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Original Article|Articles in Press

Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis

Published:February 21, 2023DOI:https://doi.org/10.1016/j.jcf.2023.02.003

      Highlights

      • Absolute abundance of fungi differed significantly among CF sputa; therefore, qPCR corrected abundance to account for total fungal abundance may be valuable for mycobiome studies.
      • Members of the Candida genus are highly abundant in sputa of adults with cystic fibrosis and are associated with pulmonary exacerbation state.
      • Higher lung function is associated with greater fungal richness and alpha-diversity and CFTR modulator use is associated with greater fungal alpha-diversity; whereas chronic azithromycin use is associated with lower fungal richness and alpha-diversity.

      Abstract

      Background

      The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics.

      Methods

      We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated.

      Results

      Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences.

      Conclusion

      The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.

      Keywords

      Abbreviations:

      FEV1 (forced expiratory volume in one second), CFQ-R (cystic fibrosis questionnaire-revised), DTT (dithiothreitol), ITS (internal transcribed spacer), QPCR (quantitative polymerase chain reaction), OTU (operational taxonomic unit), CFTR (cystic fibrosis transmembrane conductance regulator), ABPA (allergic bronchopulmonary aspergillosis), IV (intravenous), BAL (bronchoalveolar lavage)
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      References

        • 2019 Annual Data Report
        Cystic fibrosis foundation patient registry.
        Cystic Fibrosis Foundation, Bethesda, MD2020
        • Elborn J.S.
        Cystic fibrosis.
        Lancet. 2016; 388: 2519-2531
        • Sudfeld C.R.
        • Dasenbrook E.C.
        • Merz W.G.
        • Carroll K.C.
        • Boyle M.P.
        Prevalence and risk factors for recovery of filamentous fungi in individuals with cystic fibrosis.
        J Cyst Fibros. 2010; 9 (official journal of the European Cystic Fibrosis Society): 110-116
        • Hong G.
        • Psoter K.J.
        • Jennings M.T.
        • Merlo C.A.
        • Boyle M.P.
        • Hadjiliadis D.
        • et al.
        Risk factors for persistent Aspergillus respiratory isolation in cystic fibrosis.
        J Cyst Fibros. 2018; (official journal of the European Cystic Fibrosis Society)
        • Coburn B.
        • Wang P.W.
        • Diaz Caballero J.
        • Clark S.T.
        • Brahma V.
        • Donaldson S.
        • et al.
        Lung microbiota across age and disease stage in cystic fibrosis.
        Sci Rep. 2015; 5: 10241
        • Cox M.J.
        • Allgaier M.
        • Taylor B.
        • Baek M.S.
        • Huang Y.J.
        • Daly R.A.
        • et al.
        Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients.
        PLoS One. 2010; 5: e11044
        • Carmody L.A.
        • Caverly L.J.
        • Foster B.K.
        • Rogers M.A.M.
        • Kalikin L.M.
        • Simon R.H.
        • et al.
        Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis.
        PLoS One. 2018; 13e0194060
        • Mac Aogain M.
        • Chandrasekaran R.
        • Lim A.Y.H.
        • Low T.B.
        • Tan G.L.
        • Hassan T.
        • et al.
        Immunological corollary of the pulmonary mycobiome in bronchiectasis: the CAMEB study.
        Eur Respir J. 2018; 52
        • Delhaes L.
        • Monchy S.
        • Frealle E.
        • Hubans C.
        • Salleron J.
        • Leroy S.
        • et al.
        The airway microbiota in cystic fibrosis: a complex fungal and bacterial community–implications for therapeutic management.
        PLoS One. 2012; 7: e36313
        • Charlson E.S.
        • Diamond J.M.
        • Bittinger K.
        • Fitzgerald A.S.
        • Yadav A.
        • Haas A.R.
        • et al.
        Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.
