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Susan Spencer
Environmentally Integrated Dairy Management Research
Microbiologist

Phone: (715) 387-4609
Fax:

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Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Fecal source tracking and land use associations for antibiotic resistance genes in private wells - (Abstract Only)
Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources Reprint Icon - (Peer Reviewed Journal)
Burch, T.R., Stokdyk, J.P., Firnstahl, A.D., Kieke, B.A., Cook, R.M., Opelt, S.A., Spencer, S.K., Durso, L.M., Borchardt, M.A. 2022. Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources. Journal of Environmental Quality. 52(2):270-286. https://doi.org/10.1002/jeq2.20443.
Statewide quantitative microbial risk assessment for waterborne viruses, bacteria, and protozoa in public water supply wells in Minnesota Reprint Icon - (Peer Reviewed Journal)
Burch, T.R., Stokdyk, J.P., Rice, N., Anderson, A.C., Walsh, J.F., Spencer, S.K., Firnstahl, A.D., Borchardt, M.A. 2022. Statewide quantitative microbial risk assessment for waterborne viruses, bacteria, and protozoa in public water supply wells in Minnesota. Environmental Science and Technology. 56(10):6315-6324. https://doi.org/10.1021/acs.est.1c06472.
Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities Reprint Icon - (Peer Reviewed Journal)
Burch, T.R., Firnstahl, A.D., Spencer, S.K., Larson, R.A., Borchardt, M.A. 2022. Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities. Journal of Environmental Quality. 51(3):352-363. https://doi.org/10.1002/jeq2.20350.
Manure and septic systems: The microbial health risk from contaminated household wells in Kewaunee County, Wisconsin - (Abstract Only)
Burch, T.R., Stokdyk, J.P., Spencer, S.K., Kieke, B.A., Firnstahl, A.D., Muldoon, M.A., Borchardt, M.A. 2022. Manure and septic systems: The microbial health risk from contaminated household wells in Kewaunee County, Wisconsin. Meeting Abstract. March 10-11, 2022.
The environmental microbiology minimum information (EMMI) Guidelines: qPCR and dPCR quality and reporting for environmental microbiology Reprint Icon - (Peer Reviewed Journal)
Borchardt, M.A., Boehm, A.B., Salit, M., Spencer, S.K., Wigginton, K.R., Noble, R.T. 2021. The environmental microbiology minimum information (EMMI) Guidelines: qPCR and dPCR quality and reporting for environmental microbiology. Environmental Science and Technology. https://doi.org/10.1021/acs.est.1c01767.
Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin Reprint Icon - (Peer Reviewed Journal)
Borchardt, M.A., Stokdyk, J.P., Kieke, B.A., Muldoon, M.A., Spencer, S.K., Firnstahl, A.D., Bonness, D.A., Hunt, R.J., Burch, T.R. 2021. Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin. Environmental Health Perspectives. https://doi.org/10.1289/EHP7813.
Quantitative microbial risk assessment for contaminated private wells in the fractured dolomite aquifer of Kewaunee County, Wisconsin Reprint Icon - (Peer Reviewed Journal)
Burch, T.R., Stokdyk, J.P., Spencer, S.K., Kieke, B.A., Firnstahl, A.D., Muldoon, M.A., Borchardt, M.A. 2021. Quantitative microbial risk assessment for contaminated private wells in the fractured dolomite aquifer of Kewaunee County, Wisconsin. Environmental Health Perspectives. https://doi.org/10.1289/EHP7815.
Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA Reprint Icon - (Peer Reviewed Journal)
Stokdyk, J.P., Firnstahl, A.D., Walsh, J.F., Spencer, S.K., De Lambert, J.R., Anderson, A.C., Rezania, L.W., Kieke, B.A., Borchardt, M.A. 2020. Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA. Water Research. 178(1):115814. https://doi.org/10.1016/j.watres.2020.115814.
Effects of rainfall and septic systems on the occurrence of human sewage markers and traditional indicator organisms in private wells in southeastern Pennsylvania Reprint Icon - (Peer Reviewed Journal)
Murphy, H., Mcginnis, S., Blunt, R., Wu, J., Cagle, A., Denno, D., Spencer, S.K., Stokdyk, J., Firnstahl, A., Borchardt, M.A. 2020. Effects of rainfall and septic systems on the occurrence of human sewage markers and traditional indicator organisms in private wells in southeastern Pennsylvania. Environmental Science and Technology. 54(6):3159-3168. https://doi.org/10.1021/acs.est.9b05405.
