Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer

Abstract

Horizontally transferred DNA is largely responsible for the dissemination of virulence traits amongst bacteria. Rapid identification of acquired DNA remains difficult as whole-genome sequencing of outbreak strains is impractical, and microarray-based approaches, while powerful, are limited to genes present only in the reference strains. Here we present a novel bacterial comparative genomic hybridization method that directly compares the genomes of related strains at sub-kilobase resolution in order to identify acquired DNA. Bacterial comparative genomic hybridization utilizes the concept of metaphase chromosome comparative genomic hybridization, and exploits the resolving power of two-dimensional DNA electrophoresis. Comparison of isogenic variants of the pathogen Pseudomonas aeruginosa detected a single-copy gene insertion responsible for gentamicin resistance.