Publications

Steele, J.A., A.G. Zimmer-Faust, T.J. Clerkin, A. Gonzalez-Fernandez, S.A. Lowry, A.D. Blackwood, K. Raygoza, K. Langlois, A.B. Boehm, R.T. Noble, J.F. Griffith, K.C. Schiff. 2025. Survey of pathogens and human fecal markers in stormwater across a highly populated urban region. Environmental Science: Processes & Impacts 27:1354-1367.

Lowry, S.A., J.A. Steele, J.F. Griffith, K.C. Schiff, A.B. Boehm. 2025. Simulated gastrointestinal risk from recreational exposure to Southern California stormwater and relationship to human-associated Bacteroidales marker HF183. Environmental Science: Processes & Impacts DOI:10.1039/d4em00577e.

Theroux, S., A. Sepulveda, C.L. Abbott, Z. Gold, A.W. Watts, M.E. Hunter, K.E. Klymus, S.L. Hirsch, J.M. Craine, D.N. Jones, R.J. Brown, J.A. Steele, M. Takahashi, R.T. Noble, J.A. Darling. 2025. What is eDNA method standardisation and why do we need it?. Metabarcoding and Metagenomics 9:91-106.

Jimenez, K., Y. Kong, Y. Zhang, D. Ferketic, S.K. Nagori, J. Yang, A.A. Yulo, B. Kramer, O.G. Prado, T. Cason, R. Chowdhry, A. Kemsley, L.M. Espinosa, J.A. Steele, J.F. Griffith, J.A. Jay. 2025. Evaluation of a modified IDEXX method for antimicrobial resistance monitoring of extended Beta-lactamases-producing Escherichia coli in impacted waters near the U.S.-Mexico border. One Health 20:100997.

Griffith, J.F., J.A. Steele, A. Gonzalez-Fernandez, K.C. Schiff. 2025. Towards quantifying exfiltration from in situ sanitary sewer pipes. Frontiers in Environmental Science DOI:10.3389/fenvs.2024.1458146.

Steele, J.A., A. Gonzalez-Fernandez, J.F. Griffith, D. Ebentier McCarger, S. Wallace, K.C. Schiff. 2025. Extrapolating empirical measurements of wastewater exfiltration from sanitary sewers to estimate watershed-scale fecal pollution loading in urban stormwater runoff. Frontiers in Environmental Science DOI:10.3389/fenvs.2024.1458153.

Klymus, K.E., J.D. Baker, C.L. Abbott, R.J. Brown, J.M. Craine, Z. Gold, M.E. Hunter, M.D. Johnson, D.N. Jones, M.J. Jungbluth, S.P. Jungbluth, Y. Lor, A. Maloy, C.M. Merkes, R. Noble, N.V. Patin, A.J. Sepulveda, S.F. Spear, J.A. Steele, M. Takahashi, A.W. Watts, S. Theroux. 2024. The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data. Metabarcoding and Metagenomics 8:489-518.

Callejas, I.A., Y. Kong, K. Osborn, W. Hung, M. Cira, T. Cason, A. Sloane, A. Shenkiryk, A. Masikip, A. Singh, A. Jones, J.A. Steele, J.A. Jay. 2024. The influence of urbanization and water reclamation plants on fecal indicator bacteria and antibiotic resistance in the Los Angeles River watershed: A case study with complementary monitoring methods. Science of The Total Environment 957:177577.

Schiff, K.C., A. Zimmer-Faust, D. Nguyen, J.F. Griffith, J.A. Steele, D.E. McCargar, S. Wallace. 2024. Using HF183 to Estimate Watershed-Wide Annual Loadings of Human Fecal Pollution from Onsite Wastewater Treatment Systems. Sustainability 16:9503.

McLellan, S.L., A. Chariton, A. Codello, J.S. McClary-Gutierrez, M.K. Schussman, E.M. Marzinelli, J.M. O'Neil, E.J. Schott, J.L. Bowen, J.H. Vineis, L. Maignien, C. Lemonnier, M. Perennou, K.S. Gibbs, G.J. Zhou, K.M.Y. Leung, M. Kirs, J.F. Griffith, J.A. Steele, S.E. Wearer, A.L. O'Brien, D. Song, S. Liang, J. Li, L. Airoldi, F.P. Mancuso, P.S. Salomon, A.W. Silva-Lima RC Pereira, A.B. Boehm, E.W.X. Lim, S. Wuertz, E. Fernandez, E. Teira, M.L. Liao, Y.W. Dong, P.D. Steinberg. 2024. Universal microbial indicators provide surveillance of sewage contamination in harbours worldwide. Nature Water DOI:10.1038/s44221-024-00315-5.