Laboratory for infectious disease and the environment (LIDE) - (Government Publication)
Stokdyk, J.P., Bruce, J.L., Burch, T.R., Spencer, S.K., Firnstahl, A.D., Borchardt, M.A. 2019. Laboratory for infectious disease and the environment (LIDE). Government Publication/Report. 2018-3079.
Assessing groundwater quality in Kewaunee County, Wisconsin - (Government Publication)
Borchardt, M.A., Muldoon, M.A., Hunt, R.J., Bonness, D.E., Firnstahl, A.D., Kieke, B.A., Owens, D.W., Spencer, S.K., Stokdyk, J.P. 2019. Assessing groundwater quality in Kewaunee County, Wisconsin. Government Publication/Report. 2019-05.
Community Intervention with UV disinfection to estimate acute gastrointestinal illness from drinking untreated groundwater - (Abstract Only)
Effect of mixing duration on biogas production and methanogen distribution in an anaerobic digester - (Peer Reviewed Journal)
Wang, H., Larson, R., Spencer, S.K., Borchardt, M.A. 2019. Effect of mixing duration on biogas production and methanogen distribution in an anaerobic digester. Environmental Technology. DOI: 10.1080/09593330.2019.1621951.
Cryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA Reprint Icon - (Peer Reviewed Journal)
Stokdyk, J.P., Spencer, S.K., Anderson, A.C., Walsh, J.F., Firnstahl, A.D., Rezania, L.W., Borchardt, M.A. 2019. Cryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA. Environmental Science and Technology. 53(7):3391-3398. https://doi.org/10.1021/acs.est.8b05446.
The health burden of private wells contaminated by gastrointestinal pathogens in the fractured dolomite aquifer of Kewaunee County, Wisconsin - (Abstract Only)
Burch, T.R., Stokdyk, J.P., Spencer, S.K., Kieke, B.A., Firnstahl, A.D., Borchardt, M.A. 2019. The health burden of private wells contaminated by gastrointestinal pathogens in the fractured dolomite aquifer of Kewaunee County, Wisconsin. Meeting Abstract. Feb. 28 - Mar. 1, 2019.
Human-associated indicator bacteria and human-specific viruses in surface water: a spatial assessment with implications on fate and transport Reprint Icon - (Peer Reviewed Journal)
Lenaker, P.L., Corsi, S.R., Olds, H.T., McLellan, S.L., Borchardt, M.A., Dila, D.K., Spencer, S.K., Baldwin, A.K. 2018. Human-associated indicator bacteria and human-specific viruses in surface water: a spatial assessment with implications on fate and transport. Environmental Science and Technology. 52(21):12162-12171. https://doi.org/10.1021/acs.est.8b03481.
Sewage loading and microbial risk in urban waters of the Great Lakes Reprint Icon - (Peer Reviewed Journal)
McLellan, S.L., Sauer, E.P., Bootsma, M.J., Corsi, S.R., Boehm, A.B., Spencer, S.K., Borchardt, M.A. 2019. Sewage loading and microbial risk in urban waters of the Great Lakes. Elementa: Science of the Anthropocene. 6:46. https://doi.org/10.1525/elementa.301.
Human bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks Reprint Icon - (Peer Reviewed Journal)
McGinnis, S., Spencer, S.K., Firnstahl, A., Stokdyk, J., Borchardt, M.A., McCarthy, D.T., Murphy, H.M. 2017. Human bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks. Science of the Total Environment. 630:697-976.
Opportunities for optimization: fate of manure-borne pathogens during anaerobic digestion and solids separation Reprint Icon - (Peer Reviewed Journal)
Burch, T.R., Spencer, S.K., Borchardt, S.S., Larson, R.A., Borchardt, M.A. 2018. Opportunities for optimization: fate of manure-borne pathogens during anaerobic digestion and solids separation. Journal of Environmental Quality. 47:336-344.
Avian influenza virus RNA in groundwater wells supplying poultry farms affected by the 2015 influenza outbreak Reprint Icon - (Peer Reviewed Journal)
Borchardt, M.A., Spencer, S.K., Hubbard, L.E., Firnstahl, A.D., Stokdyk, J.P., Kolpin, D.W. 2017. Avian influenza virus RNA in groundwater wells supplying poultry farms affected by the 2015 influenza outbreak. Environmental Science and Technology Letters. 4:268-272.
Using enteric pathogens to assess sources of fecal contamination in the silurian dolomite aquifer: preliminary results - (Proceedings)
Muldoon, M.A., Borchardt, M.A., Spencer, S.K., Hunt, R.J., Lenaker, P. 2017. Using enteric pathogens to assess sources of fecal contamination in the silurian dolomite aquifer: preliminary results. Meeting Proceedings. p. 347.
