Changes in airway bacterial communities occur soon after initiation of antibiotic treatment of pulmonary exacerbations in cystic fibrosis


      • Changes to bacterial communities in CF lung are often observed immediately after the initiation of antibiotic therapy for exacerbation.
      • Most of the observed change in bacterial community structure occurs during the first five days of antibiotic treatment.
      • Bacterial communities remain in a perturbed state through at least two weeks of antibiotic therapy.


      Chronic polymicrobial airway infections are a hallmark of cystic fibrosis (CF) lung disease. Antibiotic therapy is a primary treatment of CF pulmonary exacerbations (PEx); however, the impact of episodic antibiotic treatment on airway bacterial communities has not been well described. We analyzed sputum samples from adults with CF obtained immediately before and during antibiotic treatment of PEx. Sequencing of the V4 region of the bacterial 16S ribosomal RNA gene was used to assess changes in bacterial community structure during antibiotic treatment. The peak impact of antibiotic treatment was observed by day four or five of treatment. These findings advance our understanding of bacterial community dynamics during antibiotic treatment of PEx and complement recent and ongoing studies evaluating the optimal duration of antibiotic therapy for PEx.


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        • Caverly L.J.
        • Lu J.
        • Carmody L.A.
        • Kalikin L.M.
        • Shedden K.
        • Opron K.
        • et al.
        Measures of cystic fibrosis airway microbiota during periods of clinical stability.
        Ann Am Thorac Soc. 2019; 16: 1534-1542
        • Lu J.
        • Carmody L.A.
        • Opron K.
        • Simon R.H.
        • Kalikin L.M.
        • Caverly L.J.
        • et al.
        Parallel analysis of cystic fibrosis sputum and saliva reveals overlapping communities and an opportunity for sample decontamination.
        mSystems. 2020; 5 (e00296-20)
        • Zhao J.
        • Li J.
        • Schloss P.D.
        • Kalikin L.M.
        • Raymond T.A.
        • Petrosino J.F.
        • et al.
        Effect of sample storage conditions on culture-independent bacterial community measures in cystic fibrosis sputum specimens.
        J Clin Microbiol. 2011; 49: 3717-3718
        • Seekatz A.M.
        • Theriot C.M.
        • Molloy C.T.
        • Wozniak K.L.
        • Bergin I.L.
        • Young V.B
        Fecal microbiota transplantation eliminates Clostridium difficile in a murine model of relapsing disease.
        Infect Immun. 2015; 83: 3838-3846
        • Callahan B.J.
        • McMurdie P.J.
        • Rosen M.J.
        • Han A.W.
        • Johnson A.J.A.
        • Holmes S.P.
        DADA2: high-resolution sample inference from Illumina amplicon data.
        Nat Methods. 2016; 13: 581-583
        • Caporaso J.G.
        • Kuczynski J.
        • Stombaugh J.
        • Bittinger K.
        • Bushman F.D.
        • Costello E.K.
        • et al.
        QIIME allows analysis of high-throughput community sequencing data.
        Nat Methods. 2010; 7: 335-336
        • Lozupone C.A.
        • Hamady M.
        • Kelley S.T.
        • Knight R.
        Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities.
        Appl Environ Microbiol. 2007; 73: 1576-1585
        • Bray J.R.
        • Curtis J.T.
        An ordination of the upland forest communities of southern Wisconsin.
        Ecol Monogr. 1957; 27: 326-349
        • Caverly L.J.
        • Zhao J.
        • LiPuma J.J.
        Cystic fibrosis lung microbiome: opportunities to reconsider management of airway infection.
        Pediatr Pulmonol. 2015; 50: S31-S38
        • Goss C.H.
        • Heltshe S.L.
        • West N.E.
        • Skalland M.
        • Sanders D.B.
        • Jain R.
        • et al.
        A randomized clinical trial of antimicrobial duration for cystic fibrosis pulmonary exacerbation treatment.
        Am J Respir Crit Care Med. 2021; 204: 1295-1305