Fig. 4: Antibiotic exposure and impact on BAL microbiome.

a, Days of antimicrobial exposure are listed for antibacterials (black), antifungals (green) and antivirals (blue). Patients are listed in the columns and the shading indicates the number of days of exposure to each antibiotic in the week preceding BAL. b, AES was calculated before each BAL as the sum of antibiotic exposure days × a broadness weighting factor, summed for all therapies received in the week preceding BAL. AES varied across the clusters (n = 127, 74, 45 and 32 for clusters 1–4, respectively) and was highest for patients in cluster 4 (Kruskal–Wallis test, P = 0.005). For all box plots: the boxes indicate the median and IQR; the whiskers extend to the largest value above the 75th percentile (or the smallest value below the 25th percentile), that is, within 1.5 times the IQR. c, Negative binomial generalized linear models were used to test for BAL microorganisms associated with AES. Microorganisms are listed in the rows, with phyla shown on the left and bacterial genera shown on the right.