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  1. Science & Research (Biologics)

Bacterial Vaccine Safety: Biomarkers of Virulence and Attenuation in Bordetella Pertussis (Whooping Cough) and Anthrax Bacteria

Principal Investigator: E. Scott Stibitz, PhD
Office / Division / Lab: OVRR / DBPAP / LESTD


General Overview

Our laboratory is studying disease-causing bacteria for which new vaccines and novel therapeutic approaches are being developed.

We are developing new ways to study respiratory infections caused by the bacterium Bordetella pertussis (whooping cough) and the mechanisms by which it causes severe disease. Although a vaccine for this organism exists, the number of whooping cough cases in the US continues to rise, making this research vital to ultimate control.

We also support the development and evaluation of vaccines against Staphylococcus aureus, which causes many infections in the US each year, some of which are extremely serious (e.g., "flesh-eating" bacteria that can cause death in a matter of hours). S. aureus also causes infections of implanted devices such as pacemakers and joint replacements that can be very difficult to treat without removing the device. Currently no vaccine for this disease exists and development of new vaccines against this organism is especially critical due to problems with antibiotic resistance typified by MRSA (methicillin-resistant Staphylococcus aureus), and the new strains of community-acquired MRSA (CA-MRSA).

We also study live biotherapeutic products (i.e., probiotics--live microorganisms that provide health benefits to an individual when consumed in appropriate quantities) to help treat and prevent bacterial infections and other conditions. The investigation of the full potential of these promising products is currently being hindered by difficulties in evaluation of the manufacturing process, purity, safety and quality of these products. We seek to solve this problem by developing better tests for the purity and safety of probiotics, thereby allowing their further testing and development in the clinic.

Diarrheal diseases are also targetted. We are investigating the use of the live attenuated Salmonella strain Ty21a as a platform for eliciting protective immune responses against other serious diseases such as Shigellosis. We are also examining ways to more fully understand some of the as yet uncharacterized genetic bases of attenuation in Ty21a as well as to confer advantageous traits such as acid resistance. We are also seeking to understand why some bacterial pathogens, such as Shigella can cause arthritis and are testing novel approaches to killed Shigella vaccines in order to control this deadly disease.

Another major worldwide health challenge and emerging problem in the US - tuberculosis - is in a class by itself in terms of its difficulty to study, its overall importance, its resistance to date to vaccine interventions, and the threat from antibiotic resistance. Our lab is working to develop and execute new ways to assess the usefullness of vaccine candidates, including the development of animal models and of in vitro tests to measure host responses.

Malaria, while not a bacterial disease, in one which also has a huge worldwide burden. Recent exciting research has brought us much closer to having a useful anti-malaria vaccine. Our lab is studying biomarkers for severe malaria in an effort to both better understand the variables that can lead to tragic outcomes as well as to better assess how current vaccine candidates control disease and infection.


Scientific Overview

Our laboratory takes a genetic approach to studies of bacterial pathogenesis and vaccine development.

In our studies of Bordetella pertussis we introduce specific mutations that affect the expression and regulation of virulence factors, such as toxins and adhesins. We then test the effects of these mutations in a mouse model of respiratory infection that uses bioluminescent B. pertussis to track infection without harming the test animal. This approach has several advantages over older methods that involve sacrificing a group of test animals at each time point, and reduces dramatically the number of animals that must be used.

Our approach to studying Bacillus anthracis pathogenesis has also been largely genetic. We developed and have recently improved, new genetic tools to introduce specific mutations into this organism. These tools, which are now used widely around the world, are significantly easier and more powerful than previous such techniques. They also allow the consecutive deletion or mutation of a unlimited number of genes. This approach has been critical to our studies of anthrax vaccine stability. For example, it has enabled us to create improved strains of the organism used to produce protective antigen (part of the anthrax toxin). These strains lack a number of secreted proteases (currently up to 16 separate deletions). This characteristic increases the production of protective antigen and leads to a purified product that has increased stability.

