Novel approach to analysis of AMR: looking at the composite resistance phenotype

Abstract

Submission of detail report with codes for the Vivli AMR Surveillance Open Data Re-use Data Challenge 2023 Team ID: 9049 [Lead: Shraddha Karve] Objectives: The escalating challenge of antimicrobial resistance (AMR) poses a significant global concern for public healthcare systems1,2. Current AMR surveillance and molecular mechanism studies traditionally focus on specific drug-bug combinations, like carbapenem-resistant Klebsiella pneumoniae, designated as a priority pathogen by the WHO3. While wastewater and environmental surveillance aim to detect Klebsiella species and genes conferring carbapenem resistance4, it is known that resistance genes for one antibiotic often coexist with genes for resistance to others5. To address these complexities, we propose a novel analysis approach using Klebsiella pneumoniae as a model. We consider the resistance profile of an isolate for a set of common antibiotics across two datasets, ATLAS and GEARS. We term this composite phenotype, encompassing resistance/sensitivity to a group of antibiotics, a 'subtype' of the pathogen. Our primary objective is to track and study the prevalence of different subtypes across time and space, enabling a more comprehensive understanding of AMR dynamics. We then explore the impact of climatic parameters on the prevalence of different Klebsiella pneumoniae subtypes, aiming to uncover additional insights into antibiotic resistance patterns. Rising temperatures and climate change have been associated with recent antibiotic resistance developments, as bacterial growth and genetic material dissemination are closely tied to temperature conditions6. Heavy rainfall has been linked to bacterial mutagenesis and antibiotic resistance gene expression7. Rising local temperatures in the United States and Europe have shown correlations with increased antibiotic resistance at the population level in various pathogens8,9. GitHub repository: https://github.com/KutumLab/amr-vivli-ashoka-submissio