        Am J Respir Crit Care Med. 2012; 186: 536-545
        • Willger S.D.
        • Grim S.L.
        • Dolben E.L.
        • Shipunova A.
        • Hampton T.H.
        • Morrison H.G.
        • et al.
        Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis.
        Microbiome. 2014; 2: 40
        • Cuthbertson L.
        • Felton I.
        • James P.
        • Cox M.J.
        • Bilton D.
        • Schelenz S.
        • et al.
        The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis.
        J Cyst Fibros. 2021; 20 (official journal of the European Cystic Fibrosis Society): 295-302
        • Soret P.
        • Vandenborght L.E.
        • Francis F.
        • Coron N.
        • Enaud R.
        • Avalos M.
        • et al.
        Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis.
        Sci Rep. 2020; 10: 3589
        • Quittner A.L.
        • Modi A.C.
        • Wainwright C.
        • Otto K.
        • Kirihara J.
        • Montgomery A.B.
        Determination of the minimal clinically important difference scores for the cystic fibrosis questionnaire-revised respiratory symptom scale in two populations of patients with cystic fibrosis and chronic Pseudomonas aeruginosa airway infection.
        Chest. 2009; 135: 1610-1618
        • Hong G.
        • Alby K.
        • Ng S.C.W.
        • Fleck V.
        • Kubrak C.
        • Rubenstein R.C.
        • et al.
        The presence of Aspergillus fumigatus is associated with worse respiratory quality of life in cystic fibrosis.
        J Cyst Fibros. 2020; 19 (official journal of the European Cystic Fibrosis Society): 125-130
        • Liu C.M.
        • Kachur S.
        • Dwan M.G.
        • Abraham A.G.
        • Aziz M.
        • Hsueh P.R.
        • et al.
        FungiQuant: a broad-coverage fungal quantitative real-time PCR assay.
        BMC Microbiol. 2012; 12: 255
        • Dollive S.
        • Peterfreund G.L.
        • Sherrill-Mix S.
        • Bittinger K.
        • Sinha R.
        • Hoffmann C.
        • et al.
        A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.
        Genome Biol. 2012; 13: R60
        • Bittinger K.
        • Charlson E.S.
        • Loy E.
        • Shirley D.J.
        • Haas A.R.
        • Laughlin A.
        • et al.
        Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.
        Genome Biol. 2014; 15: 487
        • Breuer O.
        • Schultz A.
        • Turkovic L.
        • de Klerk N.
        • Keil A.D.
        • Brennan S.
        • et al.
        Changing prevalence of lower airway infections in young children with cystic fibrosis.
        Am J Respir Crit Care Med. 2019; 200: 590-599
        • Brandt C.
        • Roehmel J.
        • Rickerts V.
        • Melichar V.
        • Niemann N.
        • Schwarz C.
        Aspergillus bronchitis in patients with cystic fibrosis.
        Mycopathologia. 2018; 183: 61-69
        • Breuer O.
        • Schultz A.
        • Garratt L.W.
        • Turkovic L.
        • Rosenow T.
        • Murray C.P.
        • et al.
        Aspergillus infections and progression of structural lung disease in children with cystic fibrosis.
        Am J Respir Crit Care Med. 2020; 201: 688-696
        • Krause R.
        • Moissl-Eichinger C.
        • Halwachs B.
        • Gorkiewicz G.
        • Berg G.
        • Valentin T.
        • et al.
        Mycobiome in the lower respiratory tract - a clinical perspective.
        Front Microbiol. 2016; 7: 2169
        • Krause R.
        • Halwachs B.
        • Thallinger G.G.
        • Klymiuk I.
        • Gorkiewicz G.
        • Hoenigl M.
        • et al.
        Characterisation of Candida within the mycobiome/microbiome of the lower respiratory tract of ICU patients.
        PLoS One. 2016; 11e0155033
        • Lepesqueur L.S.S.
        • Tanaka M.H.
        • Lima G.M.G.
        • Chiba S.M.
        • Mota A.J.
        • Santos S.F.
        • et al.
        Oral prevalence and antifungal susceptibility of Candida species in cystic fibrosis patients.
        Arch Oral Biol. 2020; 116104772
