Evolution of infectious bacteria
Epidemiological and sequence data are used to evaluate the evolution and population structure of pathogenic bacteria, including various Neisseria species, Helicobacter pylori, Salmonella enterica, Moraxella catarrhalis, Escherichia coli, Yersinia pestis and Yersinia pseudotuberculosis . Sequences of housekeeping genes from global collections have been used to define multi-locus sequence types for epidemiological purposes. Sequence relationships have also been used to determine population genetic structures. We have also developed SNP-based fine typing for Y. pestis and S. enterica Typhi, whose housekeeping genes are highly uniform.
Novel mathemical approaches were developed to extract information content from extensive sequence-based datasets. An improved version of a Bayesian program, Structure, was developed for H. pylori and E. coli in order to provide algorithms that can be used to detect phylogenetic structure and ancestry of bacterial species that experience frequent recombination.
Molecular epidemiology has been performed on a variety of organisms in an attempt to reveal the microevolution of these bacteria over periods of decades to millenia. Previously, epidemic N. meningitidis were investigated extensively but a large proportion of current efforts are addressed to the global population structure of H. pylori, S. enterica and Y. pestis.