Our new program in Staphylococcus aureus will follow a similar path, synergizing our genetic capabilities with other OVRR researchers to evaluate new vaccine candidates and identify new candidates for virulence factors and vaccine antigens. We are also examining the utility of a novel approach - bacteriophage therapy - to deal with antibiotic resistant S. aureus.

We are using bacteriophages to develop improved tests for detecting pathogens in probiotic products. We plan to exploit the exquisite specificity of these bacterial viruses to specifically kill product organisms, thereby increasing the sensitivity of detection of extraneous and potentially harmful bacterial pathogens, such as Salmonella and Shigella. Such tests are necessary to ensure the safety of these preparations, a factor that is especially important when tested in clinical trials in very sick or otherwise compromised patients.

Another application of bacteriophages is to actually treat bacterial diseases. Our lab is initiating a project to set up an animal model to examine the usefullness of phage in host decolonization of Staphylococcus aureus. If successful, this could have a major impact on carriage in hospitals and significantly improve the situation there where dangerous, highly antibiotic strains, MRSA, have a high toll.


Publications

  1. Methods Mol Biol 2024;2734:27-45
    Bacteriophage taxonomy: a continually evolving discipline.
    Turner D, Adriaenssens EM, Lehman SM, Moraru C, Kropinski AM
  2. Antimicrob Agents Chemother 2024 Feb 20 [Epub ahead of print]
    Phage-antibiotic synergy against daptomycin-nonsusceptible MRSA in an ex vivo simulated endocardial pharmacokinetic/pharmacodynamic model.
    Kunz Coyne AJ, Bleick C, Stamper K, Kebriaei R, Bayer AS, Lehman SM, Rybak MJ
  3. Microbiol Spectr 2024 Feb 27 [Epub ahead of print]
    Synergistic bactericidal effects of phage-enhanced antibiotic therapy against MRSA biofilms.
    Kunz Coyne AJ, Stamper K, Bleick C, Kebriaei R, Lehman SM, Rybak MJ
  4. AMB Express 2024 Jan 20;14(1):9
    Nanobodies as potential tools for microbiological testing of live biotherapeutic products.
    Dorosky RJ, Schreier JE, Lola SL, Sava RL, Coryell MP, Akue A, KuKuruga M, Carlson PE Jr, Dreher-Lesnick SM, Stibitz S
  5. Antimicrob Agents Chemother 2023 Nov;67(11):e0057823
    Phage-antibiotic combinations against multidrug-resistant Pseudomonas aeruginosa in in vitro static and dynamic biofilm models.
    Holger DJ, El Ghali A, Bhutani N, Lev KL, Stamper K, Kebriaei R, Kunz Coyne AJ, Morrisette T, Shah R, Alexander J, Lehman SM, Rojas LJ, Marshall SH, Bonomo RA, Rybak MJ
  6. Antimicrob Agents Chemother 2023 Nov;67(11):e0072823
    Ciprofloxacin in combination with bacteriophage cocktails against multi-drug resistant Pseudomonas aeruginosa in ex vivo simulated endocardial vegetation models.
    El Ghali A, Stamper K, Kunz Coyne AJ, Holger D, Kebriaei R, Alexander J, Lehman SM, Rybak MJ
  7. Front Microbiol 2023 Oct 31;14:1278791
    Genetic evidence for the interaction between Bacillus anthracis-encoded phage receptors and their cognate phage-encoded receptor binding proteins.
    Forrest S, Ton S, Sholes SL, Harrison S, Plaut RD, Verratti K, Wittekind M, Ettehadieh E, Necciai B, Sozhamannan S, Grady SL
  8. Viruses 2023 Sep 23;15(10):1986
