials (Basel)"},{"key":"B101","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s41374-021-00663-w","article-title":"Advancements in detection of SARS-CoV-2 infection for confronting COVID-19 pandemics","volume":"102","author":"Zhou","year":"2022","journal-title":"Lab. Invest."},{"key":"B102","doi-asserted-by":"publisher","first-page":"6675206","DOI":"10.1155\/2020\/6675206","article-title":"The applications of nanopore sequencing technology in pathogenic microorganism detection","volume":"2020","author":"Zhu","year":"2020","journal-title":"Can. J. Infect. Dis. Med. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1843102\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T05:46:18Z","timestamp":1781243178000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1843102\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,12]]},"references-count":102,"alternative-id":["10.3389\/fmicb.2026.1843102"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1843102","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,12]]},"article-number":"1843102"}}