Edward G Dudley, Ph.D.

Other Affiliations

Molecular Cellular and Integrative Biosciences

Center for Molecular Immunology and Infectious Disease

Center for Infectious Disease Dynamics

Pathobiology Graduate Program

Research Interests

My program uses molecular biology, biochemistry, and molecular biology techniques to better understand the biology and evolution of foodborne pathogens, and to develop improved methods of tracking the spread of these organisms from farm-to-fork.

Escherichia coli O157:H7 is a foodborne pathogen that causes illness through mechanisms that include the elaboration of an AB₅ protein called Shiga toxin. When I joined Penn State in 2007, the research community was just beginning to use genomic techniques to define the phylogeny of global isolates and to explain the heterogeneity observed in terms of virulence potential and toxin production. I took this opportunity to develop a program investigating the factors driving differences in toxin production using whole genomic analysis (mainly in collaboration with Dr. Mark Eppinger at the University of Texas-San Antonio), investigation of polymorphisms encoded within bacteriophage that carry the Shiga toxin genes, and interactions with members of the gut microflora. Most notably, we have found that certain strains categorized as low toxin producers synthesize high levels of toxin when co-cultured with other commensal strains of E. coli. We have also shown that inoculation of mice with such co-cultures causes more serious disease than inoculation with the pathogen alone. Future work is directed at better understanding the mechanisms behind these observations.

We are proudly a member of the US Food and Drug Administration's GenomeTrakr program, representing the Commonwealth of Pennsylvania. This program is a collaboration between Penn State and the PA Department of Health. Our goal is to help populate the whole genome sequence databases with foodborne isolates, particularly E. coli and Salmonella from food and environmental sources, and to help organizations such as our Department of Health and the food industry to gain the knowledge needed to enter this field or to gain the knowledge necessary to benefit from advances in genomic sciences.

In 2007, several high profile papers described the function of elements first discovered in bacterial genomes 30 years earlier, called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). These manuscripts and those that followed elegantly described how CRISPR is an adaptive immune system for prokaryotes designed to protect cells against foreign DNA including bacteriophage and plasmids. We were some of the first to recognize that these rapidly evolving elements could be used as molecular signatures for strain identification during foodborne outbreaks. We have studied CRISPR diversity primarily in Salmonella enterica, with additional work in Shiga toxin producing Escherichia coli. We have demonstrated their utility in molecular subtyping, and for the development of rapid methods of pathogen identification. More recent (unpublished) work has begun to elucidate the function of CRISPR in S. enterica, as it becomes more apparent that CRISPR has functions outside of those of immunity. 

Research Information

Table S5.4: Rare codon tRNA usage in E. coli O157:H7 Sakai
Table S5.5: Tandem rare codons in the E. coli O157:H7 Sakai genome

Keefer, A. B.*, Xiaoli, L.*, M'ikanatha, N. M., Yao, K., Hoffmann, M., and E. G. Dudley. 2018. Retrospective whole-genome sequencing analysis distinguished PFGE and drug resistance matched retail meat and clinical Salmonella isolates. bioRxiv 356857.

Abelman, R. L., N. M. M'ikanatha, and E. G. Dudley. 2018. Whole genome sequencing of antimicrobial-resistant Shigella sonnei associated with infection acquired from international and domestic setting reveals gene allelic variants that predict global lineages. bioRxiv 361196.

Xiaoli L, H. M. Figler, K. Goswami Banerjee, C. S. Hayes, and E. G. Dudley. 2018. Non-pathogenic Escherichia coli Enhance Stx2a Production of E. coli O157:H7 Through Both bamA-Dependent and Independent Mechanisms. Front Microbiol. 9:1325.

Zhang H, E. G. Dudley, and F. Harte. 2017, Critical synergistic concentration of lecithin phospholipids improves the antimicrobial activity of eugenol against Escherichia coli. Appl Environ Microbiol. 83: e01583-17.

Yang X, E. Huang, M. Yesil, L. Xiaoli, E. G. Dudley, and A. E. Yousef AE. 2017. Draft genome sequence of Brevibacillus laterosporus OSY-I₁, a strain that produces Brevibacillin, which combats drug-resistant Gram-positive bacteria. Genome Announc. 5: e01093-17.

Gerst M.M., E. G. Dudley, L. Xiaoli, and A. E. Yousef. 2017. Draft genome sequence of Bacillus velezensis GF610, a producer of potent anti-Listeria agents. Genome Announc. 5: e01046-17.