    Characterization of lactobacilli phage endolysins and their functional domains--potential live biotherapeutic testing reagents.
    Dorosky RJ, Lola SL, Brown HA, Schreier JE, Dreher-Lesnick SM, Stibitz S
  9. Microbiol Spectr 2023 Jun 15;11(3):e0491822
    Optimization of phage-antibiotic combinations against Staphylococcus aureus biofilms.
    Kebriaei R, Lehman SM, Shah RM, Stamper KC, Kunz Coyne AJ, Holger D, El Ghali A, Rybak MJ
  10. J Infect Dis 2023 Feb 1;227(3):311-6
    Development of host immune response to bacteriophage in a lung transplant recipient on adjunctive phage therapy for a multidrug resistant pneumonia.
    Dan JM, Lehman SM, Al-Kolla R, Penziner S, Afshar K, Yung G, Golts E, Law N, Logan C, Kovach Z, Mearns G, Schooley RT, Aslam S, Crotty S
  11. Microbiol Resour Announc 2023 Feb;12(2):e0131322
    Draft genome assemblies of phage AP50c-resistant derivatives of Bacillus anthracis Sterne strain 7702 lacking plasmid pXO2.
    Sholes SL, Harrison S, Forrest S, Ton S, Grady SL, Verratti K, Plaut RD, Goodwin BG, Sozhamannan S
  12. Arch Virol 2023 Jan 23;168(2):74
    Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.
    Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM
  13. Viruses 2022 Dec 21;15(1):17
    Phage K gp102 drives temperature-sensitive antibacterial activity on USA300 MRSA.
    Lehman SM, Kongari R, Glass AM, Koert M, Ray MD, Plaut RD, Stibitz S
  14. Comput Struct Biotechnol J 2022 Nov 6;20:6431-42
    Conformational change of the Bordetella response regulator BvgA accompanies its activation of the B. pertussis virulence gene fhaB.
    Kim D, Tracey J, Becerra Flores M, Chaudhry K, Nasim R, Correa-Medina A, Knipling L, Chen Q, Stibitz S, Jenkins LMM, Moon K, Cardozo T, Hinton DM
  15. J Appl Microbiol 2022 Sep;133(3):1636-49
    Bacteriophage-antibiotic combination therapy for multidrug-resistant Pseudomonas aeruginosa: in vitro synergy testing.
    Holger DJ, Lev KL, Kebriaei R, Morrisette T, Shah R, Alexander J, Lehman SM, Rybak MJ
  16. Microbiol Spectr 2022 Apr 27;10(2):e0041122
    Eradication of biofilm-mediated methicillin-resistant Staphylococcus aureus infections in vitro: bacteriophage-antibiotic combination.
    Kebriaei R, Lev KL, Shah RM, Stamper KC, Holger DJ, Morrisette T, Kunz Coyne AJ, Lehman SM, Rybak MJ
  17. J Orthop Res 2022 Feb;40(2):409-19
    CCR2 contributes to host defense against Staphylococcus aureus orthopedic implant-associated infections in mice.
    Wang Y, Dikeman D, Zhang J, Ackerman N, Kim S, Alphonse MP, Ortines RV, Liu H, Joyce D, Dillen CA, Thompson JM, Thomas AA, Plaut RD, Miller LS, Archer NK
  18. Antimicrob Agents Chemother 2022 Jan;66(1):e0162321
    Evaluation of bacteriophage cocktails alone and in combination with daptomycin against daptomycin-nonsusceptible Enterococcus faecium.
    Morrisette T, Lev KL, Canfield GS, Duerkop BA, Kebriaei R, Stamper KC, Holger D, Lehman SM, Willcox S, Arias CA, Rybak MJ
  19. Arch Virol 2021 Nov;166(11):3239-44
    Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021.
