Figure 1.

Alpha- and beta-diversity comparisons between patients with IPD not exposed to antibiotics before sample collection (yellow) and IPD patients with previous antibiotic exposure (blue). Boxplots showing the Chao1 richness (A) and Shannon diversity indexes (B) according to antibiotic-exposure groups at the ASV level. Differences by group were assessed with simple linear regression analyses including confounding variables as copredictors (age, gender, seasonality, vaccination, ICU admission, and length of hospital stay). Three observations from the exposed group were deleted due to missing values in vaccination variable. (C) Nonmetric multidimensional scaling (NMDS) plot based on Bray–Curtis dissimilarities of nasopharyngeal microbiota composition of samples from all patients included in the study. Samples of each group are connected with their corresponding centroids using the function “ordispider” (Vegan R package). P-value corresponds to Adonis PERMANOVA test on the antibiotic- exposure group variable and including confounding variables as covariates. Significance codes: *** ≤0.001; ** ≤0.01; * ≤0.05. MDS, nonmetric multidimensional scaling.