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Ishi Keenum (Assoc)

Ishi Keenum joined the Complex Microbial Systems Group in 2021 as an NIST-NRC Postdoctoral Research Associate mentored by with Scott Jackson. During her work in the Civil and Environmental Engineering Department at Virginia Tech, she utilized bioinformatic and culture methods to characterize the microbiology and antibiotic resistance loading in wastewater, water reuse and agricultural systems. 

Ishi’s research focuses on the development of quantitative measurements in complex environments using next generation sequencing. Additionally, she is working to develop standards for wastewater biosurveillance efforts.


  1. Keenum, I., Williams, R.K., Ray, P., Garner, E., Knowlton, K., Pruden, A. (2021) Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes. Microbiome, 9(81).
  2. Keenum, I., Crespo-Medina, M., Garner, E., Pieper, K., Pruden, A., Ramirez-Toro, G., Rhoads, W. (2021) Assessing Water Quality in Rural Drinking Water Systems in Puerto Rico Six Months after Hurricane Maria. Environmental Science and Technology,55(6), 3775–3785.
  3. Keenum, I., Brown, C., Dai, D., Vikesland, P., Pruden, A., Zhang, L. (2021) Critically evaluating short, long, and hybrid assembly for the characterization of antibiotic resistance genes in complex environmental samples. Scientific Reports. 11(1), 1-12.
  4. Wind, L., Keenum, I., Gupta, S., Ray, P., Knowlton, K. Ponder, M., Hession, W.C., Pruden, A., Krometis, L.A (2021) Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale, Frontiers in Microbiology. 12(1755),https://  doi: 10.3389/fmicb.2021.683410
  5. Liang, X., Akers, K., Keenum, I., Wind, L., Gupta, S., Aldaihani, R., Pruden, A., Zhang, L., Knowlton, K., Xia, K., Heath, L. (2021) AgroSeek: a system for computational analysis of metagenomics data and associated metadata. BMC Bioinformatics. 22 (117).
  6. Garner E., Davis B.C., Milligan E., Blair M.F., Keenum I., Maile-Moskowitz A., Pan J., Gnegy M., Liguori K., Gupta S., Prussin II A.J., Marr, L., Heath, L., Vikesland, P.J., Zhang, L., Pruden, A. (2021).Next Generation Sequencing Approaches to Evaluate Water and Wastewater Quality. Water Research. 194.
  7. Fogler K, Guron GK, Wind LL, Keenum IM, Hession WC, Krometis LA, Strawn LK, Ponder MA, Pruden A. (2019) Microbiota and Antibiotic Resistome of Lettuce Leaves and Radishes Grown in Soils Receiving Manure-Based Amendments Derived from Antibiotic-Treated Cows. Frontiers in Sustainable Food Systems. 3.


Impact of disaster research on the development of early career researchers: Lessons learned from the wastewater monitoring community pandemic response

Jeseth Delgado Vela, Jill McClary-Gutierrez, Mitham Al-faliti, Peter Arts, Robert Barbero, Cristalyne Bell, Mira Chaplin, Nishita D'Souza, Janet Baffoe, Kevin Bakker, Devrim Kaya, Raul Gonzalez, Kate Harrison, Sherin Kannoly, Ishi Keenum, Lin Li, Zachary Marsh, Brian Pecson, Sarah Philo, Hema P. Ravindran, Jatuwat Sangsanont, Rebecca Schneider, Melissa Schussman, Emily Segelhurst, Abhilasha Shrestha, Lauren Stadler, Allan Vajra, Krista R. Wigginton, Alexandria Boehm, Rolf Halden, Kyle Bibby
Created November 23, 2021, Updated August 6, 2023