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, 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 were also funded in 2022 to investigate whether the bacteriophage resistance of E. coli including serotype O157:H7 can be predicted from a genome sequence alone.

 

Representative publications:

Nawrocki, E. M., Hutchins, L. E., Eaton, K. A., and E. G. Dudley. 2022. Mcc1229, an Stx2a-amplifying microcin, is produced in vivo and requires CirA for activity. Infect. Immun. 90: e0058721.

Mosso, H. M., Xiaoli, L., Banerjee, K., Hoffmann, M., Yao, K., and E. G. Dudley. 2019. A putative microcin amplifies Shiga toxin 2a production of Escherichia coli O157:H7. J. Bacteriol. 202:1-15.

Xiaoli, L., H. M. Figler, K. Goswami, C. S. Hayes, and E. G. Dudley. 2018. Nonpathogenic Escherichia coli enhance Stx2a production by coli O157:H7 through both bamA-dependent and independent mechanisms. Front. Microbiol. 9:1325.

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.

 

Since 2016, my lab has led the state of Pennsylvania’s involvement in a US Food and Drug Administration program called GenomeTrakr. The main goals of this program are to support state agencies (Departments of Health and Agriculture primarily) as they transition to whole genome sequencing for diagnostics and source tracking, and to populate an FDA/NCBI database called Pathogen Detection with genomic data from foodborne pathogens.  We have leveraged our involvement in the latter to sequence targeted collections that allow us to ask hypothesis-driven questions.  As an example, we recently sequenced over 700 Salmonella enterica from a 30-year historic collection from migratory birds and identified genomic features that are distinct to Salmonella originating from three bird lineages.  Some of these isolates were closely related to S. enterica investigated by the Centers for Disease Control in 2020-2021 and solidified their hypothesis that the outbreak was linked to backyard bird feeders.

 

Representative publications:

Fu Y., N. M. M’ikanatha, J. M. Lorch, D. S. Blehert, B. Berlowski-Zier, C. A. Whitehouse, S. Li , X. Deng, J. C. Smith, N. W. Shariat , E. M. Nawrocki, and E. G. Dudley. 2022. Salmonella enterica serovar Typhimurium isolates from wild birds in the United States represent distinct lineages defined by bird type.  Appl Environ Microbiol. 88:e0197921.

Fu Y, J. C. Smith, N. W. Shariat, N. M. M’ikanatha, and E. G. Dudley. 2022. Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA. Microb. Genom. 8: 000775.

Fu, Y., N. M. M’ikanatha, C. A. Whitehouse, H. Tate, A. Ottesen, J. M. Lorch, D. S. Blehert, B. Berlowski-Zier, and E. G. Dudley. Low occurrence of multi-antimicrobial and heavy metal resistance in Salmonella enterica from wild birds in the United States. Environ Microbiol. 24:1380-1394.

Fu, Y., N. M. M’ikanatha, and E. G. Dudley. 2022. Comparative genomic analysis of Salmonella enterica serovar Typhimurium isolates from passerines reveals two lineages circulating in Europe, New Zealand, and the United States. Appl. Environ. Microbiol. 88:e00205-22

 

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.  While we haven’t had any active CRISPR projects in the lab for several years, we are keeping open the possibility of reengaging as this field continues to move forward.

Representative publications:

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.

Shariat, N., M. K. Kirchner, C. H. Sandt, E. Trees, R. Barrangou, and E. G. Dudley. 2013. Subtyping of Salmonella enterica serovar Newport outbreak isolates by CRISPR-MVLST and determination of the relationship between CRISPR-MVLST and PFGE results. J. Clin. Microbiol. 51:2328-2336.

Yin, S., M. Jensen, J. Bai, C. DebRoy, R. Barrangou, and E. G. Dudley. 2013. Evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in CRISPR spacer composition. Appl. Environ. Microbiol. 79:5910-5920.

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.

 

 I take my role as a mentor to the next generation of students in STEM seriously. This has been most notable in securing funds to direct a food microbiology Research Experiences for Undergraduates (REU) program called “Bugs in my Food” each summer since 2018 except for 2020 (due to the pandemic). This program is funded by the United States Department of Agriculture through 2025 and engages undergraduates from resource-limited colleges and universities in genomic and microbiome projects that demonstrate the application of these tools to improving food safety and health.  One of our goals is to have students publish their work in peer reviewed journals, which include those below.

 

Representative publications:

Méndez Acevedo, M., L. M. Carroll, M. Mukherjee, E. Mills, L. Xiaoli, E. G. Dudley, and J. Kovac. 2020. Novel effective Bacillus cereus group species “Bacillus clarus” is represented by antibiotic-producing strain ATCC 21929 isolated from soil. mSphere. 5:e00882-20.

Connolly CJ, Kaminsky L, Pinto GN, Sinclair PC, Bajracharya G, Yan R, Nawrocki EM, Dudley EG, Kovac J. Whole-genome sequences of Salmonella isolates from an ecological wastewater treatment system. Microbiol. Resour. Announc. 9:e00456-20.

Nwanosike, H., T. Chung, L. Xiaoli, M. Condello , E. G. Dudley, J. Kovac. 2019. Whole-genome sequences of Escherichia coli isolates from cocoa beans imported from Bolivia. Microbiol Resour. Announc. 8:e01516-18.