Figure 3. Bacterial cultures and the microbiome in early CF.

A) Pathogen recovery frequency (left) and burden of pathogens in samples with positive cultures (right) in BALF from subjects with CF and from non-CF controls (n=124 CF, 32 non-CF). B) Total bacterial burden, as measured by 16S qPCR, in BALF from subjects with CF and non-CF controls (n=46 CF, 15 non-CF). C) qPCR and distribution of taxa from microbiome analyses for all CF (left) and non-CF samples (right). Bar height represents total qPCR signal, with detected taxa represented proportionally within the bar. For clarity, taxa with average prevalence <1% were grouped (light gray). The pattern observed from washes of sterile bronchoscopes (w) is shown for reference (n=6). Taxa associated with environmental contamination are shown in green, taxa associated with the oral cavity, including Moraxella, Haemophilus, and Streptococcus as common upper airway commensals (72), are shown in blue, and known pathogens are shown in red. Taxa were grouped as previously described (73) D) Concentrations of MUC5B and MUC5AC as measured by IHC in mucin flakes recovered by BALF from subjects with CF with no structural lung disease (CF-NSD, n=37) and non-CF controls (n=21) (significant by parameter; p=0.054 post-multivariate analyses). E) Neutrophil (PMN) counts in CF-NSD vs. non-CF. F) qPCR in CF-NSD and non-CF samples. G) Microbiome analyses of CF-NSD. Triangles represent samples from subjects who received antibiotics ≤3 months prior to bronchoscopy. See panel 3C for taxa legend. *=p<0.05, †=p<0.05 by non-parametric analysis.