Hydrologic, land cover and seasonal patterns of waterborne pathogens in great lakes tributaries Reprint Icon - (Peer Reviewed Journal)
Lenaker, P.L., Corsi, S.R., Borchardt, M.A., Spencer, S.K., Baldwin, A.K., Lutz, M.A. 2017. Hydrologic, land cover and seasonal patterns of waterborne pathogens in great lakes tributaries. Water Research. 113:11-21.
Effects of climate and sewer condition on virus transport to groundwater Reprint Icon - (Peer Reviewed Journal)
Gotkowitz, M.B., Bradbury, K.R., Borchardt, M.A., Zhu, J., Spencer, S.K. 2016. Effects of climate and sewer condition on virus transport to groundwater. Environmental Science and Technology. 50:8497-8504. 2016.
Detection of hepatitis E virus and other livestock-related pathogens in Iowa streams Reprint Icon - (Peer Reviewed Journal)
Givens, C.E., Kolpin, D.W., Borchardt, M.A., Duris, J.W., Moorman, T.B., Spencer, S.K. 2016. Detection of hepatitis E virus and other livestock-related pathogens in Iowa streams. Science of the Total Environment. 566-567:1042-1051. doi: 10.1016/j.scitotenv.2016.05-123.
Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model Reprint Icon - (Peer Reviewed Journal)
Burch, T.R., Spencer, S.K., Stokdyk, J.P., Kieke, B.A., Larson, R.A., Firnstahl, A.D., Rule, A.M., Borchardt, M.A. 2017. Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model. Environmental Health Perspectives. https://doi.org/10.1289/EHP283.
Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR Reprint Icon - (Peer Reviewed Journal)
Stokdyk, J.P., Firnstahl, A.D., Spencer, S.K., Burch, T.R., Borchardt, M.A. 2016. Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR. Applied and Environmental Microbiology. 96:105-113.
Human and bovine viruses and bacteria at three great lakes beaches: Environmental variable associations and health risk Reprint Icon - (Peer Reviewed Journal)
Corsi, S.R., Borchardt, M.A., Carvin, R.B., Burch, T., Spencer, S.K., Lutz, M.A., McDermott, C.M., Busse, K., Kleinheinz, G.T., Zhu, J. 2015. Human and bovine viruses and bacteria at three great lakes beaches: Environmental variable associations and health risk. Environmental Science and Technology. 50:987-995.
2013 Survey of Iowa groundwater and evaluation of public well vulnerability classifications for contaminants of emerging concern - (Government Publication)
Hruby, C., Libra, R., Fields, C., Kolpin, D., Hubbard, L., Borchardt, M.A., Spencer, S.K., Wichman, M., Hall, N., Scheuller, M., Furlong, E., Weyer, P. 2015. 2013 Survey of Iowa groundwater and evaluation of public well vulnerability classifications for contaminants of emerging concern. Iowa Department of Natural Resources. May 2015.
Application of dairy slurry on alfalfa fields, and subsequent effects on nutritive value and silage fermentation characteristics of the harvested forage - (Popular Publication)
Coblentz, W.K., Muck, R.E., Borchardt, M.A., Spencer, S.K., Jokela, W.E., Bertram, M.G., Coffey, K.P. 2014. Application of dairy slurry on alfalfa fields, and subsequent effects on nutritive value and silage fermentation characteristics of the harvested forage. Popular Publication. Midwest Forage Assn. Project Reports 2013.
Effects of dairy slurry on silage fermentation characteristics and nutritive value of alfalfa Reprint Icon - (Peer Reviewed Journal)
Coblentz, W.K., Muck, R.E., Borchardt, M.A., Spencer, S.K., Jokela, W.E., Bertram, M.G., Coffey, K.P. 2014. Effects of dairy slurry on silage fermentation characteristics and nutritive value of alfalfa. Journal of Dairy Science. 97:7197-7211.
Simultaneous concentration of bovine viruses and agricultural zoonotic bacteria from water using sodocalcic glass wool filters Reprint Icon - (Peer Reviewed Journal)
Abd-Elmaksoud, S., Spencer, S.K., Gerba, C.P., Tamimi, A.H., Jokela, W.E., Borchardt, M.A. 2014. Simultaneous concentration of bovine viruses and agricultural zoonotic bacteria from water using sodocalcic glass wool filters. Food and Environmental Virology. 6:253-259.
Human and bovine viruses in the Milwaukee river watershed: hydrologically relevant representation and relations with environmental variables - (Peer Reviewed Journal)
Corsi, S.R., Borchardt, M.A., Spencer, S.K., Hughes, P.E., Baldwin, A.K. 2014. Human and bovine viruses in the Milwaukee river watershed: hydrologically relevant representation and relations with environmental variables. Science of the Total Environment. 490:849-860.
