Meaningful use of pathogen genomic data: Tracking bacterial mobile elements using published sequences

Published genomic datasets are increasing exponentially as sequencing becomes more accessible due to decreasing cost. Yet, there is tendency to generate new data when approaching a research question, even if a suitable dataset may exist.  One limitation to leveraging publish genomic data for metanalyses is the difficulty in searching myriad public repositories for genomes of interest.  Thankfully, newly developed tools are facilitating this task by allowing rapid querying of extant published genomes.  Here, we present one example of using these tools to track a genomic element of interest.  By querying all published bacterial genomes for the gene that encodes exfoliative toxin A, an epidermolytic toxin found in Staphylococcus aureus that is associated with staphylococcal scalded-skin syndrome, we gain a new understanding of the global distribution of strains harboring this toxin.  In addition, we present a new paradigm for globally tracking mobile genetic elements associated with epidemiological important phenotypes.

Bio

Dr. Taj Azarian is currently an assistant professor at the Burnett School of Biomedical Science, University of Central Florida.  His lab uses pathogen genomics to investigate the emergence and spread of bacterial infectious diseases, with a specific interest in antibiotic-resistant pathogens that are frequent causes of healthcare-associated infections. To accomplish this, they use a variety of tools including epidemiology, bioinformatics, computational biology, population genomics, and phylogenetics.  The Azarian lab’s goal is to understand the factors that contribute to pathogen success and to develop new genomic epidemiological methods to detect, monitor, and combat the growing threat of antimicrobial resistance.