Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

por Brown, Connor L., Keenum, Ishi M., Dai, Dongjuan, Zhang, Liqing, Vikesland, Peter J., Pruden, Amy
Publicado 2021

Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

por Keenum, Ishi, Williams, Robert K., Ray, Partha, Garner, Emily D., Knowlton, Katharine F., Pruden, Amy
Publicado 2021

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

por Liguori, Krista, Keenum, Ishi, Davis, Benjamin C., Calarco, Jeanette, Milligan, Erin, Harwood, Valerie J., Pruden, Amy
Publicado 2022

Metagenomic tracking of antibiotic resistance genes through a pre‐harvest vegetable production system: an integrated lab‐, microcosm‐ and greenhouse‐scale analysis

por Keenum, Ishi, Wind, Lauren, Ray, Partha, Guron, Giselle, Chen, Chaoqi, Knowlton, Katharine, Ponder, Monica, Pruden, Amy
Publicado 2022

Towards the standardization of Enterococcus culture methods for waterborne antibiotic resistance monitoring: A critical review of trends across studies

por Davis, Benjamin C., Keenum, Ishi, Calarco, Jeannette, Liguori, Krista, Milligan, Erin, Pruden, Amy, Harwood, Valerie J.
Publicado 2022

A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and S...

por Milligan, Erin G., Calarco, Jeanette, Davis, Benjamin C., Keenum, Ishi M., Liguori, Krista, Pruden, Amy, Harwood, Valerie J.
Publicado 2023

Comparison of Cefotaxime-Resistant Escherichia coli and sul1 and intI1 by qPCR for Monitoring of Antibiotic Resistance of Wastewater, Surface Water, and Recycled Water

por Liguori, Krista, Calarco, Jeanette, Maldonado Rivera, Gabriel, Kurowski, Anna, Keenum, Ishi, Davis, Benjamin C., Harwood, Valerie J., Pruden, Amy
Publicado 2023

Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications

por Keenum, Ishi, Player, Robert, Kralj, Jason, Servetas, Stephanie, Sussman, Michael D, Russell, Joseph A, Stone, Jennifer, Chandrapati, Sailaja, Sozhamannan, Shanmuga
Publicado 2023

Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale

por Wind, Lauren, Keenum, Ishi, Gupta, Suraj, Ray, Partha, Knowlton, Katharine, Ponder, Monica, Hession, W. Cully, Pruden, Amy, Krometis, Leigh-Anne
Publicado 2021

mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements

por Brown, Connor L., Mullet, James, Hindi, Fadi, Stoll, James E., Gupta, Suraj, Choi, Minyoung, Keenum, Ishi, Vikesland, Peter, Pruden, Amy, Zhang, Liqing
Publicado 2022

AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata

por Liang, Xiao, Akers, Kyle, Keenum, Ishi, Wind, Lauren, Gupta, Suraj, Chen, Chaoqi, Aldaihani, Reem, Pruden, Amy, Zhang, Liqing, Knowlton, Katharine F., Xia, Kang, Heath, Lenwood S.
Publicado 2021

ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization

por Liang, Xiao, Zhang, Jingyi, Kim, Yoonjin, Ho, Josh, Liu, Kevin, Keenum, Ishi, Gupta, Suraj, Davis, Benjamin, Hepp, Shannon L., Zhang, Liqing, Xia, Kang, Knowlton, Katharine F., Liao, Jingqiu, Vikesland, Peter J., Pruden, Amy, Heath, Lenwood S.
Publicado 2023

Structured Ethical Review for Wastewater-Based Testing

por Bowes, Devin A., Darling, Amanda, Driver, Erin M., Kaya, Devrim, Maal-Bared, Rasha, Lee, Lisa M., Goodman, Kenneth, Adhikari, Sangeet, Aggarwal, Srijan, Bivins, Aaron, Bohrerova, Zuzana, Cohen, Alasdair, Duvallet, Claire, Elnimeiry, Rasha A., Hutchison, Justin M., Kapoor, Vikram, Keenum, Ishi, Ling, Fangqiong, Sills, Deborah, Tiwari, Ananda, Vikesland, Peter, Ziels, Ryan, Mansfeldt, Cresten
Publicado 2023