Bugs, SNPs, and Maps: UF-EPI Goes the Distance

“Bugs, SNPs, and Maps: UF-EPI Goes the Distance”

Most of us have followed the story about the emergence of antibiotic resistant bacteria, the so-called ‘superbugs’, through reading newspapers or listening to NPR. Thankfully, significant attention has been focused on this important problem in our clinical and research settings. The first report of Methicillin resistant Staphylococcus aureus  (MRSA) was reported within two years of the introduction of Methicillin (1959). Over the last twenty years it has become endemic in hospitals and other healthcare settings earning the moniker HA-MRSA (healthcare-associated MRSA).

Marco Salemi  (Assistant Professor, Department of Pathology, Immunology and Laboratory Medicine and the UF Emerging Pathogens Institute) and colleagues for the first time, employ Bayesian phylogenetic methods to a bacterial pathogen to describe the temporal and spatial dynamics of HA-MRSA transmission within the population.  Their paper is titled, “Testing spatiotemporal hypothesis of bacterial evolution using Methicillin-Resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework.”Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M. Mol Biol Evol. 2011 Jan 27. [Epub ahead of print]

While Bayesian phylogenetic methods have been used to describe the temporal and spatial epidemic spread of relatively quickly evolving viruses (HIV-1, influenza, etc.), it was thought that bacteria would present insufficient phylogenetic signal to allow the measurement of evolution rates etc., requisite for such a temporal and mapping analyses.  However, the recent advances in sequencing technology have made feasible the investigation of bacterial genetic variation at the whole genome level.  Thus, sufficient bacterial genetic diversity can now be observed over short time frames.  Salemi and colleagues examined >4000 genome wide single nucleotide polymorphisms (SNPs) of HA-MRSA present within the alignment of 63 geographically-diverse sequences collected over 24 years. The study shows that the most recent common ancestor (i.e. MRSA origin) could be traced to the time of Methicillin introduction and the lineage exhibited a spread with the characteristics of a pandemic, rather than regionally restricted outbreaks.  This paper both showcases the power of phylogeographic analyses and the need for additional bacterial genome-wide data to further strengthen these approaches. Importantly, it emphasizes the public health benefit of genome-wide typing.

Most impressively, the paper highlights the impact of multidisciplinary team science, which in this case included faculty from departments of Pathology, Geography, Health Informatics, Zoology, Biomathematics, Biostatistics, and Human Genetics.  Indeed, to tackle the significant health problems that are afflicting our society, we will need to assemble additional effective problem-focused cross-disciplinary groups.  As we map the future of research endeavors at the CoM, this is the road we must take.
(see: http://stm.sciencemag.org/content/2/22/22cm9.full)

Steve P. Sugrue, Ph.D.
Senior Associate Dean for Research Affairs
College of Medicine