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  • Journal Articles

Li S, He Y, Mann DA, Deng X. 2021. Global spread of Salmonella Enteritidis via centralized sourcing and international trade of breeding stocks. Nature Communications 12, 5109 DOI:10.1038/s41467-021-25319-7

* Reported by Nature Reviews Microbiology

Deng X, Chao S, Horn A. 2021. Emerging applications of machine learning in food safety. Annual Review of Food Science and Technology 12

He Y, Chen R, Yan Q, Salazar JK, Zhang S, Tortorello ML, Deng X, Zhang W. 2021. Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits. International Journal of Food Microbiology DOI:10.1016/j.ijfoodmicro.2021.109201


Hyeon J, Li S, Mann DA, Zhang S, Kim K, Lee D, Deng X, Song C. 2021. Whole-genome sequencing analysis of Salmonella enterica serovar Enteritidis from poultry sources in South Korea 2010-2017. Pathogens DOI:10.3390/ pathogens10010045


Wang B, Shi H, Habteselassie M, Deng X, Teng Y, Wang Y, Huang Q. 2021. Simultaneous removal of multidrug-resistant Salmonella enterica serotype Typhimurium, antibiotics and antibiotic resistance genes from water by electrooxidation on Magnéli phase Ti4O7 anode. Chemical Engineering Journal DOI: 10.1016/j.cej.2020.127134


Nasser N, Sulaiman AA, Mann DA, Li S, Deng X, Kassem II. 2021. Draft Genome Sequences of Multidrug-resistant and mcr-1.1 Harboring E. coli Isolated from Drinking and Well Waters Used in Syrian Refugee Camps. Microbiology Resource Announcements DOI:10.1128/MRA.01252-20


Wu X, Luo H, Xu F, Ge C, Li S, Deng X, Wiedmann M, Baker RC, Stevenson A, Zhang G, Tang S. 2021. Evaluation of Salmonella serotype prediction with multiplex nanopore sequencing. Frontiers in Microbiology. DOI: 10.3389/fmicb.2021.637771​

Hassan J, Mann D, Li S, Deng X, Kassem II. 2021. Emergence of the mobile colistin resistance gene, mcr-1, in multidrug-resistant E. coli isolated from the fecal matter of toddlers in a community. Antimicrobial Agents and Chemotherapy. 
DOI: 10.1128/AAC.00243-21

Xu F, Ge C, Li S, Tang S, Wu X, Luo H, Deng X, Zhang G, Stevenson A, Baker RC. 2021. Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendor and Orion var. 15+, 34+. International Journal of Food Microbiology. Doi: 10.1016/j.ijfoodmicro.2021.109167

Kassem II, Mann D, Li S, Deng X. 2021. Draft genome sequences and resistome analysis of multidrug-resistant and mcr-1-harboring E. coli isolated from preharvest poultry in Lebanon. Journal of Global Antimicrobial Resistance. DOI: 10.1016/j.jgar.2021.03.00


Nasser N, Mann DA, Li S, Deng X, Kassem II. 2021. Draft genome sequences of colistin-resistant and mcr-1.1-carrying Escherichia coli isolated from irrigation water. Microbiology Resource Announcements

Li S, Mann DA, Zhang S, Yan Q, Meinersmann J, Deng X. 2020. Microbiome-informed food safety and quality: longitudinal consistency and cross-sectional distinctiveness of retail chicken breast microbiomes. mSystems DOI: 10.1128/mSystems.00589-20


Li S, Zhang S, Deng X. 2020. GC content-associated bias caused by library preparation method may infrequently affect Salmonella serotype prediction using SeqSero2. Applied and Environmental Microbiology DOI: 10.1128/AEM.00614-20


Townsend A, Li S, Mann DA, Deng X. 2020. A quasimetagenomics method for concerted detection and subtyping of Salmonella enterica and E. coli O157:H7 from romaine lettuce. Food Microbiology DOI: 10.1016/


Wang B, Shi H, Habteselassie M, Deng X, Teng Y, Wang Y, Huang Q. 2020. Simultaneous removal of multidrug-resistant Salmonella enterica serotype Typhimurium, antibiotics and antibiotic resistance genes from water by electrooxidation on Magnéli phase Ti4O7 anode. Chemical Engineering Journal DOI: 10.1016/j.cej.2020.127134


Forghani F, Li S, Zhang S, Mann DA, Deng X, den Bakker HC, Diez-Gonzalez F. 2020. Detection and serotyping of Salmonella and Escherichia coli in wheat flour by a quasimetagenomic approach assisted by magnetic capture, multiple displacement amplification and real-time sequencing. Applied and Environmental Microbiology DOI: 10.1128/AEM.00097-20


Sourenian TG, Mann DA, Li S, Deng X, Jaafar H, Kassem II. 2020. Dissemination of multidrug-resistant Escherichia coli harboring the mobile colistin resistance gene mcr-1.1 on transmissible plasmids in the Mediterranean Sea. Journal of Global Antimicrobial Resistance DOI: 10.1016/j.jgar.2020.05.007


Hassan J, Eddine RZ, Mann DA, Li S, Deng X, Saud IP, Kassem II. 2020. The mobile colistin resistance gene, mcr-1.1, is carried on IncX4 plasmids in multidrug resistant E. coli isolated from rainbow trout aquaculture. Microorganisms DOI:  10.3390/microorganisms8111636

Xu F, Ge C, Luo H, Li S, Wiedmann M, Deng X, Zhang G, Stevenson A, Baker RC, Tang S. 2020 Evaluation of real-time nanopore sequencing for Salmonella serotype prediction. Food Microbiology DOI:10.1016/

Qi Y, He Y, Beuchat LR, Zhang W, Deng X. 2020. Glove-mediated transfer of Listeria monocytogenes on fresh-cut cantaloupe. Food Microbiology 88(103396) DOI: 10.1016/

He Y, Zhou X, Chen Z, Deng X, Gehring A, Ou H, Zhang L, Shi X. 2020. PRAP: Pan Resistome analysis pipeline. BMC Bioinformatics 21:20 (2020)

Katz L, Griswold T, Morrison SS, Caravas JA, Zhang S, den Bakker HC, Deng X, Carleton HA. 2019. Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software 4(44), 1762 DOI: 10.21105/joss.01762

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

*Featured by AEM Spotlight

Diep B, Barretto C, Portmann AC, Fournier C, Karczmarek A, Voets G, Li S, Deng X, Klijn A. 2019.  Salmonella serotyping; comparison of the traditional method to a microarray-based method and an in silico platform using whole genome sequencing data. Frontiers in Microbiology DOI:10.3389/fmicb.2019.02554

​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.

  • Other papers

Aanensen D, Amid C, Baker S, Bandi C, Brown EW, Campos J, Cochrane G, Comandatore F, Dallman T, Deng X, Dougan G, Finley R, Molina AG, Gerner-Smidt P, Goodwin S, Hald T, Hernández ZIS, Hope K, Hsiao W, Jenkins C, Littler K, Lund O, Miller M, Moran-Gilad J, Gurion B, Mulder N, Nadon C, Ng’eno E, Owuor C, Parkhill J, Rossi M, Schlundt J,  Sintchenko V, Thomson NR. 2018. Whole genome sequencing for foodborne disease surveillance landscape paper. World Health Organization. ISBN 978-92-4-151386-9

  • 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

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