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Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.

Xu M, Stedtfeld RD, Wang F, Hashsham SA, Song Y, Chuang Y, Fan J, Li H, Jiang X, Tiedje JM.

Sci Total Environ. 2019 Nov 1;689:1172-1180. doi: 10.1016/j.scitotenv.2019.06.376. Epub 2019 Jun 24.


Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer.

Jha PN, Gomaa AB, Yanni YG, El-Saadany AY, Stedtfeld TM, Stedtfeld RD, Gantner S, Chai B, Cole J, Hashsham SA, Dazzo FB.

Microb Ecol. 2020 Feb;79(2):367-382. doi: 10.1007/s00248-019-01406-7. Epub 2019 Jul 25.


Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.

Williams MR, Hashsham SA.

Methods Mol Biol. 2019;1918:21-33. doi: 10.1007/978-1-4939-9000-9_2.


Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing.

Dang H, Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM.

Environ Sci Technol. 2018 Dec 4;52(23):13914-13924. doi: 10.1021/acs.est.8b04895. Epub 2018 Nov 19.


Long-Term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome.

Wang F, Xu M, Stedtfeld RD, Sheng H, Fan J, Liu M, Chai B, Soares de Carvalho T, Li H, Li Z, Hashsham SA, Tiedje JM.

Environ Sci Technol. 2018 Nov 20;52(22):13037-13046. doi: 10.1021/acs.est.8b04330. Epub 2018 Nov 8.


Antimicrobial Resistance in the Environment.

Waseem H, Williams MR, Jameel S, Hashsham SA.

Water Environ Res. 2018 Oct 1;90(10):865-884. doi: 10.2175/106143018X15289915807056. Review.


Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.

Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA.

FEMS Microbiol Ecol. 2018 Sep 1;94(9). doi: 10.1093/femsec/fiy130.


Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection.

Etchebarne BE, Li Z, Stedtfeld RD, Nicholas MC, Williams MR, Johnson TA, Stedtfeld TM, Kostic T, Khalife WT, Tiedje JM, Hashsham SA, Hughes MJ.

Front Microbiol. 2017 Dec 12;8:2211. doi: 10.3389/fmicb.2017.02211. eCollection 2017.


Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.

Williams MR, Stedtfeld RD, Engle C, Salach P, Fakher U, Stedtfeld T, Dreelin E, Stevenson RJ, Latimore J, Hashsham SA.

PLoS One. 2017 Oct 16;12(10):e0186462. doi: 10.1371/journal.pone.0186462. eCollection 2017.


Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples.

Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM.

J Microbiol Methods. 2017 Dec;143:44-49. doi: 10.1016/j.mimet.2017.10.003. Epub 2017 Oct 12.


MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome.

Williams MR, Stedtfeld RD, Tiedje JM, Hashsham SA.

Front Microbiol. 2017 Sep 27;8:1896. doi: 10.3389/fmicb.2017.01896. eCollection 2017. Review.


Antimicrobial Resistance in the Environment.

Waseem H, Williams MR, Stedtfeld RD, Hashsham SA.

Water Environ Res. 2017 Oct 1;89(10):921-941. doi: 10.2175/106143017X15023776270179. Review.


Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD.

Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA.

Front Microbiol. 2017 Sep 7;8:1708. doi: 10.3389/fmicb.2017.01708. eCollection 2017.


TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal.

Stedtfeld RD, Brett Sallach J, Crawford RB, Stedtfeld TM, Williams MR, Waseem H, Johnston CT, Li H, Teppen BJ, Kaminski NE, Boyd SA, Tiedje JM, Hashsham SA.

Appl Microbiol Biotechnol. 2017 Oct;101(19):7409-7415. doi: 10.1007/s00253-017-8460-9. Epub 2017 Aug 15.


Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs.

Trebitz AS, Hoffman JC, Darling JA, Pilgrim EM, Kelly JR, Brown EA, Chadderton WL, Egan SP, Grey EK, Hashsham SA, Klymus KE, Mahon AR, Ram JL, Schultz MT, Stepien CA, Schardt JC.

J Environ Manage. 2017 Nov 1;202(Pt 1):299-310. doi: 10.1016/j.jenvman.2017.07.045. Epub 2017 Jul 22. Review.


Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.

Munir A, Waseem H, Williams MR, Stedtfeld RD, Gulari E, Tiedje JM, Hashsham SA.

Microarrays (Basel). 2017 May 29;6(2). pii: E9. doi: 10.3390/microarrays6020009.


Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device.

Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA.

Biomed Microdevices. 2017 Sep;19(3):45. doi: 10.1007/s10544-017-0191-2.