DiMarzio M, B. Rusconi, N. H. Yennawar, M. Eppinger, A. D. Patterson, and E. G. Dudley. 2017. Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA. PLoS One. 12:e0183564

Zhang H, E. G. Dudley, P. M. Davidson, and F. Harte. 2017. Critical concentration of lecithin enhances the antimicrobial activity of eugenol against Escherichia coli. Appl Environ Microbiol. 83: e03467-16.

Scheinberg J.A., E. G. Dudley, J. Campbell, B. Roberts, M. DiMarzio, C. DebRoy, and C. N. Cutter. 2017. Prevalence and Phylogenetic Characterization of Escherichia coli and Hygiene Indicator Bacteria Isolated from Leafy Green Produce, Beef, and Pork Obtained from Farmers' Markets in Pennsylvania. J Food Prot. 80:237-244

Uhlich, G. A., G. C. Paoli, X. Zhang, E. G. Dudley, H. M. Figler, B. J. Cottrell, and E. Andreozzi. 2017. Whole-genome sequence of Escherichia coli serotype O157:H7 strain PA20. Genome Announc. 5:e01460-16.

Danagamage, T. N., P. Patterson, E. Wallner-Pendleton, D. Trampel, N. Shariat, E. G. Dudley, B. M. Jayarao, and S. Kariyawasam. 2016. Longitudinal monitoring of successive commercial layer flocks for Salmonella enteria serovar Enteritidis. 13:618-625

Very, K. J., M. K, Kirchner, N. Shariat, W. Cottrell, C. H. Sandt, E. G. Dudley, S. Kariyawasam, and B. M. Jayarao. 2016. Prevalence and spatial distribution of Salmonella infections in the Pennsylvania raccoon (Procyon lotor). Zoonoses Public Health 63:223-233.

Figler, H.M., and E. G. Dudley. 2016. The interplay of Escherichia coli O157:H7 and commensal E. coli: the importance of strain-level identification. Expert Rev. Gastroenterol Hepatol.10:415-417.

Valderrama, W. B., E. G. Dudley, S. Doores, and C. N. Cutter. 2016. Commercially available rapid methods for detection of selected foodborne pathogens. Crit. Rev. Food Sci. Nutr. 56:1519-1531.

Barrangou, R., and E. G. Dudley. 2016. CRISPR-based typing and next-generation tracking technologies. Ann. Rev. Food Sci. Technol. 7:395-411.

Ivanov, Y. V., N. Shariat, K. B. Register, B. Linz, I. Rivera, K. Hu, E. G. Dudley, and E. T. Harvill. 2015. A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease. BMC Genomics 26:863.

Park, J., Y. Zhang, C. Chen, E. G. Dudley, and E. T. Harvill. 2015. Diversity of Secretion Systems Associated with Virulence Characteristics of the Classical Bordetellae. Microbiology 161:2328-2340

Yin, S., B. Rusconi, F. Sanjar, K. Goswami, L. Xiaoli, M. Eppinger, and E. G. Dudley. 2015. Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages. BMC Genomics. 16:733.

Goswami, K., C. Chen, L. Xiaoli, K. A. Eaton, and E. G. Dudley. 2015. Co-culturing Escherichia coli O157:H7 with a non-pathogenic E. coli strain increases toxin production and virulence in a germ-free mouse model. Infect. Immun. 83:4185-4193.

Jiang, Y., S. Yin, E. G. Dudley, and C. N. Cutter. 2015. Diversity of CRISPR loci and virulence genes in pathogenic Escherichia coli isolates from various sources. Int. J. Food Microbiol. 204:41-46.

Shariat, N., R. E. Timme, J. B. Pettengill, R. Barrangou, and E. G. Dudley. 2015. Characterization and evolution of Salmonella CRISPR-cas systems. Microbiology UK. 161: 374-386.

Deng X, Shariat N, Driebe EM, Roe CC, Tolar B, Trees E, Keim P, Zhang W, Dudley EG, Fields PI, Engelthaler DM. 2015. Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica Serotype Enteritidis. J Clin Microbiol. 53:212-218.

Sanjar, J., T. H. Hazen, S. M. Shah, S. S. Koenig, S. Agrawal, S. Daugherty, L. Sadzewicz, L. J. Tallon, M. K. Mammel, P. Feng, R. Soderlund, P. I. Tarr, C. DebRoy, E. G. Dudley, T. A. Cebula, J. Ravel, C. M. Fraser, D. A. Rasko, and M. Eppinger. 2014. Genome sequence of Escherichia coli O157:H7 stain 2886-75, associated with the first reported case of human infection in the United States. Genome Announc. 2:e01120-13.

Shariat, N., C. H. Sandt, M. J. DiMarzio, R. Barrangou, and E. G. Dudley. 2013. CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates. BMC Microbiol. 13:254.

