[1] Zhong NS, Zheng BJ, Li YM, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February, 2003. Lancet, 2003; 362, 1353−8. doi:  10.1016/S0140-6736(03)14630-2
[2] Ksiazek TG, Erdman D, Goldsmith CS, et al. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med, 2003; 348, 1953−66. doi:  10.1056/NEJMoa030781
[3] Assiri AM, Biggs HM, Abedi GR, et al. Increase in Middle East Respiratory syndrome-coronavirus cases in Saudi Arabia linked to hospital outbreak with continued circulation of recombinant virus, July 1-August 31, 2015. Open Forum Infect Dis, 2016; 3, ofw165. doi:  10.1093/ofid/ofw165
[4] Al-Dorzi HM, Aldawood AS, Khan R, et al. The critical care response to a hospital outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection: an observational study. Ann Intensive Care, 2016; 6, 101. doi:  10.1186/s13613-016-0203-z
[5] Holmes EC, Dudas G, Rambaut A, et al. The evolution of Ebola virus: insights from the 2013-2016 epidemic. Nature, 2016; 538, 193−200. doi:  10.1038/nature19790
[6] Diallo MSK, Toure A, Sow MS, et al. Understanding long-term evolution and predictors of sequelae of Ebola virus disease survivors in Guinea: a 48-month prospective, longitudinal cohort study (PostEboGui). Clin Infect Dis, 2021; 73, 2166−74. doi:  10.1093/cid/ciab168
[7] Mérens A, Bigaillon C, Delaune D. Ebola virus disease: biological and diagnostic evolution from 2014 to 2017. Méd Mal Infect, 2018; 48, 83−94.
[8] De Pijper CA, Schnyder JL, Stijnis C, et al. A review of severe thrombocytopenia in Zika patients-Pathophysiology, treatment and outcome. Travel Med Infect Dis, 2022; 45, 102231. doi:  10.1016/j.tmaid.2021.102231
[9] Safford TG, Whitmore EH, Hamilton LC. Scientists, presidents, and pandemics-comparing the science-politics nexus during the Zika virus and COVID-19 outbreaks. Soc Sci Q, 2021; 102, 2482−98. doi:  10.1111/ssqu.13084
[10] Champigneulle B, Hancco I, Renan R, et al. High-altitude environment and COVID-19: SARS-CoV-2 seropositivity in the highest city in the world. High Alt Med Biol, 2021.
[11] Farooq HZ, Davies E, Brown B, et al. Real-world SARS CoV-2 testing in Northern England during the first wave of the COVID-19 pandemic. J Infect, 2021; 83, 84−91. doi:  10.1016/j.jinf.2021.04.013
[12] Zohner YE, Morris JS. COVID-TRACK: world and USA SARS-COV-2 testing and COVID-19 tracking. BioData Min, 2021; 14, 4. doi:  10.1186/s13040-021-00233-2
[13] Bello-Chavolla OY, Antonio-Villa NE, Fernández-Chirino L, et al. Diagnostic performance and clinical implications of rapid SARS-CoV-2 antigen testing in Mexico using real-world nationwide COVID-19 registry data. PLoS One, 2021; 16, e0256447. doi:  10.1371/journal.pone.0256447
[14] Maglangit F, Yu Y, Deng H. Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens). Nat Prod Rep, 2021; 38, 782−821. doi:  10.1039/D0NP00061B
[15] GBD 2019 Diseases and Injuries Collaborators. Global burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet, 2020; 396, 1204−22. doi:  10.1016/S0140-6736(20)30925-9
[16] Rajapaksha P, Elbourne A, Gangadoo S, et al. A review of methods for the detection of pathogenic microorganisms. Analyst, 2019; 144, 396−411. doi:  10.1039/C8AN01488D
[17] Li PY, Niu WK, Fang Y, et al. Development and evaluation of a loop-mediated isothermal amplification assay for rapid and specific identification of Carbapenem-resistant Acinetobacter baumannii strains harboring blaOXA-23, and the epidemiological survey of clinical isolates. Microb Drug Resist, 2020; 26, 1458−65. doi:  10.1089/mdr.2019.0441
[18] Law ILG, Loo JFC, Kwok HC, et al. Automated real-time detection of drug-resistant Mycobacterium tuberculosis on a lab-on-a-disc by recombinase polymerase amplification. Anal Biochem, 2018; 544, 98−107. doi:  10.1016/j.ab.2017.12.031
[19] Bodulev OL, Sakharov IY. Isothermal nucleic acid amplification techniques and their use in bioanalysis. Biochemistry (Mosc), 2020; 85, 147−66. doi:  10.1134/S0006297920020030
[20] Tian B, Fock J, Minero GAS, et al. Ultrasensitive real-time rolling circle amplification detection enhanced by nicking-induced tandem-acting polymerases. Anal Chem, 2019; 91, 10102−9. doi:  10.1021/acs.analchem.9b02073
[21] Simner PJ, Miller HB, Breitwieser FP, et al. Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics. J Clin Microbiol, 2018; 56, e00472−18.
