Jianfa Bai

baiProfessor

Director of Molecular Research and Development
Kansas State Veterinary Diagnostic Laboratory

Ph.D., Kansas State University
M.S., University of the Philippines at Los Baños
B.S., Northwest A&F University, Yangling, China

157 CVM East/KSU-IC, Research Park
Phone: 785-532-4332
Fax: 785-532-3909
Email: jbai@vet.ksu.edu

Research and Service

My research and service interests are to develop, validate and improve molecular diagnostic methods for the identification, quantification and characterization of animal, zoonotic and foodborne pathogens using PCR, sequencing and other technologies.

In recent years we have developed or improved a number of molecular diagnostic assays or DNA sequencing procedures. Most of which are aimed to increase diagnostic sensitivity and specificity, and reduce cost. We have recently emphasized on building syndromic diagnostic panel testing including respiratory disease, enteric diarrhea, and reproductive disorder panels for different animal species. We have made the effort to include an internal control for all newly developed assays in order to monitor nucleic acid extractions and potential PCR inhibitions, thus to reduce false negative detections.

We are also interested in exploring new molecular diagnostic technologies that can be potentially used to increase multiplexing and throughput capabilities, and to lower the cost and to reduce turnaround time for diagnostic services.

Selected Publications

(*Corresponding author)

PubMed search for Dr. Bai

Wang Y, Porter EP, Lu N, Zhu C, Noll LW, Hamill V, Brown SJ, Palinski RM, Bai J*. Whole genome classification of Rotavirus C and genetic diversity of porcine strains in the United States. J. General Virology. 2021;102:001598, DOI 10.1099/jgv.0.001598. PMID: 33950806.

Capps KM, Ludwig JB, Shridhar PB, Shi X, Roberts E, DebRoy C, Cernicchiaro N, Phebus RK, Bai J*, Nagaraja TG*. Identification, Shiga toxin subtypes and prevalence of minor serogroups of Shiga toxin‑producing Escherichia coli in feedlot cattle feces. Scientific Reports 2021, 11:8601, https://doi.org/10.1038/s41598-021-87544-w. PMID: 33883564.

Yuan F, Feng Y, Bai J, Liu X, Arruda B, Anbalagan S, Peddireddi L. Genetic diversity and prevalence of Atypical Porcine Pestivirus in the Midwest of US swine herds during 2016-2018. Transbound Emerg Dis. 2021 Feb 23. doi: 10.1111/tbed.14046. Epub ahead of print. PMID: 33621429. PMID: 33621429.

Das A, Wang Y, Babiuk S, Bai J, Dodd K, Jia W. Development of multiplex real-time PCR assays for differential detection of capripoxvirus, parapoxvirus, and foot-and-mouth disease virus. Transbound Emerg Dis. 2021 Apr 10. doi: 10.1111/tbed.14099. Epub ahead of print. PMID: 33837669.

Li Y, Sthal C, Bai J, Liu X, Anderson G, Fang Y. Development of a real-time RT-qPCR assay for the detection of porcine respirovirus 1. J Virol Methods. 2021 Mar;289:114040. https://doi.org/10.1016/j.jviromet.2020.114040. PMID: 33309757.

Ali Hroobi, Gunavanthi D. Boorgula, David Gordon, Jianfa Bai, Doug Goodin, Gary Anderson, Savannah Wilson, Alex Staggs, Ram K. Raghavan. Diversity and seasonality of host-seeking ticks in a periurban environment in the Central Midwest (USA). PLOS ONE 2021. https://doi.org/10.1371/journal.pone.0250272. PMID: 33891636.