        • Muhlebach M.S.
        • Zorn B.T.
        • Esther C.R.
        • Hatch J.E.
        • Murray C.P.
        • Turkovic L.
        • et al.
        Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children.
        PLoS Pathog. 2018; 14e1006798
        • Prevaes S.M.
        • de Steenhuijsen Piters W.A.
        • de Winter-de Groot K.M.
        • Janssens H.M.
        • Tramper-Stranders G.A.
        • Chu M.L.
        • et al.
        Concordance between upper and lower airway microbiota in infants with cystic fibrosis.
        Eur Respir J. 2017; 49
        • Gileles-Hillel A.
        • Shoseyov D.
        • Polacheck I.
        • Korem M.
        • Kerem E.
        • Cohen-Cymberknoh M.
        Association of chronic Candida albicans respiratory infection with a more severe lung disease in patients with cystic fibrosis.
        Pediatr Pulmonol. 2015; 50: 1082-1089
        • Hogan D.A.
        • Kolter R.
        Pseudomonas-Candida interactions: an ecological role for virulence factors.
        Science. 2002; 296: 2229-2232
        • McTaggart L.R.
        • Copeland J.K.
        • Surendra A.
        • Wang P.W.
        • Husain S.
        • Coburn B.
        • et al.
        Mycobiome sequencing and analysis applied to fungal community profiling of the lower respiratory tract during fungal pathogenesis.
        Front Microbiol. 2019; 10: 512
        • Esther Jr., C.R.
        • Plongla R.
        • Kerr A.
        • Lin F.C.
        • Gilligan P
        Clinical outcomes in cystic fibrosis patients with Trichosporon respiratory infection.
        J Cyst Fibros. 2016; 15 (official journal of the European Cystic Fibrosis Society): e45-e49
        • Kramer R.
        • Sauer-Heilborn A.
        • Welte T.
        • Guzman C.A.
        • Abraham W.R.
        • Höfle M.G.
        Cohort study of airway mycobiome in adult cystic fibrosis patients: differences in community structure between fungi and bacteria reveal predominance of transient fungal elements.
        J Clin Microbiol. 2015; 53: 2900-2907
        • Ming C.
        • Huang J.
        • Wang Y.
        • Lv Q.
        • Zhou B.
        • Liu T.
        • et al.
        Revision of the medically relevant species of the yeast genus Diutina.
        Med Mycol. 2019; 57: 226-233
        • Acosta N.
        • Thornton C.S.
        • Surette M.G.
        • Somayaji R.
        • Rossi L.
        • Rabin H.R.
        • et al.
        Azithromycin and the microbiota of cystic fibrosis sputum.
        BMC Microbiol. 2021; 21: 96
        • Rogers G.B.
        • Bruce K.D.
        • Martin M.L.
        • Burr L.D.
        • Serisier D.J.
        The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial.
        Lancet Respir Med. 2014; 2: 988-996
        • Slater M.
        • Rivett D.W.
        • Williams L.
        • Martin M.
        • Harrison T.
        • Sayers I.
        • et al.
        The impact of azithromycin therapy on the airway microbiota in asthma.
        Thorax. 2014; 69: 673-674
        • Einarsson G.G.
        • Ronan N.J.
        • Mooney D.
        • McGettigan C.
        • Mullane D.
        • NiChroinin M.
        • et al.
        Extended-culture and culture-independent molecular analysis of the airway microbiota in cystic fibrosis following CFTR modulation with ivacaftor.
        J Cyst Fibros. 2021; 20 (official journal of the European Cystic Fibrosis Society): 747-753
        • Graeber S.Y.
        • Boutin S.
        • Wielpütz M.O.
        • Joachim C.
        • Frey D.L.
        • Wege S.
        • et al.
        Effects of lumacaftor-ivacaftor on lung clearance index, magnetic resonance imaging, and airway microbiome in Phe508del homozygous patients with cystic fibrosis.
        Ann Am Thorac Soc. 2021; 18: 971-980
        • Hoggard M.
        • Vesty A.
        • Wong G.
        • Montgomery J.M.
        • Fourie C.
        • Douglas R.G.
        • et al.
        Characterizing the human mycobiota: a comparison of small subunit rRNA, ITS1, ITS2, and large subunit rRNA genomic targets.
        Front Microbiol. 2018; 9: 2208