On-filter direct amplification of Legionella pneumophila for rapid assessment of its abundance and viability.

Samhan FA, Stedtfeld TM, Waseem H, Williams MR, Stedtfeld RD, Hashsham SA.

Water Res. 2017 Sep 15;121:162-170. doi: 10.1016/j.watres.2017.05.028. Epub 2017 May 13.


TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.

Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen J, Zacharewski TR, Tiedje JM, Hashsham SA.

FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix058.


Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers.

Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA.

J Environ Manage. 2017 Aug 1;198(Pt 1):213-220. doi: 10.1016/j.jenvman.2017.04.079. Epub 2017 Apr 29.


Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner.

Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA.

J Microbiol Methods. 2017 Aug;139:15-21. doi: 10.1016/j.mimet.2017.04.009. Epub 2017 Apr 23.


Virulence factor activity relationships (VFARs): a bioinformatics perspective.

Waseem H, Williams MR, Stedtfeld T, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA.

Environ Sci Process Impacts. 2017 Mar 22;19(3):247-260. doi: 10.1039/c6em00689b. Review.


Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices.

Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA.

Anal Methods. 2017 Feb 28;9(8):1229-1241. doi: 10.1039/C6AY03405E. Epub 2017 Jan 31.


Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater.

Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM.

Appl Microbiol Biotechnol. 2017 Jun;101(11):4827-4835. doi: 10.1007/s00253-017-8203-y. Epub 2017 Feb 25.


Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min.

Ahmad F, Stedtfeld RD, Waseem H, Williams MR, Cupples AM, Tiedje JM, Hashsham SA.

J Microbiol Methods. 2017 Jan;132:27-33. doi: 10.1016/j.mimet.2016.11.010. Epub 2016 Nov 14.


Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils.

Wang F, Stedtfeld RD, Kim OS, Chai B, Yang L, Stedtfeld TM, Hong SG, Kim D, Lim HS, Hashsham SA, Tiedje JM, Sul WJ.

Environ Sci Technol. 2016 Dec 6;50(23):12621-12629. Epub 2016 Nov 18.


Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater.

Stedtfeld RD, Stedtfeld TM, Samhan F, Kanitkar YH, Hatzinger PB, Cupples AM, Hashsham SA.

J Microbiol Methods. 2016 Dec;131:61-67. doi: 10.1016/j.mimet.2016.09.025. Epub 2016 Oct 5.


Antimicrobial Resistance in the Environment.

Williams MR, Stedtfeld RD, Guo X, Hashsham SA.

Water Environ Res. 2016 Oct;88(10):1951-67. doi: 10.2175/106143016X14696400495974. Review.


Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay.

Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra G, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM.

PLoS One. 2016 Jun 16;11(6):e0157008. doi: 10.1371/journal.pone.0157008. eCollection 2016.


Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.

Johnson TA, Stedtfeld RD, Wang Q, Cole JR, Hashsham SA, Looft T, Zhu YG, Tiedje JM.

mBio. 2016 Apr 12;7(2):e02214-15. doi: 10.1128/mBio.02214-15.


Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens.

Stedtfeld RD, Williams MR, Fakher U, Johnson TA, Stedtfeld TM, Wang F, Khalife WT, Hughes M, Etchebarne BE, Tiedje JM, Hashsham SA.

FEMS Microbiol Ecol. 2016 Mar;92(3). pii: fiw020. doi: 10.1093/femsec/fiw020. Epub 2016 Feb 4.


Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9.

Kanitkar YH, Stedtfeld RD, Steffan RJ, Hashsham SA, Cupples AM.

Appl Environ Microbiol. 2016 Jan 8;82(6):1799-1806. doi: 10.1128/AEM.03660-15.


Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics.

Seyrig G, Stedtfeld RD, Tourlousse DM, Ahmad F, Towery K, Cupples AM, Tiedje JM, Hashsham SA.

J Microbiol Methods. 2015 Dec;119:223-7. doi: 10.1016/j.mimet.2015.11.004. Epub 2015 Nov 10.


Detection and Occurrence of Indicator Organisms and Pathogens.

Samhan FA, Kronlein MR, Fakher U, Kronlein C, Stedtfeld RD, Hashsham SA.

Water Environ Res. 2015 Oct;87(10):883-900. doi: 10.2175/106143015X14338845155147.


Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens.

Stedtfeld RD, Liu YC, Stedtfeld TM, Kostic T, Kronlein M, Srivannavit O, Khalife WT, Tiedje JM, Gulari E, Hughes M, Etchebarne B, Hashsham SA.

Biomed Microdevices. 2015 Oct;17(5):89. doi: 10.1007/s10544-015-9994-1.