Wang Y, Noll L, Porter E, Stoy C, Dong J, Anderson J, Fu J, Pogranichniy R, Woodworth J, Peddireddi L, Bai J*. Development of a differential multiplex real-time PCR assay for porcine circovirus type 2 (PCV2) genotypes PCV2a, PCV2b and PCV2d. J Virol Methods. 2020 Dec;286:113971. doi: 10.1016/j.jviromet.2020.113971. PMID: 32926893

Wang Y, Yim-im W, Porter E, Lu N, Anderson J, Noll L, Fang Y, Zhang J, Bai J*. Development of a bead-based assay for detection and differentiation of field strains and four vaccine strains of type 2 porcine reproductive and respiratory syndrome virus (PRRSV-2) in the USA. Transboundary and Emerging Diseases 2020. Accepted. doi:10.1111/tbed.13808. PMID: 32816334.

Wang Y, Xu L, Noll L, Stoy C, Porter E, Fu J, Feng Y, Peddireddi L, Liu X, Dodd KA, Jia W*, Bai J*. Development of a real-time PCR assay for detection of African swine fever virus with an endogenous internal control. Transbound Emerg Dis. 2020 Apr 19;. doi: 10.1111/tbed.13582. PMID: 32306531.

Ludwig JB, Shi X, Shridhar PB, Roberts EL, DebRoy C, Phebus RK, Bai J*, Nagaraja TG*. Multiplex PCR Assays for the Detection of One Hundred and Thirty Seven Serogroups of Shiga Toxin-Producing Escherichia coli Associated with Cattle. Front. Cell. Infect. Microbiol. 2020. 10:378. doi: 10.3389/fcimb.2020.00378. PMID: 32850480

Remfry SE, Amachawadi RG, Shi X, Bai J, Tokach MD, Dritz S, Goodband RD, DeRouchey JM, Woodworth JC, Nagaraja TG. Shiga Toxin-Producing Escherichiacoli in Feces of Finisher Pigs: Isolation, Identification and Public Health Implications of Major and Minor Serogroups. J Food Prot. 2020 Oct 1. doi: 10.4315/JFP-20-329. Online ahead of print. PMID: 33003199.

Remfry SE, Amachawadi RG, Shi X, Bai J, Woodworth JC, Tokach MD, Dritz SS, Goodband RD, DeRouchey JM, Nagaraja TG. Polymerase Chain Reaction-Based Prevalence of Serogroups of Escherichia coli Known to Carry Shiga Toxin Genes in Feces of Finisher Pigs. Foodborne Pathog Dis. 2020 Dec;17(12):782-791. doi: 10.1089/fpd.2020.2814. Epub 2020 Aug 21. PMID: 32833570.

Magossi G, Lambertini E, Noll L, Bai J, Jones C, Nagaraja TG, Phebus R, Woodworth J, Trinetta V. Potential risk-factors affecting Salmonella spp. and E. coli occurrence and distribution in Midwestern United States swine feed mills. J Appl Microbiol 2020 Dec;129(6):1744-1750. doi: 10.1111/jam.14758. Epub 2020 Jul 10. PMID: 32648660.

Zheng W, Wang B, Si M, Zou H, Song R, Gu J, Yuan Y, Liu X, Zhu G, Bai J, Bian J, Liu Z. Author Correction: Zearalenone altered the cytoskeletal structure via ER stress- autophagy- oxidative stress pathway in mouse TM4 Sertoli cells. Sci Rep. 2020 Jun 25;10(1):10658. doi: 10.1038/s41598-020-67552-y. PubMed PMID: 32581243; PubMed Central PMCID: PMC7314833.

Lerner AB, Cochrane RA, Gebhardt JT, Dritz SS, Jones CK, DeRouchey JM, Tokach MD, Goodband RD, Bai J, Porter E, Anderson J, Gauger PC, Magstadt DR, Zhang J, Bass B, Karnezos T, de Rodas B, Woodworth JC. Effects of medium chain fatty acids as a mitigation or prevention strategy against porcine epidemic diarrhea virus in swine feed. J Anim Sci. 2020 Jun 1;98(6). doi: 10.1093/jas/skaa159. PubMed PMID: 32447386; PMCID: PMC7281870.

