ariktha/mordor-spillover

Code base for Geographic spillover of antimicrobial resistance due to mass azithromycin distribution in MORDOR (Niger) at 24 months # mordor-spillover ## Geographic spillover of antimicrobial resistance (AMR) due to mass azithromycin distribution in the MORDOR trial in Niger ## Project Overview Large-scale, placebo-controlled, cluster-randomized trials in high-mortality settings in several African countries demonstrated a 14-18% reduction in childhood mortality following twice-annual mass drug administration (MDA) of azithromycin among children aged 1–59 months. Azithromycin MDA also selects for antimicrobial resistance (AMR), particularly macrolide resistance in treated populations. It is unknown whether the genetic selection of AMR from azithromycin MDA could spill over to neighboring untreated populations. We assessed between-village geographic spillover effects of genotypic resistance to macrolides and other antibiotic classes in rectal swabs collected from 1200 children in 30 monitoring villages in Niger after two years of MDA in 594 surrounding villages. Key Finding: We found no evidence of geographic spillover of macrolide resistance in untreated villages, as the genetic load of AMR remained at baseline levels in placebo-treated villages regardless of surrounding azithromycin treatment intensity. - **Preprint:** medrxiv.org - **Pre-specified analysis plan:** osf.io - **Public data repository:** osf.io - **Primary results of the trials:** - MORDOR Mortality trial: doi.org - MORDOR Morbidity (AMR-monitoring) trial: nejm.org If you have any questions about the files in this repository, please contact Ariktha Srivathsan or Ben Arnold at UCSF (ariktha.srivathsan@ucsf.edu; ben.arnold@ucsf.edu) ## Code Submission Items Following: nature.com ### System requirements `> sessionInfo()` `R version 4.5.1 (2025-06-13)` `Platform: x86_64-apple-darwin20` `Running under: macOS Sequoia 15.6.1` All analyses were run using R ve …