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Garner Research Lab
Environmental Engineering & Applied Microbiology


  • Davis, B. C., Riquelme, M. V., Ramirez-Toro, G., Bandaragoda, C., Garner, E., Rhoads, W. J., Vikesland, P., Pruden, A. (2020). Demonstrating an Integrated Antibiotic Resistance Genes Surveillance Approach in Puerto Rican Watersheds Post-Hurricane Maria. Environ. Sci. Technol. 54(23):15108-15119. doi: 10.1021/acs.est.0c05567
  • Hamilton, K. A., Garner, E., Joshi, S., Ahmed, W., Ashbolt, N., Medema, G,. Pruden, A. (2020). Antimicrobial resistant microorganisms and their genetic determinants in stormwater: A systematic review. Curr. Opin. Environ. Sci. Health. 16:101-112. doi: 10.1016/j.coesh.2020.02.012

  • Brown, C. L., Garner, E., Jospin, G., Coil, D. A., Schwake, D. O., Eisen, J. A., Mukhopadhyay, B., Pruden, A. J. (2020). Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus. PLoS ONE. 15(1):e0223033. doi: 10.1371/journal.pone.0223033

  • Logan, L. K., Zhang, L., Green, S. J., Dorevitch, S., Arango-Argoty, G. A., Reme, K., Garner, E. Aldstadt, J., Johnson-Walker, Y. J., Hayden, M. K., Weinstein, R. A., Pruden, A. (2020). A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant Enterobacteriaceae (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children. Antimicrob. Agents Chemother. 64(4):e02310-19. doi: 10.1128/AAC.02310-19

  • Arango-Argoty, G. A., Guron, G. K. P., Garner, E., Riquelme, M. V., Heath, L. S., Pruden, A., Vikesland, P. J., Zhang, L. (2020). ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. Bioinformatics. 1-8. doi: 10.1093/bioinformatics/btaa095

  • Garner, E., Brown, C., Schwake, D. O., Rhoads, W. J., Arango-Argoty, G., Zhang, L., Jospin, G., Coil, D. A., Eisen, J. A., Edwards, M. A., Pruden, A. (2019). Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016. Emerg. Infect. Dis. 25(11):2013-2020. doi: 10.3201/eid2511.181032 

