Microarray Comparative Genomic Hybridization for the Analysis of Bacterial Population Genetics and Evolution - Bacterial Pathogenesis: Methods and Protocols - page 44

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Microarray Comparative Genomic Hybridization for the
Analysis of Bacterial Population Genetics and Evolution
Caitriona M. Guinane and J. Ross Fitzgerald
Summary
Comparative genomic hybridization analyses have contributed greatly to our under-
standing of bacterial evolution, population genetics, and pathogenesis. Here, we describe
a robust protocol for microarray-based comparison of genome content, which could be
applied to any bacterial species of interest.
Key Words: Whole-genome microarrays; comparative genomics; bacterial evolution;
population genetics.
1. Introduction
Comparative genomics is a rapidly expanding discipline revolutionized
by the availability of increasing numbers of bacterial genome sequences.
DNA microarrays that represent single or multiple bacterial genomes are a
cost-effective way of comparing the genome content of large numbers of
strains of the same species. Comparative genomic hybridizations (CGHs) with
microarrays allow determination of the presence or absence of genes based
on the level of sequence homology required for hybridization to occur ( see
Note 1 ). CGH analyses can result in broad insights into bacterial genomics,
population genetics, and evolution. Moreover, whole-genome microarrays can
be used to address specific issues of bacterial pathogenesis including the basis
for host specificity, epidemic waves, and the emergence and re-emergence of
pathogenic clones (1) . Importantly, the findings of such studies could be used
in the rational design of disease-controlling strategies.