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Bronchoalveolar lavage fluid (BALF): Clinical applications for present and future

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    1. Bronchoalveolar lavage fluid has significant clinical application potential.

      Bronchoalveolar lavage fluid detection encompasses cytology, microbiology, and molecular biology.

      The omics era facilitates clinical practice based on bronchoalveolar lavage fluid.

  • Lungs are exposed to a wide range of complex internal and external environmental factors, creating a complex pulmonary microenvironment that remains challenging to detect and interpret. Bronchoalveolar lavage fluid (BALF) contains an abundance of cells, microorganisms, and active substances, thus is considered to be a clinically promising body fluid detection substance that is representative of the pulmonary microenvironment. The combination of experimental strategies with emerging omics technologies has advanced the identification and interpretation of microscopic components in BALF, underscoring its applications in clinical detection. In summary, this review provides a systematic overview of the development understanding of BALF, discusses its possible applications in clinical diagnosis, prediction, and intervention, and highlights the role of emerging omics technologies in deciphering BALF.
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  • [1] Zepp J.A. and Morrisey E.E. (2019). Cellular crosstalk in the development and regeneration of the respiratory system. Nat. Rev. Mol. Cell Biol. 20:551−566. DOI:10.1038/s41580-019-0141-3

    View in Article CrossRef Google Scholar Scopus

    [2] Zepp J.A., Morley M.P., Loebel C., et al. (2021). Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus. Science (New York, N.Y.) 371:eabc3172. DOI:10.1126/science.abc3172

    View in Article CrossRef Google Scholar Scopus

    [3] Sapoval B., Kang M. and Dinh-Xuan A.T. (2020). Modeling of gas exchange in the lungs. Compr. Physiol. 11:1289−1314. DOI:10.1002/cphy.c190019

    View in Article CrossRef Google Scholar Scopus

    [4] Melbourne C.A., Mesut Erzurumluoglu A., Shrine N., et al. (2022). Genome-wide gene-air pollution interaction analysis of lung function in 300,000 individuals. Environ. Int. 159:107041. DOI:10.1016/j.envint.2021.107041

    View in Article CrossRef Google Scholar Scopus

    [5] Feng G., Xia J., Wang X., et al. (2024). Assessing the disease burden of air pollution on children and adolescents in china from 1990 to 2019. Innov. Med. 2:100057. DOI:10.59717/j.xinn-med.2024.100057

    View in Article CrossRef Google Scholar

    [6] Olesiejuk K. and Chałubiński M. (2023). How does particulate air pollution affect barrier functions and inflammatory activity of lung vascular endothelium. Allergy 78:629−638. DOI:10.1111/all.15630

    View in Article CrossRef Google Scholar Scopus

    [7] Cai M., Su B., Hu G., et al. (2024). Long term exposure to PM2.5 chemical components associated with prevalence of cardiovascular diseases in China. Innov. Med. 2 :100077. DOI: 10.59717/j.xinn-med.2024.100077

    View in Article Google Scholar

    [8] Unger S.A. and Bogaert D. (2017). The respiratory microbiome and respiratory infections. J. Infect. 74 Suppl 1 :S84-S88. DOI: 10.1016/S0163-4453(17)30196-2

    View in Article Google Scholar

    [9] Wang C.C., Prather K.A., Sznitman J., et al. (2021). Airborne transmission of respiratory viruses. Science (New York, N.Y.) 373:eabd9149. DOI:10.1126/science.abd9149

    View in Article CrossRef Google Scholar Scopus

    [10] Falagas M.E., Agrafiotis M., Athanassa Z., et al. (2008). Administration of antibiotics via the respiratory tract as monotherapy for pneumonia. Expert Rev. Anti-Infect. Ther. 6:447−452. DOI:10.1586/14787210.6.4.447

    View in Article CrossRef Google Scholar

    [11] Hill W., Lim E.L., Weeden C.E., et al. (2023). Lung adenocarcinoma promotion by air pollutants. Nature 616:159−167. DOI:10.1038/s41586-023-05874-3

    View in Article CrossRef Google Scholar Scopus

    [12] Ravaglia C., Doglioni C., Chilosi M., et al. (2022). Clinical, radiological and pathological findings in patients with persistent lung disease following SARS-cov-2 infection. Eur. Respir. J. 60:2102411. DOI:10.1183/13993003.02411-2021

    View in Article CrossRef Google Scholar

    [13] Lim K., Donovan A.P.A., Tang W., et al. (2023). Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease. Cell Stem Cell 30:20−37. DOI:10.1016/j.stem.2022.11.013

    View in Article CrossRef Google Scholar Scopus

    [14] Youk J., Kim T., Evans K.V., et al. (2020). Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-cov-2. Cell Stem Cell 27:905−919. DOI:10.1016/j.stem.2020.10.004

    View in Article CrossRef Google Scholar

    [15] Mei J., Liu X., Tian H.X., et al. (2024). Tumour organoids and assembloids: Patient-derived cancer avatars for immunotherapy. Clin. Transl. Med. 14:e1656. DOI:10.1002/ctm2.1656

    View in Article CrossRef Google Scholar

    [16] Liao M., Liu Y., Yuan J., et al. (2020). Single-cell landscape of bronchoalveolar immune cells in patients with covid-19. Nat. Med. 26:842−844. DOI:10.1038/s41591-020-0901-9

    View in Article CrossRef Google Scholar

    [17] Li T., Liu Y., Zhang W., et al. (2020). A rapid liquid biopsy of lung cancer by separation and detection of exfoliated tumor cells from bronchoalveolar lavage fluid with a dual-layer "perfect" filter system. Theranostics 10:6517−6529. DOI:10.7150/thno.44274

    View in Article CrossRef Google Scholar

    [18] Darlington P., Kullberg S., Eklund A., et al. (2020). Subpopulations of cells from bronchoalveolar lavage can predict prognosis in sarcoidosis. Eur. Respir. J. 55:1901450. DOI:10.1183/13993003.01450-2019

    View in Article CrossRef Google Scholar Scopus

    [19] Masuhiro K., Tamiya M., Fujimoto K., et al. (2022). Bronchoalveolar lavage fluid reveals factors contributing to the efficacy of pd-1 blockade in lung cancer. JCI Insight 7:e157915. DOI:10.1172/jci.insight.157915

    View in Article CrossRef Google Scholar

    [20] Liao L. and Yang G. (2021). Clinical significance of cellular immunity function and inflammatory factors assays in alveolar lavage fluid for severe covid-19 pneumonia. J. Med. Virol. 93:2979−2987. DOI:10.1002/jmv.26827

    View in Article CrossRef Google Scholar

    [21] Daniele R.P., Elias J.A., Epstein P.E., et al. (1985). Bronchoalveolar lavage: Role in the pathogenesis, diagnosis, and management of interstitial lung disease. Ann. Intern. Med. 102:93−108

    View in Article Google Scholar

    [22] Xu P., Tang P., Song H., et al. (2019). The incremental value of bronchoalveolar lavage for the diagnosis of pulmonary tuberculosis in a high-burden urban setting. J. Infect. 79:24−29. DOI:10.1016/j.jinf.2019.05.009

    View in Article CrossRef Google Scholar Scopus

    [23] Chen S., Kang Y., Li D., et al. (2022). Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: systematic review and meta-analysis. Int. J. Infect. Dis. 122:867−873. DOI:10.1016/j.ijid.2022.07.054

    View in Article CrossRef Google Scholar

    [24] Ding W., Yue W. and Fu Y. (2010). [The current research feature and prospect of bronchoalveolar lavage in diagnosing lung cancer]. Chinese Journal of Lung Cancer 13:370−374. DOI:10.3779/j.issn.1009-3419.2010.04.19

    View in Article CrossRef Google Scholar

    [25] Niederman M.S. (2010). The argument against using quantitative cultures in clinical trials and for the management of ventilator-associated pneumonia. Clin. Infect. Dis. 51 Suppl 1 :S93-S99. DOI: 10.1086/653055

    View in Article Google Scholar

    [26] Miao Q., Ma Y., Wang Q., et al. (2018). Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin. Infect. Dis. 67:S231−S240. DOI:10.1093/cid/ciy693

    View in Article CrossRef Google Scholar

    [27] Ewig S., Torres A., Angeles Marcos M., et al. (2002). Factors associated with unknown aetiology in patients with community-acquired pneumonia. Eur. Respir. J. 20:1254−1262. DOI:10.1183/09031936.02.01942001

    View in Article CrossRef Google Scholar

    [28] Tian H.X., Mei J., Cao L., et al. (2023). Disruption of iron homeostasis to induce ferroptosis with albumin-encapsulated pt(iv) nanodrug for the treatment of non-small cell lung cancer. Small 19:e2206688. DOI:10.1002/smll.202206688

    View in Article CrossRef Google Scholar

    [29] Zöllner F. (1965). Gustav Killian, father of bronchoscopy. Arch. Otolaryngol. 82:656−659.

    View in Article Google Scholar

    [30] Boyd A.D. (1994). Chevalier Jackson: The father of American bronchoesophagoscopy. Ann. Thorac. Surg. 57:502−505.

    View in Article Google Scholar

    [31] Ikeda S., Tsuboi E., Ono R., et al. (2010). Flexible bronchofiberscope. Jpn. J. Clin. Oncol. 40:e55−e64. DOI:10.1093/jjco/hyq114

    View in Article CrossRef Google Scholar

    [32] Ikeda S., Yanai N. and Ishikawa S. (1968). Flexible bronchofiberscope. The Keio Journal of Medicine 17:1−16.

    View in Article Google Scholar

    [33] Fujino M.A., Morozumi A., Nakamura T., et al. (1994). Electronic endoscopy in perspective. J. Gastroenterol. 29 Suppl 7 :85-90.

    View in Article Google Scholar

    [34] Demling L. and Hagel H.J. (1985). Video endoscopy. Fundamentals and problems. Endoscopy 17:167−169. DOI:10.1055/s-2007-1018491

    View in Article CrossRef Google Scholar

    [35] Classen M. and Phillip J. (1984). Electronic endoscopy of the gastrointestinal tract. Initial experience with a new type of endoscope that has no fiberoptic bundle for imaging. Endoscopy 16:16−19. DOI:10.1055/s-2007-1018518

    View in Article CrossRef Google Scholar

    [36] Andersen H.A. and Fontana R.S. (1972). Transbronchoscopic lung biopsy for diffuse pulmonary diseases: Technique and results in 450 cases. Chest 62:125−128. DOI:10.1378/chest.62.2.125

    View in Article CrossRef Google Scholar

    [37] Reynolds H.Y. and Newball H.H. (1974). Analysis of proteins and respiratory cells obtained from human lungs by bronchial lavage. The Journal of Laboratory and Clinical Medicine 84:559−573.

