Comparative phylogenomics of pathogenic bacteria by microarray analysis

Abstract

DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate between bacteria, highlighting previously undetected genetic differences and population structures and providing new insight into virulence and evolution of bacterial pathogens. Recent results from such studies have generated insights into the evolution of bacterial pathogens, the levels of diversity and plasticity in the genome of a species, as well as the differences in virulence amongst pathogenic bacteria.

Introduction to Microarray‐Based Detection Methods

“…Multiple identical microarrays can be robotically printed in batches of over 100 in a single run. Most of the cost in printing such arrays is associated with the synthesis of oligonucleotide probes or primer pairs required for the amplification of the probe gene fragments [42]. Here, we briefly review various commercially available microarray formats.…”

“…This approach provides a reduction in cross-hybridization and an increase in the differentiation of overlapping genes or highly homologous regions. Theoretically, mutant alleles could be detected using such oligonucleotide microarrays owing to the shorter probe size compared to PCR product-based microarrays [42].…”

“…However, owing to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains can be vast [42]. By contrast, whole-genome sequencing comparisons allow a multitude of genes to be compared.…”

“…Whole-genome comparisons typically identify sets of core genes , which are shared by all strains in a species, and accessory genes , which are present in one or more strains in a species and often result from gene acquisition. It is these differences that can often be used to identify genes and/or genetic islands related to gain-of-function traits in pathogenic strains [42].…”

Differentiation of Escherichia coli Pathotypes by Oligonucleotide Spotted Array

“…Seventy-mer oligonucleotide probes rather than cDNA PCR probes were used in this multipletarget assay, since oligonucleotide probes are a cost-effective alternative to cDNA PCR probes. Furthermore, the oligonucleotide-based arrays provide a reduction in cross-hybridization and an increase in the differentiation of highly homologous regions (6,11,23). The microarray's ability to detect virulence, pathotype-specific, and common genes was primarily analyzed with reference strains of E. coli pathotypes, such as nonpathogenic K-12 MG1655, EHEC O157 EDL933, EAEC O42, EPEC E2348/69, and UPEC CFT073.…”