    Krupovic M, Turner D, Morozova V, Dyall-Smith M, Oksanen HM, Edwards R, Dutilh BE, Lehman SM, Reyes A, Baquero DP, Sullivan MB, Uchiyama J, Nakavuma J, Barylski J, Young MJ, Du S, Alfenas-Zerbini P, Kushkina A, Kropinski AM, Kurtböke I, Brister JR, Lood C, Sarkar BL, Yigang T, Liu Y, Huang L, Wittmann J, Chanishvili N, van Zyl LJ, Rumnieks J, Mochizuki T, Jalasvuori M, Aziz RK, Łobocka M, Stedman KM, Shkoporov AN, Gillis A, Peng X, Enault F, Knezevic P, Lavigne R, Rhee SK, Cvirkaite-Krupovic V, Moraru C, Moreno Switt AI, Poranen MM, Millard A, Prangishvili D, Adriaenssens EM
  20. Microbiol Spectr 2021 Oct;9(2):e0004421
    Identification of BvgA-dependent and BvgA-independent small RNAs (sRNAs) in Bordetella pertussis using the prokaryotic sRNA prediction toolkit ANNOgesic.
    Moon K, Sim M, Tai CH, Yoo K, Merzbacher C, Yu SH, Kim DD, Lee J, Förstner KU, Chen Q, Stibitz S, Knipling LG, Hinton DM
  21. mSphere 2021 Aug;6(4):e0065021
    RNase III and RNase E influence posttranscriptional regulatory networks involved in virulence factor production, metabolism, and regulatory RNA processing in Bordetella pertussis.
    Ifill G, Blimkie T, Lee AH, Mackie GA, Chen Q, Stibitz S, Hancock REW, Fernandez RC
  22. Sci Rep 2021 Apr 30;11(1):9373
    Four single-basepair mutations in the ptx promoter of Bordetella bronchiseptica are sufficient to activate the expression of pertussis toxin.
    Chen Q, Gray MC, Hewlett E, Stibitz S
  23. Antimicrob Agents Chemother 2020 Sep;64(9):e00993-20
    Bacteriophage-antibiotic combinations for enterococcus faecium with varying bacteriophage and daptomycin susceptibilities.
    Morrisette T, Lev KL, Kebriaei R, Abdul-Mutakabbir J, Stamper KC, Morales S, Lehman SM, Canfield GS, Duerkop BA, Arias CA, Rybak MJ
  24. Biologicals 2020 Jul;66:53-61
    Human challenge trial workshop: focus on quality requirements for challenge agents, Langen, Germany, October 22, 2019.
    Bekeredjian-Ding I, Van Molle W, Baay M, Neels P, Conrad C, van Diepen A, Fortune S, Goetz K, Gorringe A, Hoft D, Johnson RA, Kremsner P, Krut O, Levy Y, Metzger W, Oeppling V, Stibitz S, Talaat KR, Thomas S, Wildfire A, Yakubu BN
  25. Antimicrob Agents Chemother 2020 Jul;64(7):e00461-20
    Bacteriophage-antibiotic combination strategy: an alternative against methicillin-resistant phenotypes of Staphylococcus aureus.
    Kebriaei R, Lev K, Morrisette T, Stamper K, Abdul-Mutakabbir JC, Lehman S, Morales S, Rybak MJ
  26. PLoS Pathog 2020 May 13;16(5):e1008500
    Multiple weak interactions between BvgA~P and ptx promoter DNA strongly activate transcription of pertussis toxin genes in Bordetella pertussis.
    Chen Q, Boucher PE, Stibitz S
  27. Materials 2019 Dec 5;12(24):4052
    Complete killing of agar lawn biofilms by systematic spacing of antibiotic-loaded calcium sulfate beads.
    Dusane DH, Brooks JR, Sindeldecker D, Peters CW, Li A, Farrar NR, Diamond SM, Knecht CS, Plaut RD, Delury C, Aiken SS, Laycock PA, Sullivan A, Granger JF, Stoodley P
  28. Vaccine 2019 Jul 18;37(31):4256-61
    Use of controlled human infection models (CHIMs) to support vaccine development: US regulatory considerations.
    Ramanathan R, Stibitz S, Pratt D, Roberts J
  29. mSphere 2019 Jun;4(3):e00694-18
    In vivo gene essentiality and metabolism in bordetella pertussis.
    Gonyar LA, Gelbach PE, McDuffie DG, Koeppel AF, Chen Q, Lee G, Temple LM, Stibitz S, Hewlett EL, Papin JA, Damron FH, Eby JC
  30. Curr Opin Microbiol 2019 Feb;47:74-81
    The BvgASR virulence regulon of Bordetella pertussis.