Noll LW*, Stoy CPA, Wang Y, Porter EG, Lu N, Liu X, Burkland A, Peddireddi L, Hanzlicek G, Henningson J, Chengappa MM, Bai J*. Development of a nested PCR assay for detection of Streptococcus equi subspecies equi in clinical equine specimens and comparison with a qPCR assay. J Microbiol Methods. 2020 Mar 9:105887. doi: 10.1016/j.mimet.2020.105887. PMID: 32165161.

Liu X, Noll L, Shi X, Porter E, Wang Y, Stoy C, Lu N, Nagaraja TG, Anderson G, Bai J *. Single cell-based digital PCR detection and association of Shiga toxin-producing Escherichia coli serogroups and major virulence genes. J. Clinical Microbiology, 2020. DOI: 10.1128/JCM.01684-19. PMID: 31896667.

Toohey-Kurth K, Reising MM, Tallmadge RL, Goodman LB, Bai J, Bolin SR, Pedersen JC, Bounpheng MA, Pogranichniy RM, Christopher-Hennings J, Killian ML, Mulrooney DM, Maes R, Singh S, Crossley BM. Suggested guidelines for validation of real-time PCR assays in veterinary diagnostic laboratories. J Vet Diagn Invest. 2020 Sep 28;:1040638720960829. doi: 10.1177/1040638720960829. [Epub ahead of print] PubMed PMID: 32988335.

Crossley BM, Bai J, Glaser A, Maes R, Porter E, Killian ML, Clement T, Toohey-Kurth K. Guidelines for Sanger sequencing and molecular assay monitoring. J Vet Diagn Invest. 2020 Nov;32(6):767-775. doi: 10.1177/1040638720905833. PMID: 32070230

Capps KM, Amachawadi RG, Menegat MB, Woodworth JC, Perryman K, Tokach MD, Dritz SS, DeRouchey JM, Goodband RD, Bai J, Apley MD, Lubbers BV, Nagaraja TG. Impact of added copper, alone or in combination with chlortetracycline, on growth performance and antimicrobial resistance of fecal enterococci of weaned piglets. J Anim Sci. 2020 Mar 1;98(3). DOI: 10.1093/jas/skaa003. PubMed PMID: 31950170; PubMed Central PMCID: PMC7072034.

Cochrane RA, Dritz SS, Woodworth JC, Stark CR, Saensukjaroenphon M, Gebhardt JT, Bai J, Hesse RA, Poulsen EG, Chen Q, Gauger PC, Derscheid RJ, Zhang J, Tokach MD, Main RG, Jones CK. Assessing the effects of medium-chain fatty acids and fat sources on PEDV infectivity. Transl Anim Sci. 2020 Apr;4(2):txz179. eCollection 2020 Apr. PubMed PMID: 32289114; PubMed Central PMCID: PMC7107285. https://doi.org/10.1093/tas/txz179.

Wang Y, Noll L, Lu N, Porter E, Stoy C, Zheng W, Liu X, Peddireddi L, Niederwerder M, Bai J *. Genetic Diversity and Prevalence of Porcine Circovirus Type 3 (PCV3) and Type 2 (PCV2) in the Midwest of the USA during 2016-2018. Transbound Emerg Dis. 2020. DOI: 10.1111/tbed.13467. PMID: 31886622.

Yan L, Toohey-Kurth KL, Crossley BM, Bai J, Glaser AL, Tallmadge RL, Goodman LB. Inhibition monitoring in veterinary molecular testing. J Vet Diagn Invest. 2020, doi: 10.1177/1040638719889315. PMID: 31735123.

Wang Y, Das A, Zheng W, Porter E, Xu L, Noll L, Liu X, Dodd K, Jia W*, Bai J*. Development and evaluation of multiplex real time RT-PCR assays for detection and differentiation of foot-and-mouth disease virus and Seneca Valley virus-1. Transbound Emerg Dis. 2020 Mar;67(2):604-616. doi: 10.1111/tbed.13373. Epub 2019 Oct 22. PMID: 31550077.

