Abstract
Why are members of a microbial species not the same? They may be clonal, but microbial populations are often composed of multiple cocirculating lineages distinguished by large phenotypic and genetic differences. Species and the mechanisms of speciation have been notoriously challenging to study in microbes owing to pervasive horizontal gene flow, widespread geographical distribution, and cryptic ecological niches that structure microbial populations. Understanding the origins of genomic variation in microbial species and populations is fundamental to questions critical to society and public health, such as "Are emerging diseases new species or variants of existing ones?," "What makes a resistant strain successful?," and "How will a pathogen respond to selective pressures?" To explore these questions, I use whole-genome sequencing of closely related strains to understand the evolutionary, ecological, and epidemiological dynamics of bacterial pathogens to inform effective, more precisely targeted public health interventions.
Highlights
Whole-genome sequencing of microbial isolates has proven invaluable in infectious disease surveillance and response, in elucidating a pathogen’s circulation dynamics, transmission linkages, spread of antibiotic resistance, localized outbreaks, or geographical patterns of dissemination
In my recent work on Streptococcus pneumoniae, I used population genomic methods to identify the predictors of successful resistant strains
My long-term research goals are to elucidate how intrinsic genomic factors and changes in the environment together drive the success of bacterial pathogens and to use this knowledge to test predictions about transmission, spread, and outbreaks of infectious diseases
Summary
Whole-genome sequencing of microbial isolates has proven invaluable in infectious disease surveillance and response, in elucidating a pathogen’s circulation dynamics, transmission linkages, spread of antibiotic resistance, localized outbreaks, or geographical patterns of dissemination. Filling in this gap in our knowledge is important in our understanding of infectious diseases, how genetic diversity arises and the factors that favor the success of some lineages and not others.
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