Antimicrobial resistance has emerged as one of the major health threats of the 21st century. However, there is limited understanding of the distribution of antibiotic resistance globally. This is especially true in low and middle income countries with limited health care resources. Here, we are developing an extremely low cost pipeline to obtain nationally-representative estimates of antibiotic resistance gene prevalence. Cost is dramatically reduced by using novel molecular biological tools that leverage the massive data depth relative to cost of next generation short read sequencrers. The pipeline will be linked to low cost sample collection tools and automated data analysis to estimate prevalence rates of up to 30 antibiotic resistance genes in 1000s of samples simultaneously.