    Chen Q, Stibitz S
  31. MBio 2019 Jan 8;10(1):10:e02491-18
    Corynebacterium pseudodiphtheriticum exploits Staphylococcus aureus virulence components in a novel polymicrobial defense strategy.
    Hardy BL, Dickey SW, Plaut RD, Riggins DP, Stibitz S, Otto M, Merrell DS
  32. Front Immunol 2018 Nov 9;9:2612
    TACI contributes to Plasmodium yoelii host resistance by controlling T follicular helper cell response and germinal center formation.
    Parra M, Yang J, Weitner M, Derrick S, Yang A, Schmidt T, Singh B, Moreno A, Akkoyunlu M
  33. J Bacteriol 2018 Oct;200(20):e00175-18
    A novel Bvg-repressed promoter causes vrg-like transcription of fim3 but does not result in the production of serotype 3 Fimbriae in the Bvg(-) mode Bordetella pertussis.
    Chen Q, Lee G, Craig C, Ng V, Carlson PE Jr, Hinton DM, Stibitz S
  34. Emerg Infect Dis 2018 Apr;24(4):691-9
    Avirulent Bacillus anthracis strain with molecular assay targets as surrogate for irradiation-inactivated virulent spores.
    Plaut RD, Staab AB, Munson MA, Gebhardt JS, Klimko CP, Quirk AV, Cote CK, Buhr TL, Rossmaier RD, Bernhards RC, Love CE, Berk KL, Abshire TG, Rozak DA, Beck LC, Stibitz S, Goodwin BG, Smith MA, Sozhamannan S
  35. Clin Vaccine Immunol 2017 Dec 5;24(12):e00181-17
    Stable chromosomal expression of Shigella flexneri 2a and 3a O-antigens in the live Salmonella oral vaccine vector Ty21a.
    Dharmasena MN, Osorio M, Takeda K, Stibitz S, Kopecko DJ
  36. J Bacteriol 2017 Nov;199(22):e00475-17
    Activation of Bvg-repressed genes in Bordetella pertussis by RisA requires cross-talk from a non co-operonic histidine kinase RisK.
    Chen Q, Ng V, Warfel JM, Merkel TJ, Stibitz S
  37. J Infect Dis 2017 Nov 15;216(10):1264-72
    A novel gametocyte biomarker for superior molecular detection of the Plasmodium falciparum infectious reservoirs.
    Essuman E, Grabias B, Verma N, Chorazeczewski JK, Tripathi AK, Mlambo G, Addison EA, Amoah AGB, Quakyi I, Oakley MS, Kumar S
  38. Cell Host Microbe 2017 Nov 8;22(5):653-66
    Staphylococcus aureus epicutaneous exposure drives skin inflammation via IL-36-mediated T cell responses.
    Liu H, Archer NK, Dillen CA, Wang Y, Ashbaugh AG, Ortines RV, Kao T, Lee SK, Cai SS, Miller RJ, Marchitto MC, Zhang E, Riggins DP, Plaut RD, Stibitz S, Geha RS, Miller LS
  39. Genome Announc 2017 Nov 9;5(45):e01231-17
    Whole-genome sequences of variants of Bacillus anthracis Sterne and their toxin gene deletion mutants.
    Staab A, Plaut RD, Pratt C, Lovett SP, Wiley MR, Biggs TD, Bernhards RC, Beck LC, Palacios GF, Stibitz S, Jones KL, Goodwin BG, Smith MA, Sozhamannan S
  40. MBio 2017 Oct 10;8(5):e01526-17
    The BvgAS regulon of Bordetella pertussis.
    Moon K, Bonocora RP, Kim DD, Chen Q, Wade JT, Stibitz S, Hinton DM
  41. Microbiol Spectr 2017 Sep;5(5):BAD-0017-2017
    U.S. regulatory considerations for development of live biotherapeutic products as drugs.
    Dreher-Lesnick SM, Stibitz S, Carlson PE Jr
  42. NPJ Vaccines 2017 Jun 15;2:17
    Protection against inhalation anthrax by immunization with Salmonella enterica serovar Typhi Ty21a stably producing protective antigen of Bacillus anthracis.
    Sim BKL, Li ML, Osorio M, Wu Y, Wai TT, Peterson JW, James ER, Chakravarty S, Gao LX, Xu R, Natasha KC, Stafford RE, Lawrence WS, Yeager LA, Peel JE, Sivasubramani SK, Chopra AK, Filippova S, Hoffman SL