[22] Li YM, Xiu LS, Liu JW, et al. A multiplex assay for characterization of antimicrobial resistance in Neisseria gonorrhoeae using multi-PCR coupled with mass spectrometry. J Antimicrob Chemother, 2020; 75, 2817−25. doi:  10.1093/jac/dkaa269
[23] Zhang C, Xiao Y, Du J, et al. Application of multiplex PCR coupled with matrix-assisted laser desorption ionization-time of flight analysis for simultaneous detection of 21 common respiratory viruses. J Clin Microbiol, 2015; 53, 2549−54. doi:  10.1128/JCM.00943-15
[24] Zhang C, Xiu LS, Xiao Y, et al. Simultaneous detection of key bacterial pathogens related to pneumonia and meningitis using multiplex PCR coupled with mass spectrometry. Front Cell Infect Microbiol, 2018; 8, 107. doi:  10.3389/fcimb.2018.00107
[25] Hernández OH, Gutiérrez-Escolano AL, Cancio-Lonches C, et al. Multiplex PCR method for the detection of human norovirus, Salmonella spp. , Shigella spp. , and Shiga toxin producing Escherichia coli in blackberry, coriander, lettuce and strawberry. Food Microbiol, 2022; 102, 103926.
[26] Xiu L, Li YM, Wang F, et al. Multiplex high-resolution melting assay for simultaneous identification of molecular markers associated with extended-spectrum cephalosporins and azithromycin resistance in Neisseria gonorrhoeae. J Mol Diagn, 2020; 22, 1344−55. doi:  10.1016/j.jmoldx.2020.08.003
[27] Xiu L, Zhang C, Li YM, et al. High-resolution melting analysis for rapid detection of the internationally spreading ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone. J Antimicrob Chemother, 2020; 75, 106−9. doi:  10.1093/jac/dkz395
[28] Naccache SN, Federman S, Veeraraghavan N, et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res, 2014; 24, 1180−92. doi:  10.1101/gr.171934.113
[29] Van Dijk EL, Auger H, Jaszczyszyn Y, et al. Ten years of next-generation sequencing technology. Trends Genet, 2014; 30, 418−26. doi:  10.1016/j.tig.2014.07.001
[30] Zhao L, Zhang H, Kohnen MV, et al. Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and Nanopore-based direct RNA sequencing. Front Genet, 2019; 10, 253. doi:  10.3389/fgene.2019.00253
[31] Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science, 2009; 323, 133−8. doi:  10.1126/science.1162986
[32] Giusti B, Sticchi E, De Cario R, et al. Genetic bases of bicuspid aortic valve: the contribution of traditional and high-throughput sequencing approaches on research and diagnosis. Front Physiol, 2017; 8, 612. doi:  10.3389/fphys.2017.00612
[33] Niedringhaus TP, Milanova D, Kerby MB, et al. Landscape of next-generation sequencing technologies. Anal Chem, 2011; 83, 4327−41. doi:  10.1021/ac2010857
[34] Wang Y, Yang QP, Wang ZM. The evolution of nanopore sequencing. Front Genet, 2015; 5, 449.
