Genomic Insight and Molecular Approaches to Understanding and Tracking Pathogens in Nature.

Microbial species are comprised of a set of related organisms but, in contrast to higher organisms, have a more varied set of genes in members of a species. This phenomenon is now described as the pangenome, in other words all the genes explored by a species. This means that, beyond the common and basic metabolic core, many genes and hence some functions will vary among members of a species.  Furthermore, the divergence of sequence, common in these rather ancient and fast evolving organisms, also adds to strain variation. Both of these features can make tracking of target bacteria problematic if methods rely one only one or a few genes. We have studied the pangenome of several populations, namely Escherichia, Burkholderia and Shewanella, and from this have learned of gene patterns, the core gene set and apparent adaptations to habitat.  Furthermore, we have tracked over 300 antibiotic resistance genes, as a variable and important trait of commensal and in pathogen populations, to learn of practices that affect their selection and possible horizontal transfer.