Graham Hatfull

Mycobacterium tuberculosis kills more people than any other single infectious agent. Since antibiotics are available and the BCG vaccine is in widespread use, why do two million people die each year from TB? The answer, in part, is that we really don't understand this curious bacterium or what parts of its genetic instructions make this such a deadly pathogen. At the heart of our strategies to understand mycobacterial genetics is the mycobacteriophages - viruses that infect the mycobacteria. These are easy to grow and manipulate and offer advantages over working with the slow-growing mycobacteria (such as M. tuberculosis) that can take up to a month to produce a colony on an agar plate. Phages are also rich sources of  potential genetic and molecular tools that can be used to study - and to modify - their bacterial hosts.

Here's just a flavor of some of the current studies going on in the lab:

Exploring bacteriophage genomics. In collaboration with Dr. Hendrix we have spearheaded an initiative to understand viral diversity and evolution. Our specific focus is on the genomic characterization of mycobactriophages, and a collection of about 250 complete genome sequences have been determined. Many of these phages were isolated and sequenced through three programs in which phage discovery and genomics is a platform for integrating our science and educational missions. These are the Pittsburgh Phage Hunters Integrating Research and Education (PHIRE) program, the Howard Hughes Medical Institute Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program, and a Univiersity of KwaZulu-Natal and KwaZulu-Nalat Research in TB and HIV (UKZN/K-RITH) workshop.  These studies have not only provided valuable insights into phage diveristy and evolution, but present a rich and easily-accessible reservoir of genetic and mechanistic novelty for further study. A database of mycobaectriophage genomic infomration is available at http://www.phagesdb.org.

Exploiting mycobacteriophages. We are dissecting the mycobacteriophages to understand the functional roles of the thousands of genes we have identified, and to deternine if and when they are expressed, and how this expression is regulated.  We are exploiting this information to develop tools and approaches that not only generate new tools for genetic manipulation for tuberculosis, but also to gain advances in diagnosis, prevention and treatment of the disease.

Site-specific recombination. Many if not most of the mycobacteriophages we have sequenced integrate their DNA into the host chromosome (and can excise them too). We are studying the mechanism of integrase-mediated site-specific recombination with a primary current focus on the serine-integrases.  We are partiualrly interested in understanding how recomibnational directionality is determine in phage integration systems.

Tools - Genetic and Clinical. Studying the mycobacteria and their phages has great potential for the development of novel tools for their genetics but also for a more direct clinical involvement. Two systems we have been involved in developing are multivalent recombinant BCG vaccines and Luciferase Reporter Phages, but there are numerous additional strategies awaiting further development!