    View in Article Google Scholar

    [38] Springmeyer S.C., Hackman R., Carlson J.J., et al. (1983). Bronchiolo-alveolar cell carcinoma diagnosed by bronchoalveolar lavage. Chest 83:278−279. DOI:10.1378/chest.83.2.278

    View in Article CrossRef Google Scholar

    [39] Goel S., Yeshvanth S.K., Asnani R., et al. (2022). Accuracy of bronchial cytological diagnosis in lung lesions in comparison with histopathology. J. Cytol. 39:163−168. DOI:10.4103/joc.joc_44_22

    View in Article CrossRef Google Scholar Scopus

    [40] Bezel P., Valaperti A., Steiner U., et al. (2021). Evaluation of cytokines in the tumor microenvironment of lung cancer using bronchoalveolar lavage fluid analysis. Cancer Immunol. Immunother. 70:1867−1876. DOI:10.1007/s00262-020-02798-z

    View in Article CrossRef Google Scholar Scopus

    [41] Tanaka Y., Nakai T., Suzuki A., et al. (2023). Clinicopathological significance of peritumoral alveolar macrophages in patients with resected early-stage lung squamous cell carcinoma. Cancer Immunol. Immunother. 72:2205−2215. DOI:10.1007/s00262-023-03393-8

    View in Article CrossRef Google Scholar Scopus

    [42] Meyer K.C., Raghu G., Baughman R.P., et al. (2012). An official american thoracic society clinical practice guideline: The clinical utility of bronchoalveolar lavage cellular analysis in interstitial lung disease. Am. J. Respir. Crit. Care Med. 185:1004−1014. DOI:10.1164/rccm.201202-0320ST

    View in Article CrossRef Google Scholar

    [43] Frye B.C., Schupp J.C., Rothe M.E., et al. (2020). The value of bronchoalveolar lavage for discrimination between healthy and diseased individuals. J. Intern. Med. 287:54−65. DOI:10.1111/joim.12973

    View in Article CrossRef Google Scholar Scopus

    [44] Chen C., Liu F., Quan S., et al. (2023). Microplastics in the bronchoalveolar lavage fluid of chinese children: Associations with age, city development, and disease features. Environ. Sci. Technol. 57:12594−12601. DOI:10.1021/acs.est.3c01771

    View in Article CrossRef Google Scholar

    [45] Catinon M., Cavalin C., Chemarin C., et al. (2018). Sarcoidosis, inorganic dust exposure and content of bronchoalveolar lavage fluid: the minasarc pilot study. Sarcoidosis Vasc. Diffuse Lung Dis. 35:327−332. DOI:10.36141/svdld.v35i4.7058

    View in Article CrossRef Google Scholar

    [46] Hastie A.T., Bishop A.C., Khan M.S., et al. (2024). Protein-protein interactive networks identified in bronchoalveolar lavage of severe compared to nonsevere asthma. Clin. Exp. Allergy 54:265−277. DOI:10.1111/cea.14447

    View in Article CrossRef Google Scholar

    [47] Mayr C.H., Simon L.M., Leuschner G., et al. (2021). Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers. EMBO Mol. Med. 13:e12871. DOI:10.15252/emmm.202012871

    View in Article CrossRef Google Scholar Scopus

    [48] Stjärne Aspelund A., Hammarström H., Inghammar M., et al. (2018). Heparin-binding protein, lysozyme, and inflammatory cytokines in bronchoalveolar lavage fluid as diagnostic tools for pulmonary infection in lung transplanted patients. Am. J. Transplant. 18:444−452. DOI:10.1111/ajt.14458

    View in Article CrossRef Google Scholar

    [49] Man W.H., de Steenhuijsen Piters W.A.A. and Bogaert D. (2017). The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat. Rev. Microbiol. 15:259−270. DOI:10.1038/nrmicro.2017.14

    View in Article CrossRef Google Scholar

    [50] Thibeault C., Suttorp N. and Opitz B. (2021). The microbiota in pneumonia: from protection to predisposition. Sci. Transl. Med. 13:eaba501. DOI:10.1126/scitranslmed.aba0501

    View in Article CrossRef Google Scholar

    [51] Wypych T.P., Wickramasinghe L.C. and Marsland B.J. (2019). The influence of the microbiome on respiratory health. Nat. Immunol. 20:1279−1290. DOI:10.1038/s41590-019-0451-9

    View in Article CrossRef Google Scholar Scopus

    [52] Xiang L. and Meng X. (2022). Emerging cellular and molecular interactions between the lung microbiota and lung diseases. Crit. Rev. Microbiol. 48:577−610. DOI:10.1080/1040841X.2021.1992345

    View in Article CrossRef Google Scholar Scopus

    [53] Natalini J.G., Singh S. and Segal L.N. (2023). The dynamic lung microbiome in health and disease. Nat. Rev. Microbiol. 21:222−235. DOI:10.1038/s41579-022-00821-x

    View in Article CrossRef Google Scholar Scopus

    [54] de Blic J., Midulla F., Barbato A., et al. (2000). Bronchoalveolar lavage in children. ERS Task Force on bronchoalveolar lavage in children. European Respiratory Society. Eur. Respir. J. 15:217−231. DOI:10.1183/09031936.00.15121700

    View in Article CrossRef Google Scholar

    [55] Du Rand I.A., Blaikley J., Booton R., et al. (2013). British thoracic society guideline for diagnostic flexible bronchoscopy in adults: accredited by nice. Thorax 68 Suppl 1 :i1-i44. DOI: 10.1136/thoraxjnl-2013-203618

    View in Article Google Scholar

    [56] Qu J., Zhou J. and Yu Y. (2017). [Chinese expert consensus on pathogen detection of bronchoalveolar lavage for pulmonary infectious diseases (2017)]. Chinese Journal of Tuberculosis and Respiratory Diseases 40:578−583. DOI:10.3760/cma.j.issn.1001-0939.2017.08.007

    View in Article CrossRef Google Scholar

    [57] Connett G.J. (2000). Bronchoalveolar lavage. Paediatr. Respir. Rev. 1:52−56. DOI:10.1053/prrv.2000.0007

    View in Article CrossRef Google Scholar Scopus

    [58] Zhou D., Wu M., Xu S., et al. (2020). [Consensus of chinese experts on morphological examination of bronchoalveolar lavage fluid cells (2020)]. Journal of Modern Laboratory Medicine 35:4−8. DOI:10.3969/j.issn.1671-7414.2020.06.002

    View in Article CrossRef Google Scholar

    [59] Xiao G., Cai Z., Guo Q., et al. (2022). Insights into the unique lung microbiota profile of pulmonary tuberculosis patients using metagenomic next-generation sequencing. Microbiol. Spectr. 10:e190121. DOI:10.1128/spectrum.01901-21

    View in Article CrossRef Google Scholar

    [60] Zhang H., Deng D., Li S., et al. (2023). Bronchoalveolar lavage fluid assessment facilitates precision medicine for lung cancer. Cancer Biol. Med. 21:230−251. DOI:10.20892/j.issn.2095-3941.2023.0381

    View in Article CrossRef Google Scholar Scopus

    [61] Kadota N., Nakahira N., Miyauchi M., et al. (2022). Usefulness of bronchoalveolar lavage (BAL) in the diagnosis of pulmonary alveolar proteinosis. QJM 115:767−768. DOI:10.1093/qjmed/hcac168

    View in Article CrossRef Google Scholar Scopus

    [62] Patolia S., Tamae Kakazu M., Chami H.A., et al. (2020). Bronchoalveolar lavage lymphocytes in the diagnosis of hypersensitivity pneumonitis among patients with interstitial lung disease. Ann. Am. Thorac. Soc. 17:1455−1467. DOI:10.1513/AnnalsATS.202005-420OC

    View in Article CrossRef Google Scholar Scopus

    [63] Barcik W., Boutin R.C.T., Sokolowska M., et al. (2020). The role of lung and gut microbiota in the pathology of asthma. Immunity 52:241−255. DOI:10.1016/j.immuni.2020.01.007

    View in Article CrossRef Google Scholar

    [64] Sommariva M., Le Noci V., Bianchi F., et al. (2020). The lung microbiota: Role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy. Cell. Mol. Life Sci. 77:2739−2749. DOI:10.1007/s00018-020-03452-8

    View in Article CrossRef Google Scholar

    [65] Gosens R., Hiemstra P.S., Adcock I.M., et al. (2020). Host-microbe cross-talk in the lung microenvironment: implications for understanding and treating chronic lung disease. The Eur. Respir. J. 56:1902320. DOI:10.1183/13993003.02320-2019

    View in Article CrossRef Google Scholar

    [66] Scholte J.B.J., van Dessel H.A., Linssen C.F.M., et al. (2014). Endotracheal aspirate and bronchoalveolar lavage fluid analysis: Interchangeable diagnostic modalities in suspected ventilator-associated pneumonia. J. Clin. Microbiol. 52:3597−3604. DOI:10.1128/JCM.01494-14

    View in Article CrossRef Google Scholar

    [67] Zhang R., Wu Y., Deng G., et al. (2022). Value of sputum gram stain, sputum culture, and bronchoalveolar lavage fluid gram stain in predicting single bacterial pathogen among children with community-acquired pneumonia. BMC Pulm. Med. 22:427. DOI:10.1186/s12890-022-02234-1

    View in Article CrossRef Google Scholar

    [68] Zhao D., Yang X., Chen Q., et al. (2012). A modified acid-fast staining method for rapid detection of mycobacterium tuberculosis. J. Microbiol. Methods 91:128−132. DOI:10.1016/j.mimet.2012.07.024

    View in Article CrossRef Google Scholar

    [69] Doering T.L. (2009). How sweet it is! Cell wall biogenesis and polysaccharide capsule formation in cryptococcus neoformans. Annu. Rev. Microbiol. 63:223−247. DOI:10.1146/annurev.micro.62.081307.162753

    View in Article CrossRef Google Scholar

    [70] De Pauw B., Walsh T.J., Donnelly J.P., et al. (2008). Revised definitions of invasive fungal disease from the european organization for research and treatment of cancer/invasive fungal infections cooperative group and the national institute of allergy and infectious diseases mycoses study group (eortc/msg) consensus group. Clin. Infect. Dis. 46:1813−1821. DOI:10.1086/588660

    View in Article CrossRef Google Scholar

    [71] Rohner P., Jacomo V., Studer R., et al. (2009). Detection of pneumocystis jirovecii by two staining methods and two quantitative PCR assays. Infection 37:261−265. DOI:10.1007/s15010-008-8027-x