Zhang H, Wang Y, Porter E, Lu N, Li Y, Yuan F, Lohman M, Noll L, Zheng W, Stoy C, Lang Y, Huber VC, Ma W, Peddireddi L, Fang Y, Shi J, Anderson G, Liu X, Bai J*. Development of a multiplex real-time RT-PCR assay for simultaneous detection and differentiation of Influenza A, B, C and D viruses. Diagn Microbiol Infect Dis. 2019 Sep;95(1):59-66. doi: https://doi.org/10.1016/j.diagmicrobio.2019.04.011. Epub 2019 Apr 29. PMID: 31130238.

Wang Y, Feng Y, Zheng W, Noll L, Porter E, Potter M, Cino G, Peddireddi L, Liu X, Anderson G, Bai J*. A multiplex real-time PCR assay for the detection and differentiation of the newly emerged porcine circovirus type 3 and continuously evolving type 2 strains in the United States. Journal of Virological Methods. 2019, 269, 7-12. https://doi.org/10.1016/j.jviromet.2019.03.011.

Zheng W, Porter E, Noll L, Stoy C, Lu N, Wang Y, Liu X, Purvis T, Peddireddi L, Lubbers B, Hanzlicek G, Henningson J, Liu Z, Bai J*. A multiplex real-time PCR assay for the detection and differentiation of five bovine pinkeye pathogens. J Microbiol Methods. 2019, 160, 87-92. https://doi.org/10.1016/j.mimet.2019.03.024.

Zheng W.; Fan W.; Feng N.; Lu N.; Zou H.; Gu J.; Yuan Y.; Liu X.; Bai J.; Bian J.; Liu Z. The Role of miRNAs in Zearalenone-Promotion of TM3 Cell Proliferation. Int. J. Environ. Res. Public Health 2019, 16, 1517. https://doi.org/10.3390/ijerph16091517.

Zheng W, Feng N, Wang Y, Noll L, Xu S, Liu X, Lu N, Zou H, Gu J, Yuan Y, Liu X, Zhu G, Bian J, Bai J, Liu Z. Effects of zearalenone and its derivatives on the synthesis and secretion of mammalian sex steroid hormones: A review. Food Chem Toxicol. 2019, 126:262-276. doi: 10.1016/j.fct.2019.02.031. Epub 2019 Feb 27. Review. PMID: 30825585.

Neill JD, Workman AM, Hesse R, Bai J, Porter EP, Meadors B, Anderson J, Bayles DO, Falkenberg SM. Identification of BVDV2b and 2c subgenotypes in the United States: Genetic and antigenic characterization. Virology 528, 2019, 19-29. https://doi.org/10.1016/j.virol.2018.12.002.

Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Nagaraja TG. DNA Microarray-Based Genomic Characterization of the Pathotypes of Escherichia coli O26, O45, O103, O111, and O145 Isolated from Feces of Feedlot Cattle. J Food Prot 2019. 82(3):395-404. https://doi.org/10.4315/0362-028X.JFP-18-393.

Shridhar PB, Worley JN, Gao X, Yang X, Noll LW, Shi X, Bai J, Meng J, Nagaraja TG. Analysis of virulence potential of Escherichia coli O145 isolated from cattle feces and hide samples based on whole genome sequencing. PLoS One. 2019, e0225057. doi: 10.1371/journal.pone.0225057. eCollection 2019. PMID: 31774847. PMID: 31774847.

Magossi G, Bai J, Cernicchiaro N, Jones C, Porter E, Trinetta V. Seasonal Presence of Salmonella spp., Salmonella Typhimurium and Its Monophasic Variant Serotype I 4,[5],12:i:-, in Selected United States Swine Feed Mills. Foodborne Pathog Dis. 2019. 16(4), 276-281. https://doi.org/10.1089/fpd.2018.2504.

Zhang H, Porter EP, Lohman M, Lu N, Peddireddi L, Hanzlicek G, Marthaler D, Liu X*, and Bai J*. Influenza C Virus in Cattle with Respiratory Disease, United States, 2016–2018. 2018. Emerg Infect Dis. 24(10), 1926-1929. https://dx.doi.org/10.3201/eid2410.180589.

