2016 Clayton, J.B., Vangay, P., Huang, H., Ward, T., Hillmann, B.M., Al-Ghalith, G.A., Travis, D.A., Long, H.T., Tuan, B.V., Minh, V.V., Cabana, F., Nadler, T., Toddes, B., Murphy, T., Glander, K.E., Johnson, T.J., and Knights, D. Captivity humanizes the primate microbiome. Proceedings of the National Academy of Sciences USA, 13:10376-81.

2016 Meason-Smith, C., Diesel, A., Patterson, A.P., Older, C.E., Johnson, T.J. Mansell, J.M., Suchodolski, J.S., and Rodrigues-Hoffmann, A.R. Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing. Veterinary Dermatology, In Press, doi:10.1111/vde.12373.

2016 Lang, K.S., and Johnson, T.J. Characterization of Acr2, an H-NS-like protein encoded on A/C2-type plasmids. Plasmid, In Press, doi:10.1016/j.plasmid.2016.07.004.

2016 Gohl, D.M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T., Clayton, J.B., Johnson, T.J., Hunter, R., Knights, D., and Beckman, K.B. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology, 34:942-9.

2016 Johnson, T.J., Danzeisen, J.L., Youmans, B., Case, K., Llop, K., Munoz-Aguayo, J., Flores-Figueroa, C., Aziz, M., Stoesser, N., Sokurenko, E., Price, L.B., and Johnson, J.R. Separate F-type plasmids have shaped the evolution of the H30 subclone of Escherichia coli sequence type 131. mSphere 1:e00121-16.

2016 Mishra, H.K., Johnson, T.J., Seelig, D.M., and Walcheck, B. Targeting ADAM17 in leukocytes increases neutrophil recruitment and reduces bacterial spread during polymicrobial sepsis. J Leukoc Biol, Epub ahead of print.

2016 Stoesser, N., Sheppard, A.E., Pankhurst, L., De Maio, N., Moore, C.E., Sebra, R., Turner, P., Anson, L.W., Kasarskis, A., Batty, E.M., Kos, V., Wilson, D.J., Phetsouvanh, R., Wylie, D., Sokurenko, E., Manges, A.R., Johnson, T.J., Price. L.B., Peto, T.E., Johnson, J.R., Didelot, X., Walker, A.S., Crook, D.W. Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131. mBio 7(2):e02162-15.

2016 Banerjee, S., Sindberg, G., Wang, F., Meng, J., Sharma, U., Zhang, L., Dauer, P., Chen, C., Dalluge, J., Johnson, T., and Roy, S. Opioid-induced gut microbial disruption and bile dysregulation leads to gut barrier compromise and sustained systemic inflammation. Mucosal Immunology Epub ahead of print.

2015 Hargreaves, M.L., Shaw, K.M., Dobbins, G., Snippes Vagnone, P.M., Harper, J.E., Bxrud, D., Lynfield, R., Aziz, M., Price, L.B., Silverstein, K.A., Danzeisen, J.L., Youmans, B., Case, K., Sreevatsan, S., and Johnson, T.J. Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States. Antimicrobial Agents and Chemotherapy 59:7723-7734.

2015 Danzeisen, J.L., Clayton, J.B., Huang, H., Knights, D., McComb, B., Hayer, S.S., Johnson, T.J. Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment. Frontiers in Veterinary Science 2:56.

2015 Liu, C., Tan, C., Zheng, H., Yang, M., Xu, Z., Wang, X., Wei, L., Tang, B., Liu, F., Zhang, Y., Ding, Y., Tang, X., Wu, B., Chen, H., Johnson, T.J. Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033. BMC Genomics 16:717.

2015 Johnson, J.R., Porter, S.B., Thuras, P., Johnson, T.J., Price, L.B., Tchesnokova, V., and Sokurenko, E.V. Greater Ciprofloxacin Tolerance as a Possible Selectable Phenotype Underlying the Pandemic Spread of the H30 Subclone of Sequence Type 131. Antimicrobial Agents and Chemotherapy 59:7132-7135.

2015 LaPara, T., Madson, M., Borchardt, S., Lang, K., and Johnson, T.J. Multiple Discharges of Treated Municipal Wastewater Have a Small Effect on the Quantities of Numerous Antibiotic Resistance Determinants in the Upper Mississippi River. Environmental Science and Technology 49:11509-11515.