[35] Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell, 2015; 58, 586−97. doi:  10.1016/j.molcel.2015.05.004
[36] Yahara K, Suzuki M, Hirabayashi A, et al. Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. Nat Commun, 2021; 12, 27. doi:  10.1038/s41467-020-20199-9
[37] Leggett RM, Clark MD. A world of opportunities with nanopore sequencing. J Exp Bot, 2017; 68, 5419−29. doi:  10.1093/jxb/erx289
[38] Imai K, Tamura K, Tanigaki T, et al. Whole genome sequencing of influenza A and B viruses with the MinION sequencer in the clinical setting: a pilot study. Front Microbiol, 2018; 9, 2748. doi:  10.3389/fmicb.2018.02748
[39] Mcintyre ABR, Rizzardi L, Yu AM, et al. Nanopore sequencing in microgravity. npj Microgravity, 2016; 2, 16035. doi:  10.1038/npjmgrav.2016.35
[40] Castro-Wallace SL, Chiu CY, John KK, et al. Nanopore DNA sequencing and genome assembly on the international space station. Sci Rep, 2017; 7, 18022. doi:  10.1038/s41598-017-18364-0
[41] Pennisi E. Genome sequencing. Search for pore-fection. Science, 2012; 336, 534−7.
[42] Jain M, Koren S, Miga KH, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol, 2018; 36, 338−45. doi:  10.1038/nbt.4060
[43] Badenes ML, Martí AFI, Ríos G, et al. Application of genomic technologies to the breeding of trees. Front Genet, 2016; 7, 198.
[44] Sereika M, Kirkegaard RH, Karst SM, et al. Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. bioRxiv, 2021.
[45] Roychowdhury S, Chinnaiyan AM. Translating cancer genomes and transcriptomes for precision oncology. CA Cancer J Clin, 2016; 66, 75−88. doi:  10.3322/caac.21329
[46] Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature, 2011; 473, 174−80. doi:  10.1038/nature09944
[47] De Vlaminck I, Khush KK, Strehl C, et al. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell, 2013; 155, 1178−87. doi:  10.1016/j.cell.2013.10.034
[48] Teng L, Lee S, Ginn A, et al. Genomic comparison reveals natural occurrence of clinically relevant multidrug-resistant extended-spectrum-β-Lactamase-producing Escherichia coli strains. Appl Environ Microbiol, 2019; 85, e03030−18.
[49] Díaz-Viraqué F, Pita S, Greif G, et al. Nanopore sequencing significantly improves genome assembly of the protozoan parasite Trypanosoma cruzi. Genome Biol Evol, 2019; 11, 1952−7. doi:  10.1093/gbe/evz129
[50] Moss EL, Maghini DG, Bhatt AS. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nat Biotechnol, 2020; 38, 701−7. doi:  10.1038/s41587-020-0422-6
[51] Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet, 2019; 20, 631−56. doi:  10.1038/s41576-019-0150-2
[52] Garalde DR, Snell EA, Jachimowicz D, et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods, 2018; 15, 201−6. doi:  10.1038/nmeth.4577
[53] Workman RE, Tang AD, Tang PS, et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat Methods, 2019; 16, 1297−305. doi:  10.1038/s41592-019-0617-2
[54] Zhang C, Xiu LS, Li YM, et al. Multiplex PCR and nanopore sequencing of genes associated with antimicrobial resistance in Neisseria gonorrhoeae directly from clinical samples. Clin Chem, 2021; 67, 610−20. doi:  10.1093/clinchem/hvaa306
[55] Seedorf H, Griffin NW, Ridaura VK, et al. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell, 2014; 159, 253−66. doi:  10.1016/j.cell.2014.09.008
[56] Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA, 2011; 108, 4554−61. doi:  10.1073/pnas.1000087107
[57] Djemiel C, Dequiedt S, Karimi B, et al. BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. BMC Bioinf, 2020; 21, 492. doi:  10.1186/s12859-020-03829-3
[58] Quick J, Grubaugh ND, Pullan ST, et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc, 2017; 12, 1261−76. doi:  10.1038/nprot.2017.066
[59] Wang M, Fu AS, Hu B, et al. Nanopore targeted sequencing for the accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses. Small, 2020; 16, 2002169. doi:  10.1002/smll.202002169
[60] Moore SC, Penrice-Randal R, Alruwaili M, et al. Amplicon-based detection and sequencing of SARS-CoV-2 in nasopharyngeal swabs from patients with COVID-19 and identification of deletions in the viral genome that encode proteins involved in interferon antagonism. Viruses, 2020; 12, 1164. doi:  10.3390/v12101164
[61] Chew KL, Octavia S, Jureen R, et al. Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles. Lett Appl Microbiol, 2021; 73, 286−93.
