U.S. flag An official website of the United States government
  1. Home
  2. Animal & Veterinary
  3. Science & Research
  4. Chih-Hao Hsu
  1. Science & Research

Chih-Hao Hsu PhD.

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

Division of Emerging Technologies


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.


  • Serve as a primary investigator of basic/conceptual computational research projects to lead new complex initiatives which will improve FDA capabilities to detect and monitor disease and antimicrobial resistance in foodborne bacteria.
  • Perform highly complex computer-science-based research in developing techniques for the processing and reduction of microbial sampling data.
  • Assist and advise CVM/OR staffs on matters concerning the planning, research, purchase, implementation and use of advanced computational techniques.
  • Represent FDA as an authoritative judgement on theoretical and applied computer science on interagency, FDA, and industrial groups.

Select Publications

C. Li, G.H. Tyson, C. Hsu, L. Harrison, E. Strain, T. Tran, G. Tillman, U. Dessai, P. McDermott, S. Zhao. Long-read sequencing reveals evolution and acquisition of antimicrobial resistance and virulence genes in Salmonella enterica. Front. Microbiol 12:777817. (2021)

G.H. Tyson, C. Li, L. Harrison, G. Martin, C. Hsu, H. Tate, T. Tran, E. Strain, S. Zhao. A multidrug-resistant Salmonella Infantis clone is spreading and recombining in the United States. Microbial Drug Resistance 27:792-799. (2021)

L. Harrison, S. Mukherjee, C. Hsu, S. Young, E. Strain, Q. Zhang, G. Tillman, C. Morales, J. Haro, S. Zhao. Core genome MLST for source attribution of Campylobacter coli. Front Microbiol 12:703890. (2021)

C. Hsu, L. Harrison, S. Mukherjee, E. Strain, P. McDermott, Q. Zhang, S. Zhao. Core genome multilocus sequence typing for food animal source attribution of human Campylobacter jejuni infections. Pathogens. 9(7): 532 (2020)

S. Zhao, C. Li, C. Hsu, G. Tyson, E. Strain, H. Tate, T. Tran, J. Abbott, P. McDermott. Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals. Genes. 11(9): 1025 (2020)

G. Tyson, C. Li, C. Hsu, S. Ayers, S. Borenstein, S. Mukherjee, T. Tran, P. McDermott, and S. Zhao. The mcr-9 Gene of Salmonella and E. coli is Not Associated with Colistin Resistance in the United States. Antimicrob Agents Chemother. 64(8): e00573-20 (2020)

G. Tyson, C. Li, L. Harrison, G. Martin, C. Hsu, H. Tate, T. Tran, E. Strain, S. Zhao. A Multidrug-Resistant Salmonella Infantis Clone Is Spreading and Recombining in the United States. Microb Drug Resist. DOI: 10.1089/mdr.2020.0389 (2020)

J.B. Pettengill JB, H. Tate, K. Gensheimer, C. Hsu, J. Ihrie, A. Markon, P. McDermott, S. Zhao, E. Strain, M. Bazaco. Distribution of antimicrobial resistance genes across Salmonella enterica isolates from various foods. J. of Food Protection. DOI: 10.4315/0362-028X.JFP-19-310 (2020)

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. 25(8): 1238–1249. (2019)

Contact Information
Chih-Hao Hsu
Back to Top