    View in Article CrossRef Google Scholar

    [72] Liu X., Hou X., Gao L., et al. (2018). Indicators for prediction of mycobacterium tuberculosis positivity detected with bronchoalveolar lavage fluid. Infect. Dis. Poverty 7:22. DOI:10.1186/s40249-018-0403-x

    View in Article CrossRef Google Scholar

    [73] Ashitani J., Kumamoto K., Matsukura S. (2000). Paragonimiasis westermani with multifocal lesions in lungs and skin. Intern. Med. 39:433−436. DOI:10.2169/internalmedicine.39.433

    View in Article CrossRef Google Scholar

    [74] S Pavia C. and M Plummer M. (2021). The evolution of rapid antigen detection systems and their application for covid-19 and other serious respiratory infectious diseases. J. Microbiol. Immunol. Infect. 54:776−786. DOI:10.1016/j.jmii.2021.06.003

    View in Article CrossRef Google Scholar

    [75] The committee of chinese laboratory medical education, chinese thoracic society of the chinese medical association. (2023). [Expert consensus on nucleic acid of amplification techniques test for the diagnosis of pathogens in adult respiratory tract infections (2023)]. Medical Journal of Peking Union Medical College Hospital 14:959−971. DOI: 10. 12290 / xhyxzz. 2023-0338. DOI:10.12290/xhyxzz.2023-0338

    View in Article CrossRef Google Scholar

    [76] Goodwin S., Mcpherson J.D. and Mccombie W.R. (2016). Coming of age: Ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17:333−351. DOI:10.1038/nrg.2016.49

    View in Article CrossRef Google Scholar

    [77] Deng W., Xu H., Wu Y., et al. (2022). Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia. Front. Cell. Infect. Microbiol. 12:950531. DOI:10.3389/fcimb.2022.950531

    View in Article CrossRef Google Scholar Scopus

    [78] Wyres K.L., Lam M.M.C. and Holt K.E. (2020). Population genomics of klebsiella pneumoniae. Nat. Rev. Microbiol. 18:344−359. DOI:10.1038/s41579-019-0315-1

    View in Article CrossRef Google Scholar

    [79] Wyres K.L. and Holt K.E. (2018). Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr. Opin. Microbiol. 45:131−139. DOI:10.1016/j.mib.2018.04.004

    View in Article CrossRef Google Scholar

    [80] Sanchez G.V., Master R.N., Clark R.B., et al. (2013). Klebsiella pneumoniae antimicrobial drug resistance, united states, 1998-2010. Emerg. Infect. Dis. 19:133−136. DOI:10.3201/eid1901.120310

    View in Article CrossRef Google Scholar

    [81] Zhang S., Abbas M., Rehman M.U., et al. (2020). Dissemination of antibiotic resistance genes (args) via integrons in escherichia coli: A risk to human health. Environ. Pollut. 266:115260. DOI:10.1016/j.envpol.2020.115260

    View in Article CrossRef Google Scholar

    [82] Tang Z., Zhang Y., Xiao S., et al. (2022). Insight into the impacts and mechanisms of ketone stress on the antibiotic resistance in Escherichia coli. Environ. Sci. Pollut. Res. Int. 29:83746−83755. DOI:10.1007/s11356-022-21600-4

    View in Article CrossRef Google Scholar Scopus

    [83] Boolchandani M., D'Souza A.W. and Dantas G. (2019). Sequencing-based methods and resources to study antimicrobial resistance. Nat. Rev. Genet. 20:356−370. DOI:10.1038/s41576-019-0108-4

    View in Article CrossRef Google Scholar Scopus

    [84] Vehreschild M.J.G.T., Hamprecht A., Peterson L., et al. (2014). A multicentre cohort study on colonization and infection with ESBL-producing Enterobacteriaceae in high-risk patients with haematological malignancies. J. Antimicrob. Chemother. 69:3387−3392. DOI:10.1093/jac/dku305

    View in Article CrossRef Google Scholar

    [85] Ha Y.E., Kang C., Cha M.K., et al. (2013). Epidemiology and clinical outcomes of bloodstream infections caused by extended-spectrum β-lactamase-producing Escherichia coli in patients with cancer. Int. J. Antimicrob. Agents 42:403−409. DOI:10.1016/j.ijantimicag.2013.07.018

    View in Article CrossRef Google Scholar

    [86] Margalit I., Lebeaux D., Tishler O., et al. (2021). How do I manage nocardiosis. Clin. Microbiol. Infect. 27:550−558. DOI:10.1016/j.cmi.2020.12.019

    View in Article CrossRef Google Scholar Scopus

    [87] Bickett T.E. and Karam S.D. (2020). Tuberculosis-cancer parallels in immune response regulation. Int. J. Mol. Sci. 21:6136. DOI:10.3390/ijms21176136

    View in Article CrossRef Google Scholar

    [88] Fol M., Koziński P., Kulesza J., et al. (2021). Dual nature of relationship between mycobacteria and cancer. International J. Mol. Sci. 22:8332. DOI:10.3390/ijms22158332

    View in Article CrossRef Google Scholar Scopus

    [89] Erkes D.A., Wilski N.A. and Snyder C.M. (2017). Intratumoral infection by cmv may change the tumor environment by directly interacting with tumor-associated macrophages to promote cancer immunity. Hum. Vaccin. Immunother. 13:1778−1785. DOI:10.1080/21645515.2017.1331795

    View in Article CrossRef Google Scholar

    [90] Cobbs C. (2019). Cytomegalovirus is a tumor-associated virus: Armed and dangerous. Curr. Opin. Virol. 39:49−59. DOI:10.1016/j.coviro.2019.08.003

    View in Article CrossRef Google Scholar

    [91] Lin Y., Lau H.C., Liu Y., et al. (2022). Altered mycobiota signatures and enriched pathogenic aspergillus rambellii are associated with colorectal cancer based on multicohort fecal metagenomic analyses. Gastroenterology 163:908−921. DOI:10.1053/j.gastro.2022.06.038

    View in Article CrossRef Google Scholar

    [92] Ullmann A.J., Aguado J.M., Arikan-Akdagli S., et al. (2018). Diagnosis and management of aspergillus diseases: executive summary of the 2017 escmid-ecmm-ers guideline. Clin. Microbiol. Infect. 24 Suppl 1 :e1-e38. DOI: 10.1016/j.cmi.2018.01.002

    View in Article Google Scholar

    [93] Schmalzle S.A., Buchwald U.K., Gilliam B.L., et al. (2016). Cryptococcus neoformans infection in malignancy. Mycoses 59:542−552. DOI:10.1111/myc.12496

    View in Article CrossRef Google Scholar

    [94] Nematollahi S. and Dioverti-Prono V. (2020). Cryptococcal infection in haematologic malignancies and haematopoietic stem cell transplantation. Mycoses 63:1033−1046. DOI:10.1111/myc.13153

    View in Article CrossRef Google Scholar Scopus

    [95] Fillatre P., Decaux O., Jouneau S., et al. (2014). Incidence of pneumocystis jiroveci pneumonia among groups at risk in HIV-negative patients. Am. J. Med. 127:1211−1242. DOI:10.1016/j.amjmed.2014.07.010

    View in Article CrossRef Google Scholar

    [96] Maschmeyer G., Helweg-Larsen J., Pagano L., et al. (2016). ECIL guidelines for treatment of pneumocystis jirovecii pneumonia in non-HIV-infected haematology patients. J. Antimicrob. Chemother. 71:2405−2413. DOI:10.1093/jac/dkw158

    View in Article CrossRef Google Scholar

    [97] Classen A.Y., Henze L., von Lilienfeld-Toal M., et al. (2021). Primary prophylaxis of bacterial infections and pneumocystis jirovecii pneumonia in patients with hematologic malignancies and solid tumors: 2020 updated guidelines of the infectious diseases working party of the german society of hematology and medical oncology (agiho/dgho). Ann. Hematol. 100:1603−1620. DOI:10.1007/s00277-021-04452-9

    View in Article CrossRef Google Scholar

    [98] Pena T. and Klesney-Tait J. (2017). Mycobacterial infections in solid organ and hematopoietic stem cell transplantation. Clin. Chest. Med. 38:761−770. DOI:10.1016/j.ccm.2017.07.011

    View in Article CrossRef Google Scholar

    [99] Russo R.L., Dulley F.L., Suganuma L., et al. (2010). Tuberculosis in hematopoietic stem cell transplant patients: case report and review of the literature. Int. J. Infect. Dis. 14 Suppl 3 :e187-e191. DOI: 10.1016/j.ijid.2009.08.001

    View in Article Google Scholar

    [100] Haidar G., Boeckh M. and Singh N. (2020). Cytomegalovirus infection in solid organ and hematopoietic cell transplantation: state of the evidence. J. Infect. Dis. 221:S23−S31. DOI:10.1093/infdis/jiz454

    View in Article CrossRef Google Scholar

    [101] De La Cruz O. and Silveira F.P. (2017). Respiratory fungal infections in solid organ and hematopoietic stem cell transplantation. Clin. Chest Med. 38:727−739. DOI:10.1016/j.ccm.2017.07.013

    View in Article CrossRef Google Scholar

    [102] Sprute R., Nacov J.A., Neofytos D., et al. (2023). Antifungal prophylaxis and pre-emptive therapy: When and how. Mol. Aspects. Med. 92:101190. DOI:10.1016/j.mam.2023.101190

    View in Article CrossRef Google Scholar Scopus

    [103] Trapnell B.C., Whitsett J.A. and Nakata K. (2003). Pulmonary alveolar proteinosis. N. Engl. J. Med. 349:2527−2539. DOI:10.1056/NEJMra023226

    View in Article CrossRef Google Scholar

    [104] De Giacomi F., Vassallo R., Yi E.S., et al. (2018). Acute eosinophilic pneumonia. Causes, diagnosis, and management. Am. J. Respir. Crit. Care Med. 197:728−736. DOI:10.1164/rccm.201710-1967CI

    View in Article CrossRef Google Scholar

    [105] Newman L.S., Mroz M.M., Balkissoon R., et al. (2005). Beryllium sensitization progresses to chronic beryllium disease: A longitudinal study of disease risk. Am. J. Respir. Crit. Care Med. 171:54−60. DOI:10.1164/rccm.200402-190OC

    View in Article CrossRef Google Scholar

    [106] Grommes J. and Soehnlein O. (2011). Contribution of neutrophils to acute lung injury. Mol. Med. 17:293−307. DOI:10.2119/molmed.2010.00138

    View in Article CrossRef Google Scholar

    [107] Reisinger A.C., Hatzl S., Prattes J., et al. (2024). Soluble urokinase plasminogen activator receptor (supar) in bronchoalveolar fluid and blood in critically ill patients-a prospective cohort study. Infection 52:249−252. DOI:10.1007/s15010-023-02127-3

