Overview of Research Program

• Genomic epidemiology
• Bioinformatics and genomics
• Applied and molecular food microbiology

Lab website
https://www.denglab.site/

Publications

(2010-present)

Li H, Wu Y, Feng D, Jiang Q, Li S, Rong J, Zhong L, Methner U, Baxter L, Ott S, Falush D, Li Z, Deng X, Lu X, Ren Y, Kan B, Zhou Z. 2024. Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica. Nat Food. 5(5):413-422. doi: 10.1038/s43016-024-00968-1. Epub 2024 May 9. MID: 38724686

Kassem II, Osman M, Hassan J, Sulaiman AA, Mann D, Esseili MA, Naas T, Deng X. 2023. First report of the mobile colistin resistance gene, mcr-1.26, in multidrug-resistant Escherichia coli isolated from retail chicken meat. J Glob Antimicrob Resist. 34:176-178. doi: 10.1016/j.jgar.2023.07.005.

Liao J, Guo X, Li S, Anupoju SMB, Cheng RA, Weller DL, Sullivan G, Zhang H, Deng X, Wiedmann M. 2023. Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments.  ISME Commun. 3(1):85. doi: 10.1038/s43705-023-00293-x.

Wang W, Cui J, Liu F, Hu Y, Li F, Zhou Z, Deng X, Dong Y, Li S, Xiao J. 2023. Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China. Front Microbiol. 14:1295769. doi: 10.3389/fmicb.2023.1295769.

Wu X, Luo H, Ge C, Xu F, Deng X, Wiedmann M, Baker RC, Stevenson AE, Zhang G, Tang S. 2023. Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection. Front Microbiol. 13:1073057. doi: 10.3389/fmicb.2022.1073057.

Xian Z, Yoo J, Patel C, Yang H, Deng X, Hammack T, Chen Y. 2023. Comparison between qPCR, VIDAS immunoassays, and agar streaking for the detection of Listeria monocytogenes from food and environmental surfaces containing and not containing Listeria innocua. J Food Prot. 86(5):100013. doi: 10.1016/j.jfp.2022.11.005.

Zhong L, Zhang M, Sun L, Yang Y, Wang B, Yang H, Shen Q, Xia Y, Cui J, Hang H, Ren Y, Pang B, Deng X, Zhan Y, Li H, Zhou Z. 2023. Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century. Nat Commun. 14(1):7706. doi: 10.1038/s41467-023-43528-0.

Fu Y, M'ikanatha NM, Lorch JM, Blehert DS, Berlowski-Zier B, Whitehouse CA, Li S, Deng X, Smith JC, Shariat NW, Nawrocki EM, Dudley EG. 2022. Salmonella enterica serovar Typhimurium from wild birds in the United States represent distinct lineages defined by bird type. Appl Environ Microbiol. AEM0197921. doi: 10.1128/AEM.01979-21. Epub ahead of print. PMID: 35108089. 

Hassan J, Esseili MA, Mann D, Osman M, Li S, Deng X, Kassem II. 2022. Draft genome sequences of antibiotic-resistant Serratia sp. strains isolated from raw sewage and sediment sludge in Georgia, USA. Microbiol Resour Announc.11(12):e0096522. doi: 10.1128/mra.00965-22. Epub 2022 Nov 16. PMID: 36383023; PMCID: PMC9753650. 

Hassan J, Mann D, Li S, Deng X, Kassem II. 2022. First report of the mobile colistin resistance gene, mcr-9.1, in Morganella morganii isolated from sewage in Georgia, USA. J Glob Antimicrob Resist. 9:S2213-7165(21)00267-8. doi: 10.1016/j.jgar.2021.11.013. 

He Y, Xu T, Li S, Mann DA, Britton B, Oliver HF, den Bakker HC, Deng X. 2022. Integrative assessment of reduced Listeria monocytogenes susceptibility to benzalkonium chloride in produce processing environments. Appl Environ Microbiol. 13:e0126922. doi: 10.1128/aem.01269-22.  