Surface runoff from manured cropping systems assessed by the paired-watershed method, part 2: pathogen transport - (Abstract Only)
Borchardt, M.A., Spencer, S.K., Jokela, W.E. 2014. Surface runoff from manured cropping systems assessed by the paired-watershed method, part 2: pathogen transport. American Water Resources Association Conference Proceedings. March 13-14, 2014.
Effects of precipitation events on virus presence in groundwater - (Abstract Only)
Gotkowitz, M.B., Bradbury, K.R., Borchardt, M.A., Spencer, S.K., Krause, J.J. 2014. Effects of precipitation events on virus presence in groundwater. American Water Resources Association Conference Proceedings. March 13-14, 2014.
Characterization of preferential flow pathways in a siliciclastic aquifer system using human enteric viruses and groundwater geochemistry - (Abstract Only)
Gellasch, C.A., Borchardt, M.A., Bradbury, K.R., Spencer, S.K., Bahr, J.M. 2014. Characterization of preferential flow pathways in a siliciclastic aquifer system using human enteric viruses and groundwater geochemistry. Geological Society of America Meeting. March 23-25, 2014.
Accumulation and inactivation of avian influenza virus by the filter feeding invertebrate daphnia magna Reprint Icon - (Peer Reviewed Journal)
Meixell, B.W., Borchardt, M.A., Spencer, S.K. 2013. Accumulation and inactivation of avian influenza virus by the filter feeding invertebrate daphnia magna. Applied and Environmental Microbiology. 79:7249-7255.
Ranking filter methods for concentrating pathogens in lake water Reprint Icon - (Peer Reviewed Journal)
Borchardt, M.A., Kieke, B.A., Spencer, S.K. 2013. Ranking filter methods for concentrating pathogens in lake water. Applied and Environmental Microbiology. 79:5418-5419.
Source and transport of human enteric viruses in deep municipal water supply wells - (Peer Reviewed Journal)
Bradbury, K.R., Borchardt, M.A., Gotkowitz, M., Spencer, S.K., Zhu, J., Hunt, R.J. 2013. Source and transport of human enteric viruses in deep municipal water supply wells. Journal of Environmental Science and Technology. 47:4096-4103.
Inactivation of dairy manure-borne pathogens by anaerobic digestion - (Abstract Only)
Borchardt, M.A., Spencer, S.K., Larson, R.A., Alkan-Ozkaynak, A. 2013. Inactivation of dairy manure-borne pathogens by anaerobic digestion. Meeting Abstract. May 18-21, 2013.
Improved HF183 reverse primer and probe for greater analytical sensitivity of human bacteroides in the environment - (Abstract Only)
Millen, H.T., Spencer, S.K., Shanks, O.C., Green, H.C., Haugland, R.A., Gonnering, J.C., Borchardt, M.A. 2013. Improved HF183 reverse primer and probe for greater analytical sensitivity of human bacteroides in the environment. Meeting Abstract. May 18-21, 2013.
Risk of viral acute gastrointestinal illness from non-disinfected drinking water distribution systems - (Peer Reviewed Journal)
Lambertini, E., Borchardt, M.A., Kieke, B.A., Spencer, S.K., Loge, F.J. 2012. Risk of viral acute gastrointestinal illness from non-disinfected drinking water distribution systems. Environmental Science and Technology. 46:9299-9307.
Viruses in non-disinfected drinking water from municipal wells are related to community rates of acute gastrointestinal illness - (Peer Reviewed Journal)
Borchardt, M.A., Spencer, S.K., Kieke, B.A., Lambertini, E., Loge, F.J. 2012. Viruses in non-disinfected drinking water from municipal wells are related to community rates of acute gastrointestinal illness. Proceedings of the National Academy of Sciences. 120:1272-1279.
Comparative effectiveness of membrane bioreactors, conventional secondary treatment, and disinfection to remove microorganisms from municipal wastewaters - (Peer Reviewed Journal)
Francy, D.S., Stelzer, E.A., Bushon, R.N., Brady, A.M., Williston, A.G., Riddell, K.R., Borchardt, M.A., Spencer, S.K., Gellner, T.M. 2012. Comparative effectiveness of membrane bioreactors, conventional secondary treatment, and disinfection to remove microorganisms from municipal wastewaters. Water Research. 46:4164-4178.