    View in Article CrossRef Google Scholar

    [108] Caparrós-Martín J.A., Saladie M., Agudelo-Romero S.P., et al. (2023). Detection of bile acids in bronchoalveolar lavage fluid defines the inflammatory and microbial landscape of the lower airways in infants with cystic fibrosis. Microbiome 11:132. DOI:10.1186/s40168-023-01543-9

    View in Article CrossRef Google Scholar Scopus

    [109] Mccarthy C., Carey B.C., Trapnell B.C. (2022). Autoimmune pulmonary alveolar proteinosis. Am. J. Respir. Crit. Care Med. 205:1016−1035. DOI:10.1164/rccm.202112-2742SO

    View in Article CrossRef Google Scholar

    [110] Wicks I.P. and Roberts A.W. (2016). Targeting GM-CSF in inflammatory diseases. Nat. Rev. Rheumatol. 12:37−48. DOI:10.1038/nrrheum.2015.161

    View in Article CrossRef Google Scholar

    [111] Church D.L., Cerutti L., Gürtler A., et al. (2020). Performance and application of 16s rRNA gene cycle sequencing for routine identification of bacteria in the clinical microbiology laboratory. Clin. Microbiol. Rev. 33:e19−e53. DOI:10.1128/CMR.00053-19

    View in Article CrossRef Google Scholar

    [112] Chiu C.Y. and Miller S.A. (2019). Clinical metagenomics. Nat. Rev. Genet. 20:341−355. DOI:10.1038/s41576-019-0113-7

    View in Article CrossRef Google Scholar Scopus

    [113] Liu Y., Qin Y., Chen T., et al. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell 12:315−330. DOI:10.1007/s13238-020-00724-8

    View in Article CrossRef Google Scholar Scopus

    [114] Eisenhofer R., Minich J.J., Marotz C., et al. (2019). Contamination in low microbial biomass microbiome studies: Issues and recommendations. Trends Microbiol. 27:105−117. DOI:10.1016/j.tim.2018.11.003

    View in Article CrossRef Google Scholar

    [115] Rajar P., Dhariwal A., Salvadori G., et al. (2022). Microbial DNA extraction of high-host content and low biomass samples: optimized protocol for nasopharynx metagenomic studies. Front. Microbiol. 13:1038120. DOI:10.3389/fmicb.2022.1038120

    View in Article CrossRef Google Scholar

    [116] Clarridge J.E.R. (2004). Impact of 16s rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 17:840−862. DOI:10.1128/CMR.17.4.840-862.2004

    View in Article CrossRef Google Scholar

    [117] Zemanick E.T., Wagner B.D., Robertson C.E., et al. (2017). Airway microbiota across age and disease spectrum in cystic fibrosis. Eur. Respir. J. 50:1700832. DOI:10.1183/13993003.00832-2017

    View in Article CrossRef Google Scholar

    [118] Schneeberger P.H.H., Prescod J., Levy L., et al. (2019). Microbiota analysis optimization for human bronchoalveolar lavage fluid. Microbiome 7:141. DOI:10.1186/s40168-019-0755-x

    View in Article CrossRef Google Scholar Scopus

    [119] Rodino K.G. and Simner P.J. (2024). Status check: Next-generation sequencing for infectious-disease diagnostics. J. Clin. Invest. 134:e178003. DOI:10.1172/JCI178003

    View in Article CrossRef Google Scholar

    [120] Jia H., Liu H., Tu M., et al. (2023). Diagnostic efficacy of metagenomic next generation sequencing in bronchoalveolar lavage fluid for proven invasive pulmonary aspergillosis. Front. Cell. Infect. Microbiol. 13:1223576. DOI:10.3389/fcimb.2023.1223576

    View in Article CrossRef Google Scholar Scopus

    [121] Shi C., Han P., Tang P., et al. (2020). Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J. Infect. 81:567−574. DOI:10.1016/j.jinf.2020.08.004

    View in Article CrossRef Google Scholar Scopus

    [122] Jin X., Li J., Shao M., et al. (2022). Improving suspected pulmonary infection diagnosis by bronchoalveolar lavage fluid metagenomic next-generation sequencing: A multicenter retrospective study. Microbiol. Spectr. 10:e247321. DOI:10.1128/spectrum.02473-21

    View in Article CrossRef Google Scholar

    [123] Wang J., Yuan D., Yang X., et al. (2023). Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: A retrospective study. Front. Cell. Infect. Microbiol. 13:1291980. DOI:10.3389/fcimb.2023.1291980

    View in Article CrossRef Google Scholar

    [124] Shen H., Liu T., Shen M., et al. (2023). Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort. Front. Cell. Infect. Microbiol. 13:1200806. DOI:10.3389/fcimb.2023.1200806

    View in Article CrossRef Google Scholar Scopus

    [125] Wang C., Yin X., Ma W., et al. (2024). Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia. Respir. Res. 25:68. DOI:10.1186/s12931-023-02654-5

    View in Article CrossRef Google Scholar Scopus

    [126] Chen Q., Chen X., Mo P., et al. (2024). Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for pneumocystis jirovecii pneumonia in HIV-infected patients. Front. Microbiol. 15:1421660. DOI:10.3389/fmicb.2024.1421660

    View in Article CrossRef Google Scholar

    [127] Peng J., Du B., Qin H., et al. (2021). Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J. Infect. 82:22−27. DOI:10.1016/j.jinf.2021.01.029

    View in Article CrossRef Google Scholar Scopus

    [128] Combs M.P., Wheeler D.S., Luth J.E., et al. (2021). Lung microbiota predict chronic rejection in healthy lung transplant recipients: A prospective cohort study. Lancet Respir. Med. 9:601−612. DOI:10.1016/S2213-2600(20)30405-7

    View in Article CrossRef Google Scholar

    [129] Wang Y., Yu X., Liu F., et al. (2023). Respiratory microbiota imbalance in children with mycoplasma pneumoniae pneumonia. Emerg. Microbes Infect. 12:2202272. DOI:10.1080/22221751.2023.2202272

    View in Article CrossRef Google Scholar

    [130] Fenn D., Abdel-Aziz M.I., van Oort P.M.P., et al. (2022). Composition and diversity analysis of the lung microbiome in patients with suspected ventilator-associated pneumonia. Crit. Care 26:203. DOI:10.1186/s13054-022-04068-z

    View in Article CrossRef Google Scholar Scopus

    [131] Wu X., Li Y., Zhang M., et al. (2020). Etiology of severe community-acquired pneumonia in adults based on metagenomic next-generation sequencing: A prospective multicenter study. Infect. Dis. Ther. 9:1003−1015. DOI:10.1007/s40121-020-00353-y

    View in Article CrossRef Google Scholar

    [132] Yang A., Chen C., Hu Y., et al. (2022). Application of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) in diagnosing pneumonia of children. Microbiol. Spectr. 10:e148822. DOI:10.1128/spectrum.01488-22

    View in Article CrossRef Google Scholar

    [133] Wang B., Zhang L., Wang Y., et al. (2022). Alterations in microbiota of patients with covid-19: potential mechanisms and therapeutic interventions. Signal Transduct. Target. Ther. 7:143. DOI:10.1038/s41392-022-00986-0

    View in Article CrossRef Google Scholar

    [134] Dickson R.P. (2021). Lung microbiota and covid-19 severity. Nat. Microbiol. 6:1217−1218. DOI:10.1038/s41564-021-00969-x

    View in Article CrossRef Google Scholar

    [135] Chen L., Liu W., Zhang Q., et al. (2020). RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerg. Microbes Infect. 9:313−319. DOI:10.1080/22221751.2020.1725399

    View in Article CrossRef Google Scholar Scopus

    [136] Huang L., Zhang X., Pang L., et al. (2023). Viral reactivation in the lungs of patients with severe pneumonia is associated with increased mortality, a multicenter, retrospective study. J. Med. Virol. 95:e28337. DOI:10.1002/jmv.28337

    View in Article CrossRef Google Scholar Scopus

    [137] Ren L., Zhang R., Rao J., et al. (2018). Transcriptionally active lung microbiome and its association with bacterial biomass and host inflammatory status. Msystems 3:e118−e199. DOI:10.1128/mSystems.00199-18

    View in Article CrossRef Google Scholar

    [138] Zhou Z., Ren L., Zhang L., et al. (2020). Heightened innate immune responses in the respiratory tract of covid-19 patients. Cell Host Microbe 27:883−890. DOI:10.1016/j.chom.2020.04.017

    View in Article CrossRef Google Scholar

    [139] Sulaiman I., Chung M., Angel L., et al. (2021). Microbial signatures in the lower airways of mechanically ventilated covid-19 patients associated with poor clinical outcome. Nat. Microbiol. 6:1245−1258. DOI:10.1038/s41564-021-00961-5

    View in Article CrossRef Google Scholar

    [140] Wang L., Cao J., Xia B., et al. (2023). Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated covid-19 omicron patients. Signal Transduct. Target. Ther. 8:432. DOI:10.1038/s41392-023-01684-1

    View in Article CrossRef Google Scholar

    [141] Zinter M.S., Lindemans C.A., Versluys B.A., et al. (2021). The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury. Blood 137:1679−1689. DOI:10.1182/blood.2020009246

    View in Article CrossRef Google Scholar Scopus

    [142] Spottiswoode N., Bloomstein J.D., Caldera S., et al. (2022). Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in uganda: A cross-sectional study. Lancet Microbe 3:e357−e365. DOI:10.1016/S2666-5247(21)00357-8

    View in Article CrossRef Google Scholar

    [143] Saberi R., Nakhaei M., Fakhar M., et al. (2022). Molecular identification and genotyping of acanthamoeba spp. , in bronchoalveolar lavage fluid from immunocompetent patients with chronic respiratory disorders (CRD). Parasitol. Res. 121:3013−3017. DOI:10.1007/s00436-022-07609-1

    View in Article CrossRef Google Scholar

    [144] Lin C., Ying F., Lai Y., et al. (2019). Use of nested PCR for the detection of trichomonads in bronchoalveolar lavage fluid. BMC Infect. Dis. 19:512. DOI:10.1186/s12879-019-4118-9

    View in Article CrossRef Google Scholar Scopus

    [145] Sing A., Leitritz L., Roggenkamp A., et al. (1999). Pulmonary toxoplasmosis in bone marrow transplant recipients: Report of two cases and review. Clin. Infect. Dis. 29:429−433. DOI:10.1086/520228

