Supplementary Material 10

Grouping antimicrobial resistance (AMR) genes based on their association with 16 antimicrobial classes used in antimicrobial susceptibility testing (AST) and E. coli treatment in ICU sepsis patients is crucial for understanding resistance patterns, guiding treatment decisions, and tracking the evolution of resistant strains.
Enhanced treatment strategies: By categorizing AMR genes based on antimicrobial classes, clinicians can predict resistance trends in ICU E. coli sepsis cases, aiding in selecting effective antibiotics and reducing treatment failures.Understanding phylogenetic distribution: Phylogenetic grouping helps reveal whether specific resistance genes are associated with particular E. coli lineages, providing insights into the evolutionary dynamics and horizontal gene transfer events contributing to multidrug resistance.Surveillance and outbreak tracking: Clustering AMR genes by antimicrobial classes allows researchers to monitor the spread of resistant E. coli strains in ICU settings, identifying high-risk clones and resistance hotspots.Correlation with phenotypic resistance: Linking AMR gene clusters with AST results helps validate genotype-phenotype relationships, ensuring that genetic predictions align with observed drug resistance patterns.Personalized medicine approaches: Understanding the phylogenetic distribution of AMR genes supports the development of targeted therapies, potentially enabling the use of combination treatments to overcome specific resistance mechanisms.AMR mechanism identification: Categorizing resistance genes among antimicrobial classes provides deeper insights into resistance mechanisms, such as enzymatic degradation (e.g., β-lactamases for β-lactams), efflux pump activity, or target site modifications.Antibiotic stewardship programs: The data generated from such phylogenetic groupings can inform antimicrobial stewardship efforts by highlighting the most concerning resistance patterns and promoting the judicious use of antibiotics in ICU settings.By analyzing AMR gene distributions across antimicrobial classes and integrating phylogenetic data, researchers can develop robust strategies for combating drug-resistant E. coli infections in ICU patients with sepsis, ultimately improving clinical outcomes and slowing the spread of antimicrobial resistance.