Clinical Antibiotic Resistance Patterns Across 70 Countries

Abstract

We sought global patterns of antibiotic resistant pathogenic bacteria within the AMR Research Initiative database, Atlas. This consists of 6.5M clinical minimal inhibitory concentrations (MICs) observed in 70 countries in 633k patients between 2004 and 2017. Stratifying MICs according to pathogens (P), antibiotics (A) and countries (C), we found that the frequency of resistance was higher in Atlas than other publicly available databases. We determined global MIC distributions and, after showing they are coherent between years, we predicted MIC changes for 43 pathogens and 827 pathogen-antibiotic (PAs) pairings that exhibit significant resistance dynamics, including MIC increases and even decreases. However, many MIC distributions are multi-modal and some PA pairs exhibit sudden changes in MIC. We therefore analysed Atlas after replacing the clinical classification of pathogens into ‘susceptible’, ‘intermediate’ and ‘resistant’ with an information-optimal, cluster-based classifier to determine subpopulations with differential resistance that we denote S and R. Accordingly, S and R clusters for different PA pairs exhibit signatures of stabilising, directional and disruptive selection because their respective MICs can have different dynamics. Finally, we discuss clinical applications of a (R, dR/dt) ‘phase plane’ whereby the MIC of R is regressed against change in MIC (dR/dt), a methodology we use to detect PA pairs at risk of developing clinical resistance.