ARG-MATEE Automated Pipeline for Detection of Antimicrobial Resistance in WGS Data Collected from Pig Farms and Surrounding Communities

Abstract: As part of recognizing the interconnected nature of different sectors in relation to health, AMR (antimicrobial resistance) has emerged as an issue of high global importance. E. coli isolates were taken from pig farms in Thailand, which serves as a point of interest in the study of ARGs (antimicrobial resistance genes) in emerging economies. The fecal samples were collected from pigs, humans who came in contact with the pigs, and humans who did not have contact with pigs to be analyzed for ARGS, virulence genes, and plasmids. Data was analyzed with an automated pipeline in the form of ARG-MATEE, the Antimicrobial Resistance Gene Multi-Analysis Tool for Enteric E. coli, a tool designed in this study to be used here and in future investigations. ARG-MATEE regulates and records internal software versions in a produced report which also includes data tables for all non phylogeny results in Boyce–Codd normal form and data visualizations for plasmids, ARGs, virulence genes, and phylogeny. Through the use of ARG-MATEE, the iss virulence gene was seen to be significantly different between testing groups as it is present in only human testing groups, suggesting the loss of function of the iss gene in pigs, showing host specialization.