Zhang H, Porter EP, Lohman M, Lu N, Peddireddi L, Liu X*, and Bai J*. Complete genome sequence of an influenza C virus strain identified from a sick calf in the United States. Microbiol Resour Announc. 7(1): e00828-18. https://doi.org/10.1128/MRA.00828-18.

Ekong P, Sanderson M, Shridhar P, Cernicchiaro N, Renter D, Bello N, Bai J, and Nagaraja TG. Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces. Preventive Veterinary Medicine. 2018. 161:90-99. https://doi.org/10.1016/j.prevetmed.2018.10.012.

Gebhardt JT, Cochrane RC, Woodworth JC, Jones CK, Niederwerder MC, Muckey MB, Stark CR, Tokach MD, DeRouchey JM, Goodband RD, Bai J, Gauger PC, Chen Q, Zhang J, Main RG, and Dritz SS. Evaluation of the effects of flushing feed manufacturing equipment with chemically treated rice hulls on porcine epidemic diarrhea virus (PEDV) cross contamination during feed manufacturing. J Animal Sci. 2018. sky295, https://doi.org/10.1093/jas/sky295.

Noll LW, Chall R., Shridhar PB, Liu X, Bai J*, Delannoy S, Fach P, and Nagaraja TG*. Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces. J. Food Protection, 81 (7), 2018, 1157–1164. https://doi.org/10.4315/0362-028X.JFP-18-049 .

Bai J*, Trinetta V*, Shi X, Noll LW, Magossi GB, Zheng W, Porter EP, Cernicchiaro N, Renter DG, and Nagaraja TG. A Multiplex Real-Time PCR Assay, Based on invA and pagC Genes, for the Detection and Quantification of Salmonella enterica from Cattle Lymph Nodes. J Microbiol Methods. 2018, 148, 110-116. https://doi.org/10.1016/j.mimet.2018.03.019.

Bai J*, Trinetta V, Shi X, Noll LW, Magossi G, Zheng W, Porter EP, Cernicchiaro N, Renter DG, and Nagaraja TG. Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes. Data in Brief. 2018. https://doi.org/10.1016/j.dib.2018.04.051.

Shepherd F, Herrera-Ibata D, Porter EP, Homwong N, Hesse R, Bai J, and Marthaler D. Whole genome classification and phylogenetic analyses of Rotavirus B strains from the United States. Pathogens. 2018. 7, 44. https://doi:10.3390/pathogens7020044.

Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, and Nagaraja TG. DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces. PLoS One. 2018;13(4):e0196490. https://doi.org/10.1371/journal.pone.0196490.

Noll LW, Worley JN, Yang X, Shridhar PB, Ludwig JB, Shi X, Bai J, Caragea D, Meng J, and Nagaraja TG. Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin. PLoS ONE 2018; 13(2): e0191362. https://doi.org/10.1371/journal.pone.0191362.

Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Elkins CA, Strockbine NA, and Nagaraja TG. Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated from Cattle Feces Using Whole Genome Sequencing. Front. Microbiol. 2018. 9:341. https://doi.org/10.3389/fmicb.2018.00341.

Zheng W, Wang B, Wang L, Shan Y, Zou H, Song R, Wang T, Gu J, Yuan Y, Liu X, Zhu G, Bai J, Liu Z, and Bian J. ROS mediated cell cycle arrest and apoptosis induced by zearalenone in sertoli cells via ER stress- ATP- AMPK pathway. Toxins. 2018. 10, 24; https://doi.org/10.3390/toxins10010024.

Zheng W, Wang B, Li X, Wang T, Zou H, Gu J, Yuan Y, Liu X, Bai J, Bian J, and Liu Z. Zearalenone Promotes Cell Proliferation or Causes Cell Death? Toxins 2018, 10, 184; https://doi.org/10.3390/toxins10050184.