[62] Yang Y, Che Y, Liu L, et al. Rapid absolute quantification of pathogens and ARGs by nanopore sequencing. Sci Total Environ, 2022; 809, 152190. doi:  10.1016/j.scitotenv.2021.152190
[63] Alili R, Belda E, Le P, et al. Exploring semi-quantitative metagenomic studies using oxford nanopore sequencing: a computational and experimental protocol. Genes, 2021; 12, 1496. doi:  10.3390/genes12101496
[64] Karlsson FH, Tremaroli V, Nookaew I, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature, 2013; 498, 99−103. doi:  10.1038/nature12198
[65] Caussy C, Hsu C, Lo MT, et al. Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD. Hepatology, 2018; 68, 918−32. doi:  10.1002/hep.29892
[66] Zhao N, Cao JB, Xu JY, et al. Targeting RNA with next- and third-generation sequencing improves pathogen identification in clinical samples. Adv Sci, 2021; 8, 2102593. doi:  10.1002/advs.202102593
[67] Hoenen T, Groseth A, Rosenke K, et al. Nanopore sequencing as a rapidly deployable Ebola outbreak tool. Emerg Infect Dis, 2016; 22, 331−4.
[68] Mbala-Kingebeni P, Villabona-Arenas CJ, Vidal N, et al. Rapid confirmation of the Zaire Ebola virus in the outbreak of the Equateur Province in the Democratic Republic of Congo: Implications for public health interventions. Clin Infect Dis, 2019; 68, 330−3. doi:  10.1093/cid/ciy527
[69] Yang MY, Cousineau A, Liu XB, et al. Direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on nanopore MinION-Promising strategies for multiplex identification of viable pathogens in food. Front Microbiol, 2020; 11, 514. doi:  10.3389/fmicb.2020.00514
[70] Petersen LM, Martin IW, Moschetti WE, et al. Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of nanopore sequencing. J Clin Microbiol, 2020; 58, e01315−19.
[71] Zhang LL, Zhang C, Zeng YL, et al. Emergence and characterization of a ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone evolving moderate-level resistance to azithromycin in Shenzhen, China. Infect Drug Resist, 2021; 14, 4271−6. doi:  10.2147/IDR.S336212
[72] Quick J, Loman NJ, Duraffour S, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature, 2016; 530, 228−32. doi:  10.1038/nature16996
[73] Faria NR, Sabino EC, Nunes MRT, et al. Mobile real-time surveillance of Zika virus in Brazil. Genome Med, 2016; 8, 97. doi:  10.1186/s13073-016-0356-2
[74] Kim D, Lee JY, Yang JS, et al. The architecture of SARS-CoV-2 transcriptome. Cell, 2020; 181, 914−21.e10. doi:  10.1016/j.cell.2020.04.011
[75] Bull RA, Adikari TN, Ferguson JM, et al. Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nat Commun, 2020; 11, 6272. doi:  10.1038/s41467-020-20075-6
[76] Tyson JR, James P, Stoddart D, et al. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. bioRxiv, 2020.
[77] Lu RJ, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet, 2020; 395, 565−74. doi:  10.1016/S0140-6736(20)30251-8
[78] Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature, 2020; 579, 265−9. doi:  10.1038/s41586-020-2008-3
[79] Mahmood TB, Saha A, Hossan MI, et al. A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Curr Res Microb Sci, 2021; 2, 100065.