Keenum, I., N.J. Lin, A. Logan-Jackson, A.J. Gushgari, N. D'Souza, J.A. Steele, D. Kaya, L.R. Gushgari. 2024. Optimizing Wastewater Surveillance: The Necessity of Standardized Reporting and Proficiency for Public Health. American Journal of Public Health 114:859-863.

Schiff, K.C., J.F. Griffith, J.A. Steele, A. Gonzalez-Fernandez. 2024. Summary of Technical Research: Quantifying Sources of Human Fecal Pollution in the Lower San Diego River Watershed. Technical Report 1380. Southern California Coastal Water Research Project. Costa Mesa, CA.

Rothman, J.A., A. Saghir, A.G. Zimmer-Faust, K. Langlois, K. Raygoza, J.A. Steele, J.F. Griffith, K.L. Whiteson. 2024. Longitudinal Sequencing and Variant Detection of SARS-CoV-2 across Southern California Wastewater. Applied Microbiology 4:635-649.

Hinds, J.B., T. Garg, S. Hutmacher, A. Nguyen, Z. Zheng, J.F. Griffith, J.A. Steele, A. Gonzalez Fernandez, K.C. Schiff. 2024. Assessing the defecation practices of unsheltered individuals and their contributions to microbial water quality in an arid, urban watershed. Science of the Total Environment 920:170708.

Kelly, R.P., D.M. Lodge, K.N. Lee, S. Theroux, A.J. Sepulveda, C.A. Scholin, J.M. Craine, E.A. Allan, K.M. Nichols, K.M. Parsons, K.D. Goodwin, Z. Gold, F.P. Chavez, R.T. Noble, C.L. Abbott, M.R. Baerwald, A.M. Naaum, P.M. Thielen, A.L. Simons, C.L. Jerde, J.J. Duda, M.E. Hunter, J.A. Hagan, R.S. Meyer, J.A. Steele, M.Y. Stoeckle, H.M. Bik, C.P. Meyer, E.D. Stein, K.E. James, A.C. Thomas, E. Demir-Hilton, M.A. Timmers, J.F. Griffith, M.J. Weise, S.B. Weisberg. 2024. Toward a national eDNA strategy for the United States. Environmental DNA DOI:10.1002/edn3.432.

Philo, S.E., K.B. De Leon, R.T. Noble, N.A. Zhou, R. Alghafri, I. Bar-Or, A. Darling, N. D'Souza, O. Hachimi, D. Kaya, S. Kim, K. Gaardbo Kuhn, B.A. Layton, C. Mansfeldt, B. Oceguera, T.S. Radniecki, J.L. Ram, L.P. Saunders, A. Shrestha, L.B. Stadler, J.A. Steele, B.S. Steveson, J.R. Vogel, K. Bibby, A.B. Boehm, R.U. Halden, J. Delgado Vela. 2023. Wastewater surveillance for bacterial targets: current challenges and future goals. Applied and Environmental Microbiology DOI:10.1128/aem.01428-23.

Rabe, A., S. Ravuri, E. Burnor, J.A. Steele, R.S. Kantor, S. Choi, S. Forman, R. Batjiaka, S. Jain, T.M. León, D.J. Vugia, A.T. Yu. 2023. Correlation between wastewater and COVID-19 case incidence rates in major California sewersheds across three variant periods. Journal of Water & Health 21:1303-1317.

Rothman, J.A., A. Saghir, S. Chung, N. Boyajian, T. Dinh, J. Kim, J. Oval, V. Sharavanan, C. York, A.G. Zimmer-Faust, K. Langlois, J.A. Steele, J.F. Griffith, K.L. Whiteson. 2023. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020–21 reveals widespread transcription of antibiotic resistance genes. Journal of Water Research 329:119421.

