Table 2

Relative abundance of classical CF pathogens and core CF microbiome constituents, as a function of clinical outcomes

Progression to eESLDAbsolute rate of lung function declineRelative rate of lung function decline
nESLD (n=87)eESLD (n=17)P valuesAb-Nrp (n=46)Ab-RP (n=58)P valuesRe-Nrp (n=57)Re-RP (n=47)P values
Classical pathogens
Pseudomonas 0.45 (0.03–37)47.8 (0.1–91.3)0.0410.7 (0.04–51.1)1.1 (0.03–44.2)0.462.17 (0.03–47.8)3.28 (0.03–48.5)0.84
Streptococcus 30.6 (12.4–56.6)7.37 (0.4–19.9)0.0132.3 (16.1–50.1)22.8 (5.1–59)0.2734.1 (18.7–56)15.1 (4.02–56.04)0.05
Staphylococcus 0.32 (0.01–14.3)0.01 (0.002–7)0.090.16 (0.01–5.1)1.62 (0.01–18.3)0.520.12 (0.01–5.04)2.58 (0.008–22.8)0.17
Haemophilus 1.8 (0.16–16.4)0.01 (0.01–0.05)<0.0011.71 (0.18–7.6)0.52 (0.02–9.8)0.211.62 (0.1–8.7)0.28 (0.01–7.9)0.06
Stenotrophomonas 0 (0–0.002)0.001 (0–0.07)0.080 (0–0.002)0 (0–0.004)0.310 (0–0.002)0 (0–0.003)0.42
‘Non-Classical’ core microbiome*
Granulicatella 0.79 (0.1–1.89)0.07 (0.002–0.3)0.0010.93 (0.23–2.13)0.35 (0.02–1.1)0.011.07 (0.2–2.13)0.26 (0.02–0.81)<0.001
Gemella 0.73 (0.14–1.9)0.06 (0.01–0.6)0.011.25 (0.35–1.9)0.31 (0.02–0.9)0.0021.03 (0.31–2.1)0.24 (0.02–0.8)<0.001
Rothia 1.16 (0.23–3.4)0.4 (0.02–0.7)0.031.6 (0.2–3.4)0.73 (0.08–2.8)0.081.61 (0.2–4.1)0.62 (0.03–2.1)0.01
Veillonella 0.26 (0.04–0.7)0.05 (0.01–0.5)0.110.23 (0.06–0.73)0.25 (0.02–0.5)0.260.35 (0.07–0.7)0.15 (0.01–0.4)0.02
Prevotella 0.57 (0.08–2.8)0.43 (0.04–1)0.340.68 (0.1–2.2)0.49 (0.04–2.8)0.500.81 (0.2–2.3)0.41 (0.03–2.8)0.17
Fusobacterium 0.21 (0.03–0.5)0.06 (0.01–0.3)0.230.26 (0. 03–0. 7)0.14 (0.01–0.4)0.120.27 (0.04–0.72)0.09 (0.01–0.43)0.03
  • Data are presented as median (%) (IQR) and Wilcoxon rank-sum test was conducted.

  • *Core microbiome refers to those genera recovered from the cystic fibrosis microbiome that is commonly found in patients, in high prevalence amounts.47

  • Ab, absolute; CF, cystic fibrosis; eESLD, early end-stage lung disease (defined as death/transplantation prior to age 25); nESLD, no eESLD; Nrp, non-rapid progressors; Re, relative; RP, rapid progressors.