Publications

  • Ryan T. Botts, Brooke A. Apffel, C. Joy Walters, Kelly E. Davidson, Ryan S. Echols, Michael R. Geiger, Victoria L. Guzman, Victoria S. Haase, Michal A. Hoenecke, Chip A. La Chat, Jenna A. Mielke, Kelly L. Mullen, Cierra C. Virtue, Celeste J. Brown, Eva M. Top, and David E. Cummings. Genomic and functional analysis of four multidrug resistance plasmids captured from the sediments of an urban coastal wetland. (In preparation.)
  • T.R. Borgogna, J.-L Borgogna, J. A. Mielke, C. J. Brown, E. M. Top, R. T. Botts, D. E. Cummings. High Diversity of CTX-M Extended-Spectrum β-Lactamases in Municipal Wastewater and Urban Wetlands. Microbial Drug Resistance ahead of print. doi:10.1089/mdr.2015.0197 (2015).
  • Cummings, D. E., K. F. Archer, D. J. Arriola, P. A. Baker, K. G. Faucett, J. B. Laroya, K. L. Pfeil, C. R. Ryan, K. R. U. Ryan, and D. E. Zuill. 2011. Broad dissemination of plasmid- mediated quinolone resistance genes in sediments of two urban coastal wetlands. Environ. Sci. Technol. 45:447-454.
  • Cummings, D. E., A. E. Zimmerman, K. R. Unruh, and S. Spring. 2010. Influence of microbially reducible Fe(III) on the bacterial community structure of estuarine surface sediments. Geomicrobiol. J. 27:292-302.

  • Cummings, D. E. 2014. Environmental reservoirs of drug-resistant bacteria. San Diego Zoo Institute for Conservation Research, San Diego, CA. (invited speaker, scheduled for 7/16/14)
  • Cummings, D. E. 2012. Environmental reservoirs of antibiotic resistance. Annual Meeting of the Southern California Academy of Sciences, Occidental College, Los Angeles, CA. (plenary speaker)
  • Cummings, D. E., K. F. Archer, D. J. Arriola, P. A. Baker, K. G. Faucett, J. B. Laroya, K. L. Pfeil, C., R. Ryan, and K. R. Unruh. 2010. Antibiotic resistance genes as emerging contaminants in California’s coastal environment. San Diego Microbiology Group meeting, Scripps Institute of Oceanography, San Diego, CA. (invited talk)
  • Cummings, D. E., K. F. Archer, D. A. Arriola, J. B. Laroya, C. R. Ryan, N. J. Singh, and K. R. Unruh. 2008. “Antibiotic-resistant bacteria and antibiotic resistance genes in urban coastal wetlands.” Montana State University, Bozeman, MT. (invited talk)
  • Cummings, D. E., K. F. Archer, D. A. Arriola, J. B. Laroya, C. R. Ryan, N. J. Singh, and K. R. Unruh. 2008. “Antibiotic-resistant bacteria in California’s coastal wetlands.” Tijuana Estuary Summer Speaker Series. San Diego, CA. (invited talk)
  • Cummings, D. E., D. A. Arriola, C. R. Ryan, N. J. Singh, and K. R. Unruh. 2007. “Bacteria – the wetland’s most underappreciated members.” Tijuana Estuary Summer Speaker Series. San Diego, CA. (invited talk)
  • Cummings, D. E., D. A. Arriola, C. R. Ryan, N. J. Singh, and K. R. Unruh. 2007. Microbiology at the Tijuana River Estuary. Loyola Marymount University, Los Angeles, CA. (invited talk)
  • R. Botts. Antibiotic Resistance in Urban Wetlands and the Bioinformatics Challenges it Presents. IBEST Seminar Series. Moscow, ID, July 2014.


