The overarching goal of our research program is to contribute to modernizing bacterial microbiology by allowing the rapid diagnosis and personalized treatment of infections using molecular tools coupled with informatics. We plan to achieve this through microbial genome wide association to identify genetic biomarkers of infectious disease determinants, including drug resistance, transmissibility, and organ tropism among others. Our work has a current strong focus on M. tuberculosis and its drug resistance phenotype.

Maha Farhat is a practicing pulmonary and critical care physician at Massachusetts General Hospital and an Assistant Professor of Biomedical Informatics at Harvard Medical School. Her group is interdisciplinary spanning epidemiology, bioinformatics, computational and evolutionary biology. Specifically the group has focused on the interpretation of microbial gene expression and whole genome sequence data and the development of biostatistical methods. For example, we developed a method for the detection of signatures of natural selection in M. tuberculosis whole genome sequences to uncover novel genes and cellular mechanisms associated with drug resistance in tuberculosis. We have followed this up with methodological work where we developed a general matched study design and power calculator for microbial genome-wide association studies. Further we are developing a web-based Mycobacterium tuberculosis genotype-phenotype analysis platform that allows users, including laboratory personnel and clinicians, to use state of the art methods to predict the tuberculosis drug resistance phenotype from genomic data. We have the long term vision to grow this tool to a clinical and surveillance tool for the use for both individual patient care and disease surveillance in resource poor settings.

At the moment we have several projects geared to cover these aims spanning methods development to application in field sites of tuberculosis clinical care including India and Peru.