Detection of Antibiotic Resistance in the Environment using Functional Metagenomics

Abstract

Metagenomicshas the potential to discover novel phenotypes that are not recognizable by DNA sequence analysis. In this study,functional metagenomic analysis of Niangua River soil detected spectinomycin (NR-YP1) and nalidixic acid (NR-YP3) resistance expressed in E. coli EPI300. Subclonesof eachwere generated and screened on spectinomycin ornalidixic acid containingmedia for NR-YP1and NR-YP3, respectively. No subclones were identified conferring resistance to either of the antibiotics. Random DNA sequencing and BLAST analysis of both NR-YP1 and NR-YP3 subclones matchedan environmental clone, termed zdt-9n2, with almost 100% sequence identity. However, proteomic analysis of zdt-9n2 yielded no proteins with the potential to conferantibiotic resistance. Thus, the two clones, NR-YP1 and NR-YP3, appear to be nearly 100% identical in their cloned DNA but yet express two different antibiotic resistance phenotypes.Genetic loci responsible for the resistance could not be identified in this study.