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  Home > VBS Faculty > Timothy Johnson

Timothy Johnson

Tim Johnson

Johnson Lab site



e-mail: joh04207@umn.edu  

Johnson Lab Facebook page                                                          




205 Veterinary Science Building                              

1971 Commonwealth Ave.

University of Minnesota

St. Paul, MN 55108  





B.S., North Dakota State University, 2000
Ph.D., North Dakota State University, 2004


Honors and Awards


Arnold S. Rosenwald Poster Award Winner, AVMA/AAAP Annual Meeting in Boston, July 2001


Richard B. Rimler Memorial Paper Award Winner, AVMA/AAAP Annual Meeting in Nashville, July 2002


CRWAD Oral Presentation Award in Molecular Biology, Chicago, IL, 2004


Brian Wilkins Young Investigator Award in Plasmid Biology, Meeting of the Plasmid Biology Society in Gdansk, Poland, 2008


Bayer-Snoeyenbos New Investigator Award in Avian Research, AVMA/AAAP Annual Meeting in Atlanta, August 2010


Research Interests


About the Lab
The Johnson Lab is located on the Saint Paul campus of the University of Minnesota in the College of Veterinary Medicine. I have two primary research areas: 1) understanding the mechanisms of plasmid dissemination associated with antibiotic resistance in bacterial pathogens; and 2) understanding the succession of the microbial communities in the animal gastrointestinal tract related to health and development. I work primarily with multidrug resistance-encoding plasmids of E. coli and Salmonella humans and production animals. The goal of this work is to understand the spread of these plasmids within and between human and animal bacterial populations. I also work closely with the poultry industries to study the bacterial populations inhabiting the gastrointestinal tracts of turkeys and chickens. The goal of this work is to understand the succession of bacterial communities over time, and how the modulation of these communities can be achieved using non-antibiotic alternatives.

My lab uses combinations of high throughput sequencing approaches, molecular biology, and classical microbiology tied with natural models of infection and development to study these problems. Much of this work aligns with the mission of the University of Minnesota College of Veterinary Medicine’s One Health concept.

Interested in Microbiology?
I am always in search of hard-working scientists on all levels, including postgraduate, graduate, and undergraduate. If you are interested in training in microbiology, genomics, and microbial evolution, or interested in an undergraduate laboratory experience, please email me.


Selected Publications


Foley, S.L., Johnson, T.J., Ricke, S.R., Nayak, R., and Danzeisen, J.L. Salmonella Pathogenicity and Host Adaptation in Chicken-associated Serovars. Accepted for publication in Microbiology and Molecular Biology Reviews, August 2013.

Johnson, T.J., Abrahante, J.E., Hunter, S.S., Hauglund, M., Tatum, F.M., Maheswaran, S.K., and Briggs, R.E. 2013. 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 (link to pdf.)

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

Danzeisen, J.L., Wannemuehler, W., Nolan, L.K., and Johnson, T.J. 2013. 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.

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

Logue, C.M., Doetkott, C., Mangiamele, P., Wannemuehler, Y.M., Johnson, T.J., Tivendale, K.A., Li, G., Sherwood, J., and Nolan, L.K. 2012. 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 (link to pdf.)

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

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.

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

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. 2012. Leukocyte Transcriptome from Chickens Infected with Avian Pathogenic Escherichia coli Identifies Pathways Associated with Resistance. Results In Immunology 2:44-53.

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

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

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

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

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

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. 2012. Recombinant Iss as a potential vaccine for avian colibacillosis. Avian Diseases 56:192-199.

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. 2011. Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. BMC Genomics 12:469 (link to pdf.)

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

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

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.

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

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.  Infect Immun., In Press (link to pdf.)

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.  2010.  Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky.  PLoS One 22:e15524 (link to pdf.)


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.  2010.  A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.  J. Bacteriol. 192:5822-5831 (link to pdf.)


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.  2010.  Sequence analysis and characterization of a transferrable hybrid plasmid encoding multidrug resistance and enabling zoonotic potential for extraintestinal pathogenic Escherichia coli.  Infect. Immun. 78:1931-1942.


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


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


Johnson, T.J., and Nolan, L.K.  2009.  Pathogenomics of the virulence plasmids of Escherichia coli.  Microbiol. Mol. Biol. Rev. 73:750-774.


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.  2009. Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry.  Appl. Environ. Microbiol. 75:5963-5971.


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


Johnson, T.J. and Nolan, L.K.  2009.  Plasmid replicon typing.  Methods Mol. Biol. 551:27-35.


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.  2008.  Comparison of extraintestinal pathogenic Escherichia coli from human and avian sources reveals a mixed subset representing potential zoonotic pathogens.  Appl. Environ. Microbiol. 74:7043-7050.


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


Johnson, T.J., Wannemuehler, Y.M., and Nolan, L.K.  2008.  Evolution of the iss gene in Escherichia coli.  Appl. Environ. Microbiol. 74:2360-2369.


Skyberg, J.A., Johnson, T.J., and Nolan, L.K.  2008. Mutational and transcriptional analyses of an avian pathogenic Escherichia coli ColV plasmid.  BMC Microbiol. 8:24.


