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Kansas State University



Bai, J.





Jianfa Bai
Assistant Professor
Ph.D. 2000, Kansas State University
M.S. 1990, University of the Philippines at Los Baños

Office: 157 Research Park
Phone: 785-532-4332
Fax: 785-532-4481





My service interests are to validate, improve, and develop new molecular detection methods for identification of animal pathogens using PCR, sequencing and microarray-based technologies. Regular PCR, real-time PCR, and multiplex PCR methods are being developed and used for the identification of animal viral and bacterial pathogens including zoonotic pathogens.  Some molecular tests that we have recently developed include:

  • A duplex real-time PCR test to detect and differentiate PCV2a and PCV2b strains;
  • A duplex real-time PCR test to detect all Brucella species, and B. canis specifically;
  • A real-time PCR detecting type I and type II porcine torque teno virus;
  • A multiplex PCR detecting eae, hlyA, stx1, stx2, fliC and rfbE virulence genes in E. coli O157:H7 strains;
  • A multiplex PCR detecting and differentiating E. coli O26, O45, O103, O111, O121, O145, and O157 serotypes;
  • A multiplex PCR detecting eae, hlyA, stx1, stx2, fliC and rfbE virulence genes, at the same time, detecting and differentiating O26, O45, O103, O111, O121, O145, and O157 E. coli serotypes;
  • A triplex real-time PCR detecting stx1, stx2, fliC in Shiga toxin producing E. coli O157 strains;

I am in charge of DNA sequencing services at the Kansas State Veterinary Diagnostic Laboratory.  Partial or full genome sequencing, especially on viral pathogens, becomes an important tool to reveal the potential source of a given pathogen, and pathogen genomic variations due to mutations and adaptation.  We provide service on sample preparations for sequencing, and provide clients with assembled sequences, identity tables and phylogenetic trees that are generated with some reference strains of known genotypes.  We also provide similar analysis with client’s own sequence collections. 


In addition to animal pathogen identifications, I am interested in a few research areas. The first one is the genomic diversity of porcine torque teno viruses (PTTV). PTTV becomes increasingly important in swine production as it serves as a cofactor in PPRS and/or PCV2 infected pigs, and enhances disease severity. An amazing feature of PTTV is that multiple strains with very different genomic identities are commonly co-exist in the same host. We have cloned and sequenced full genomes of two type I and six type II PTTV strains, and partial genomes of four additional type I strains. Phylogenetic analysis indicating that they are very diverged strains. Within each type, multiple distinct subtypes exist. Infectious clones are being generated for animal challenging studies.

The second project I am currently working on is the diversity of VP4 and VP7 encoding RNA segments in group A rotavirus. Rotavirus causes enteritis and diarrhea in human and many animal species. Viral protein VP4 and VP7 form the outer layer of the triple-layered particle (capsid) of a mature viral particle, and are considered the major antigens that induce neutralizing antibodies. Understand the diversity of VP4 and VP7 encoding segments may help generating new vaccines. The emphasis of the project is on amplification, cloning, sequencing and phylogenetic analysis of VP4 and VP7 segments of group A rotaviruses from about 250 cattle samples that we have accumulated for the past years.

Cattle are not infected by Escherichia coli (E. coli), but serve as major reservoir, and allow the organism to propagate inside the cattle gut. E. coli shed in cattle feces can contaminate our food and cause human infections. A small percentage of the E. coli strains are shed in higher concentrations, i.e., greater than 103-104 CFU/g of feces. These strains are referred to as high-shedder strains. They are the major source of food contaminations and human infections. My interest is to identify factors in E. coli that may influence bacterial shedding levels using whole genome microarray and sequencing information.

Selected Publications

Ada G. Cino-Ozuna, Richard Hesse,H. Jerome C. Nietfeld, Steven Henry, Jianfa Bai, Morgan Scott, Raymond R.R. Rowland. 2011. Characterization of a new disease syndrome associated with porcine circovirus type 2 (PCV2) in previously vaccinated herds. J. Clinical Microbiol. doi:10.1128/JCM.02543-10.

Jianfa Bai, Xiaorong Shi and T. G. Nagaraja. 2010. A Multiplex PCR Procedure for Detection of Six Major Virulence Genes in Escherichia coli O157:H7. J. Microbiol. Methods. 82: 85-89.

Greg Peterson, Jianfa Bai, T.G. Nagaraja, Sanjeev Narayanan. 2010. Diagnostic microarray for human and animal bacterial diseases and their virulence and antimicrobial resistance genes. J. Microbiol. Methods. 80: 223-230.

C. M. Smith, X. Liu, L. Wang, X. Liu, M. Chen, S. Starkey, and J Bai. 2010. Aphid Feeding Activates Expression of a Transcriptome of Oxylipin-Based Defense Signals in Wheat Involved in Resistance to Herbivory. J. Chem. Ecol. 36: 260–276.

Bhupinder Bawa, Jianfa Bai, Mike Whitehair, Tanya Purvis, Brad M. DeBey. 2010. Bovine abortion associated with Nocardia farcinica. J Vet Diagn Invest, 22: 108-111.

Yuwen W Zhang, Elizabeth G Davis, Jianfa Bai. 2009. Internal control issues for gene expression studies in equine tissues and cell culture using quantitative RT-PCR. Veterinary Immunology and Immunopathology, 130: 114-119.

Greg Peterson, Jianfa Bai and Sanjeev Narayanan. 2009. A co-printed oligomer to enhance reliability of spotted microarrays. J. Microbiol. Methods. 77: 261-266.

Myron Bruce, Ann Hess, Jianfa Bai, Ramil Mauleon, M. Genaleen Diaz, Nobuko Sugiyama, Alicia Bordeos, Guo-Liang Wang, Hei Leung and Jan E. Leach. 2009. Detection of genomic deletions in rice using oligonucleotide microarrays. BMC Genomics, 10: 129.

Michael Pumphrey, Jianfa Bai, Debbie Laudencia-Chingcuanco, Olin Anderson and Bikram S. Gill. 2009. Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat. Genetics 181: 1147–1157.

Liu, X.L. Bai. J., Zhu, L., Liu, X., Reese J.C., Harris, M., Stuart, J.J., and Chen, M.S. 2007. Gene Expression of Different Wheat Genotypes during Attack by Virulent and Avirulent Hessian Fly (Mayetiola destructor) Larvae. J Chem Ecol 33: 2171–2194.

J. F. Bai, L. A. Pennill, J. C. Ning, S. W. Lee, J. Ramalingam, C. A. Webb, B. Y. Zhao, Q. Sun, J. C. Nelson, J. E. Leach, and S. H. Hulbert. 2002. Diversity in Nucleotide Binding Site-Leucine-Rich Repeat genes in cereals. Genome Research. 12, 1871-1884.