    View in Article CrossRef Google Scholar

    [146] Demir M., Lang S., Hartmann P., et al. (2022). The fecal mycobiome in non-alcoholic fatty liver disease. J. Hepatol. 76:788−799. DOI:10.1016/j.jhep.2021.11.029

    View in Article CrossRef Google Scholar Scopus

    [147] Panaiotov S., Hodzhev Y., Tsafarova B., et al. (2021). Culturable and non-culturable blood microbiota of healthy individuals. Microorganisms 9:1464. DOI:10.3390/microorganisms9071464

    View in Article CrossRef Google Scholar

    [148] Li Z., Wang M., Xu T., et al. (2022). Development and clinical implications of a novel CRISPR-based diagnostic test for pulmonary aspergillus fumigatus infection. J. Microbiol. Immunol. Infect. 55:749−756. DOI:10.1016/j.jmii.2021.11.008

    View in Article CrossRef Google Scholar

    [149] Pang Y., Hu D., Dang Y., et al. (2022). Bronchial artery-pulmonary artery shunt by Apiotrichum mycotoxinivorans infection in a recurrent hemoptysis case. Infect. Drug Resist. 15:4611−4615. DOI:10.2147/IDR.S373615

    View in Article CrossRef Google Scholar

    [150] Murphy S.G., Smith C., Lapierre P., et al. (2023). Direct detection of drug-resistant mycobacterium tuberculosis using targeted next generation sequencing. Front. Public Health 11:1206056. DOI:10.3389/fpubh.2023.1206056

    View in Article CrossRef Google Scholar

    [151] Li S., Tong J., Li H., et al. (2023). L. Pneumophila infection diagnosed by tNGS in a lady with lymphadenopathy. Infect. Drug Resist. 16:4435−4442. DOI:10.2147/IDR.S417495

    View in Article Google Scholar

    [152] Li X., Liu Y., Li M., et al. (2023). Epidemiological investigation of lower respiratory tract infections during influenza a (h1n1) pdm09 virus pandemic based on targeted next-generation sequencing. Front. Cell. Infect. Microbiol. 13:1303456. DOI:10.3389/fcimb.2023.1303456

    View in Article CrossRef Google Scholar

    [153] Bhatia S., Pooja and Yadav S.K. (2023). CRISPR-Cas for genome editing: Classification, mechanism, designing and applications. Int. J. Biol. Macromol. 238:124054. DOI:10.1016/j.ijbiomac.2023.124054

    View in Article CrossRef Google Scholar Scopus

    [154] Gootenberg J.S., Abudayyeh O.O., Lee J.W., et al. (2017). Nucleic acid detection with CRISPR-Cas13a/c2c2. Science (New York, N.Y.) 356:438−442. DOI:10.1126/science.aam9321

    View in Article CrossRef Google Scholar

    [155] Zhou J., Xiao F., Fu J., et al. (2023). Rapid, ultrasensitive and highly specific diagnosis of mycoplasma pneumoniae by a CRISPR-based detection platform. Front. Cell. Infect. Microbiol. 13:1147142. DOI:10.3389/fcimb.2023.1147142

    View in Article CrossRef Google Scholar

    [156] Lou H., Wang X., Jiang Q., et al. (2024). Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: A prospective cohort study. Infect. Dis. 57:167−177. DOI:10.1080/23744235.2024.2402921

    View in Article CrossRef Google Scholar

    [157] Guo H., Zhao L., Zhu J., et al. (2022). Microbes in lung cancer initiation, treatment, and outcome: boon or bane. Semin. Cancer. Biol. 86:1190−1206. DOI:10.1016/j.semcancer.2021.05.025

    View in Article CrossRef Google Scholar

    [158] Hogea S., Tudorache E., Pescaru C., et al. (2020). Bronchoalveolar lavage: Role in the evaluation of pulmonary interstitial disease. Expert Rev. Respir. Med. 14:1117−1130. DOI:10.1080/17476348.2020.1806063

    View in Article CrossRef Google Scholar

    [159] Yang Q., Qi F., Ye T., et al. (2023). The interaction of macrophages and cd8 t cells in bronchoalveolar lavage fluid is associated with latent tuberculosis infection. Emerg. Microbes Infect. 12:2239940. DOI:10.1080/22221751.2023.2239940

    View in Article CrossRef Google Scholar

    [160] Huang J. and Ren K. (2023). Detection of changes in CEA and ProGRP levels in BALF of patients with peripheral lung cancer and the relationship with CT signs. Contrast Media Mol. Imaging 2023:1421709. DOI:10.1155/2023/1421709

    View in Article CrossRef Google Scholar

    [161] Kim I.A., Hur J.Y., Kim H.J., et al. (2023). A prospective phase 2 study of expeditious EGFR genotyping and immediate therapeutic initiation through extracellular vesicles (EV)-based bronchoalveolar lavage fluid (BALF) liquid biopsy in advanced NSCLC patients. Transl. Lung Cancer Res. 12:1425−1435. DOI:10.21037/tlcr-22-892

    View in Article CrossRef Google Scholar

    [162] Slimmen L.J.M., Giacalone V.D., Schofield C., et al. (2023). Airway macrophages display decreased expression of receptors mediating and regulating scavenging in early cystic fibrosis lung disease. Front. Immunol. 14:1202009. DOI:10.3389/fimmu.2023.1202009

    View in Article CrossRef Google Scholar Scopus

    [163] Nakagome K. and Nagata M. (2020). Possible mechanisms of eosinophil accumulation in eosinophilic pneumonia. Biomolecules 10:638. DOI:10.3390/biom10040638

    View in Article CrossRef Google Scholar Scopus

    [164] Todd J.L., Weber J.M., Kelly F.L., et al. (2023). Bal fluid eosinophilia associates with chronic lung allograft dysfunction risk: A multicenter study. Chest 164:670−681. DOI:10.1016/j.chest.2023.03.033

    View in Article CrossRef Google Scholar

    [165] Chen X., Liu F., Zheng B., et al. (2021). Exhausted and apoptotic BALF T cells in proinflammatory airway milieu at acute phase of severe mycoplasma pneumoniae pneumonia in children. Front. Immunol. 12:760488. DOI:10.3389/fimmu.2021.760488

    View in Article CrossRef Google Scholar

    [166] Tasdemir-Yilmaz O.E., Druckenbrod N.R., Olukoya O.O., et al. (2021). Diversity of developing peripheral glia revealed by single-cell RNA sequencing. Dev. Cell 56:2516−2535. DOI:10.1016/j.devcel.2021.08.005

    View in Article CrossRef Google Scholar Scopus

    [167] Halpern K.B., Shenhav R., Massalha H., et al. (2018). Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells. Nat. Biotechnol. 36:962−970. DOI:10.1038/nbt.4231

    View in Article CrossRef Google Scholar

    [168] Subramanian S., Busch C.J., Molawi K., et al. (2022). Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo. Nat. Immunol. 23:458−468. DOI:10.1038/s41590-022-01146-w

    View in Article CrossRef Google Scholar Scopus

    [169] Wang M., Liu X., Chang G., et al. (2018). Single-cell RNA sequencing analysis reveals sequential cell fate transition during human spermatogenesis. Cell Stem Cell 23:599−614. DOI:10.1016/j.stem.2018.08.007

    View in Article CrossRef Google Scholar

    [170] Bheda P., Aguilar-Gómez D., Becker N.B., et al. (2020). Single-cell tracing dissects regulation of maintenance and inheritance of transcriptional reinduction memory. Mol. Cell 78:915−925. DOI:10.1016/j.molcel.2020.04.016

    View in Article CrossRef Google Scholar

    [171] Liu Y., Wang H., Taylor M., et al. (2022). Classification of human chronic inflammatory skin disease based on single-cell immune profiling. Sci. Immunol. 7:eabl9165. DOI:10.1126/sciimmunol.abl9165

    View in Article CrossRef Google Scholar Scopus

    [172] Li X., Kolling F.W., Aridgides D., et al. (2022). ScRNA-seq expression of IFI 27 and APOC 2 identifies four alveolar macrophage superclusters in healthy BALF. Life Sci. Alliance 5:e202201458. DOI:10.26508/lsa.202201458

    View in Article CrossRef Google Scholar

    [173] Bost P., Giladi A., Liu Y., et al. (2020). Host-viral infection maps reveal signatures of severe covid-19 patients. Cell 181:1475−1488. DOI:10.1016/j.cell.2020.05.006

    View in Article CrossRef Google Scholar

    [174] Li H., Wang H., Sokulsky L., et al. (2021). Single-cell transcriptomic analysis reveals key immune cell phenotypes in the lungs of patients with asthma exacerbation. J. Allergy Clin. Immunol. 147:941−954. DOI:10.1016/j.jaci.2020.09.032

    View in Article CrossRef Google Scholar Scopus

    [175] Cao C., Memete O., Shao Y., et al. (2022). Single-cell RNA-sequencing reveals epithelial cell signature of multiple subtypes in chemically induced acute lung injury. Int. J. Mol. Sci. 24:277. DOI:10.3390/ijms24010277

    View in Article CrossRef Google Scholar

    [176] Franken A., Van Mol P., Vanmassenhove S., et al. (2022). Single-cell transcriptomics identifies pathogenic T-helper 17.1 cells and pro-inflammatory monocytes in immune checkpoint inhibitor-related pneumonitis. J. Immunother. Cancer 10 :e5323. DOI: 10.1136/jitc-2022-005323

    View in Article Google Scholar

    [177] Wang K.C. and Chang H.Y. (2018). Epigenomics: Technologies and applications. Circ. Res. 122:1191−1199. DOI:10.1161/CIRCRESAHA.118.310998

    View in Article CrossRef Google Scholar

    [178] Vistain L.F. and Tay S. (2021). Single-cell proteomics. Trends Biochem. Sci. 46:661−672. DOI:10.1016/j.tibs.2021.01.013

    View in Article CrossRef Google Scholar

    [179] Zhang X., Xu J., Wang Y., et al. (2023). Respiratory viral infections in the elderly: From the perspective of the aging immune system. Innov. Med. 1:100022. DOI:10.59717/j.xinn-med.2023.100022

    View in Article CrossRef Google Scholar

    [180] Galazzo G., van Best N., Benedikter B.J., et al. (2020). How to count our microbes. The effect of different quantitative microbiome profiling approaches. Front. Cell. Infect. Microbiol. 10:403. DOI:10.3389/fcimb.2020.00403

    View in Article CrossRef Google Scholar

    [181] Li L., Ye Z., Yang S., et al. (2021). Diagnosis of pulmonary nodules by DNA methylation analysis in bronchoalveolar lavage fluids. Clin. Epigenetics 13:185. DOI:10.1186/s13148-021-01163-w

