Understanding the impact of antibiotic therapies on the respiratory tract resistome: a novel pooled-template metagenomic sequencing strategy

Abstract

By combining metagenomic screening of pooled DNA extracts with validatory quantitative PCR-based analysis of candidate markers in individual samples, we identify population-level changes in the relative abundance of specific macrolide resistance genes. Keywords * Antibiotic therapy * DNA * Metagenomic screening Introduction As in all clinical disciplines, the management of patients with chronic respiratory diseases is subject to a process of ongoing refinement, including through the development of novel antimicrobial drugs and treatment strategies. Resistance genes grouped by function as defined by CARD where: brown = aminoglycoside resistance genes, red = beta-lactam resistance genes, orange = efflux pump resistance genes, yellow = glycopeptide resistance genes, green = tetracycline resistance genes, blue = other resistance genes A substantial proportion of the genes identified through resistome analysis were chromosomally-encoded, non-transmissible, resistance determinants. Ethics approval and consent to participate The study was approved by the Mater Health Service human research ethics committee (ACTRN12609000578202), and all participants provided written, informed consent.