Extended Data Fig. 9: Distribution of canonical resistance mechanisms across antibiotic treatments.
From: ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro
(A) Distribution of canonical resistance mechanisms across antibiotic treatments in adaptive laboratory evolution and frequency of resistance assay. Unique de novo genomic mutations were assigned to four major resistance mechanisms based on homology to genes featured in the CARD and ResFinder databases. Those antibiotic treatments were disregarded that did not yield at least 10 unique mutations during the course of laboratory evolution. The four major resistance categories include reduced membrane permeability, antibiotic target alteration, antibiotic inactivation, and antibiotic efflux. The distribution of mutations belonging to each resistance mechanism differs across the antibiotics (two-sided proportion test, p < 0.001). For antibiotic abbreviations, see Table 1. (B) Distribution of resistance mechanisms across antibiotic treatments in functional metagenomics screens. The barplot shows the fraction of ARGs per antibiotic resistance mechanisms across functional metagenomics screens in the presence of different antibiotics (blue and orange indicate control and recent antibiotics, respectively). ARGs were assigned to five major resistance mechanisms (vertical panels) based on homology to genes featured in the CARD and ResFinder databases. The five major resistance categories include antibiotic efflux. antibiotic inactivation, antibiotic target alteration, antibiotic target protection, and reduced permeability to antibiotics. The distribution of ARGs belonging to each resistance mechanism shows heterogeneity across the antibiotics (two-sided roportion test, p < 0.001). For antibiotic abbreviations, see Table 1.