  • Borgogna, T. R., J.-L. Borgogna, J. A. Mielke, C. J. Brown, E. M. Top, R. T. Botts, and D. E. Cummings. 2014. Abundance and diversity of CTX-M extended-spectrum ß-lactamases in urban wetlands and associated waste water treatment plants. General Meeting of the American Society for Microbiology, Boston, MA. (poster)
  • Frye, William, Ryan Botts, and David Cummings. 2014. Aminoglycoside resistance plasmids in Pseudomonas species isolated from the Tijuana River Estuary. West Coast Biological Sciences Undergraduate Research Conference, Azusa Pacific University, Azusa, CA. (oral presentation)
  • Petersen, Kristen, Lori Carter, David Cummings, and Ryan Botts. 2014. Plasmid Identification Using Gene Clusters. 2014. Mathematical Association of America Sectional Meeting, Concordia University, Irvine, CA. (poster presentation, won outstanding undergraduate poster)
  • Borgogna, Joanna-Lynn, Timothy Borgogna, Lori Carter, Ryan Botts, and David Cummings. 2014. Diversity, abundance, and persistence of antibiotic resistance genes in urban wetlands in San Diego County. West Coast Biological Sciences Undergraduate Research Conference, Azusa Pacific University, Azusa, CA. (poster presentation)
  • Collins, Brooke, Lori Carter, Ryan Botts, and David Cummings. 2014. The identification and annotation of novel plasmids carrying drug resistance from urban wetlands. Point Loma Nazarene University Honors Conference, San Diego, CA. (poster presentation)
  • Borgogna, Timothy, Joanna-Lynn Borgogna, Matthieu Rouffet, Ryan Botts, and David Cummings. West 2014. Detection and Quantification of CTX-M Extended-Spectrum ß-lactamases in Urban Wetlands and Associated Waste Water Treatment Plants. Coast Biological Sciences Undergraduate Research Conference, Azusa Pacific University, Azusa, CA. (oral presentation, won outstanding undergraduate presentation)
  • Zuill, Doug. 2012. West Coast Biological Sciences Undergraduate Research Conference, Loyola Marymount University, Los Angeles, CA. (oral presentation)
  • Geiger, M., K. Schroeder, V. Haase, J. Lavenuta, D. Zuill, and D. Cummings. 2012. Self- transmissible antibiotic resistance plasmids in urban coastal wetlands. West Coast Biological Sciences Undergraduate Research Conference, Loyola Marymount University, Los Angeles, CA. (poster)
  • Archer, Karisa, David Arriola, Pieter Baker, Grace Faucett, Jonathan Laroya, Jenna Lavenuta, Kelly Pfeil, Cody Ryan, Kelsey Ryan, Douglas Zuill, and David Cummings. 2011. Contamination of the urban coastal environment with plasmid-encoded antibiotic resistance genes. West Coast Biological Sciences Undergraduate Research Conference, Tacoma, WA. (poster)
  • Archer, Karisa F., David J. Arriola, Pieter A. Baker, Jonathan B. Laroya, Cody R. Ryan, Kelsey R. Unruh, Kelly L. Pfeil, and David E. Cummings. 2010. Spread of drug-resistance genes in a sewage-impacted coastal wetland. West Coast Biological Sciences Undergraduate Research Conference, Santa Clara, CA. (poster)
  • Unruh, K., D. Arriola, C. Ryan, J. Laroya, K. Archer, and David Cummings. 2009. The search for antibiotic-resistant bacteria in coastal wetlands using growth-based methods. West Coast Biological Sciences Undergraduate Research Conference, San Diego, CA. (oral presentation)
  • Archer, K. F., D. A. Arriola, J. B. Laroya, C. R. Ryan, N. J. Singh, K. R. Unruh, and D. E. Cummings. 2009. Investigation of antibiotic resistance genes in urban wetland sediments. West Coast Biological Sciences Undergraduate Research Conference, San Diego, CA. (oral presentation)
  • Arriola, D. A., K. F. Archer, J. B. Laroya, C. R. Ryan, N. J. Singh, K. R. Unruh, and D. E. Cummings. 2008. Antibiotic resistance genes in the metagenome of urban wetland sediments. 16th Annual International Meeting on Microbial Genomics, Lake Arrowhead, CA. (poster
  • Unruh, K. R., C. Ryan, N. Singh, D. Arriola, and D. Cummings. 2008. The search for antibiotic- resistant bacteria in coastal wetlands using DNA-based and growth-based methods. West Coast Biological Sciences Undergraduate Research Conference, San Diego, CA. (poster)
  • Unruh, K. R., A. E. Hebling, S. Spring, and D. E. Cummings. 2007. Microbial diversity of native and Fe(III)-enriched consortia from the sediment-water interface of an estuarine coastal wetland. American Society for Microbiology, General Meeting, Toronto, Canada. (poster)
  • Unruh, K. R., A. E. Hebling, S. Spring, and D. E. Cummings. 2007. Microbial diversity of native and Fe(III)-enriched consortia from the sediment-water interface of an estuarine coastal wetland. West Coast Biological Sciences Undergraduate Research Conference, Los Angeles, CA. (poster)