Publications

Articles in Refereed Journals

  1. Liang, X., Zhang, J., Kim, Y., Ho, J., Liu, K., Keenum, I., Gupta, S., Davis, B., Hepp,S. L.,  Zhang, L., Xia, K., Knowlton, K. F., Liao, J., Vikesland, P., Pruden, A., Heath, L.S. (2023) “ARGem: A New Metagenomics Pipeline for Antibiotic Resistance Genes: Metadata, Analysis, and Visualization”, Frontiers in Genetics,  https://doi.org/10.3389/fgene.2023.1219297
  2. Keenum, I.*, Player, R., Kralj, J., Servetas, S., Sussman, M., Russell, J., Stone, J., Chandrapati, S., Sozhamannan, S., AOAC SPADA-NGS Working Group (2023), “Amplicon Sequencing Minimum Information (AsqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications” AOAC International, https://doi.org/10.1093/jaoacint/qsad047
  3. Bowes, D.A., Darling, A., Driver, E.M., Kaya, D., Maal-Bared, R., Lee, L. M., Goodman, K., Adhikari, S., Bivins, A., Bohrerova, Z., Cohen, A., Duvallet, C., Rasha, A., Elnimeiry, R.A., Hutchison, J.M., Kapoor, V., Keenum, I., Ling, Fangqiong, Sills, D., Tiwari, A., Vikesland, Ziels, R., Mansfeldt, C. (2023)“Structured Ethical Review for Wastewater-Based Testing in Support of Public Health”, Environmental Science and Technology, https://doi.org/10.1021/acs.est.3c04529
  4. Davis, B.C., Brown, C., Gupta, S., Calarco, J., Liguori,K., Milligan, E., Harwood, V.J., Pruden, A, Keenum,I.* (2023)Towards Standardization of Metagenomics for Monitoring Antibiotic Resistance in Wastewater and Impacted Aquatic Environments. Critical Reviews in Environmental Science and Technology, https://doi.org/10.1080/10643389.2023.2181620
  5. Liguori, K., Calarco, J., Maldonado Rivera, G., Kurowski, A., Keenum, I., Davis, B., Harwood, V.J., Pruden, A. (2023) “Comparison of Cefotaxime-Resistant Escherichia coli versus sul1 and intI1 qPCR-Based Assessment of Antibiotic Resistance of Wastewater, Surface Water, and Recycled Water” Antibiotics, https://doi.org/10.3390/antibiotics12081252
  6. Milligan, E., Calarco, J.,  Davis, B., Keenum, I., Liguori, K., Harwood, V.J., Pruden, A. (2023) “A systematic review of culture-based methods for monitoring antibiotic resistant Acinetobacter, Aeromonas, and Pseudomonas as environmentally-relevant pathogens in wastewater and surface water” Current Environmental Health Reports. https://doi.org/10.1007/s40572-023-00393-9
  7. Keenum, I., Wind, L., Ray, P., Guron, G., Chen, C., Knowlton, K., Ponder, M.,Pruden, A. (2022) Metagenomic Tracking of Antibiotic Resistance Genes through a Pre‐harvest Vegetable Production System: An Integrated Lab‐, Microcosm‐, and Greenhouse‐Scale Study. Environmental Microbiology. https://doi.org/10.1111/1462-2920.16022
  8. Davis, B.C., Harwood, V.J., Keenum, I., Calaraco, J., Liguori, K., Milligan, E., Pruden, A., “Towards the Standardization of Enterococcus Culture Methods for Waterborne Antibiotic Resistance Monitoring: A Critical Review of Trends Across Studies” Water Research X, https://doi.org/10.1016/j.wroa.2022.100161
  9. Brown, C. L., Mullet, J., Hindi, F., Stoll, J.E., Gupta, S., Choi, M., Keenum, I., Vikesland, P., Pruden, A., Zhang, L. (2022) “mobileOG-db: a manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements.”Applied and Environmental Microbiology, https://doi.org/10.1128/aem.00991-22
  10. Liguori, K., Keenum, I., Davis, B., Calarco, J., Milligan, E., Harwood, V.J., Pruden, A. (2022) Antimicrobial Resistance Monitoring of Water Environments: A Call for Standardized Methods and Quality Control. Environmental Science and Technology, https://doi.org/10.1021/acs.est.1c08918
  11. Keenum,I., Liguori,K., Calarco, J., Davis, B.C., Milligan, E., Harwood, V.J., Pruden, A (2021) A framework for standardized qPCR-targets and protocols for quantifying antibiotic resistance in surface water, recycled water and wastewater. Critical Reviews in Environmental Science and Technology, https://doi.org/10.1080/10643389.2021.2024739
  12. 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). https://doi.org/10.1186/s40168-021-01006-z
  13. 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. https://doi.org/10.1021/acs.est.0c08814
  14. Brown, C., Keenum, I., 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. https://doi.org/10.1038/s41598-021-83081-8
  15. 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
  16. 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). https://doi.org/10.1186/s12859-021-04035-5
  17. 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. https://doi.org/10.1016/j.watres.2021.116907
  18. 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. https://doi.org/10.3389/fsufs.2019.00022

Book Chapters and Commentaries

  1. Mansfeldt, C., Maal-Bared, R., Kaya, D., Bowes, D., Keenum, I., Aggarwal, S., Tiwari, A., Hutchinson, J., (2023) “Unveiling the targeted opportunities and universal challenges of wastewater-based surveillance for public health” (2023)  Environmental Science and Technology: Water, https://doi.org/10.1021/acsestwater.3c00291
  2. Delgado Vela, J., McClary-Gutierrez, J.; Al-Faliti, M., Allan, V., Arts, P., Barbero, R., Bell, C., D’Souza, N., Bakker, K., Kaya, D., Gonzalez, R., Harrison, K., Kannoly, Sh., Keenum, I., Li, L., Pecson, B. M., Philo, S., Schneider, R., Schussman, M., Shrestha, A., Stadler, L., Wigginton, K., Boehm, A., Halden, R., Bibby, K. (2022) Impact of disaster research on the development of early career researchers: Lessons learned from the wastewater monitoring pandemic response efforts. Environmental Science & Technology, https://doi.org/10.1021/acs.est.2c01583
  3. Hasan, R., Nordin, A.C., Shakoor, S., Keenum, I. and Vinneras, B. (2019). Salmonella, Enteric Fevers, and Salmonellosis. In: J.B. Rose and B. Jiménez-Cisneros, (eds) Global Water Pathogen Project. A. Pruden, N. Ashbolt and J. Miller (eds) Part 3 Bacteria http://www.waterpathogens.org/book/salmonella-enteric-fevers-salmonellosis. Michigan State University, E. Lansing, MI, UNESCO. https://doi.org/10.14321/waterpathogens.27

Physical Reference Material

  1. Keenum, I., Kralj, J., Jackson, S., Dootz, J., Hunter, M., Servetas, S., NIST Research Grade Test Material 10223 Mpox (MPXV) Synthetic DNA Plasmid (2022).