    View in Article CrossRef Google Scholar Scopus

    [182] Zareba L., Szymanski J., Homoncik Z., et al. (2021). EVs from BALF-mediators of inflammation and potential biomarkers in lung diseases. Int. J. Mol. Sci. 22:3651. DOI:10.3390/ijms22073651

    View in Article CrossRef Google Scholar

    [183] Liu Z., Yan J., Tong L., et al. (2022). The role of exosomes from BALF in lung disease. J. Cell. Physiol. 237:161−168. DOI:10.1002/jcp.30553

    View in Article CrossRef Google Scholar Scopus

    [184] Carnino J.M., Lee H. and Jin Y. (2019). Isolation and characterization of extracellular vesicles from broncho-alveolar lavage fluid: A review and comparison of different methods. Respir. Res. 20:240. DOI:10.1186/s12931-019-1210-z

    View in Article CrossRef Google Scholar

    [185] Xu R., Greening D.W., Zhu H., et al. (2016). Extracellular vesicle isolation and characterization: toward clinical application. J. Clin. Invest. 126:1152−1162. DOI:10.1172/JCI81129

    View in Article CrossRef Google Scholar

    [186] O'Brien K., Breyne K., Ughetto S., et al. (2020). RNA delivery by extracellular vesicles in mammalian cells and its applications. Nat. Rev. Mol. Cell Biol. 21:585−606. DOI:10.1038/s41580-020-0251-y

    View in Article CrossRef Google Scholar Scopus

    [187] Sun H., Gao W., Chen R., et al. (2023). CircRNAs in BALF exosomes and plasma as diagnostic biomarkers in patients with acute respiratory distress syndrome caused by severe pneumonia. Front. Cell. Infect. Microbiol. 13:1194495. DOI:10.3389/fcimb.2023.1194495

    View in Article CrossRef Google Scholar Scopus

    [188] Kaur G., Maremanda K.P., Campos M., et al. (2021). Distinct exosomal miRNA profiles from BALF and lung tissue of COPD and IPF patients. Int. J. Mol. Sci. 22:11830. DOI:10.3390/ijms222111830

    View in Article CrossRef Google Scholar

    [189] Aksoy M.O., Kim V., Cornwell W.D., et al. (2017). Secretion of the endoplasmic reticulum stress protein, grp78, into the BALF is increased in cigarette smokers. Respir. Res. 18:78. DOI:10.1186/s12931-017-0561-6

    View in Article CrossRef Google Scholar

    [190] Testa A., Venturelli E. and Brizzi M.F. (2021). Extracellular vesicles as a novel liquid biopsy-based diagnosis for the central nervous system, head and neck, lung, and gastrointestinal cancers: Current and future perspectives. Cancers 13:2792. DOI:10.3390/cancers13112792

    View in Article CrossRef Google Scholar

    [191] Sathe N.A., Morrell E.D., Bhatraju P.K., et al. (2023). Alveolar biomarker profiles in subphenotypes of the acute respiratory distress syndrome. Crit. Care Med. 51:e13−e18. DOI:10.1097/CCM.0000000000005704

    View in Article CrossRef Google Scholar

    [192] Kim I.A., Hur J.Y., Kim H.J., et al. (2022). Extracellular vesicle-based bronchoalveolar lavage fluid liquid biopsy for EGFR mutation testing in advanced non-squamous NSCLC. Cancers 14:2744. DOI:10.3390/cancers14112744

    View in Article CrossRef Google Scholar

    [193] Hur J.Y., Kim H.J., Lee J.S., et al. (2018). Extracellular vesicle-derived DNA for performing EGFR genotyping of NSCLC patients. Mol. Cancer 17:15. DOI:10.1186/s12943-018-0772-6

    View in Article CrossRef Google Scholar

    [194] Shaba E., Landi C., Carleo A., et al. (2021). Proteome characterization of BALF extracellular vesicles in idiopathic pulmonary fibrosis: Unveiling undercover molecular pathways. Int. J. Mol. Sci. 22:5696. DOI:10.3390/ijms22115696

    View in Article CrossRef Google Scholar

    [195] Yu W., He Y., Shang Y., et al. (2023). Metabolic landscape dysregulation in bronchoalveolar lavage fluid of checkpoint inhibitor pneumonitis. Clin. Immunol. 247:109230. DOI:10.1016/j.clim.2023.109230

    View in Article CrossRef Google Scholar Scopus

    [196] Lee H., Groot M., Pinilla-Vera M., et al. (2019). Identification of miRNA-rich vesicles in bronchoalveolar lavage fluid: Insights into the function and heterogeneity of extracellular vesicles. J. Control. Release 294:43−52. DOI:10.1016/j.jconrel.2018.12.008

    View in Article CrossRef Google Scholar Scopus

    [197] Holtzman J. and Lee H. (2020). Emerging role of extracellular vesicles in the respiratory system. Exp. Mol. Med. 52:887−895. DOI:10.1038/s12276-020-0450-9

    View in Article CrossRef Google Scholar Scopus

    [198] Yang Q., Luo Y., Ge P., et al. (2023). Emodin ameliorates severe acute pancreatitis-associated acute lung injury in rats by modulating exosome-specific miRNA expression profiles. Int. J. Nanomed. 18:6743−6761. DOI:10.2147/IJN.S428924

    View in Article CrossRef Google Scholar

    [199] Huang J., Ding M., Lu Y., et al. (2023). MiR-1246b, a novel miRNA molecule of extracellular vesicles in bronchoalveolar lavage fluid, promotes nodule growth through FGF14 in patients with lung cancer. Cell Death Dis. 14:789. DOI:10.1038/s41419-023-06218-9

    View in Article CrossRef Google Scholar

    [200] Lee H., Hong R. and Jin Y. (2024). Altered circular RNA expressions in extracellular vesicles from bronchoalveolar lavage fluids in mice after bacterial infections. Front. Immunol. 15:1354676. DOI:10.3389/fimmu.2024.1354676

    View in Article CrossRef Google Scholar Scopus

    [201] Chen W., Xu J., Wu Y., et al. (2023). The potential role and mechanism of circRNA/miRNA axis in cholesterol synthesis. Int. J. Biol. Sci. 19:2879−2896. DOI:10.7150/ijbs.84994

    View in Article CrossRef Google Scholar Scopus

    [202] Tang R., Hu Y., Mei S., et al. (2023). Non-coding RNA alterations in extracellular vesicles from bronchoalveolar lavage fluid contribute to mechanical ventilation-induced pulmonary fibrosis. Front. Immunol. 14:1141761. DOI:10.3389/fimmu.2023.1141761

    View in Article CrossRef Google Scholar Scopus

    [203] Luo H., Xiao T., Sun X., et al. (2023). The regulation of circRNA_kif26b on alveolar epithelial cell senescence via miR-346-3p is involved in microplastics-induced lung injuries. Sci. Total Environ. 882:163512. DOI:10.1016/j.scitotenv.2023.163512

    View in Article CrossRef Google Scholar Scopus

    [204] Slebos D., Scholma J., Boezen H.M., et al. (2002). Longitudinal profile of bronchoalveolar lavage cell characteristics in patients with a good outcome after lung transplantation. Am. J. Respir. Crit. Care Med. 165:501−507. DOI:10.1164/ajrccm.165.4.2107035

    View in Article CrossRef Google Scholar

    [205] Takei R., Arita M., Kumagai S., et al. (2017). Impact of lymphocyte differential count > 15% in BALF on the mortality of patients with acute exacerbation of chronic fibrosing idiopathic interstitial pneumonia. BMC Pulm. Med. 17:67. DOI:10.1186/s12890-017-0412-8

    View in Article CrossRef Google Scholar

    [206] Hellyer T.P., Morris A.C., Mcauley D.F., et al. (2015). Diagnostic accuracy of pulmonary host inflammatory mediators in the exclusion of ventilator-acquired pneumonia. Thorax 70:41−47. DOI:10.1136/thoraxjnl-2014-205766

    View in Article CrossRef Google Scholar

    [207] Hellyer T.P., Mcauley D.F., Walsh T.S., et al. (2020). Biomarker-guided antibiotic stewardship in suspected ventilator-associated pneumonia (vaprapid2): A randomised controlled trial and process evaluation. Lancet Respir. Med. 8:182−191. DOI:10.1016/S2213-2600(19)30367-4

    View in Article CrossRef Google Scholar

    [208] Hoser G., Domagała-Kulawik J., Droszcz P., et al. (2003). Lymphocyte subsets differences in smokers and nonsmokers with primary lung cancer: A flow cytometry analysis of bronchoalveolar lavage fluid cells. Med. Sci. Monit. 9:BR310−BR315.

    View in Article Google Scholar

    [209] Rossides M., Darlington P., Kullberg S., et al. (2023). Sarcoidosis: Epidemiology and clinical insights. J. Intern. Med. 293:668−680. DOI:10.1111/joim.13629

    View in Article CrossRef Google Scholar Scopus

    [210] Wauters E., Van Mol P., Garg A.D., et al. (2021). Discriminating mild from critical covid-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages. Cell Res. 31:272−290. DOI:10.1038/s41422-020-00455-9

    View in Article CrossRef Google Scholar

    [211] King A. (2024). Exploring the lung microbiome's role in disease. Nature DOI: 10.1038/d41586-024-01123-3

    View in Article Google Scholar

    [212] Lal C.V., Travers C., Aghai Z.H., et al. (2016). The airway microbiome at birth. Sci. Rep. 6:31023. DOI:10.1038/srep31023

    View in Article CrossRef Google Scholar

    [213] Toivonen L., Hasegawa K., Waris M., et al. (2019). Early nasal microbiota and acute respiratory infections during the first years of life. Thorax 74:592−599. DOI:10.1136/thoraxjnl-2018-212629

    View in Article CrossRef Google Scholar Scopus

    [214] Wu B.G., Sulaiman I., Tsay J.J., et al. (2021). Episodic aspiration with oral commensals induces a myd88-dependent, pulmonary T-helper cell type 17 response that mitigates susceptibility to streptococcus pneumoniae. Am. J. Respir. Crit. Care Med. 203:1099−1111. DOI:10.1164/rccm.202005-1596OC

    View in Article CrossRef Google Scholar

    [215] Sun W., Zheng L., Kang L., et al. (2024). Comparative analysis of metagenomic and targeted next-generation sequencing for pathogens diagnosis in bronchoalveolar lavage fluid specimens. Front. Cell. Infect. Microbiol. 14:1451440. DOI:10.3389/fcimb.2024.1451440

    View in Article CrossRef Google Scholar Scopus

    [216] Sun Y., Liu Y., Li J., et al. (2023). Characterization of lung and oral microbiomes in lung cancer patients using culturomics and 16s rRNA gene sequencing. Microbiol. Spectr. 11:e31423. DOI:10.1128/spectrum.00314-23