Measuring and mitigating inhibition during real-time, quantitative PCR analysis of viral nucleic acid extracts from large-volume environmental water samples - (Peer Reviewed Journal)
Gibson, K.E., Schwab, K.J., Spencer, S.K., Borchardt, M.A. 2012. Measuring and mitigating inhibition during real-time, quantitative PCR analysis of viral nucleic acid extracts from large-volume environmental water samples. Water Research. 46:4281-4291.
Pathogen transport in surface runoff from manured agricultural fields - (Abstract Only)
Borchardt, M.A., Jokela, W.E., Spencer, S.K. 2012. Pathogen transport in surface runoff from manured agricultural fields. Meeting Abstract. September 23-26, 2012.
Glass wool filters for concentrating waterborne viruses and agricultural zoonotic pathogens - (Peer Reviewed Journal)
Millen, H., Gonnering, J., Berg, R., Spencer, S.K., Jokela, W.E., Pearce, J.M., Borchardt, J.S., Borchardt, M.A. 2012. Glass wool filters for concentrating waterborne viruses and agricultural zoonotic pathogens. Journal of Visualized Experiments. DOI: 10.3791/3930.
Human and bovine viruses in urban and rural streams: Hydrologic and season patterns of wastewater influence - (Abstract Only)
Hydrogeological and statistical evidence for wide-spread enteric virus contamination of deep municipal wells - (Abstract Only)
Viruses in non-disinfected groundwater used for municipal drinking water and the incidence of acute gastrointestinal illness - (Abstract Only)
Quantifying viruses and bacteria in wastewater - results, quality control, and interpretation methods - (Government Publication)
Francy, D.S., Stelzer, E.A., Bushon, R.N., Brady, A.M., Mailot, B.E., Spencer, S.K., Borchardt, M.A., Elber, A.G., Riddell, K.R., Gellner, T.M. 2011. Quantifying viruses and bacteria in wastewater - results, quality control, and interpretation methods. United States Geological Survey Technical Report. 5150, 44p.
Virus contamination from operation and maintenance practices in small drinking water distribution systems - (Peer Reviewed Journal)
Lambertini, E., Spencer, S.K., Kieke, B.A., Loge, F.J., Borchardt, M.A. 2011. Virus contamination from operation and maintenance practices in small drinking water distribution systems. Journal of Water and Health. 9:799-812.
Method 1615 measurment of Enterovirus and Norovirus occurrence in water by culture and qRT-PCR - (Government Publication)
Fout, G.S., Brinkman, N.E., Cashdollar, J.L., Griffin, S.M., Mcminn, B.R., Rhodes, E.R., Varughese, E.A., Grimm, A.G., Spencer, S.K., Borchardt, M.A. 2011. Method 1615 measurment of Enterovirus and Norovirus occurrence in water by culture and qRT-PCR. Government Publication/Report. EPA/600/R-10/181.
Pathogen losses in surface runoff from dairy manure applied to corn fields - (Abstract Only)
Borchardt, M.A., Jokela, W.E., Spencer, S.K. 2011. Pathogen losses in surface runoff from dairy manure applied to corn fields. American Society for Microbiology. Abstract #1436.
Human viruses as tracers of wastewater pathways into deep municipal wells - (Government Publication)
Bradbury, K.R., Borchardt, M.A., Gotkowski, M., Spencer, S.K. 2010. Human viruses as tracers of wastewater pathways into deep municipal wells. Government Publication/Report. Final Report to the Wisconsin Department of Natural Resources, Open-File Report 2010-04A, 47p.
Presence of human enteric viruses in deep urban groundwater - (Abstract Only)
Bradbury, K., Borchardt, M.A., Gotkowitz, M.B., Hunt, R., Spencer, S.K. 2010. Presence of human enteric viruses in deep urban groundwater. Meeting Abstract. Vol. 42, No. 5, page 378.
Groundwater sampling methods using glass wool filtration to trace human enteric viruses in Madison, Wisconsin - (Abstract Only)
Gellasch, C.A., Bahr, J.M., Borchardt, M.A., Bradbury, K.E., Chase, P.M., Spencer, S.K. 2010. Groundwater sampling methods using glass wool filtration to trace human enteric viruses in Madison, Wisconsin. Geological Society of America Meeting. Vol. 42, No. 5, p. 603.
Assessment of Sewer Source Contamination of Drinking Water Wells Using Tracers and Human Enteric Viruses - (Peer Reviewed Journal)
Hunt, R.J., Borchardt, M.A., Richards, K.D., Spencer, S.K. 2010. Assessment of Sewer Source Contamination of Drinking Water Wells Using Tracers and Human Enteric Viruses. Environmental Science and Technology. Environ. Sci. Technol.44:7956-7963..