Kassem II, Assi A, Osman M, Mann D, Li S, Deng X. 2022. First Report of the Detection of the Plasmid-Borne Colistin Resistance Gene, mcr-1.26, in Multidrug-Resistant Escherichia coli Isolated from a Domesticated Pigeon. Microb Drug Resist. 28:821-823. doi: 10.1089/mdr.2021.0359.  

Kassem II, Hassan J, Esseili MA, Mann D, Osman M, Li S, Deng X. 2022. Draft genome sequences of multidrug-resistant Escherichia coli isolated from river water. Microbiol Resour Announc. e0082722. doi: 10.1128/mra.00827-22. Epub ahead of print. PMID: 36222705.

Xian Z, Li S, Mann DA, Huang Y, Xu F, Wu X, Tang S, Zhang G, Stevenson A, Ge C, Deng X. 2022. Subtyping evaluation of Salmonella Enteritidis using single nucleotide polymorphism and core genome multilocus sequence typing with nanopore reads. Appl Environ Microbiol. 88(15):e0078522. doi: 10.1128/aem.00785-22. Epub 2022 Jul 12. PMID: 35867567; PMCID: PMC9361833. 

Deng X, Cao S, Horn AL. 2021. Emerging applications of machine learning in food safety. Annu Rev Food Sci Technol. doi: 10.1146/annurev-food-071720-024112.

He Y, Chen R, Qi Y, Salazar JK, Zhang S, Tortorello ML, Deng X, Zhang W. 2021. Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits. Int J Food Microbiol. 348:109201. doi: 10.1016/j.ijfoodmicro.2021.109201

Hyeon J-Y, Li S, Mann DA, Zhang S, Kim K-J, Lee D-H, Deng X, Song C-S. 2021 Whole-genome sequencing analysis of Salmonella Enterica serotype enteritidis isolated from poultry sources in South Korea, 2010–2017. Pathogens. 10(1):45. https://doi.org/10.3390/pathogens10010045.

Kassem II, Mann D, Li S, Deng X. 2021. Draft genome sequences and resistome analysis of multidrug-resistant mcr-1-harbouring Escherichia coli isolated from pre-harvest poultry in Lebanon. J Glob Antimicrob Resist. 25:114-116. doi: 10.1016/j.jgar.2021.03.001.

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

Nasser NA, Alhaj Sulaiman A, Mann D, Li S, Deng X, Kassem II. 2021. Draft genome sequences of multidrug-resistant and mcr-1.1- harboring Escherichia coli isolated from drinking and well waters used in Syrian refugee camps. Microbiol Resour Announc 10:e01252-20. https://doi.org/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. Front Microbiol. 12:637771. doi: 10.3389/fmicb.2021.637771. eCollection 2021.

37.  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. Kunzendorf and Orion var. 15+, 34. Int J Food Microbiol. 346:109167. doi: 10.1016/j.ijfoodmicro.2021.109167.

Forghani F, Li S, Zhang S, Mann DA, Deng X, den Bakker HC, Diez-Gonzalez F. 2020. Salmonella enterica and Escherichia coli in wheat flour: detection and serotyping by a quasimetagenomic approach assisted by magnetic capture, multiple-displacement amplification, and real-time sequencing. Appl Environ Microbiol. 86(13):e00097-20. doi: 10.1128/AEM.00097-20.

Sourenian T, Mann D, 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. J Glob Antimicrob Resist. 22:84-86. doi: 10.1016/j.jgar.2020.05.007

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 Microbiol. 89:103452 https://doi.org/10.1016/j.fm.2020.103452

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

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. J Open So Soft 4(44), 1762 DOI: 10.21105/joss.01762

Qi Y, He Y, Beuchat LR, Zhang W, Deng X. 2020. Glove-mediated transfer of Listeria monocytogenes on fresh-cut cantaloupe. Food Microbiol 88(103396) DOI: 10.1016/j.fm.2019.103396

Diep b, Barretto C, Portmann A-C, 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. Front. Microbiol. 10, 2554.

