A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure
Bo Li, Xu Li, Bing Wang, Tao Yan
Abstract
Bacterial antibiotic resistance genes in the environment are ubiquitous and can pose different levels of human health risks due to their bacterial host association and subsequent mobility. This study introduced a population metagenomic approach to study ARGs and their mobility in specific bacterial populations through a combination of selective cultivation followed by next generation sequencing and bioinformatic analysis of the combined metagenome of isolates. The utility of this approach was demonstrated with the E. coli population in cattle manure samples, which showed that ARGs detected in the E. coli population corresponded to the observed resistance phenotypes, co-location of multiple ARGs on the same mobile genetic elements.