Zimmer-Faust, A.G., J.F. Griffith, J.A. Steele, B. Santos, Y. Cao, L. Asato, T. Chiem, S. Choi, A. Diaz, J. Guzman, D. Laak, M. Padilla, J. Quach-Cu, M. Woo, S.B. Weisberg. 2023. Relationship between coliphage and Enterococcus at southern California beaches and implications for beach water quality management. Journal of Water Research 230:119383.

Schiff, K.C., J.F. Griffith, J.A. Steele, A.G. Zimmer-Faust. 2023. Dry and Wet Weather Survey for Human Fecal Sources in the San Diego River Watershed. Water 15:2239.

Simons, A.L., S. Theroux, M. Osborne, S. Nuzhdin, R.D. Mazor, J.A. Steele. 2023. Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment. Ecological Applications DOI:10.1002/eap.2812.

Kim, S., L.C. Kennedy, M.K. Wolfe, C.S. Criddle, D.H. Duong, A. Topol, B.J. White, R.S. Kantor, K.L. Nelson, J.A. Steele, K. Langlois, J.F. Griffith, A.G. Zimmer-Faust, S.L. McLellan, M.K. Schussman, M. Ammerman, K.R. Wigginton, K.M. Bakker, A.B. Boehm. 2022. SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works. Environmental Science Water Research and Technology 8:757-770.

Zimmer-Faust, A.G., J.F. Griffith, J.A. Steele, L. Asato, T. Chiem, S. Choi, A. Diaz, J. Guzman, M. Padilla, J. Quach-Cu, V. Ruiz, B. Santos, M. Woo, S.B. Weisberg. 2022. Assessing cross-laboratory performance for quantifying coliphage using EPA Method 1642. Journal of Applied Microbiology DOI:10.1111/jam.15523.

Ahmed, W., S.L. Simpson, P.M. Bertsch, K. Bibby, A. Bivins, L.L. Blackall, S. Bofill-Mas, A. Bosch, J. Brandão, P.M. Choi, M. Ciesielski, E. Donner, N. D'Souza, A.H. Farnleitner, D. Gerrity, R. Gonzalez, J.F. Griffith, P. Gyawali, C.N. Haas, K.A. Hamilton, H.C. Hapuarachchi, V.J. Harwood, R. Haque, G. Jackson, S.J. Khan, W. Khan, M. Kitajima, A. Korajkic, G. La Rosa, B.A. Layton, E. Lipp, S.L. McLellan, B. McMinn, G. Medema, S. Metcalfe, W.G. Meijer, J.F. Mueller, H. Murphy, C.C. Naughton, R.T. Noble, S. Payyappat, S. Petterson, T. Pitkänen, V.B. Rajal, B. Reyneke, F.A. Roman Jr, J.B. Rose, M. Rusiñol, M.J. Sadowsky, L. Sala-Comorera, Y.X. Setoh, S.P. Sherchan, K. Sirikanchana, W. Smith, J.A. Steele, R. Sabburg, E.M. Symonds, P. Thai, K.V. Thomas, J. Tynan, S. Toze, J. Thompson, A.S. Whiteley, J.C. Wong, D. Sano, S. Wuertz, I. Xagoraraki, Q. Zhang, A.G. Zimmer-Faust, O.C. Shanks. 2022. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. Science of the Total Environment DOI:10.1016/j.scitotenv.2021.149877.

Rothman, J.A., T.B. Loveless, J. Kapcia III, E.D. Adams, J.A. Steele, A.G. Zimmer-Faust, D. Wanless, M.L. Griffith, L. Mao, J. Chokry, J.F. Griffith, K.L. Whiteson, K. Langlois. 2021. RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants. Applied and Environmental Microbiology 87:e01448-21.

Zimmer-Faust, A.G., J.A. Steele, X. Xiong, C. Staley, M.L. Griffith, M.J. Sadowsky, M. Diaz, J.F. Griffith. 2021. A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border. Frontiers in Marine Science DOI:10.3389/fmicb.2021.674214.

Diner, R.E., D. Kaul, A. Rabines, H. Zheng, J.A. Steele, J.F. Griffith, A.E. Allen. 2021. Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes. mSystems DOI:10.1128/mSystems.00571-21.