[80] Badua CLDC, Baldo KAT, Medina PMB. Genomic and proteomic mutation landscapes of SARS-CoV-2. J Med Virol, 2021; 93, 1702−21. doi:  10.1002/jmv.26548
[81] Chan WM, Ip JD, Chu AWH, et al. Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole-genome sequencing. J Med Virol, 2020; 92, 2725−34. doi:  10.1002/jmv.26140
[82] Olsen RJ, Christensen PA, Long SW, et al. Trajectory of growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in Houston, Texas, January through May 2021, based on 12, 476 genome sequences. Am J Pathol, 2021; 191, 1754−73. doi:  10.1016/j.ajpath.2021.07.002
[83] Ruan Z, Zou SM, Wang YZ, et al. Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids. Brief Bioinform, 2022; 23, bbac004. doi:  10.1093/bib/bbac004
[84] Gu W, Deng XD, Lee M, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med, 2021; 27, 115−24. doi:  10.1038/s41591-020-1105-z
[85] Leggett RM, Alcon-Giner C, Heavens D, et al. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nat Microbiol, 2020; 5, 430−42. doi:  10.1038/s41564-019-0626-z
[86] Chng KR, Li CH, Bertrand D, et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat Med, 2020; 26, 941−51. doi:  10.1038/s41591-020-0894-4
[87] Wi T, Lahra MM, Ndowa F, et al. Antimicrobial resistance in Neisseria gonorrhoeae: global surveillance and a call for international collaborative action. PLoS Med, 2017; 14, e1002344. doi:  10.1371/journal.pmed.1002344
[88] Unemo M, Del Rio C, Shafer WM. Antimicrobial resistance expressed by Neisseria gonorrhoeae: a major global public health problem in the 21st century. Microbiol Spectr, 2016; 4.
[89] Młynarczyk-Bonikowska B, Majewska A, Malejczyk M, et al. Multiresistant Neisseria gonorrhoeae: a new threat in second decade of the XXI century. Med Microbiol Immunol, 2020; 209, 95−108. doi:  10.1007/s00430-019-00651-4
[90] Zhang C, Wang F, Zhu CS, et al. Determining antimicrobial resistance profiles and identifying novel mutations of Neisseria gonorrhoeae genomes obtained by multiplexed MinION sequencing. Sci China Life Sci, 2020; 63, 1063−70. doi:  10.1007/s11427-019-1558-8
[91] Karst SM, Ziels RM, Kirkegaard RH, et al. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat Methods, 2021; 18, 165−9. doi:  10.1038/s41592-020-01041-y
[92] World Health Organization. Global Tuberculosis Report 2020.https://www.who.int/teams/global-tuberculosis-programme/tb-reports/9789240013131. [2020-10-15].
[93] Dalberto PF, De Souza EV, Abbadi BL, et al. Handling the hurdles on the way to anti-tuberculosis drug development. Front Chem, 2020; 8, 586294. doi:  10.3389/fchem.2020.586294
[94] Oh S, Trifonov L, Yadav VD, et al. Tuberculosis drug discovery: a decade of hit assessment for defined targets. Front Cell Infect Microbiol, 2021; 11, 611304. doi:  10.3389/fcimb.2021.611304
[95] Cabibbe AM, Spitaleri A, Battaglia S, et al. Application of targeted next-generation sequencing assay on a portable sequencing platform for culture-free detection of drug-resistant tuberculosis from clinical samples. J Clin Microbiol, 2020; 58, e00632−20.
[96] Taxt AM, Avershina E, Frye SA, et al. Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Sci Rep, 2020; 10, 7622. doi:  10.1038/s41598-020-64616-x
[97] Zhou ML, Wu YR, Kudinha T, et al. Comprehensive pathogen identification, antibiotic resistance, and virulence genes prediction directly from simulated blood samples and positive blood cultures by nanopore metagenomic sequencing. Front Genet, 2021; 12, 620009. doi:  10.3389/fgene.2021.620009
[98] Peter S, Bosio M, Gross C, et al. Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by nanopore sequencing. mSphere, 2020; 5, e00525−20.
[99] Feng Y, Zou SM, Chen HF, et al. BacWGSTdb 2. 0:a one-stop repository for bacterial whole-genome sequence typing and source tracking. Nucleic Acids Res, 2021; 49, D644−50.
