Fig. 4: Co-occurrence of mcr-9 and mcr-10 with antimicrobial resistance (AMR) genes in the global plasmid dataset (n = 326).
a Multivariate principal component analysis (PCA) showing the distribution of AMR genes harbored by plasmids carrying mcr-9 and mcr-10. Ellipses represent 95% confidence with three specified clusters. The PCA plot was generated using the Jaccard measure of distance. Variants mcr-9.1, mcr-9.2, and mcr-10.1 are labeled in blue for visual clarity. b Heatmap matrix showing the conditional probabilities of AMR gene co-occurrence calculated for all pairs of genes using ReGAIN50. Conditional probability refers to the probability of observing gene A given the presence of gene B50. Antimicrobial class of every AMR gene is indicated by colored blocks on the left and top of the matrix. (c) Association network showing the co-occurrence of mcr alleles and AMR genes based on relative risk. Relative risk is the ratio of the conditional probability of observing gene A given gene B to the conditional probability of only observing gene A in the absence of gene B50. Nodes represent AMR genes and are colored by antimicrobial class. Edges are colored by relative risk values. Details of the co-occurrence analysis are presented in Supplementary Data 8.
