Zhao (Jack) Chen Ph.D.

Employment

Education

1. Application of genomics and metagenomics to improve food safety
2. Stress responses of foodborne pathogens
3. Development of innovative food processing technologies to control foodborne pathogens

Recent Publications:

1. Huang, X., Toro, M., Reyes-Jara, A., Moreno-Switt, A.I., Adell, A.D., Oliveira, C.J.B., Bonelli, R.R., Gutiérrez. S., Álvarez, F.P., Rocha, A.D.L., Kraychete, G.B., Chen, Z., Grim, C.J., Brown, E.W., Bell, R.L., Meng, J. (2024). Integrative genome-centric metagenomics for surface water surveillance: elucidating microbiomes, antimicrobial resistance, and their associations. Water Research. In revision.


2. Chen, Z., Moreno-Switt, A.I., Reyes-Jara, A., Delgado-Suárez, E.J., Adell, A.D., Oliveira, C.J.B., Bonelli, R.R., Huang, X., Brown, E.W., Allard, M., Grim, C.J., Bell, R.L., Meng, J., Toro, M. (2024). A multicenter genomic epidemiological investigation in Brazil, Chile, and Mexico reveals the diversity and persistence of Salmonella populations in surface waters. mBio. In press.


3. Chen, Z.*, Meng, J. (2024). Illumina short read-based shotgun metagenomic data sets of simulated bacterial communities derived from fresh spinach and surface water. Microbiology Resource Announcements. In press.


4. Chen, Z.*, Grim, C.J., Ramachandran, P., Meng, J. (2024). Advancing metagenome-assembled genome-based pathogen identification: Unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing. Microbiology Spectrum. In press.


5. Chen, Z.*, Toro, M., Moreno-Switt, A.I., Adell, A.D., Delgado-Suárez, E.J., Bonelli, R.R., Oliveira, C.J.B., Reyes-Jara, A., Huang, X., Albee, B., Grim, C.J., Allard, M., Tallent, S.M., Brown, E.W., Bell, R.L., Meng, J. (2024). Unveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis isolates from Latin American surface waters: A comparative analysis. Microbiology Spectrum, 12, e00047-24.


6. Cao, G., Zhao, S., Kuang, D., Hsu, C., Yin, L., Luo, Y., Chen, Z., Xu, X., Strain, E., McDermott, P., Allard, M., Brown, E., Meng, J., & Zheng, J. (2023). Geography shapes the genomics and antimicrobial resistance of Salmonella enterica serovar Enteritidis isolated from humans. Scientific Reports, 13, 1331.


7. Chen, Z.* & Meng, J. (2022). Critical assessment of short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Microorganisms, 10, 2416.


8. Chen, Z.* (2022). Application of chlorine dioxide-based hurdle technology to improve microbial food safety–A review. International Journal of Food Microbiology, 379, 109848.


9. Ballesteros-Nova, N. E., Sánchez, S., Steffani, J. L., Sierra, L.C., Chen, Z., Ruíz-López F. A., Rubio, M. S., Soberanis, O., Barona, F., Meng, J., Allard, M. W., & Delgado-Suárez, E. J. (2022). Genomic epidemiology of Salmonella enterica circulating in surface waters used in agriculture and aquaculture in Mexico. Applied and Environmental Microbiology, 88, e02149-21.


10. Wang, Z., Zhu, T., Chen, Z., Meng, J., Simpson, D. J., & Gänzle, M. G. (2021). Genetic determinants of stress resistance in desiccated Salmonella enterica. Applied and Environmental Microbiology, 87, e01683-21.


11. Chen, Z. & Meng, J. (2021). Persistence of Salmonella enterica and Enterococcus faecium NRRL B-2354 on baby spinach subjected to temperature abuse after exposure to sub-lethal stresses. Foods, 10(9), 2141.


12. Chen, Z., Erickson, D. L., & Meng, J. (2021). Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses. Genomics, 113(3), 1366-1377.


13. Chen, Z., Erickson, D. L., & Meng, J. (2020). Benchmarking long-read assemblers for genomic analyses of bacterial pathogens using Oxford Nanopore sequencing. International Journal of Molecular Sciences, 21(23), 9161.


14. Chen, Z., Erickson, D. L., & Meng, J. (2020). Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing. BMC Genomics, 21(1), 1-21.


15. Kwon, H. J., Chen, Z., Evans, P., Meng, J., & Chen, Y. (2020). Characterization of mobile genetic elements using long-read sequencing for tracking Listeria monocytogenes from food processing environments. Pathogens, 9(10), 822.


16. Chen, Z., Kuang, D., Xu, X., González-Escalona, N., Erickson, D. L., Brown, E., & Meng, J. (2020). Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies. PloS ONE, 15(7), e0235641.

Grant Awards:

• 2022 – 2025. PI. “Control of Persistent Salmonella enterica on Foods with Prior Exposure to Sub-Lethal Food Production-Related Stresses Using a Hurdle Concept”, U.S. Department of Agriculture - National Institute of Food and Agriculture. $288,000.


• 2024 – 2027. Co-PI. "Production and Application of Biochar in Agricultural Practices at Small and Underserved Farms: Soil enhancement, Carbon Sequestration, and Productivity Improvement", U.S. Department of Agriculture - Natural Resources Conservation Service. $4,855,000.

Certificates:

• Certified Produce Safety Alliance Trainer


• Certified HACCP Principles and GAPs for Fresh Produce Industries

Editorial Board Memberships:

• International Journal of Food Microbiology


• Food Control


• LWT - Food Science and Technology

Professional Memberships:

• International Association for Food Protection


• American Society for Microbiology