Topological data analysis captures Horizontal Gene Transfer in Antimicrobial Resistance gene families among clinically relevant bacteria

Antibiotic resistance, causing 10 million deaths annually by 2050, is driven by horizontal gene transfer in hospitals. The Critical Assessment of Massive Data Analysis 2023 challenge analyzed resistance markers from 146 Johns Hopkins bacterial isolates using persistent homology, a topological data analysis method. The study found that on average, two 1-holes form for every group of three genomes undergoing horizontal gene transfer. Persistent homology offers a framework for understanding complex clinical patterns, offering an alternative to genomic sequencing methods.