McClary-Gutierrez, J.S., Z.T. Aanderud, M. Al-faliti, C. Duvallet, R. Gonzalez, J. Guzman, R.H. Holm, M.A. Jahne, R.S. Kantor, P. Katsivelis, K.G. Kuhn, L.M. Langan, C. Mansfeldt, S.L. McLellan, L.M. Mendoza-Grijalva, K.S. Murnane, C.C. Naughton, A.I. Packman, S. Paraskevopoulos, T.S. Radniecki, F.A. Roman, A. Shrestha, L.B. Stadler, J.A. Steele, B.M. Swalla, P. Vikesland, B. Wartell, C.J. Wilusz, J.C. Ching-Wong, A.B. Boehm, R.U. Halden, K. Bibby, J.D. Vela. 2021. Standardizing data reporting in the research community to enhance the utility of open data for SARS-CoV-2 wastewater surveillance. Environmental Science Water Research & Technology DOI:10.1039/d1ew00235j.

Crain, C., K. Kezer, S. Steele, J. Owiti, S. Rao, M. Victorio, B. Austin, A. Volner, W. Draper, J.F. Griffith, J.A. Steele, M. Seifert. 2021. Application of ddPCR for detection of Enterococcus spp. in coastal water quality monitoring. Journal of Microbiological Methods DOI:10.1016/j.mimet.2021.106206.

Rothman, J.A., T.B. Loveless, M.L. Griffith, J.A. Steele, J.F. Griffith, K.L. Whiteson. 2020. Metagenomics of Wastewater Influent from Southern California Wastewater Treatment Facilities in the Era of COVID-19. Microbiology Resource Announcements 9:e00907-20.

Zimmer-Faust, A.G., J.A. Steele, J.F. Griffith, K.C. Schiff. 2020. The challenges of microbial source tracking at urban beaches for Quantitative Microbial Risk Assessment (QMRA). Marine Pollution Bulletin DOI:10.1016/j.marpolbul.2020.111546.

Steele, J.A., D. Ebentier, A.G. Zimmer-Faust, J.F. Griffith, K.C. Schiff. 2019. Los Coches Creek Microbial Source Tracking Study. Technical Report 1087. Southern California Coastal Water Research Project. Costa Mesa, CA.

Schiff, K.C., J.F. Griffith, J.A. Steele, A.G. Zimmer-Faust, J.A. Soller. 2019. Inner Cabrillo Beach Microbial Source Tracking and Quantitative Microbial Risk Assessment (QMRA). Technical Report 1068. Southern California Coastal Water Research Project. Costa Mesa, CA.

Steele, J.A., A.D. Blackwood, J.F. Griffith, R.T. Noble, K.C. Schiff. 2018. Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California. Water Research 136:137-149.

Arnold, B.F., K.C. Schiff, A. Ercumen, J. Benjamin-Chung, J.A. Steele, J.F. Griffith, S.J. Steinberg, P.D. Smith, C.D. McGee, R. Wilson, C. Nelsen, S.B. Weisberg, J.M. Colford Jr. 2017. Acute Illness Among Surfers After Exposure to Seawater in Dry- and Wet-Weather Conditions. American Journal of Epidemiology 186:866-875.

Steele, J.A., J.F. Griffith, R. Noble, K.C. Schiff. 2017. Tracking Human Fecal Sources in an Urban Watershed During Wet Weather. Technical Report 1002. Southern California Coastal Water Research Project. Costa Mesa, CA.

Soller, J.A., M. Schoen, J.A. Steele, J.F. Griffith, K.C. Schiff. 2017. Incidence of gastrointestinal illness following wet weather recreational exposures: Harmonization of quantitative microbial risk assessment with an epidemiologic investigation of surfers. Water Research 121:280-289.

Schiff, K.C., J.F. Griffith, J.A. Steele, B. Arnold, A. Ercumen, J. Benjamin-Chung, J.M. Colford Jr, J. Soller, R. Wilson, C. McGee. 2016. The Surfer Health Study: A Three-Year Study Examining Illness Rates Associated with Surfing During Wet Weather. Technical Report 943. Southern California Coastal Water Research Project Authority. Costa Mesa, CA.