Zheng W, Wang B, Si M, Zou H, Song R, Gu J, Yuan Y, Liu X, Zhu G, Bai J, Bian J, and Liu Z. Zearalenone altered the cytoskeletal structure via ER stress- autophagy- oxidative stress pathway in mouse TM4 Sertoli cells. Sci Rep. 2018, 8(1): 3320. https://doi.org/10.1038/s41598-018-21567-8.

Peddireddi L, Foster KA, Poulsen EG, An B, Hoang QH, O’Connell C, Anderson JW, Thomson DU, Hanzlicek GA, Bai J, Hesse RA, Oberst RD, and Anderson GA. Molecular detection/characterization of transient bovine viral diarrhea virus (BVDV) infections in cattle commingled with ten BVDV persistently infected cattle. J Vet Diag Invest. 2018. https://doi.org/10.1177/1040638717753962.

Yang Y, Wang Y, Poulsen EP, Ransburgh R, Liu X, An B, Lu N, Anderson G, Wang C*, and Bai J*. Genotyping Brucella canis isolates using a highly discriminatory multilocus variable-number tandem-repeat analysis (MLVA) assay. Scientific Reports. Sci Rep. 2017, 7(1):1067. https://doi.org/10.1038/s41598-017-01114-7.

Schumacher LL, Huss AR, Cochrane RA, Stark CR, Woodworth JC, Bai J, Poulsen EG, Chen Q, Main RG, Zhang J, Gauger PC, Ramirez A, Derscheid RJ, Magstadt DM, Dritz SS, and Jones CK. Characterizing the rapid spread of porcine epidemic diarrhea virus (PEDV) through an animal food manufacturing facility. PLOS ONE, 2017, https://doi.org/10.1371/journal.pone.0187309.

Noll LW, Worley JN, Yang X, Shridhar PB, Bai J, Meng J, Caragea D, and Nagaraja TG. Draft Genome Sequences of Enterohemorrhagic Escherichia coli O103:H2 Strains Isolated from Feces of Feedlot Cattle. Genome Announc 2017, 5:e00094-17. doi: 10.1128/genomeA.00387-17.

Noll LW, Worley JN, Yang X, Shridhar PB, Bai J, Meng J, Caragea D, and Nagaraja TG. 2017. Draft genome sequences of enteropathogenic Escherichia coli O103 strains isolated from feces of feedlot cattle. Genome Announc 5:e00387-17. doi: 10.1128/genomeA.00387-17.

Shridhar P, Patel I, Gangiredla J, Mammel M, Noll L, Shi X, Bai J, Elkins C, Strockbine N, and Nagaraja T. Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin. Genome Announc. 2017, 17;5(33). pii: e00630-17. doi: 10.1128/genomeA.00630-17.

Shridhar P, Siepker C, Noll L, Shi X, Nagaraja TG*, and Bai J*. Shiga Toxin Subtypes of Non-O157 Escherichia coli Serogroups Isolated from Cattle Feces. Front. Cell. Infect. Microbiol. 2017. 7:121. doi: 10.3389/fcimb.2017.00121.

Shridhar PB, Noll LW, Cull CA, Shi X, Cernicchiaro N, Renter DG, Bai J, and Nagaraja TG. Spiral Plating Method to Quantify the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces. J. Food Protection: 2017, 80, 848-856. DOI: 10.4315/0362-028X.JFP-16-360.

Ekong PS, Sanderson MW, Bello NM, Noll LW, Cernicchiaro N, Renter DG, Bai J, and Nagaraja TG. Bayesian estimation of true prevalence, sensitivity and specificity of three diagnostic tests for detection of Escherichia coli O157 in cattle feces. Preventive Veterinary Medicine. 2017, 148, 21-27.

Fowler VL, Ransburgh RH, Poulsen EG, Wadsworth J, King DP, Mioulet V, Knowles NJ, Williamson S, Liu X, Anderson GA, Fang Y, and Bai J*. Development of a novel real-time RT-PCR assay to detect Seneca Valley virus-1 associated with emerging cases of vesicular disease in pigs. J Virol Methods. 2017. 239, 34–37. doi:10.1016/j.jviromet.2016.10.012.