Data for Discovery of a Geographically Distinct blaTEM Lineage in the Urban Public Transit Network of Quito, Ecuador

This dataset contains the supplementary analytical files, reference sequences, and custom scripts supporting the genomic characterization and phylogeographic analysis of blaTEM extended-spectrum beta-lactamase (ESBL) lineages identified within the "Trolebús" mass transit network in Quito, Ecuador. The study utilized Oxford Nanopore Technologies (ONT) long-read environmental sequencing combined with Bayesian phylodynamic inference to track plasmid-mediated antimicrobial resistance genes (ARGs) across high-touch urban surfaces. This repository houses the downstream alignment, profiling, and geographical mapping files used to generate the evolutionary coalescent dynamics and consensus networks discussed in the manuscript. Note: The raw environmental consensus sequences generated via ONT are not included in this repository and have been deposited separately in the NCBI BioProject database.