Center for Pathogen Genomics and Microbial Evolution
Providing specialized expertise in pathogen-specific sequence analysis and bioinformatics for emerging and ongoing infectious disease threats.
The development of next generation DNA sequencing approaches has revolutionized genomics. As these technologies have become more affordable, easier to use and widely available, there has been an explosion of genomic sequence generated with hundreds of thousands of bacterial, viral and fungal genome sequences currently available through public databases. The wealth of microbial sequence data available, however, has far outpaced expertise and tools for analysis of these data. Owing in part to the considerable biological diversity among microbes - including bacteria, fungi and viruses - microbial genome sequence analysis has been difficult to standardize. Often, analysis approaches are not “one-size-fits-all” and a technique that is successful for studying one organism may not be directly applicable to another. To fully leverage the power of these tools, diverse expertise is required across several fields including microbiology, infectious disease clinical care, epidemiology and computational bioinformatics.
When properly harnessed through an integrated pipeline from sample acquisition to sequencing and bioinformatic analysis, pathogen genomics and molecular epidemiology can define the determinants of pathogen transmission, pathogenesis and evolution and so inform best practices in clinical care and public health. Indeed, the essentiality of rapid and effective microbial sequence analysis has been underscored by the global COVID-19 pandemic. Novel and creative approaches to SARS-CoV-2 viral sequencing and analysis have been central to important discoveries throughout the pandemic that have dictated diagnostic paradigms, facilitated drug discovery, charted routes of transmission and helped define best public health practices.
Our Mission and Vision
Why It's Important
Microbial genomics: the study of the complete genetic code of pathogenic organisms
Successful Clinical Response in Pneumonia Therapy (SCRIPT)
This U19 systems biology center funded by the NIAID investigates host/pathogen interactions that result in unsuccessful responses to therapy in severe pneumonia. The study combines clinical phenomics, host transcriptomics and epigenomics, pathogen genomics and alveolar metagenomics to model disease dynamics during ventilator-associated pneumonia.