Publications

Underlined names are those of lab members. A complete publication list can be found at MyBibliography.

Post-2018, this page only tracks our preprints and other publications that cannot be found in PubMed.

Submitted to bioRxiv November 2022:

, , , and E. G. Dudley. Population structure and genetic diversity of Salmonella Typhimurium in avian hosts.

2018

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. Microbiology UK 165:270-286.

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. Microb. Genom. 5:e000270.

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.

2017

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.

2016

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

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.

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. 10:415-417.

Barrangou, R., and E. G. Dudley. 2016. CRISPR-based typing and next-generation technologies. Ann. Rev. Food Sci. Technol. In press.

2015

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. In press.

Yin, S., B. Rusconi, F. Sanjar, K. Goswami, L. Xiaoli, M. Eppinger, and E. G. Dudley. 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.

2014

Wijetunge DS, Karunathilake KH, Chaudhari A, Katani R, Dudley EG, Kapur V, DebRoy C, Kariyawasam S. 2014. Complete nucleotide sequence of pRS218, a large virulence plasmid, that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218. BMC Microbiol. 14:203.

Shariat, N., and E. G. Dudley. 2014. CRISPRs: Molecular signatures used for pathogen subtyping. Appl. Environ. Microbiol. 80:430-439.

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.

2013

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. 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. 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. 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.

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.