Seminar: Harnessing Metagenomic Data and Computational Resources in the War Against Antimicrobial Resistance
Amy Pruden, Lenny Heath, Liqing Zhang
Civil and Environmental Engineering
Computer Science
Virginia Tech
Friday, October 27, 2023
2:30 - 3:30 PM
3100 Torgersen Hall
Abstract
Antibiotic resistance is a grand societal challenge, undermining the efficacy of life-saving antibiotics. Thousands of antibiotic resistance genes (ARGs) have been identified to date, encoding a variety of
mechanisms that allow bacteria to resist specific antibiotics. Better understanding the conditions under which ARGs evolve and spread to new bacterial hosts is needed to inform health policies aimed at combating the spread of resistance and preserving the efficacy of antibiotics for future
generations. Applying metagenomic sequencing of water and other samples for the purpose of environmental surveillance holds promise for identifying hot spots for evolution and spread of resistance where such efforts could be most fruitfully focused. In this presentation, we learn how life scientists and computer scientists collaborate to gain insights into antibiotic resistance through metagenomic data in general. Computer scientists in computational biology and bioinformatics (CBB) are especially interested developing sequence-based algorithms and tools for the purpose of metagenomic analysis. For example, computer scientists develop deep learning models for identifying ARGs in a fast and accurate
manner in large metagenomic data sets that usually contain hundreds of gigabytes of data. In collaboration with life scientists and environmental engineers, they have also developed a number of programs and web services that domain scientists can productively use to process and analyze even terabytes of data. In the realm of graduate education, the Convergence at the Interfaces of Policy, Data Science, Environmental Science and Engineering to Combat the Spread of Antimicrobial Resistance (CIP-CAR) NSF Research Traineeship (NRT) program provides a forum for interdisciplinary training of PhD students to address grand societal challenges such as the spread of antibiotic resistance and of infectious diseases.
Biography
Amy Pruden, Civil and Environmental Engineering
https://pruden.cee.vt.edu/
Lenwood S. Heath, Computer Science
https://people.cs.vt.edu/~heath/
Liqing Zhang, Computer Science
https://people.cs.vt.edu/~lqzhang/