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. 2016 Dec 8;11(12):e0167649.
doi: 10.1371/journal.pone.0167649. eCollection 2016.

Airway Microbiota in Bronchoalveolar Lavage Fluid From Clinically Well Infants With Cystic Fibrosis

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Free PMC article

Airway Microbiota in Bronchoalveolar Lavage Fluid From Clinically Well Infants With Cystic Fibrosis

Theresa A Laguna et al. PLoS One. .
Free PMC article

Abstract

Background: Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics.

Methods: BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening. BALF was analyzed for total bacterial load by qPCR and for bacterial community composition by 16S ribosomal RNA sequencing. Clinical characteristics and standard BALF and NP culture results were recorded over five years of longitudinal follow-up.

Results: 12 BALF samples were collected from 8 infants with CF. Streptococcus, Burkholderia, Prevotella, Haemophilus, Porphyromonas, and Veillonella had the highest median relative abundance in infant CF BALF. Two of the 3 infants with repeat BALF had changes in their microbial communities over six months (Morisita-Horn diversity index 0.36, 0.38). Although there was excellent percent agreement between standard NP and BALF cultures, these techniques did not routinely detect all bacteria identified by sequencing.

Conclusions: BALF in asymptomatic CF infants contains complex microbiota, often missed by traditional culture of airway secretions. Anaerobic bacteria are commonly found in the lower airways of CF infants.

Conflict of interest statement

(1) T.A.L. - is a member of an advisory board for Gilead Pharmaceuticals; receives grant funding from the Cystic Fibrosis Foundation. (2) E.T.Z./B.D.W./J.K.H. - receive grant funding from the Cystic Fibrosis Foundation. Otherwise, the authors have declared that no other competing interests exist. In addition, this does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Total bacterial load and sequencing results from CF infant BALF samples.
(A) The top graph shows the relative abundance (RA) of specific taxon identified in the eight cross-sectional BALF samples. In specimens where total RA displayed is < 100%, the proportion not displayed was made up of other taxa present in low RA (< 5%). The samples are ordered by total bacterial load (TBL) detected in each sample. (B) The lower graph shows the TBL detected from each sample. The black horizontal line indicates the value obtained from one of the two negative controls included on the TBL qPCR plate, the other control produced a 0 value. Each letter represents an individual patient. Each taxon was required to have a RA of > 5% in at least 1 sample to be represented.
Fig 2
Fig 2. Comparison of the BALF microbiota communities in CF infants with repeat BALF performed 6 months apart.
Two BALF pairs had large shifts in their microbial communities as represented by a MH index of < 0.38. Each letter represents an individual patient.
Fig 3
Fig 3. The three samples with larger RA of Burkholderia had low TBL values in CF infant BALF samples.
Dark circles represent bronchoscopies performed at 6 months and light circles represent those performed at 12 months. Each letter represents an individual patient.
Fig 4
Fig 4. A positive correlation was observed between an increased RA of Streptococcus and a higher FEV0.5% predicted was observed in our CF infants during the first year of life.
Dark circles represent bronchoscopies performed at 6 months and light circles represent those performed at 12 months. Each letter represents an individual patient.

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