Representing antibiotic relationships using measurements of efficacy against clinical isolates

Antimicrobial resistance (AMR) is a worrying and confusing problem for both patients and medical professionals. Current antimicrobial nomenclature makes it difficult to understand how different antibiotics are related to one another, and their empirical uses and efficacy. Here, I attempt to address this problem by using experimental data from hundreds of thousands of clinical isolates to infer relationships between antibiotics and represent them with simple diagrams.This dataset (Supplementary File 1) is a cleaned version of the Pfizer ATLAS dataset made publicly available as part of the Wellcome Data Re-use Prize. With an additional metadata file on antibiotics (Supplementary File 2) the R code (Supplementary File 3) reproduces Table 1 and Figure 2 of the associated paper.