Zhao (Jack) Chen

*Open position in Spring 2025: Graduate Research Assistant

For more information, please refer to Job Description.

Professional Experiences

Postdoctoral associate, University of Maryland

Postdoctoral associate, University of California, Davis

Recent Publications (Google Scholar)

Chen, Z.*, Delgado-Suárez, E.J., Bonelli, R.R., Oliveira, C.J.B., Moreno-Switt, A.I., Toro, M., Adell, A.D., Reyes-Jara, A., Grim, C.J., Allard, M.W., Brown, E.W., Bell, R.L., Meng, J. Exploring the genomic and antimicrobial resistance tapestry: Comparative insights into Salmonella enterica serotypes Agona, Braenderup, Muenchen, and Panama in Latin American surface waters. Microbiology Spectrum. In press.

Chen, Z.*, Grim, C.J., Ramachandran, P., Meng, J. (2024). Oxford Nanopore long read-based shotgun metagenomic data sets of simulated bacterial communities originating from fresh spinach and surface water. Microbiology Resource Announcements, 13, e00586-24.

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, 264, 122208.

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, 15, e00777-24.

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, 13, e00375-24.

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, 12, e00117-24.

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.

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.

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.

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

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.

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.

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, 2141.

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, 1366-1377.

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, 9161.

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, 1-21.

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, 822.

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, 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 Members

International Journal of Food Microbiology

Food Control

LWT - Food Science and Technology

Professional Members

International Association for Food Protection

American Society for Microbiology