Thirty-minute screening of antibiotic resistance genes in bacterial isolates with minimal sample preparation in static self-dispensing 64 and 384 assay cards.

Kostić T, Ellis M, Williams MR, Stedtfeld TM, Kaneene JB, Stedtfeld RD, Hashsham SA.

Appl Microbiol Biotechnol. 2015 Sep;99(18):7711-22. doi: 10.1007/s00253-015-6774-z. Epub 2015 Jul 31.


DNA extraction-free quantification of Dehalococcoides spp. in groundwater using a hand-held device.

Stedtfeld RD, Stedtfeld TM, Kronlein M, Seyrig G, Steffan RJ, Cupples AM, Hashsham SA.

Environ Sci Technol. 2014 Dec 2;48(23):13855-63.


Detection and characterization of human pathogenic viruses circulating in community wastewater using multi target microarrays and polymerase chain reaction.

Wong MV, Hashsham SA, Gulari E, Rouillard JM, Aw TG, Rose JB.

J Water Health. 2013 Dec;11(4):659-70. doi: 10.2166/wh.2013.322.


Diverse and abundant antibiotic resistance genes in Chinese swine farms.

Zhu YG, Johnson TA, Su JQ, Qiao M, Guo GX, Stedtfeld RD, Hashsham SA, Tiedje JM.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3435-40. doi: 10.1073/pnas.1222743110. Epub 2013 Feb 11.


Evaluation of sample recovery efficiency for bacteriophage P22 on fomites.

Herzog AB, Pandey AK, Reyes-Gastelum D, Gerba CP, Rose JB, Hashsham SA.

Appl Environ Microbiol. 2012 Nov;78(22):7915-22. doi: 10.1128/AEM.01370-12. Epub 2012 Aug 31.


Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review.

Ahmad F, Hashsham SA.

Anal Chim Acta. 2012 Jul 6;733:1-15. doi: 10.1016/j.aca.2012.04.031. Epub 2012 May 3. Review. Erratum in: Anal Chim Acta. 2013 Jan 14;760:100.


A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification.

Tourlousse DM, Ahmad F, Stedtfeld RD, Seyrig G, Tiedje JM, Hashsham SA.

Biomed Microdevices. 2012 Aug;14(4):769-78. doi: 10.1007/s10544-012-9658-3.


Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.

Baushke SW, Stedtfeld RD, Tourlousse DM, Ahmad F, Wick LM, Gulari E, Tiedje JM, Hashsham SA.

J Microbiol Methods. 2012 Jul;90(1):29-35. doi: 10.1016/j.mimet.2012.04.003. Epub 2012 Apr 17.


Gene-Z: a device for point of care genetic testing using a smartphone.

Stedtfeld RD, Tourlousse DM, Seyrig G, Stedtfeld TM, Kronlein M, Price S, Ahmad F, Gulari E, Tiedje JM, Hashsham SA.

Lab Chip. 2012 Apr 21;12(8):1454-62. doi: 10.1039/c2lc21226a. Epub 2012 Feb 29.


In-feed antibiotic effects on the swine intestinal microbiome.

Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, Sul WJ, Stedtfeld TM, Chai B, Cole JR, Hashsham SA, Tiedje JM, Stanton TB.

Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1691-6. doi: 10.1073/pnas.1120238109. Epub 2012 Jan 17.


Criteria for selection of surrogates used to study the fate and control of pathogens in the environment.

Sinclair RG, Rose JB, Hashsham SA, Gerba CP, Haas CN.

Appl Environ Microbiol. 2012 Mar;78(6):1969-77. doi: 10.1128/AEM.06582-11. Epub 2012 Jan 13.


A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips.

Ahmad F, Seyrig G, Tourlousse DM, Stedtfeld RD, Tiedje JM, Hashsham SA.

Biomed Microdevices. 2011 Oct;13(5):929-37. doi: 10.1007/s10544-011-9562-2.


Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples.

Iwai S, Johnson TA, Chai B, Hashsham SA, Tiedje JM.

Appl Environ Microbiol. 2011 Jun;77(11):3551-7. doi: 10.1128/AEM.00331-11. Epub 2011 Apr 15. Review.


Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.

Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM.

ISME J. 2010 Feb;4(2):279-85. doi: 10.1038/ismej.2009.104. Epub 2009 Sep 24.


Implications of limits of detection of various methods for Bacillus anthracis in computing risks to human health.

Herzog AB, McLennan SD, Pandey AK, Gerba CP, Haas CN, Rose JB, Hashsham SA.

Appl Environ Microbiol. 2009 Oct;75(19):6331-9. doi: 10.1128/AEM.00288-09. Epub 2009 Jul 31.

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