Johnson, T.J., Wannemuehler, Y.M., Johnson, S.J., and Nolan, L.K.  2007.  Plasmid Replicon Typing of Commensal and Pathogenic Types of Escherichia coli.  Antimicrob Agents Chemother. 73:1976-1983. (20 citations)


Johnson, T.J., Kariyawasam, S., Wannemuehler, Y.M., Mangiamele, P.M., Johnson, S.J., Doetkott, C., Skyberg, J.A., Johnson, J.R., Lynne, A.L., and Nolan, L.K.  2007.  Genome Sequence of Avian Pathogenic Escherichia coli Strain O1:K1:H7 Shares Strong Similarities with Human ExPEC Genomes.  J Bacteriol. 189:3228-3236. (54 citations)


Skyberg, J.A., Johnson, T.J., Logue, C.M., and Nolan, L.K.  2006.  Acquisition of a Large ColV Plasmid by an Avirulent Escherichia coli Isolate Enhances Its Virulence and Ability to Grow in Human Urine.  Infect Immun. 74:6287-6292.


Johnson, T.J., Wannemuehler, Y.M., Scaccianoce, J., Johnson, S.J., and Nolan, L.K.  2006.  Complete DNA Sequence, Comparative Genomics, and Prevalence of an IncHI2 Plasmid Occurring among Extraintestinal Pathogenic Escherichia coli.  Antimicrob Agents Chemother. 50:3929-3933. (17 citations)


Johnson, T.J., Johnson, S.J., and Nolan, L.K.  2006.  Complete DNA Sequence of a ColBM Plasmid from an Avian Pathogenic Escherichia coli Suggests that it Evolved from Closely Related ColV Virulence Plasmids.  J Bacteriol. 188:5975-5983. (36 citations)


Kariyawasam, S., Johnson,T.J., and Nolan, L.K.  2006.  Occurrence of Pathogenicity Island APEC-O1 Genes Among Escherichia coli Implicated in Avian Colibacillosis.  Avian Dis. 50:405-410.


Kariyawasam, S., Johnson, T.J., and Nolan, L.K.  2006.  Unique DNA Sequences of Avian Pathogenic Escherichia coli Isolates as Determined by Genomic Suppressive Subtractive Hybridization.  FEMS Microbiol Letters 262:193-200.


Johnson, T.J., Siek, K.E., Johnson, S.J., and Nolan, L.K.  2006.  DNA Sequence of a ColV Plasmid and Prevalence of Selected Plasmid-Encoded Virulence Genes Among Avian Escherichia coli.  J Bacteriol. 188:745-788. (54 citations)


Kariyawasam, S., Johnson, T.J., and Nolan, L.K.  2006.  The pap Operon of Avian Pathogenic Escherichia coli Strain APEC O1:K1 is Located on a Novel Pathogenicity Island.  Infect Immun. 74:744-749.


Johnson, T.J., Siek, K.E., Johnson, S.J., and Nolan, L.K.  2005.  DNA Sequence and Comparative Genomics of pAPEC-O2-R, an Avian Pathogenic Escherichia coli (APEC) Transmissible R Plasmid.  Antimicrob Agents Chemother. 49:4681-4688. (26 citations)


Rodriguez-Siek, K., Giddings, C.W., Doetkott, C., Johnson, T.J., and Nolan, L.K.  2005.  Characterizing the APEC Pathotype.  Vet Res. 35:241-256. (59 citations)


Rodriguez-Siek, K.E., Giddings, C.W., Johnson, T.J., Fakhr, M., Doetkott, C., and Nolan, L.K.  2005.  Comparison of Escherichia coli Implicated in Human Urinary Tract Infection and Avian Colibacillosis.  Microbiol. 151: 2097-2110. (64 citations)


Johnson, T.J., Siek, K., Skyberg, J., Doetkott, C., and Nolan, L.K.  2005.  Plasmid-Linked Virulence Factors among Avian Pathogenic Escherichia coli.  Plasmid Biology 2004: International Symposium on Molecular Biology of Plasmids and Other Mobile Genetic Elements, Kanoni, Corfu, Greece, September 2004.  Plasmid 53: 23-96.


Johnson, T.J., Skyberg, J. and Nolan, L.K.  2004.  Multiple Antimicrobial Resistance Region of a Putative Virulence Plasmid from an Escherichia coli Isolate Incriminated in Avian Colibacillosis.  Avian Dis. 48:351-360.


Nolan, L.K., Horne, S.M., Giddings, C.W., Foley, S.L., Johnson, T.J., Lynne, A.M., and Skyberg, J.  2003.  Resistance to Serum Complement, iss, and Virulence of Avian Escherichia coli.  Vet Res Commun. 2003 27:101-10.


Johnson, T.J., Giddings, C.W., Horne, S.M., Gibbs, P.S., Wooley, R.E., Skyberg, J., Olah, P., Kercher, R., Sherwood, J.S., Foley, S.F. and Nolan, L.K.  2001.  Location of Increased Serum Survival Gene and Selected Virulence Traits on a Conjugative R Plasmid in an Avian Escherichia coli Isolate.  Avian Dis. 46:342-352.





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