PUBLICATIONS

  • Journal Articles

 

Li S, Zhang S, Baert L, Jagadeesan B, Ngom-Bru C, Griswold T, Katz LS, Carleton HA, Deng X. 2019. Implications of mobile genetic elements for Salmonella enterica single nucleotide polymorphism subtyping and source tracking investigations. Applied and Environmental Microbiology DOI: 10.1128/AEM.01985-19

Zhang S, den Bakker H, Li S, Chen J, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. 2019. SeqSero2: Rapid and improved Salmonella serotype determination using whole genome sequencing data. 2019. Applied and Environmental Microbiology DOI: 10.1128/AEM.01746-19

​Hyeon J, Mann DA, Wang J, Kim W, Deng X. 2019. Rapid detection of Salmonella in poultry environmental samples using real-time PCR coupled with immunomagnetic separation and whole genome amplification. Poultry Science DOI:10.3382/ps/pez425

Zhang S, Li S, Gu W, den Bakker H, Boxrud D, Taylor A, Roe C, Driebe E, Engelthaler DM, Allard M, Brown E, McDermott P, Zhao S, Bruce BB, Trees Eija, Fields PI, Deng X. 2019. Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States. Emerging Infectious Diseases 25(1): 82-91

*Featured by CDC/EID podcast 
*Reported by the Verge

*Featured by Nature Reviews Microbiology

 

Hyeon J, Mann DA, Townsend AM, Deng X. 2018 Quasi-metagenomics analysis of Salmonella from food and environmental samples. Journal of Visualized Experiments. (140), e58612, doi:10.3791/58612 (2018)

Hyeon J, Li S, Mann DA, Zhang S, Li Z, Chen Y, Deng X. 2018. Quasimetagenomics-based and real-time-sequencing-aided detection and subtyping of Salmonella enterica from food samples. Applied and Environmental Microbiology 84 e02340-17

*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 61:252-259

 

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 53:212-218

 

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 20:1481-1489

 

Deng X, Salazar JK, Frezet S, MacCannell D, Ribot EM, Fields PI, Fricke WF, Zhang W. 2013. Genome sequence of Salmonella enterica serotype Tennessee strain CDC07-0191 implicated in the 2006-2007 multi-state foodborne outbreak linked to peanut butter in the United States. Genome Announcements 1:e00260-13.

 

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

 

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

Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. 2010. Probing the pan genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics 11:500.

 

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

 

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

  • Books and Book Chapters

Gerner-Smidt P, Trees E, Carleton H, Katz L, den Bakker HC, Deng X 2019. Molecular source tracking and molecular subtyping. In Food Microbiology: Fundamentals and Frontiers, 5th edition, edited by Doyle MP, Diez-Gonzalez F, Hill C. ASM Press. Washington DC, USA

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

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