    View in Article CrossRef Google Scholar

    [217] Xue M., Zhang T., Lin R., et al. (2022). Clinical utility of heparin-binding protein as an acute-phase inflammatory marker in interstitial lung disease. J. Leukoc. Biol. 112:861−873. DOI:10.1002/JLB.3MA1221-489R

    View in Article CrossRef Google Scholar Scopus

    [218] Lin W., Lin C., Chen C., et al. (2010). Prediction of outcome in patients with acute respiratory distress syndrome by bronchoalveolar lavage inflammatory mediators. Exp. Biol. Med. (Maywood) 235:57−65. DOI:10.1258/ebm.2009.009256

    View in Article CrossRef Google Scholar

    [219] Larsen E.L., Nilius H., Studt J., et al. (2024). Accuracy of diagnosing heparin-induced thrombocytopenia. Jama Netw. Open 7:e243786. DOI:10.1001/jamanetworkopen.2024.3786

    View in Article CrossRef Google Scholar

    [220] Dong X., Xu X., Huang Y., et al. (2023). Prognostic value of secretory autophagosomes in patients with acute respiratory distress syndrome. Biomark. Res. 11:79. DOI:10.1186/s40364-023-00519-z

    View in Article CrossRef Google Scholar Scopus

    [221] Li Y., He Y., Chen S., et al. (2022). S100a12 as biomarker of disease severity and prognosis in patients with idiopathic pulmonary fibrosis. Front. Immunol. 13:810338. DOI:10.3389/fimmu.2022.810338

    View in Article CrossRef Google Scholar

    [222] Ji J., Zheng S., Liu Y., et al. (2023). Increased expression of OPN contributes to idiopathic pulmonary fibrosis and indicates a poor prognosis. J. Transl. Med. 21:640. DOI:10.1186/s12967-023-04279-0

    View in Article CrossRef Google Scholar Scopus

    [223] Fisher A.J., Donnelly S.C., Hirani N., et al. (2001). Elevated levels of interleukin-8 in donor lungs is associated with early graft failure after lung transplantation. Am. J. Respir. Crit. Care Med. 163:259−265.

    View in Article Google Scholar

    [224] Ruppert A., Baud L., Rabbe N., et al. (2019). Calpain 1 in bronchoalveolar lavage fluid is associated with poor prognosis in lepidic predominant pulmonary adenocarcinoma. Bull. Cancer 106:179−188. DOI:10.1016/j.bulcan.2018.11.014

    View in Article CrossRef Google Scholar Scopus

    [225] Chang C., Armstrong D., Corry D.B., et al. (2023). Alveolar macrophages in lung cancer: opportunities challenges. Front. Immunol. 14:1268939. DOI:10.3389/fimmu.2023.1268939

    View in Article CrossRef Google Scholar Scopus

    [226] Xue Y., Chen Y., Sun S., et al. (2024). Tet2-stat3-cxcl5 nexus promotes neutrophil lipid transfer to fuel lung adeno-to-squamous transition. J. Exp. Med. 221:e20240111. DOI:10.1084/jem.20240111

    View in Article CrossRef Google Scholar

    [227] Tian Y., Li M., Song W., et al. (2019). Effects of probiotics on chemotherapy in patients with lung cancer. Oncol. Lett. 17:2836−2848. DOI:10.3892/ol.2019.9906

    View in Article CrossRef Google Scholar Scopus

    [228] Katayama Y., Yamada T., Shimamoto T., et al. (2019). The role of the gut microbiome on the efficacy of immune checkpoint inhibitors in Japanese responder patients with advanced non-small cell lung cancer. Transl. Lung Cancer Res. 8:847−853. DOI:10.21037/tlcr.2019.10.23

    View in Article CrossRef Google Scholar Scopus

    [229] Zhang L., Jin Q., Chai D., et al. (2022). The correlation between probiotic use and outcomes of cancer patients treated with immune checkpoint inhibitors. Front. Pharmacol. 13:937874. DOI:10.3389/fphar.2022.937874

    View in Article CrossRef Google Scholar Scopus

    [230] Shenoy A.T., Lyon De Ana C., Arafa E.I., et al. (2021). Antigen presentation by lung epithelial cells directs cd4(+) t(rm) cell function and regulates barrier immunity. Nat. Commun. 12:5834. DOI:10.1038/s41467-021-26045-w

    View in Article CrossRef Google Scholar

    [231] Mondoni M., Rinaldo R.F., Carlucci P., et al. (2022). Bronchoscopic sampling techniques in the era of technological bronchoscopy. Pulmonology 28:461−471. DOI:10.1016/j.pulmoe.2020.06.007

    View in Article CrossRef Google Scholar Scopus

    [232] Lerner A.D. and Feller-Kopman D. (2017). Bronchoscopic techniques used in the diagnosis and staging of lung cancer. J. Natl. Compr. Canc. Netw. 15:640−647. DOI:10.6004/jnccn.2017.0065

    View in Article CrossRef Google Scholar

    [233] Sung J.Y., Hwang Y., Shin M.H., et al. (2018). Utility of conventional culture and MALDI-TOF MS for identification of microbial communities in bronchoalveolar lavage fluid in comparison with the GS junior next generation sequencing system. Ann. Lab. Med. 38:110−118. DOI:10.3343/alm.2018.38.2.110

    View in Article CrossRef Google Scholar

    [234] Criner G.J., Eberhardt R., Fernandez-Bussy S., et al. (2020). Interventional bronchoscopy. Am. J. Respir. Crit. Care Med. 202:29−50. DOI:10.1164/rccm.201907-1292SO

    View in Article CrossRef Google Scholar Scopus

    [235] Baysoy A., Bai Z., Satija R., et al. (2023). The technological landscape and applications of single-cell multi-omics. Nat. Rev. Mol. Cell Biol. 24:695−713. DOI:10.1038/s41580-023-00615-w

    View in Article CrossRef Google Scholar Scopus

    [236] Aggarwal N., Kitano S., Puah G.R.Y., et al. (2023). Microbiome and human health: Current understanding, engineering, and enabling technologies. Chem. Rev. 123:31−72. DOI:10.1021/acs.chemrev.2c00431

    View in Article CrossRef Google Scholar

    [237] Cullin N., Azevedo Antunes C., Straussman R., et al. (2021). Microbiome and cancer. Cancer Cell 39:1317−1341. DOI:10.1016/j.ccell.2021.08.006

    View in Article CrossRef Google Scholar Scopus

    [238] Hilty M., Burke C., Pedro H., et al. (2010). Disordered microbial communities in asthmatic airways. Plos One 5:e8578. DOI:10.1371/journal.pone.0008578

    View in Article CrossRef Google Scholar

    [239] Aagaard K., Ma J., Antony K.M., et al. (2014). The placenta harbors a unique microbiome. Sci. Transl. Med. 6:237ra65. DOI:10.1126/scitranslmed.3008599

    View in Article CrossRef Google Scholar

    [240] Chang D., Dela Cruz C.S. and Sharma L. (2020). Challenges in understanding lung microbiome: It is not like the gut microbiome. Respirology (Carlton, Vic.) 25:244−245. DOI:10.1111/resp.13759

    View in Article CrossRef Google Scholar

    [241] Yan Z., Chen B., Yang Y., et al. (2022). Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions. Nat. Microbiol. 7:1361−1375. DOI:10.1038/s41564-022-01196-8

    View in Article CrossRef Google Scholar

    [242] Chotirmall S.H., Bogaert D., Chalmers J.D., et al. (2022). Therapeutic targeting of the respiratory microbiome. Am. J. Respir. Crit. Care Med. 206:535−544. DOI:10.1164/rccm.202112-2704PP

    View in Article CrossRef Google Scholar

    [243] de Vos W.M., Tilg H., Van Hul M., et al. (2022). Gut microbiome and health: mechanistic insights. Gut 71:1020−1032. DOI:10.1136/gutjnl-2021-326789

    View in Article CrossRef Google Scholar Scopus

    [244] Yagi K., Huffnagle G.B., Lukacs N.W., et al. (2021). The lung microbiome during health and disease. Int. J. Mol. Sci. 22:10872. DOI:10.3390/ijms221910872

    View in Article CrossRef Google Scholar Scopus

    [245] Dickson R.P., Martinez F.J. and Huffnagle G.B. (2014). The role of the microbiome in exacerbations of chronic lung diseases. Lancet 384:691−702. DOI:10.1016/S0140-6736(14)61136-3

    View in Article CrossRef Google Scholar

    [246] Li R., Li J. and Zhou X. (2024). Lung microbiome: New insights into the pathogenesis of respiratory diseases. Signal Transduct. Target. Ther. 9:19. DOI:10.1038/s41392-023-01722-y

    View in Article CrossRef Google Scholar

    [247] Rogers G.B., Shaw D., Marsh R.L., et al. (2015). Respiratory microbiota: Addressing clinical questions, informing clinical practice. Thorax 70:74−81. DOI:10.1136/thoraxjnl-2014-205826

    View in Article CrossRef Google Scholar

    [248] Yuan X., Xie L., Shi Z., et al. (2023). Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers. Front. Cell. Infect. Microbiol. 13:1200157. DOI:10.3389/fcimb.2023.1200157

    View in Article CrossRef Google Scholar Scopus

    [249] Puschhof J. and Elinav E. (2023). Human microbiome research: Growing pains and future promises. Plos Biol. 21:e3002053. DOI:10.1371/journal.pbio.3002053

    View in Article CrossRef Google Scholar Scopus

    [250] Hosang L., Canals R.C., van der Flier F.J., et al. (2022). The lung microbiome regulates brain autoimmunity. Nature 603:138−144. DOI:10.1038/s41586-022-04427-4

    View in Article CrossRef Google Scholar Scopus

    [251] Achouiti A., Vogl T., Endeman H., et al. (2014). Myeloid-related protein-8/14 facilitates bacterial growth during pneumococcal pneumonia. Thorax 69:1034−1042. DOI:10.1136/thoraxjnl-2014-205668

    View in Article CrossRef Google Scholar

    [252] Awasthi S., Magee D.M. and Coalson J.J. (2004). Coccidioides posadasii infection alters the expression of pulmonary surfactant proteins (SP)-A and SP-D. Respir. Res. 5:28. DOI:10.1186/1465-9921-5-28

    View in Article CrossRef Google Scholar

    [253] Whiteside S.A., Mcginniss J.E. and Collman R.G. (2021). The lung microbiome: Progress and promise. J. Clin. Invest. 131:e150473. DOI:10.1172/JCI150473

