References
- Aksamit TR, O’Donnell AE, Barker A, Olivier KN, Winthrop KL, Daniels MLA, Johnson M, Eden E, Griffith D, Knowles M, et al. Adult patients with bronchiectasis: A first look at the US Bronchiectasis Research Registry. Chest. 2017 May;151(5):982–992. https://doi.org/10.1016/j.chest.2016.10.055
- Aliberti S, Lonni S, Dore S, McDonnell MJ, Goeminne PC, Dimakou K, Fardon TC, Rutherford R, Pesci A, Restrepo MI, et al. Clinical phenotypes in adult patients with bronchiectasis. Eur Respir J. 2016 Apr;47(4):1113–1122. https://doi.org/10.1183/13993003.01899-2015
- Amati F, Simonetta E, Gramegna A, Tarsia P, Contarini M, Blasi F, Aliberti S. The biology of pulmonary exacerbations in bronchiectasis. Eur Respir Rev. 2019 Nov;28(154):190055. https://doi.org/10.1183/16000617.0055-2019
- Bilton D, Henig N, Morrissey B, Gotfried M. Addition of inhaled tobramycin to ciprofloxacin for acute exacerbations of Pseudomonas aeruginosa infection in adult bronchiectasis. Chest. 2006 Nov; 130(5):1503–1510. https://doi.org/10.1378/chest.130.5.1503
- Bronchiectasis Expert Consensus Writing Group, Pulmonary Infection Assembly of Chinese Thoracic Society. [Expert consensus on the diagnosis and treatment of adult bronchiectasis in China] (in Chinese). Zhonghua Jie He He Hu Xi Za Zhi. 2021 Apr;44(4):311–321. https://doi.org/10.3760/cma.j.cn112147-20200617-00717
- Byun MK, Chang J, Kim HJ, Jeong SH. Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis. PLoS One. 2017 Aug;12(8):e0183553. https://doi.org/10.1371/journal.pone.0183553
- Chalmers JD, Chang AB, Chotirmall SH, Dhar R, McShane PJ. Bronchiectasis. Nat Rev Dis Primers. 2018 Nov;4(1):45. https://doi.org/10.1038/s41572-018-0042-3
- Chalmers JD, Goeminne P, Aliberti S, McDonnell MJ, Lonni S, Davidson J, Poppelwell L, Salih W, Pesci A, Dupont LJ, et al. The bronchiectasis severity index. An international derivation and validation study. Am J Respir Crit Care Med. 2014 Mar;189(5): 576–585. https://doi.org/10.1164/rccm.201309-1575OC
- Chalmers JD, Smith MP, McHugh BJ, Doherty C, Govan JR, Hill AT. Short- and long-term antibiotic treatment reduces airway and systemic inflammation in non-cystic fibrosis bronchiectasis. Am J Respir Crit Care Med. 2012 Oct;186(7):657–665. https://doi.org/10.1164/rccm.201203-0487OC
- Chandrasekaran R, Mac Aogáin M, Chalmers JD, Elborn SJ, Chotirmall SH. Geographic variation in the aetiology, epidemiology and microbiology of bronchiectasis. BMC Pulm Med. 2018 May; 18(1):83. https://doi.org/10.1186/s12890-018-0638-0
- Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep;34(17):i884–i890. https://doi.org/10.1093/bioinformatics/bty560
- Chen Y, Feng W, Ye K, Guo L, Xia H, Guan Y, Chai L, Shi W, Zhai C, Wang J, et al. Application of metagenomic next-generation sequencing in the diagnosis of pulmonary infectious pathogens from bronchoalveolar lavage samples. Front Cell Infect Microbiol. 2021 Mar;11:541092. https://doi.org/10.3389/fcimb.2021.541092
- Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019 Jun;20(6):341–355. https://doi.org/10.1038/s41576-019-0113-7
- Cox MJ, Turek EM, Hennessy C, Mirza GK, James PL, Coleman M, Jones A, Wilson R, Bilton D, Cookson WO, et al. Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients. PLoS One. 2017 Feb;12(2):e0170622. https://doi.org/10.1371/journal.pone.0170622
- Davies J, Denyer T, Hadfield J. Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA. Biotechniques. 2016 Apr;60(4):197–199. https://doi.org/10.2144/000114403
- de Sena Brandine G, Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Res. 2019 Nov; 8:1874. https://doi.org/10.12688/f1000research.21142.2
- Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections. J Adv Res. 2021 Sep;38:201–212. https://doi.org/10.1016/j.jare.2021.09.012
- Evans DJ, Greenstone M. Long-term antibiotics in the management of non-CF bronchiectasis--do they improve outcome? Respir Med. 2003 Jul;97(7):851–858. https://doi.org/10.1016/s0954-6111(03)00063-5
- Feng J, Sun L, Sun X, Xu L, Liu L, Liu G, Wang J, Gao P, Zhan S, Chen Y, et al. Increasing prevalence and burden of bronchiectasis in urban Chinese adults, 2013–2017: A nationwide population-based cohort study. Respir Res. 2022 May 4;23(1):111. https://doi.org/10.1186/s12931-022-02023-8
- Flume PA, Chalmers JD, Olivier KN. Advances in bronchiectasis: endotyping, genetics, microbiome, and disease heterogeneity. Lancet. 2018 Sep;392(10150):880–890. https://doi.org/10.1016/S0140-6736(18)31767-7
- Gao L, Qin KR, Li T, Wang HL, Pang M. The clinical phenotype of bronchiectasis and its clinical guiding implications. Exp Biol Med. 2021 Feb;246(3):275–280. https://doi.org/10.1177/1535370220972324
- Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol. 2019 Jan; 14:319–338. https://doi.org/10.1146/annurev-pathmechdis-012418-012751
- Guarner J, Brandt ME. Histopathologic diagnosis of fungal infections in the 21st century. Clin Microbiol Rev. 2011 Apr;24(2):247–280. https://doi.org/10.1128/CMR.00053-10
- He Y, Fang K, Shi X, Yang D, Zhao L, Yu W, Zheng Y, Xu Y, Ma X, Chen L, et al. Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia. J Transl Med. 2022 May;20(1):195. https://doi.org/10.1186/s12967-022-03397-5
- Hill AT, Welham SA, Sullivan AL, Loebinger MR. Updated BTS Adult Bronchiectasis Guideline 2018: A multidisciplinary approach to comprehensive care. Thorax. 2019 Jan;74(1):1–3. https://doi.org/10.1136/thoraxjnl-2018-212468
- Huang HY, Lo CY, Chung FT, Huang YT, Ko PC, Lin CW, Huang YC, Chung KF, Wang CH. Risk factors for influenza-induced exacerbations and mortality in non-cystic fibrosis bronchiectasis. Viruses. 2023 Feb;15(2):537. https://doi.org/10.3390/v15020537
- Jeon YJ, Zhou Y, Li Y, Guo Q, Chen J, Quan S, Zhang A, Zheng H, Zhu X, Lin J, et al. The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform. PLoS One. 2014 Oct;9(10):e110240. https://doi.org/10.1371/journal.pone.0110240
- Kosmidis C, Denning DW. Republished: The clinical spectrum of pulmonary aspergillosis. Postgrad Med J. 2015 Jul;91(1077): 403–410. https://doi.org/10.1136/postgradmedj-2014-206291rep
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul;25(14):1754–1760. https://doi.org/10.1093/bioinformatics/btp324
- Li S, Qin J, Zhou P, Peng M, Qian J, Cai Y, Shi Q, Tung TH, Shen B, Yu S. The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections. Front Cell Infect Microbiol. 2022 Dec;12:961746. https://doi.org/10.3389/fcimb.2022.961746
- Li X, Liang S, Zhang D, He M, Zhang H. The clinical application of metagenomic next-generation sequencing in sepsis of immunocompromised patients. Front Cell Infect Microbiol. 2023 Apr; 13:1170687. https://doi.org/10.3389/fcimb.2023.1170687
- Ma D, Cruz MJ, Ojanguren I, Romero-Mesones C, Varona-Porres D, Munoz X. Risk factors for the development of bronchiectasis in patients with asthma. Sci Rep. 2021 Nov;11(1):22820. https://doi.org/10.1038/s41598-021-02332-w
- Maartens G, Griesel R, Dube F, Nicol M, Mendelson M. Etiology of pulmonary infections in human immunodeficiency virus-infected inpatients using sputum multiplex real-time polymerase chain reaction. Clin Infect Dis. 2020 Mar;70(6):1147–1152. https://doi.org/10.1093/cid/ciz332
- Martinez-Garcia MA, Athanazio RA, Girón R, Máiz-Carro L, de la Rosa D, Olveira C, de Gracia J, Vendrell M, Prados-Sánchez C, Gramblicka G, et al. Predicting high risk of exacerbations in bronchiectasis: The E-FACED score. Int J Chron Obstruct Pulmon Dis. 2017 Jan;12:275–284. https://doi.org/10.2147/COPD.S121943
