Fig. 1. Shifts in gut microbial ecology associated with CPE colonization.
a, PCoA plot showing how gut microbial community composition varies in relation to CPE colonization status (genus-level Bray–Curtis dissimilarity; Unifrac plot in Extended Data Fig. 1). Contour lines indicate similar density with regions of locally higher density associated with distinct community configurations (defined by average linkage clustering in Extended Data Fig. 1; marked with labels I, II, III and IV). b, Box plots showing genus-level Shannon diversity distributions for different timepoints for index patients (‘CPE positive’, during colonization; ‘At clearance’, within 1 month of decolonization; ‘2 months post-clearance’, timepoints that were >2 months after decolonization) and all timepoints for family members (n = 347 timepoints; two-sided Wilcoxon rank-sum test P values: CPE positive versus 2 months post-clearance, 1.15 × 10−4; CPE positive versus family members, 2.46 × 10−12). c, Species that were found to be enriched in CPE-positive (red) and CPE-negative (blue) samples along with their linear discriminant analysis (LDA) scores based on LEfSe analysis. Results that were significant on the basis of Songbird analysis as well are indicated with a solid circle. d, Violin plots showing the standard deviation of relative abundances (ignoring relative abundances <0.1% to avoid the effect of detection limit for metagenomics) over time of various taxa in different individuals (subjects and family members) (n = 43 individuals, two-sided Wilcoxon rank-sum test P values: E. coli, 0.021; K. pneumoniae, 4.96 × 10−5; Enterobacteriaceae, 0.011). For all subfigures: *P < 0.1, **P < 0.05, ***P < 0.01 based on the Wilcoxon rank-sum test, and all other comparisons were not statistically significant. Centre lines in the boxplots represent median values, box limits represent upper and lower quartile values, and whiskers represent 1.5 times the interquartile range above the upper quartile and below the lower quartile.