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Research Articles

The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study

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Pages 128-137 | Received 25 Aug 2023, Accepted 12 Oct 2023, Published online: 07 Nov 2023

References

  • Rajapaksha P, Elbourne A, Gangadoo S, et al. A review of methods for the detection of pathogenic microorganisms. Analyst. 2019;144(2):396–411. doi: 10.1039/c8an01488d.
  • 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(9):e00472–e00518. doi: 10.1128/jcm.00472-18.
  • Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol. 2019;14(1):319–338. doi: 10.1146/annurev-pathmechdis-012418-012751.
  • Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333–351. doi: 10.1038/nrg.2016.49.
  • Fu Y, Chen Q, Xiong M, et al. Clinical performance of nanopore targeted sequencing for diagnosing infectious diseases. Microbiol Spectr. 2022;10(2):e0027022. doi: 10.1128/spectrum.00270-22.
  • Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol. 2019;37(7):783–792. doi: 10.1038/s41587-019-0156-5.
  • Cheng J, Hu H, Kang Y, et al. Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis. Ann Clin Microbiol Antimicrob. 2018;17(1):43. doi: 10.1186/s12941-018-0294-5.
  • Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother. 2017;72(1):104–114. doi: 10.1093/jac/dkw397.
  • Au CH, Ho DN, Ip BBK, et al. Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing. Cancer Genet. 2019;239:22–25. doi: 10.1016/j.cancergen.2019.08.005.
  • Yu MC, Hung CS, Huang CK, et al. Integrative utility of long read sequencing-based whole genome analysis and phenotypic assay on differentiating isoniazid-resistant signature of Mycobacterium tuberculosis. J Biomed Sci. 2021;28(1):86. doi: 10.1186/s12929-021-00783-x.
  • Jain M, Koren S, Miga KH, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36(4):338–345. doi: 10.1038/nbt.4060.
  • Cao B, Huang Y, She DY, et al. Diagnosis and treatment of community-acquired pneumonia in adults: 2016 clinical practice guidelines by the Chinese thoracic society, Chinese medical association. Clin Respir J. 2018;12(4):1320–1360. doi: 10.1111/crj.12674.
  • Torres A, Niederman MS, Chastre J, et al. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia: guidelines for the management of Hospital-Acquired Pneumonia (HAP)/Ventilator-Associated Pneumonia (VAP) of the European Respiratory Society (ERS), European Society of Intensive Care Medicine (ESICM), European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and asociación latinoamericana del tórax (ALAT). Eur Respir J. 2017;50(3):1700582. doi: 10.1183/13993003.00582-2017.
  • Zhou H, Larkin PMK, Zhao D, et al. Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and management of pneumonia: a multicenter prospective observational study. J Mol Diagn. 2021;23(10):1259–1268. doi: 10.1016/j.jmoldx.2021.06.007.
  • Langelier C, Zinter MS, Kalantar K, et al. Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients. Am J Respir Crit Care Med. 2018;197(4):524–528. doi: 10.1164/rccm.201706-1097LE.
  • Bittinger K, Charlson ES, Loy E, et al. Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biol. 2014;15(10):487. doi: 10.1186/s13059-014-0487-y.
  • Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med. 2017;141(6):776–786. doi: 10.5858/arpa.2016-0539-RA.
  • Doughty EL, Sergeant MJ, Adetifa I, et al. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ. 2014;2:e585. doi: 10.7717/peerj.585.
  • Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis. 2018;66(5):778–788. doi: 10.1093/cid/cix881.
  • van Ingen J, Kohl TA, Kranzer K, et al. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. Lancet Infect Dis. 2017;17(10):1033–1041. doi: 10.1016/s1473-3099(17)30324-9.
  • Özçolpan OO, Sürücüoğlu S, Özkütük N, et al. Distribution of nontuberculous mycobacteria isolated from clinical specimens and identified with DNA sequence analysis. Mikrobiyol Bul. 2015;49(4):484–493. doi: 10.5578/mb.9698.
  • Graf EH, Simmon KE, Tardif KD, et al. Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. J Clin Microbiol. 2016;54(4):1000–1007. doi: 10.1128/jcm.03060-15.
  • Hill UG, Floto RA, Haworth CS. Non-tuberculous mycobacteria in cystic fibrosis. J R Soc Med. 2012;105(Suppl 2):S14–S18. doi: 10.1258/jrsm.2012.12s003.
  • Webb BJ, Sorensen J, Jephson A, et al. Broad-spectrum antibiotic use and poor outcomes in community-onset pneumonia: a cohort study. Eur Respir J. 2019;54(1):1900057. doi: 10.1183/13993003.00057-2019.
  • Holter JC, Müller F, Bjørang O, et al. Etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in Norway. BMC Infect Dis. 2015;15(1):64. doi: 10.1186/s12879-015-0803-5.
  • Jain S, Self WH, Wunderink RG, et al. Community-acquired pneumonia requiring hospitalization among U.S. Adults. N Engl J Med. 2015;373(5):415–427. doi: 10.1056/NEJMoa1500245.
  • Gadsby NJ, Russell CD, McHugh MP, et al. Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia. Clin Infect Dis. 2016;62(7):817–823. doi: 10.1093/cid/civ1214.
  • Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J. 2021;19:1497–1511. doi: 10.1016/j.csbj.2021.02.020.
  • Zhang Y, Lu X, Tang LV, et al. Nanopore-targeted sequencing improves the diagnosis and treatment of patients with serious infections. mBio. 2023;14(1):e0305522. doi: 10.1128/mbio.03055-22.
  • Yu G, Wang X, Zhu P, et al. Comparison of the efficacy of metagenomic next-generation sequencing and xpert MTB/RIF in the diagnosis of tuberculous meningitis. J Microbiol Methods. 2021;180:106124. doi: 10.1016/j.mimet.2020.106124.
  • Wang J, Han Y, Feng J. Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis. BMC Pulm Med. 2019;19(1):252. doi: 10.1186/s12890-019-1022-4.