[100] Ruan Z, Wu JY, Chen HF, et al. Hybrid genome assembly and annotation of a pandrug-resistant Klebsiella pneumoniae strain using nanopore and Illumina sequencing. Infect Drug Resist, 2020; 13, 199−206. doi:  10.2147/IDR.S240404
[101] Chen HF, Jiang T, Wu JY, et al. Genomic and phylogenetic analysis of a multidrug-resistant mcr-1-carrying Klebsiella pneumoniae recovered from a urinary tract infection in China. J Glob Antimicrob Resist, 2021; 27, 222−4. doi:  10.1016/j.jgar.2021.10.002
[102] Yue MN, Liu D, Hu X, et al. Genomic characterisation of a multidrug-resistant Escherichia coli strain carrying the mcr-1 gene recovered from a paediatric patient in China. J Glob Antimicrob Resist, 2021; 24, 370−2. doi:  10.1016/j.jgar.2021.02.002
[103] Zheng W, Yue MN, Zhang J, et al. Coexistence of two blaCTX-M-14 genes in a blaNDM-5-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China. J Glob Antimicrob Resist, 2021; 26, 11−4. doi:  10.1016/j.jgar.2021.05.002
[104] Runtuwene LR, Tuda JSB, Mongan AE, et al. Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum. Sci Rep, 2018; 8, 8286. doi:  10.1038/s41598-018-26334-3
[105] Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet, 2012; 13, 260−70. doi:  10.1038/nrg3182
[106] Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol, 2019; 37, 783−92. doi:  10.1038/s41587-019-0156-5
[107] Lourenço TGB, Heller D, Silva-Boghossian CM, et al. Microbial signature profiles of periodontally healthy and diseased patients. J Clin Periodontol, 2014; 41, 1027−36. doi:  10.1111/jcpe.12302
[108] Nayfach S, Shi ZJ, Seshadri R, et al. New insights from uncultivated genomes of the global human gut microbiome. Nature, 2019; 568, 505−10. doi:  10.1038/s41586-019-1058-x
[109] Heikema AP, Horst-Kreft D, Boers SA, et al. Comparison of Illumina versus Nanopore 16S rRNA gene sequencing of the human nasal microbiota. Genes, 2020; 11, 1105. doi:  10.3390/genes11091105
[110] Yang LB, Haidar G, Zia H, et al. Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study. Respir Res, 2019; 20, 265. doi:  10.1186/s12931-019-1218-4
[111] Benítez-Páez A, Portune KJ, Sanz Y. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer. GigaScience, 2016; 5, 4. doi:  10.1186/s13742-016-0111-z
[112] Cuscó A, Catozzi C, Viñes J, et al. Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon. F1000Res, 2018; 7, 1755. doi:  10.12688/f1000research.16817.1
[113] Huang YJ, Charlson ES, Collman RG, et al. The role of the lung microbiome in health and disease. A national heart, lung, and blood institute workshop report. Am J Respir Crit Care Med, 2013; 187, 1382−7.
[114] Bunyavanich S, Schadt EE. Systems biology of asthma and allergic diseases: a multiscale approach. J Allergy Clin Immunol, 2015; 135, 31−42. doi:  10.1016/j.jaci.2014.10.015
[115] Benítez-Páez A, Sanz Y. Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer. Gigascience, 2017; 6, gix043.
[116] Nygaard AB, Tunsjø HS, Meisal R, et al. A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. Sci Rep, 2020; 10, 3209. doi:  10.1038/s41598-020-59771-0
[117] Gonçalves AT, Collipal-Matamal R, Valenzuela-Muñoz V, et al. Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens. Sci Rep, 2020; 10, 2895. doi:  10.1038/s41598-020-59747-0
[118] Zhu XJ, Yan SS, Yuan FH, et al. The applications of nanopore sequencing technology in pathogenic microorganism detection. Can J Infect Dis Med Microbiol, 2020; 2020, 6675206.
[119] Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform, 2021; 22, bbaa403. doi:  10.1093/bib/bbaa403
[120] Tedersoo L, Albertsen M, Anslan S, et al. Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Appl Environ Microbiol, 2021; 87, e0062621. doi:  10.1128/AEM.00626-21
[121] Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J, 2021; 19, 1497−511. doi:  10.1016/j.csbj.2021.02.020
[122] Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol Mech Dis, 2019; 14, 319−38. doi:  10.1146/annurev-pathmechdis-012418-012751