Seeking patterns of antibiotic resistance in ATLAS, an open, raw MIC database with patient metadata

Abstract

This is the final version. Available on open access from Nature Research via the DOI in this record ; Data availability: ATLAS is available following website registration*. Data and further information can be downloaded from the following links: Project overview: https://amr.theodi.org/project-overview Project description: https://wellcome.ac.uk/sites/default/files/antimicrobial-resistance-surveillance-sharing-industry-data.pdf Data download*: https://www.synapse.org/#!Synapse:syn17009517/wiki/585653 The same dataset is available from this link: https://s3-eu-west-1.amazonaws.com/amr-prototype-data/Open+Atlas_Reuse_Data.xlsx Data was extracted from the English Surveillance Programme for Antimicrobial Utilisation and Resistance (ESPAUR) report from years 2013-2018. These were downloaded from the following UK government website: https://www.gov.uk/government/publications/english-surveillance-programme-antimicrobial-utilisation-and-resistance-espaur-report ResistanceMap data is published by the Centre for Disease, Dynamics Economics and Policy28, it can be downloaded from https://github.com/gwenknight/empiricprescribing/tree/master/data, Data for the European Centre for Disease Prevention and Control (ECDC) can be downloaded from https://atlas.ecdc.europa.eu/public/index.aspx?Dataset=27#x00026;HealthTopic=4. The file we used in this paper can be downloaded from https://github.com/PabloCatalan/atlas/tree/master/data/europe_resistance_data.csv EUCAST data can only be obtained by contacting individuals named on their website https://www.eucast.org/mic_distributions_and_ecoffs/ and requesting access to MIC histograms, which we were granted. ; Code availability: Analysis codes66 written in Python 3.0 using pandas can be downloaded here: https://github.com/PabloCatalan/atlas or https://doi.org/10.5281/zenodo.6390565. Codes have been written to provide straightforward access to data so that figures from this manuscript can be reproduced and to help facilitate the development of new analyses. Interested readers are ...