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

Pablo Catalán (), Emily Wood, Jessica M. A. Blair, Ivana Gudelj, Jonathan R. Iredell and Robert E. Beardmore ()
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Pablo Catalán: Biosciences, College of Life and Environmental Sciences, University of Exeter
Emily Wood: Biosciences, College of Life and Environmental Sciences, University of Exeter
Jessica M. A. Blair: Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham
Ivana Gudelj: Biosciences, College of Life and Environmental Sciences, University of Exeter
Jonathan R. Iredell: Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research
Robert E. Beardmore: Biosciences, College of Life and Environmental Sciences, University of Exeter

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Antibiotic resistance represents a growing medical concern where raw, clinical datasets are under-exploited as a means to track the scale of the problem. We therefore sought patterns of antibiotic resistance in the Antimicrobial Testing Leadership and Surveillance (ATLAS) database. ATLAS holds 6.5M minimal inhibitory concentrations (MICs) for 3,919 pathogen-antibiotic pairs isolated from 633k patients in 70 countries between 2004 and 2017. We show most pairs form coherent, although not stationary, timeseries whose frequencies of resistance are higher than other databases, although we identified no systematic bias towards including more resistant strains in ATLAS. We sought data anomalies whereby MICs could shift for methodological and not clinical or microbiological reasons and found artefacts in over 100 pathogen-antibiotic pairs. Using an information-optimal clustering methodology to classify pathogens into low and high antibiotic susceptibilities, we used ATLAS to predict changes in resistance. Dynamics of the latter exhibit complex patterns with MIC increases, and some decreases, whereby subpopulations’ MICs can diverge. We also identify pathogens at risk of developing clinical resistance in the near future.

Date: 2022
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DOI: 10.1038/s41467-022-30635-7

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