  43. Proc Natl Acad Sci U S A 2017 Feb 21;114(8):E1519-27
    Bordetella PlrSR regulatory system controls BvgAS activity and virulence in the lower respiratory tract.
    Bone MA, Wilk AJ, Perault AI, Marlatt SA, Scheller EV, Anthouard R, Chen Q, Stibitz S, Cotter PA, Julio SM
  44. Clin Vaccine Immunol 2017 Jan 5;24(1):e00509-16
    Trained immunity and susceptibility to HIV.
    Derrick SC
  45. PLoS One 2016 Dec 2;11(12):e0166814
    Molecular markers of radiation induced attenuation in intrahepatic Plasmodium falciparum parasites.
    Oakley MS, Verma N, Zheng H, Anantharaman V, Takeda K, Gao Y, Myers TG, Pham PT, Mahajan B, Kumar N, Sangweme D, Tripathi AK, Mlambo G, Aravind L, Kumar S
  46. Pathog Dis 2016 Nov;74(8):ftw098
    Stable expression of Shigella dysenteriae serotype 1 O-antigen genes integrated into the chromosome of live Salmonella oral vaccine vector Ty21a.
    Dharmasena MN, Osorio M, Filipova S, Marsh C, Stibitz S, Kopecko DJ
  47. PLoS One 2016 Sep 27;11(9):e0163511
    Development of an Acid-Resistant Salmonella Typhi Ty21a Attenuated Vector For Improved Oral Vaccine Delivery.
    Dharmasena MN, Feuille CM, Starke CE, Bhagwat AA, Stibitz S, Kopecko DJ
  48. J Microbiol Methods 2016 Dec;131:7-9
    A simplified mycobacterial growth inhibition assay (MGIA) using direct infection of mouse splenocytes and the MGIT system.
    Yang AL, Schmidt TE, Stibitz S, Derrick SC, Morris SL, Parra M
  49. Sci Rep 2016 Sep 13;6:32774
    The multifaceted RisA regulon of Bordetella pertussis.
    Coutte L, Huot L, Antoine R, Slupek S, Merkel TJ, Chen Q, Stibitz S, Hot D, Locht C
  50. Clin Vaccine Immunol 2016 Jul 5;23(7):638-47
    Induction of unconventional T cells by a mutant BCG strain formulated in cationic liposomes correlates with protection against M. tuberculosis infections of immunocompromised mice.
    Derrick SC, Yabe I, Morris S, Cowley S
  51. Viruses 2015 Dec 16;7(12):6675-88
    Development of phage lysin LysA2 for use in improved purity assays for live biotherapeutic products.
    Dreher-Lesnick SM, Schreier JE, Stibitz S
  52. PLoS One 2015 Dec 1;10(12):e0142758
    Improvements to a markerless allelic exchange system for Bacillus anthracis.
    Plaut RD, Stibitz S
  53. PLoS One 2015 Oct 27;10(10):e0141141
    Co-expression of Interleukin-15 enhances the protective immune responses induced by immunization with a murine malaria MVA-based vaccine encoding the circumsporozoite protein.
    Parra M, Liu X, Derrick SC, Yang A, Molina-Cruz A, Barillas-Mury C, McGavern DB, Zheng H, Thao Pham P, Sedegah M, Belmonte A, Litilit DD, Waldmann TA, Kumar S, Morris SL, Perera LP
  54. Proc Natl Acad Sci U S A 2015 Feb 10;112(6):E526-35
    Bordetella pertussis fim3 gene regulation by BvgA: Phosphorylation controls the formation of inactive vs. active transcription complexes.
    Boulanger A, Moon K, Decker KB, Chen Q, Knipling L, Stibitz S, Hinton DM
  55. Vaccine 2015 Jan 1;33(1):126-32
    Effect of cationic liposomes on BCG trafficking and vaccine-induced immune responses following a subcutaneous immunization in mice.
    Derrick SC, Yang A, Parra M, Kolibab K, Morris SL
 
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