2015 Lang, K., and Johnson, T.J. Transcriptome modulations due to A/C2 plasmid acquisition. Plasmid 80:83-89.

2015 Johnson, T.J., Singer, R.S., Isaacson, R.E., Danzeisen, J.L., Lang, K., Kobluk, K., Rivet, B., Borewicz, K., Frye, J.G., Englen, M., Anderson, J., and Davies, P.R. In Vivo transmission of an IncA/C plasmid in Escherichia coli depends on tetracycline concentration, and acquisition of the plasmid results in a variable cost of fitness. Applied and Environmental Microbiology 81:3561-70.

2014 Clayton, J.B., Danzeisen, J.L., Trent, A.M., Murphy, T., Johnson, T.J. Longitudinal characterization of Escherichia coli in healthy non-human primates. Frontiers in Veterinary Science 1:24.

2014 Kudirkien, E., Bager, R.J., Johnson, T.J., Bojesen, A.M. Chaperone-usher fimbriae in a diverse selection of Gallibacterium genomes. BMC Genomics 15:1093.

2014 Oakley, B.B., Lillehoj, H.S., Kogut, M.H., Kim, W.K., Maurer, J.J., Pedroso, A., Lee, M.D., Collett, S.R., Johnson, T.J., Cox, N.A. The chicken gastrointestinal microbiome. FEMS Microbiology Letters 360:100-112.

2014 Reiland, H.A., Omolo, M.A., Johnson, T.J., and Baumler, D.J. 2014. A survey of Escherichia coli O157:H7 virulence factors: the first 25 years and 13 genomes. Advances in Microbiology 4:390-423.

2014 Kim, H.B., Singer, R.S., Borewicz, K., White, B.A., Sreevatsan, S., Johnson, T.J., Espejo, L.A., Isaacson, R.E. Effects of tylosin administration on C-reactive protein concentration and carriage of Salmonella enterica in pigs. American Journal of Veterinary Research 75:460-467.

2013 Foley, S.L., Johnson, T.J., Ricke, S.R., Nayak, R., and Danzeisen, J.L. Salmonella Pathogenicity and Host Adaptation in Chicken-associated Serovars. Microbiology and Molecular Biology Reviews 77:582-607.

2013 Danzeisen, J.L., Calvert, A.J., Noll, S.L., McComb, B., Sherwood, J.S., Logue, C.M., and Johnson, T.J. Succession of the turkey gastrointestinal bacterial microbiome related to weight gain. PeerJ 1:e237.

2013 Johnson, T.J., Abrahante, J.E., Hunter, S.S., Hauglund, M., Tatum, F.M., Maheswaran, S.K., and Briggs, R.E. Comparative genome analysis of an avirulent and two virulent strains of avian Pasteurella multocida reveals candidate genes involved in fitness and pathogenicity. BMC Microbiology 13:106.

2012 Johnson, T.J., Danzeisen, J.L., Trampel, D., Nolan, L.K., Seemann, T., Bager, R.J., and Bojesen, A.M. Genome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry. PLoS ONE 8: e54844.

2013 Danzeisen, J.L., Wannemuehler, W., Nolan, L.K., and Johnson, T.J. Comparison of multilocus sequence analysis and virulence genotyping of Escherichia coli from live birds, retail poultry meat, and human extraintestinal infection. Avian Diseases 57:104-108.

2012 Sandford, E.E., Orr, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S. Strong Concordance Between Transcriptomic Patterns of Spleen and Peripheral Blood Leukocytes in Response to Avian Pathogenic Escherichia coli. Avian Diseases 56:732-736.

2012 Logue, C.M., Doetkott, C., Mangiamele, P., Wannemuehler, Y.M., Johnson, T.J., Tivendale, K.A., Li, G., Sherwood, J., and Nolan, L.K. Genotypic and phenotypic traits that distinguish neonatal meningitis Escherichia coli from fecal E. coli isolates of healthy human hosts. Applied and Environmental Microbiology 78:5824-5830.

2012 Patterson, S.K., Borewicz, K., Johnson, T.J., Xu, W., and Isaacson, R.E. Characterization and differential gene expression between two phenotypic phase variants in Salmonella enterica serovar Typhimurium. PLoS ONE 7:e43592.