Shariat, N., and E. G. Dudley. 2013. CRISPRs: Molecular signatures used for pathogen subtyping. Appl. Environ. Microbiol. 80:430-439.

Shariat N., and E. G. Dudley. 2013. Where are we heading with Salmonella molecular subtyping? Future Microbiol. 8:1231–1233

Loquasto, J. R., R. Barrangou, E. G. Dudley, B. Stahl, C. Chen, and R. F. Roberts. Bifidobacterium animalis subsp. lactis ATCC 27673 is a genomically unique strain within this conserved subspecies. Appl. Environ. Microbiol. 79:6903-6910.

Yin, S., M. Jensen, J. Bai, C. DebRoy, R. Barrangou, and E. G. Dudley. Evolutionary Divergence of Shiga Toxin-producing Escherichia coli is Reflected in CRISPR Spacer Composition. Appl. Environ. Microbiol. 79:5910-5920.

Chen, C., C. A. Blumentritt, M. M. Curtis, V. Sperandio, A. G. Torres, and E. G. Dudley. 2013. Restrictive streptomycin-resistant mutations decrease the formation of attaching and effacing lesions in Escherichia coli O157:H7 strains. Antimicrob. Agents Chemother. 57:4260-4266.

DiMarzio, M., N. Shariat, S. Kariyawasam, R. Barrangou, and E. G. Dudley. 2013. Antibiotic resistance in Salmonella Typhimurium associates with CRISPR sequence type. Antimicrob. Agents Chemother. 57:4282-4289.

Uhlich, G. A., C. Y. Chen, B. J. Cottrell, C. S. Hofmann, E. G. Dudley, T. P. Strobaugh, and L. H. Nguyen. 2013. Phage insertion in mlrA and variations in rpoS limit curli expression and biofilm formation in Escherichia coli serotype O157:H7. Microbiology UK. 159:1586-1596.

Shariat, N., M. K. Kirchner, C. H. Sandt, E. Trees, R. Barrangou, and E. G. Dudley. 2013. CRISPR-MVLST Subtyping of Salmonella serovar Newport Outbreak Isolates and Determination of the Relationship Between CRISPR-MVLST and PFGE. J. Clin. Microbiol. 51:2328-2336.

Valderrama, W. B., E. G. Dudley, S. Doores, and C. N. Cutter. Commercially available rapid methods for detection of selected foodborne pathogens. Accepted in Crit. Rev. Fd. Sc. Nutr.

Svoboda, A. L., E. G. Dudley, C. DebRoy, E. W. Mills, and C. N. Cutter. Presence of Shiga toxin-producing Escherichia coli O-groups in small and very small beef processing plants and resulting ground beef detected by a multiplex polymerase chain reaction assay. Foodborne Pathog. Dis. 10:789-795.

Eppinger, M., S. Daugherty, S. Agrawai, K. Galens, N. Sengamalay, L. Sadzewicz, L. Tallon, T. A. Cebula, M. K. Mammel, P. Feng, R. Soderlund, P. I. Tarr, C. DebRoy, E. G. Dudley, C. M. Fraser, J. Ravel. 2013. Whole-genome draft sequences of 26 enterohemorrhagic Escherichia coli O157:H7 strains. Genom. Announc. 1:e00134-12.

Chen C., C. R. Lewis, K. Goswami, E. L. Roberts, C. Debroy, and E. G. Dudley. 2013. Identification and Characterization of Spontaneous Deletions within the Sp11-Sp12 Prophage Region of Escherichia coli O157:H7 Sakai. Appl. Environ. Microbiol. 79:1934-1941.

Shariat, N., M. J. DiMarzio, S. Yin, L. Dettinger, C. H. Sandt, J. R. Lute, R. Barrangou, and E. G. Dudley. 2013. The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis. Food Microbiol. 34:164-173.

Weyrich L.S., O. Y. Rolin, S. J. Muse, J. Park, N. Spidale, M. J. Kennett, S. E. Hester, C Chen, E. G. Dudley, and E. T. Harvill. 2012. A Type VI secretion system encoding locus is required for Bordetella bronchiseptica immunomodulation and persistence in vivo. PloS One 7:e45892

Verghese B., N. D. 3^rd Schwalm, E. G. Dudley, and S. J. Knabel. 2012. A combined multi-virulence-locus sequence typing and Staphylococcal Cassette Chromosome mec typing scheme possesses enhanced discriminatory power for genotyping MRSA. Infect Genet Evol. 12:1816-1821.

Miller D.M., E. G. Dudley, and R. F. Roberts. 2012. Technical note: development of a quantitative PCR method for monitoring strain dynamics during yogurt manufacture. J. Dairy Sci. 95:4868-4872.

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