    View in Article CrossRef Google Scholar Scopus

    [254] Mortaz E., Adcock I.M., Folkerts G., et al. (2013). Probiotics in the management of lung diseases. Mediat. Inflamm. 2013:751068. DOI:10.1155/2013/751068

    View in Article CrossRef Google Scholar

    [255] Wang Q. and Liu S. (2023). The effects and pathogenesis of PM2.5 and its components on chronic obstructive pulmonary disease. Int. J. Chronic Obstr. Pulm. Dis. 18 :493-506. DOI: 10.2147/COPD.S402122

    View in Article Google Scholar

    [256] Li J., Hu Y., Liu L., et al. (2020). PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice. Sci. Total Environ. 721 :137432. DOI: 10.1016/j.scitotenv.2020.137432

    View in Article Google Scholar

    [257] de Toro-Martín J., Arsenault B.J., Després J., et al. (2017). Precision nutrition: A review of personalized nutritional approaches for the prevention and management of metabolic syndrome. Nutrients 9:913. DOI:10.3390/nu9080913

    View in Article CrossRef Google Scholar

    [258] Wang J., Ghosh D. and Maniruzzaman M. (2023). Using bugs as drugs: Administration of bacteria-related microbes to fight cancer. Adv. Drug Deliv. Rev. 197:114825. DOI:10.1016/j.addr.2023.114825

    View in Article CrossRef Google Scholar Scopus

    [259] Cao Y., Xia H., Tan X., et al. (2024). Intratumoural microbiota: A new frontier in cancer development and therapy. Signal Transduct. Target. Ther. 9:15. DOI:10.1038/s41392-023-01693-0

    View in Article CrossRef Google Scholar

    [260] Nejman D., Livyatan I., Fuks G., et al. (2020). The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science (New York, N.Y.) 368:973−980. DOI:10.1126/science.aay9189

    View in Article CrossRef Google Scholar Scopus

    [261] Wang S., Yao X., Ma S., et al. (2021). A single-cell transcriptomic landscape of the lungs of patients with covid-19. Nat. Cell Biol. 23:1314−1328. DOI:10.1038/s41556-021-00796-6

    View in Article CrossRef Google Scholar

    [262] Fang C., Mei J., Tian H., et al. (2020). CSF3 is a potential drug target for the treatment of covid-19. Front. Physiol. 11:605792. DOI:10.3389/fphys.2020.605792

    View in Article CrossRef Google Scholar

    [263] Shawaf T., Schuberth H. and Hussen J. (2022). Immune cell composition of the bronchoalveolar lavage fluid in healthy and respiratory diseased dromedary camels. BMC Vet. Res. 18:353. DOI:10.1186/s12917-022-03446-7

    View in Article CrossRef Google Scholar Scopus

    [264] Ergan B. and Nava S. (2018). The use of bronchoscopy in critically ill patients: Considerations and complications. Expert Rev. Respir. Med. 12:651−663. DOI:10.1080/17476348.2018.1494576

    View in Article CrossRef Google Scholar

    [265] Yu Y., Liu C., Zhang Z., et al. (2019). Bronchoalveolar lavage fluid dilution in ICU patients: What we should know and what we should do. Crit. Care 23:23. DOI:10.1186/s13054-018-2300-x

    View in Article CrossRef Google Scholar Scopus

    [266] Meyer K.C. and Raghu G. (2011). Bronchoalveolar lavage for the evaluation of interstitial lung disease: Is it clinically useful. Eur. Respir. J. 38:761−769. DOI:10.1183/09031936.00069509

    View in Article CrossRef Google Scholar

    [267] Zhang H., Wang N., Xu Y., et al. (2023). Comparative analysis of peripheral blood immunoinflammatory landscapes in patients with acute cholangitis and its secondary septic shock using single-cell RNA sequencing. Biochem. Biophys. Res. Commun. 683:149121. DOI:10.1016/j.bbrc.2023.149121

    View in Article CrossRef Google Scholar Scopus

    [268] Crowley E., Di Nicolantonio F., Loupakis F., et al. (2013). Liquid biopsy: Monitoring cancer-genetics in the blood. Nat. Rev. Clin. Oncol. 10:472−484. DOI:10.1038/nrclinonc.2013.110

    View in Article CrossRef Google Scholar

    [269] Chen C.K., Liao J., Li M.S., et al. (2020). Urine biopsy technologies: Cancer and beyond. Theranostics 10:7872−7888. DOI:10.7150/thno.44634

    View in Article CrossRef Google Scholar Scopus

    [270] Kaczor-Urbanowicz K.E., Wei F., Rao S.L., et al. (2019). Clinical validity of saliva and novel technology for cancer detection. Biochim. Biophys. Acta Rev. Cancer 1872:49−59. DOI:10.1016/j.bbcan.2019.05.007

    View in Article CrossRef Google Scholar Scopus

    [271] Nonaka T. and Wong D.T.W. (2022). Saliva diagnostics. Ann. Rev. Anal. Chem. (Palo Alto, Calif.) 15:107−121. DOI:10.1146/annurev-anchem-061020-123959

    View in Article CrossRef Google Scholar

    [272] Kim C.K. and Hagan J.B. (2004). Sputum tests in the diagnosis and monitoring of asthma. Ann. Allergy Asthma Immunol. 93 :112-122, 122-124, 184. DOI: 10.1016/S1081-1206(10)61462-7

    View in Article Google Scholar

    [273] Scheja A., Larsen K., Todorova L., et al. (2007). BALF-derived fibroblasts differ from biopsy-derived fibroblasts in systemic sclerosis. Eur. Respir. J. 29:446−452. DOI:10.1183/09031936.00135205

    View in Article CrossRef Google Scholar

    [274] Mei J., Tian H., Huang H., et al. (2021). Cellular models of development of ovarian high-grade serous carcinoma: A review of cell of origin and mechanisms of carcinogenesis. Cell Prolif. 54:e13029. DOI:10.1111/cpr.13029

    View in Article CrossRef Google Scholar Scopus

    [275] In T Veld S.G.J.G., Arkani M., Post E., et al. (2022). Detection and localization of early- and late-stage cancers using platelet RNA. Cancer Cell 40:999−1009. DOI:10.1016/j.ccell.2022.08.006

    View in Article CrossRef Google Scholar Scopus

    [276] Reggiardo R.E., Maroli S.V., Peddu V., et al. (2023). Profiling of repetitive RNA sequences in the blood plasma of patients with cancer. Nat. Biomed. Eng. 7:1627−1635. DOI:10.1038/s41551-023-01081-7

    View in Article CrossRef Google Scholar Scopus

    [277] Mei J., Tian H., Huang H.S., et al. (2023). Ccne1 is a potential target of metformin for tumor suppression of ovarian high-grade serous carcinoma. Cell Cycle 22:85−99. DOI:10.1080/15384101.2022.2109362

    View in Article CrossRef Google Scholar

    [278] Larsen G.L., Presley D.M., Graves J.P., et al. (1991). The effect of intravascular complement activation and brief episodes of hypoxia on protein in bronchoalveolar lavage fluid in c5 sufficient and deficient mice. Pediatr. Pulmonol. 11:302−309. DOI:10.1002/ppul.1950110406

    View in Article CrossRef Google Scholar

    [279] Zeng D., Wang C., Mu C., et al. (2021). Cell-free DNA from bronchoalveolar lavage fluid (BALF): A new liquid biopsy medium for identifying lung cancer. Ann. Transl. Med. 9:1080. DOI:10.21037/atm-21-2579

    View in Article CrossRef Google Scholar

    [280] Kang Y.P., Lee W.J., Hong J.Y., et al. (2014). Novel approach for analysis of bronchoalveolar lavage fluid (BALF) using HPLC-QTOF-MS-based lipidomics: Lipid levels in asthmatics and corticosteroid-treated asthmatic patients. J. Proteome Res. 13:3919−3929. DOI:10.1021/pr5002059

    View in Article CrossRef Google Scholar

    [281] Zheng L., Liu C., Wang H., et al. (2024). Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury. Microbiome 12:56. DOI:10.1186/s40168-024-01772-6

    View in Article CrossRef Google Scholar Scopus

    [282] Erturk-Hasdemir D. and Kasper D.L. (2018). Finding a needle in a haystack: Bacteroides fragilis polysaccharide a as the archetypical symbiosis factor. Ann. N. Y. Acad. Sci. 1417:116−129. DOI:10.1111/nyas.13660

    View in Article CrossRef Google Scholar

    [283] Fu A., Yao B., Dong T., et al. (2022). Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell 185:1356−1372. DOI:10.1016/j.cell.2022.02.027

    View in Article CrossRef Google Scholar Scopus

    [284] Qiu L., Lu W., Tu C., et al. (2023). Evidence of microplastics in bronchoalveolar lavage fluid among never-smokers: A prospective case series. Environ. Sci. Technol. 57:2435−2444. DOI:10.1021/acs.est.2c06880

    View in Article CrossRef Google Scholar

    [285] Wu P., Chan C., Tan H., et al. (2024). A threat or not? A global-scale investigation on microplastics inhalation during the first-ever worldwide face-mask wearing against the covid-19 pandemic. Innov. Med. 2 :100097. DOI: 10.59717/j.xinn-med.2024.100097

    View in Article Google Scholar

    [286] Chen Q., Wei X., Xie R., et al. (2024). Beyond physical particles: A holistic assessment of human health risks from real-world micro-nanoplastic exposure. Innov. Med. 2:100104. DOI:10.59717/j.xinn-med.2024.100104

    View in Article CrossRef Google Scholar Scopus

    [287] Du T., Yu X., Shao S., et al. (2023). Aging of nanoplastics significantly affects protein corona composition thus enhancing macrophage uptake. Environ. Sci. Technol. 57:3206−3217. DOI:10.1021/acs.est.2c05772

    View in Article CrossRef Google Scholar

    [288] Hu Q., Bian Q., Rong D., et al. (2023). Jak/stat pathway: Extracellular signals, diseases, immunity, and therapeutic regimens. Front. Bioeng. Biotechnol. 11:1110765. DOI:10.3389/fbioe.2023.1110765

    View in Article CrossRef Google Scholar

  • Cite this article:

    Mei J., Chen Y.-S., Tian H.-X., et al. (2025). Bronchoalveolar lavage fluid (BALF): Clinical applications for present and future. The Innovation Medicine 3:100115. https://doi.org/10.59717/j.xinn-med.2025.100115
    Mei J., Chen Y.-S., Tian H.-X., et al. (2025). Bronchoalveolar lavage fluid (BALF): Clinical applications for present and future. The Innovation Medicine 3:100115. https://doi.org/10.59717/j.xinn-med.2025.100115

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