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Chih-Hao Hsu PhD.

Chih-Hao Hsu, PhD
Chih-Hao Hsu PhD.

Division of Animal and Food Microbiology


Dr. Hsu got his PhD in computer science and engineering from the Pennsylvania State University in 2009. Since graduation, Dr. Hsu has worked as a Visiting Fellow in the National Center for Biotechnology Information (NCBI) and as a Research Fellow in the National Cancer Institute (NCI). Dr. Hsu joined the FDA in 2015 and has provided his bioinformatics expertise in support of the study of antimicrobial resistance for the National Antimicrobial Resistance Monitoring System (NARMS) project.


  • Provides bioinformatics expertise in support of next-generation sequencing and metagenomics data analyses.
  • Initiates and performs studies in accordance with Center priorities in collaboration with microbiologists in the Division of Food and Animal Microbiology and other scientists within the Center for Veterinary Medicine’s Office of Research.
  • Works with principal investigators to understand their bioinformatics analysis needs and turns ideas into practical design and implementation, optimizes non-production code, constructs pipelines from building blocks, and conducts advanced data analysis and modeling.
  • Leads experiments in which experimental theories and new analysis methods are developed and applied to problems whose analyses are not supported by usual data analysis methods.

Select Publications

C. Hsu, C. Li, M. Hoffmann, P. McDermott, J. Abbott, S. Ayers, G.H. Tyson, H. Tate, K. Yao, M. Allard, and S. Zhao. Comparative Genomic Analysis of Multidrug-resistant Salmonella Dublin from Sick Cattle and Retail Beef. Microb Drug Resist. DOI: 10.1089/mdr.2019.0045 (2019)

S. Zhao, S. Mukherjee, C. Hsu, S. Yang, C. Li, H. Tate, C. Morales, J. Haro, S. Thitaram, G. Tillman, and P. McDermott. Genomic Analysis of Emerging Florfenicol Resistant Campylobacter coli isolated from Cattle in the U.S. mSphere DOI: 10.1128/mSphere.00367-19 (2019)

D.A. Tadesse, C. Li, S. Mukherjee, C. Hsu, S. Bodeis Jones, S.A. Gaines, C. Kabera, G.H. Loneragan, T. S. Edrington, M. Torrence, D.M. Harhay, P.F. McDermott and S. Zhao. Whole Genome Sequence Analysis of CTX-M Containing Escherichia coli Isolates from Retail Meats and Cattle in the United States. Microb Drug Resist. 24(7): 939-948. (2018) 

C.A. Whitehouse, S. Young, C. Li, C. Hsu, G. Martin, P.F. McDermott, and S. Zhao. Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015. Food Microbiol. 73: 122-128. (2018)

G.H. Tyson, J.L. Sabo, M. Hoffman, C. Hsu, S. Mukherjee, J. Hernandez, G. Tillman, J. L. Wasilenko, J. Haro, M. Simmons, U. Dessai, and P. F. McDermott. Novel Linezolid Resistance Plasmids in Enterococcus in the United States. J Antimicrob Chemother. 73(12): 3254-3258 (2018)

H. Tate, J.P. Folster, C. Hsu, J. Chen, M. Hoffmann, C. Li, C. Morales, G.H. Tyson, S. Mukherjee, A.C. Brown, A. Green, W. Wilson, U. Dessai, J. Abbott, L. Joseph, J. Haro, S. Ayers, P.F. McDermott, S. Zhao. Comparative Analysis of Extended-Spectrum-beta-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States. Antimicrob Agents Chemother, 61: 00488-17. (2017)

B. Ge, S. Mukherjee, C. Hsu, J. A. Davis, T. Tran, Q. Yang, J.W. Abbott, S.L. Ayers, S.R. Young, E.T. Crarey, N.A. Womack, S. Zhao, P.F. McDermott. MRSA and Multidrug-Resistant Staphylococcus aureus in Retail Meats, USA, 2010-2011. Food Microbiol. 62: 289-297. (2017)

Contact Information
Chih-Hao Hsu
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