  • Vikesland, P., Garner, E., Gupta, S., Kang, S., Maile-Moskowitz, A., Zhu, N. (2019). Differential Drivers of Antimicrobial Resistance across the World. Acc. Chem. Res., 52(4):916-924. doi: 10.1021/acs.accounts.8b00643
  • Garner, E., Inyang, M., Garvey, E., Parks, J., Glover, C., Grimaldi, A., Dickenson, E., Sutherland, J., Salveson, A., Edwards, M. A., Pruden A. (2019). Impact of blending for direct potable reuse on premise plumbing microbial ecology and regrowth of opportunistic pathogens and antibiotic resistant bacteria. Water Research. 151:75-96. doi: 10.1016/j.watres.2018.12.003
  • Singh, R. R., Angeles, L. F., Butryn, D. M., Metch, J., Garner, E., Vikesland, P. J., Aga, D. S. (2019). Towards a harmonized method for the global reconnaissance of multi-class antimicrobials and other pharmaceuticals in wastewater and receiving surface waters. Environ. Int. 124:361-369. doi: 10.1016/j.envint.2019.01.025
  • Garner, E., McLain, J., Bowers, J., Engelthaler D. M., Edwards, M. A., Pruden, A. (2018). Microbial ecology and water chemistry impact regrowth of opportunistic pathogens in full-scale reclaimed water distribution systems. Environ. Sci. Technol. 52(16):9056-9068. doi: 10.1021/acs.est.8b02818
  • Garner, E., Chen, C., Xia, K., Bowers, J., Engelthaler D. M., McLain, J., Edwards, M. A., Pruden, A. (2018). Metagenomic characterization of antibiotic resistance genes in full-scale reclaimed water distribution systems and corresponding potable systems. Environ. Sci. Technol. 52(11):6113-6125. doi: 10.1021/acs.est.7b05419
  • Wallace, J., Garner, E., Pruden, A., Aga, D. (2018). Occurrence and transformation of veterinary antibiotics and antibiotic resistance genes in dairy manure treated by advanced anaerobic digestion and conventional treatment methods. Environ. Pollut. 15(236):764-772. doi: 10.1016/j.envpol.2018.02.024
  • Arango, G., Garner, E., Pruden, A., Heath, L. S., Vikesland, P., Zhang, L. (2018). DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome. 6:23. doi: 10.1186/s40168-018-0401-z
  • Li, A.-D., Metch, J., Wang, Y., Garner, E., Zhang, A. N., Riquelme, M., Vikesland, P., Pruden, A., and Zhang, T. (2017). Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater. FEMS Microbiol. Ecol. 94(2). doi: 10.1093/femsec/fix189
  • Guo, X., Yang, Y., Lu, D., Niu, Z., Feng, J., Chen, Y., Tou, F., Garner, E., Liu, M., Hochella, M. F. (2017). Biofilms as a sink for antibiotic resistance genes (ARGs) in the Yangtze Estuary. Water Research. 129:277-286. doi: 10.1016/j.watres.2017.11.029
  • Rhoads, W., Garner, E., Ji, P., Zhu, N., Parks, J., Schwake, D. O., Pruden, A., Edwards, M. (2017). Distribution System Operational Deficiencies Coincide with Reported Legionnaires’ Disease Clusters in Flint, MI. Environ. Sci. Technol. 51(20):11986-11995. doi: 10.1021/acs.est.7b01589
  • Garner, E., Benitez, R., von Wagoner, E., Sawyer, R., Shaberg, E., Hession, C., Krometis, L. A., Badgley, B., Pruden, A. (2017). Stormwater loadings of antibiotic resistance genes in urban stream. Water Research. 123:144-152. doi: 10.1016/j.watres.2017.06.046
  • Garner, E., Wallace, J. S., Argoty, G. A., Wilkinson, C., Fahrenfeld, N., Heath, L., Zhang, L., Arabi, M., Aga, D. S., Pruden, A. (2016). Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes. Scientific Reports. 6:38432. doi:
  • Schwake, D. O., Garner, E., Strom, O. R., Pruden, A., Edwards, M. A. (2016). Legionella DNA Markers in Tap Water Coincident with a Spike in Legionnaires’ Disease in Flint, MI. Environ. Sci. Technol. Lett. 3(9):311-315. doi: 10.1021/acs.estlett.6b00192
  • Garner, E., Zhu, N., Strom, L., Edwards, M., Pruden, A. (2016). A human exposome framework for guiding risk management and holistic assessment of recycled water quality. Environ. Sci.: Water Res Technol. 2:580-598. [2016 Editor’s Choice Paper] doi: 10.1039/C6EW00031B
  • Weidhaas, J., Garner, E., Basden, T., Harwood, V. (2014). Run-off studies demonstrate parallel transport behavior for a marker of poultry fecal contamination and Staphylococcus aureus. J. Appl. Microbiol., 117:417-429. doi: 10.1111/jam.12543
  • Fahrenfeld, N., Knowlton, K., Krometis, L. A., Hession, W. C., Xia, K., Lipscomb, E., Libuit, K., Green, B. L., Pruden, A. (2014). Effect of Manure Application on Abundance of Antibiotic Resistance Genes and Their Attenuation Rates in Soil: Field-Scale Mass Balance Approach. Environ. Sci. Technol. 48(5):2643-2650. doi: 10.1021/es404988k
  • Weidhaas, J. and Lipscomb, E. (2013). A new method for tracking poultry litter in the Potomac Basin headwaters of West Virginia. J. Appl. Microbiol., 115(2):445-454. doi: 10.1111/jam.12231