2012 Johnson, T.J., Bielek, E.M., Fortini, D., Hansen, L.H., Hasman, H., Debroy, C., Nolan, L.K., and Carattoli, A. 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae. Plasmid 68:43-50.

2012 Gnanandarajah, J.S., Johnson, T.J., Kim, H.B., Abrahante, J.E., Lulich, J.P., and Murtaugh, M.P. Comparative fecal microbiota of dogs with and without calcium oxalate stones. Journal of Applied Microbiology 113:745-756.

2012 Sandford, E.E., Orr, M., Shelby, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S.J. Leukocyte Transcriptome from Chickens Infected with Avian Pathogenic Escherichia coli Identifies Pathways Associated with Resistance. Results In Immunology 2:44-53.

2012 Johnson, T.J. and Lang, K. IncA/C plasmids: an emerging threat to human and animal health? Mobile Genetic Elements 2:55-58.

2012 Clayton, J.B., Kim, H.B., Glander, K.E., Isaacson, R.E., and Johnson, T.J. Fecal bacterial diversity of the wild mantled howling monkey (Alouatta palliata). Amer J Phys Anthropol 147:116-117.

2012 Lang, K.L., Danzeisen, J.L., Xu, W., and Johnson, T.J. Transcriptome mapping of pAR060302, a blaCMY-2 positive, IncA/C broad host range plasmid. Applied and Environmental Microbiology 78:3379-3386.

2012 Johnson, T.J., Wannemuehler, Y.W., Kariyawasam, S., Johnson, J.R., Logue, C.M., and Nolan, L.K. Prevalence of avian pathogenic Escherichia coli strain APEC O1 genomic islands and assessment of its zoonotic potential. Journal of Bacteriology 194:2846-2853.

2012 Shepard, S.M., Danzeisen, J.L., Isaacson, R.E., Seemann, T., Achtman, M., and Johnson, T.J. Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli. Journal of Bacteriology 194:395-405.

2012 Lynne, A.M., Kariyawasam, S., Wannemeuhler, Y.M., Johnson, T.J., Johnson, S.J., Sinha, A.S., Lynne, D.K., Moon H.W., Jordan D.M., Logue, C.M., Foley, S.L., and Nolan, L.K. Recombinant Iss as a potential vaccine for avian colibacillosis. Avian Diseases 56:192-199.

2012 Johnson, T.J., Logue, C.M., Johnson, J.R., Kuskowski, M.A., Sherwood, J.S., Barnes, H.J., DebRoy, C., Wannemuehler, Y.M., Obata-Yasuoka, M., Spanjaard, L., and Nolan, L.K. 2012. Associations between multidrug resistance, plasmid content, and virulence potential among extraintestinal pathogenic and commensal Escherichia coli from humans and poultry. Foodborne Pathogens and Disease 9:37-46.

2011 Danzeisen, J.L., Kim, H.B., Isaacson, R.E., Tu, Z.J., and Johnson, T.J. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PLoS ONE 6:e27949.

2011 Cayton, J.B., Johnson, T.J., and Trent, A.M. Examination of Escherichia coli populations in a captive zoological collection of nonhuman primates. Amer J Phys Anthropol 144:110.

2011 Sandford, E.E., Orr, M., Balfanz, E., Bowerman, N., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S.J. Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. BMC Genomics 12:469.

2011 Johnson, T.J., Shepard, S.M., Rivet, B., Danzeisen, J.L., and Carattoli, A. Comparative Genomics and Phylogeny of the IncI1 Plasmids, a Common Plasmid Type Among Porcine Enterotoxigenic Escherichia coli. Plasmid 66:144-151.

2011 Fernandez-Alarcon, C., Singer, R.S., and Johnson, T.J. Comparative Genomics of Multidrug Resistance-Encoding IncA/C Plasmids from Commensal and Pathogenic Escherichia coli from Multiple Animal Sources. PLoS One 6:e2341.

2011 Foley, S.L., Nayak, R., Hanning, I.B., Johnson, T.J., Han, J., and Ricke, S.C. Population Dynamics of Salmonella enterica Serotypes in Commercial Egg and Poultry Production. Applied and Environmental Microbiology 77:4273-4279.