- Martinez-García MA. Pseudomonas aeruginosa infection and exacerbations in bronchiectasis: More questions than answers. Eur Respir J. 2018 Jan;51(2):1702497. https://doi.org/10.1183/13993003.02497-2017
- Mei J, Hu H, Zhu S, Ding H, Huang Z, Li W, Yang B, Zhang W, Fang X. Diagnostic role of mNGS in polymicrobial periprosthetic joint infection. J Clin Med. 2023 Feb;12(5):1838. https://doi.org/10.3390/jcm12051838
- Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 2018 Nov;67(suppl_2):S231–S240. https://doi.org/10.1093/cid/ciy693
- Qi C, Hountras P, Pickens CO, Walter JM, Kruser JM, Singer BD, Seed P, Green SJ, Wunderink RG. Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing. J Med Microbiol. 2019 Jul;68(7):996–1002. https://doi.org/10.1099/jmm.0.000968
- Qian YY, Wang HY, Zhou Y, Zhang HC, Zhu YM, Zhou X, Ying Y, Cui P, Wu HL, Zhang WH, et al. Improving pulmonary infection diagnosis with metagenomic next generation sequencing. Front Cell Infect Microbiol. 2021 Jan;10:567615. https://doi.org/10.3389/fcimb.2020.567615
- Quint JK, Millett ER, Joshi M, Navaratnam V, Thomas SL, Hurst JR, Smeeth L, Brown JS. Changes in the incidence, prevalence and mortality of bronchiectasis in the UK from 2004 to 2013: A population-based cohort study. Eur Respir J. 2016 Jan;47(1):186–193. https://doi.org/10.1183/13993003.01033-2015
- Ren D, Ren C, Yao R, Zhang L, Liang X, Li G, Wang J, Meng X, Liu J, Ye Y, et al. The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis. BMC Infect Dis. 2021 Dec;21(1):1257. https://doi.org/10.1186/s12879-021-06934-7
- Ringshausen FC, Rademacher J, Pink I, de Roux A, Hickstein L, Ploner T, Welte T, Diel R. Increasing bronchiectasis prevalence in Germany, 2009–2017: A population-based cohort study. Eur Respir J. 2019 Dec;54(6):1900499. https://doi.org/10.1183/13993003.00499-2019
- Ruppé E, Baud D, Schicklin S, Guigon G, Schrenzel J. Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia. Future Microbiol. 2016;11(3):427–439. https://doi.org/10.2217/fmb.15.144
- Sibila O, Suarez-Cuartin G, Rodrigo-Troyano A, Fardon TC, Finch S, Mateus EF, Garcia-Bellmunt L, Castillo D, Vidal S, Sanchez-Reus F, et al. Secreted mucins and airway bacterial colonization in non-CF bronchiectasis. Respirology. 2015 Oct;20(7):1082–1088. https://doi.org/10.1111/resp.12595
- Wang J, Han Y, Feng J. Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis. BMC Pulm Med. 2019 Dec;19(1):252. https://doi.org/10.1186/s12890-019-1022-4
- Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019 Nov;20(1):257. https://doi.org/10.1186/s13059-019-1891-0
- Yan L, Sun W, Lu Z, Fan L. Metagenomic Next-Generation Sequencing (mNGS) in cerebrospinal fluid for rapid diagnosis of Tuberculosis meningitis in HIV-negative population. Int J Infect Dis. 2020 Jul; 96:270–275. https://doi.org/10.1016/j.ijid.2020.04.048
- Yang A, Chen C, Hu Y, Zheng G, Chen P, Xie Z, Fan H, Sun Y, Wu P, Jiang W, et al. Application of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) in diagnosing pneumonia of children. Microbiol Spectr. 2022 Oct;10(5):e0148822. https://doi.org/10.1128/spectrum.01488-22
- Zhang P, Chen Y, Li S, Li C, Zhang S, Zheng W, Chen Y, Ma J, Zhang X, Huang Y, et al. Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. Peer J. 2020 Jul;8:e9623. https://doi.org/10.7717/peerj.9623
- Zhao L, Luo JL, Ali MK, Spiekerkoetter E, Nicolls MR. The human respiratory microbiome: Current understandings and future directions. Am J Respir Cell Mol Biol. 2023 Mar;68(3): 245–255. https://doi.org/10.1165/rcmb.2022-0208TR