Xiangyu Deng Assistant Professor Center for Food Safety
Contact Information xdeng@uga.edu 770-233-5495

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Description of Research Interests

Genomics and molecular biology of foodborne pathogens; pathogen subtyping and genomic epidemiology; bioinformatics; microbial phylogenetics and evolution; food microbiology.

Visit laboratory website at www.denglab.site 

Selected Recent Publications

Hyeon J, Li S, Mann DA, Zhang S, Li Z, Chen Y, Deng X. 2017. Quasimetagenomics-based and real-time-sequencing-aided detection and subtyping of Salmonella enterica from food samples. Applied and Environmental Microbiology (Featured by AEM spotlight)

Zhang H, Qi Y, Wang L, Zhang S, Deng X. 2017. Salmonella survival during thermal dehydration of fresh garlic and storage of dehydrated garlic products. International Journal of Food Microbiology 263:26-31

Wang W, Zhou X, Suo Y, Deng X, Cheng M, Shi C, Shi X. 2017. Prevalence, serotype diversity, biofilm-forming ability and eradication of Listeria monocytogenes isolated from diverse foods in Shanghai, China. Food Control 73:1068-1073

Katz LS, Griswold T, Williams-Newkirk AJ, Wagner D, Petkau A, Sieffert C, Domselaar GV, Deng X, Carleton HA. 2017. A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology for foodborne pathogens. Frontiers in Microbiology doi:10.3389/fmicb.2017.00375

Hyeon J and Deng X. 2017. Rapid detection of Salmonella in raw chicken breast using real-time PCR combined with immunomagnetic separation and whole genome amplification. Food Microbiology 63:111-116.

Feasey AN, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X et al (47 co-authors). 2016. Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nature Genetics 48:1211-1217

Peng Y, Deng X, Harrison MA, Alali W. 2016. Salmonella levels associated with turkey skin. Journal of Food Protection 79:801-805.

Deng X, den Bakker HC, Hendriksen RS. 2016. Genomic epidemiology: Whole-genome Sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens. Annual Review of Food Science and Technology 7:353-374.

Zhang S, Yin Y, Jones MB, Zhang Z, Kaiser BLD, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. 2015. Salmonella serotype determination utilizing high-throughput genome sequencing. Journal of Clinical Microbiology 53:1685-1692

Doyle MP, Erickson MC, Alali W, Cannon J, Deng X, Ortega Y, Smith MA, Zhao T. 2015. The food industry's current and future role in preventing microbial foodborne illness within the United States. Clinical Infectious Diseases 61:252-2

Deng X, Shariat N, Driebe E, Roe C, Tolar B, Trees E, Keim PS, Zhang W, Dudley EG, Fields PI, Engelthaler DM. 2015. Comparative analysis of subtyping methods against a whole genome sequencing standard in Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology; 53(1):212-218.

Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye, JG, Porwolik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland. 2014. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerging Infectious Diseases 2014 Sep; 20(9):1481-9.

Deng X, Salazar JK, Frezet S, MacCannell D, Ribot EM, Fields PI, Fricke WF, Zhang W: Genome sequence of Salmonella enterica Serotype Tennessee strain CDC07-0191, implicated in the 2006-2007 multistate food-borne outbreak linked to peanut butter in the United States. Genome Announcements. 2013 May/June; 1(3): e00260-13.

Deng X, Allen KJ, Zhang W: Pathogen identification using high-density microarrays. In Encyclopedia of Biotechnology in Agriculture and Food. CRC Press. 2012.

Deng X, Li X, Zhang W: Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil. Food Microbiology. 2012 May; 30(1): 311-315.

Wen J, Deng X, Li Z, Dudley EG, Anantheswaran RC, Knabel SJ, Zhang W: Transcriptomic response of Listeria monocytogenes during transition to long-survival-phase. Applied and Environmental Microbiology. 2011 Sep; 77(17): 5966-5972.     

Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W: Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification.  BMC Genomics. 2010 Sep 16;11(1):500.

Wang S, Deng K, Zaremba S, Deng X, Lin C, Wang Q, Tortorello ML, Zhang W: Transcriptomic response of Escherichia coli O157:H7 to oxidative stress. Applied and Environmental Microbiology. 2009 Oct 75(19):6110-6123.

Phillippy AM, Deng X, Zhang W, Salzberg SL: Efficient oligonucleotide probe selection for pan-genomic tiling microarrays.  BMC Bioinformatics. 2009 Sep 16;10:293.

Books

Deng X, den Bakker HC, Hendriksen RS (Eds.) Applied Genomics of Foodborne Pathogens. Springer, New York, USA 2017

Book chapters

den Bakker HC, Strawn LK, Deng X 2016. Bioinformatics aspects of foodborne pathogen research. In Applied Genomics of Foodborne Pathogens, edited by Deng X, den Bakker HC, Hendriksen RS. Springer. New York, USA

Deng X, Katz LS, Fields PI, Zhang W 2014. High-throughput sequencing. In DNA Methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens, edited by Oyarzabal, OA and Kathariou, S. Wiley-Blackwell. West Sussex, United Kingdom. ISBN 9781118278673

Deng X, Allen K, Zhang W 2012. Pathogen identification using high-density microarrays. In: Heldman DR, Hoover D, Wheeler MB, Bamania AB (eds.), Encyclopedia of Biotechnology in Agriculture and Food. Taylor & Francis Group, New York, USA. ISBN 0849350271.