2011 Li, G., Tivendale, K.A., Liu, P., Feng, Y., Wannemuehler, Y.M., Cai, W., Mangiamele, P., Johnson, T.J., Penn, C.W., and Nolan, L.K. Transcriptome analysis of avian pathogenic Escherichia coli O1:K1:H7 in chicken serum reveals adaptive responses to systemic infection. Infection and Immunity 79:1951-1960.

2010 Johnson, T.J., Thorsness, J.L., Anderson, C.P., Lynne, A.M., Foley, S.L., Han, J., Fricke, W.F., McDermott, P.F., White, D.G., Khatri, M., Stell, A.L., Flores, C., and Singer R.S. Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky. PLoS One 22:e15524.

2010 Crossman, L.C., Chaudhuri, R.R., Beatson, S.A., Wells, T.J., Desvaux, M., Cunningham, A.F., Petty, N.K., Mahon, V., Brinkley, C., Hobman, J.L., Savarino, S.J., Turner, S.M., Pallen, M.J., Penn, C.W., Parkhill, J., Turner, A.K., Johnson, T.J., Thomson, N.R., Smith, S.G., and Henderson, I.R. A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. Journal of Bacteriology 192:5822-5831.

2010 Johnson, T.J., Jordan, D., Kariyawasam, S., Stell, A.L., Bell, N.P., Wannemuehler, Y.M., Alarcon, C.F., Tivendale, K.A., Logue, C.M., and Nolan, L.K. Sequence analysis and characterization of a transferrable hybrid plasmid encoding multidrug resistance and enabling zoonotic potential for extraintestinal pathogenic Escherichia coli. Infection and Immunity 78:1931-1942.

2010 Johnson, T.J., DebRoy, C., Belton, S., Williams, M.L., Lawrence, M.L., Nolan, L.K., and Thorsness, J. Pyrosequencing of the Vir plasmid of necrotoxigenic Escherichia coli. Veterinary Microbiology 144:100-109.

2010 Debroy, C., Sidhu, M.S., Sarker, U., Jayarao, B.M., Stell, A.L., Bell, N.P., and Johnson, T.J. Complete sequence of pEC14_114, a highly conserved IncFIB/FIIA plasmid associated with uropathogenic Escherichia coli cystitis strains. Plasmid 63:53-60.

2009 Johnson, T.J., and Nolan, L.K. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiology and Molecular Biology Reviews 73:750-774.

2009 Fricke, W.F., McDermott, P.F., Mammel, M.K., Zhao, S., Johnson, T.J., Rasko, D.A., Fedorka-Cray, P.J., Pedroso, A., Whichard, J.M., Leclerc, J.E., White, D.G., Cebula, T.A., and Ravel, J. Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry. Applied and Environmental Microbiology 75:5963-5971.

2009 Johnson, T.J., Logue, C.M., Wannemuehler, Y.M., Kariyawasam, S., Doetkott, C., Debroy, C., White, D.G., and Nolan, L.K. Examination of the source and extended virulence genotypes of Escherichia coli contaminating retail poultry meat. Foodborne Pathogens and Disease 6:657-667.

2009 Johnson, T.J. and Nolan, L.K. Plasmid replicon typing. Methods in Molecular Biology 551:27-35.

2008 Johnson, T.J., Wannemuehler, Y.M., Johnson, S.J., Stell, A.L., Doetkott, C., Johnson, J.R., Kim, K.S., Spanjaard, L., and Nolan, L.K. Comparison of extraintestinal pathogenic Escherichia coli from human and avian sources reveals a mixed subset representing potential zoonotic pathogens. Applied and Environmental Microbiology 74:7043-7050.

2008 Johnson, T.J., Wannemuehler, Y.M., Doetkott, C., Johnson, S.J., Rosenberger, S.C., and Nolan, L.K. Identification of minimal predictors of avian pathogenic Escherichia coli virulence for use as a rapid diagnostic tool. Journal of Clinical Microbiology 46:3987-3996.

2008 Johnson, T.J., Wannemuehler, Y.M., and Nolan, L.K. Evolution of the iss gene in Escherichia coli. Applied and Environmental Microbiology 74:2360-2369.  link to pdf