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. Appl Environ Microbiol. doi: 10.1128/AEM.01985-19. [Epub ahead of print]

Zhang S, Den-Bakker HC, 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. Appl Environ Microbiol. doi: 10.1128/AEM.01746-19. [Epub ahead of print]

Hyeon JY, Mann DA, Wang J, Kim WK, Deng X. 2019. Rapid detection of Salmonella in poultry environmental samples using real-time PCR coupled with immunomagnetic separation and whole genome amplification. Poult Sci. 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

Hyeon JY, Mann DA, Townsend AM, Deng X. 2018. Quasi-metagenomic analysis of Salmonella from food and environmental samples. J Vis Exp. doi: 10.3791/58612.

Hyeon, J.-Y., L. S. Li, D.A. Mann, S. Zhang, Z. Li2, Y. Chen, and X. Deng. 2018. Quasi-metagenomics and realtime sequencing aided detection and subtyping of Salmonella enterica from food samples. Appl. Environ. Microbiol. doi: 10.1128/AEM.02340-17.

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. Int J Food Microbiol. 263:26-31. doi: 10.1016/j.ijfoodmicro.2017.10.010

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 JY, Deng X. 2017. Rapid detection of Salmonella in raw chicken breast using real-time PCR combined with immunomagnetic separation and whole genome amplification. Food Microbiol. 2017 May;63:111-116.

Deng, X., H.C. den Bakker, and R.S. Hendriksen. 2016. Genomic epidemiology: whole-genome-sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens. Annu. Rev. Food Sci. Technol. 7:353-374.

Peng, Y., X.Y. Deng, M.A. Harrison, and W.Q. Alali. 2016. Salmonella levels associated with skin of turkey parts. J. Food Prot. 79:801-805.

Deng, X., S. Nikki, E. M. Driebe, C.C. Roe, B. Tolar, E. Trees, P. Keim, W. Zhang, E.G. Dudley, P.I. Fields, and D.M. Engelthaler. 2015. Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis. J. Clin. Microbiol. 53:212-218.

Doyle, M.P., M.C. Erickson, W. Alali, J. Cannon, X. Deng, Y. Ortega, M.A. Smith, and T. Zhao. 2015. Food industry's current and future role in preventing microbial foodborne illness within the United States. Clin. Infect. Dis. 61:252-259.

Zhang, S.K., Y.L. Yin, M.B. Jones, Z.Z. Zhang, B.L.D. Kaiser, B.A. Dinsmore, C. Fitzgerald, P.I. Fields, and X.Y. Deng. 2015. Salmonella serotype determination using high-throughput genome sequencing data.  J. Clin. Microbiol. 53:1685-1692.

Deng, X.Y., N. Shariat, E.M. Driebe, C.C. Roe, B. Tolar, E. Trees, P. Keim, W. Zhang, E.G. Dudley, P.I. Fields,and D.M. Engelthaler. 2014. Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis.  J. Clin. Microbiol. 53:212-218.

Deng, X.Y., P.T. Desai, H.C. den Bakker, M. Mikoleit, B. Tolar, E. Trees, R.S. Hendriksen, J.G. Frye, S. Porwollik, B.C. Weimer,m M. Wiedmann, G.M. Weinstock, P.I. Fields, and M. McClelland. 2014. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerg. Infect. Dis. 20:1481-1489.

Deng, X, J.K. Salazar, S. Frezet, D. MacCannell, E.M. Ribot, P.I. Fields, W.F. Fricke, and W. Zhang. 2013. Genome sequence of Salmonella enterica CDC07-0191, implicated in the 2006-2007 multistate food-borne outbreak linked to peanut butter in the United States. Genome Announcements 1(3): e00260-13.

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

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

Wen, J., X. Deng, Z. Li, E.G. Dudley, R.C. Anantheswaran, S.J. Knabel, and W. Zhang. 2011. Transcriptomic response of Listeria monocytogenes during transition to long-survival-phase. Appl. Environ. Microbiol. 77:5966-5972.

Deng, X., A.M. Phillippy, Z. Li, S.L. Salzberg, and W. Zhang. 2010. Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification. BMC Genomics 11:500.