Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Challenges and opportunities in mRNA vaccine development against bacteria

Nature Microbiology volume 10, pages 1816–1828 (2025)Cite this article

Subjects

Abstract

The global surge in antimicrobial resistance presents a critical threat to public health, emphasizing the urgent need for the development of new and more effective bacterial vaccines. Since the success of mRNA vaccines during the COVID-19 pandemic, this vaccine strategy has rapidly advanced, with most efforts focused on cancer immunotherapy and targeting viral pathogens. Recently, mRNA vaccines have entered the early phases of clinical development for bacterial diseases. However, bacteria present greater biological complexity compared with viruses, posing additional challenges for vaccine design, such as antigen selection, immune response and mRNA construct design. Here, we discuss critical aspects in the development of bacterial mRNA vaccines, from antigen selection to construct design. We also highlight the current preclinical landscape and discuss remaining translational challenges and future potential for mRNA vaccines against bacterial infections.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Antigen discovery methods in bacterial vaccine development.
Fig. 2: Inclusion of different signalling peptides and trafficking motifs directs intracellular processing and localization of the mRNA-encoded antigen after ribosomal translation.
Fig. 3: Optimization of mRNA construct design to enhance protein expression or to direct expressed antigens towards specific antigen presentation pathways.

Similar content being viewed by others

References

  1. Patel, J. et al. Measuring the global response to antimicrobial resistance, 2020–21: a systematic governance analysis of 114 countries. Lancet Infect. Dis. 23, 706–718 (2023).

    Article  PubMed  Google Scholar 

  2. Urgent call for better use of existing vaccines and development of new vaccines to tackle AMR. World Health Organization https://www.who.int/news/item/12-07-2022-urgent-call-for-better-use-of-existing-vaccines-and-development-of-new-vaccines-to-tackle-amr (2022).

  3. CDC. Antibiotic Resistance Threats in the United States 2019 (US Department of Health and Human Services, 2019).

  4. Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).

    Article  CAS  Google Scholar 

  5. Bacterial Vaccines in Clinical and Preclinical Development 2021 (World Health Organization, 2021).

  6. Bloom, D. E., Black, S., Salisbury, D. & Rappuoli, R. Antimicrobial resistance and the role of vaccines. Proc. Natl Acad. Sci. USA 115, 12868–12871 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Frost, I. et al. The role of bacterial vaccines in the fight against antimicrobial resistance: an analysis of the preclinical and clinical development pipeline. Lancet Microbe 4, e113–e125 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Moore, M. R. et al. Effectiveness of 13-valent pneumococcal conjugate vaccine for prevention of invasive pneumococcal disease in children in the USA: a matched case-control study. Lancet Respir. Med. 4, 399–406 (2016).

    Article  CAS  PubMed  Google Scholar 

  9. Micoli, F., Bagnoli, F., Rappuoli, R. & Serruto, D. The role of vaccines in combatting antimicrobial resistance. Nat. Rev. Microbiol. 19, 287–302 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Baker, S. J., Payne, D. J., Rappuoli, R. & De Gregorio, E. Technologies to address antimicrobial resistance. Proc. Natl Acad. Sci. USA 115, 12887–12895 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Adepoju, P. New TB vaccine on trial. Nat. Africa 10.1038/d44148-024-00101-1 (2024).

  12. Olivier, V. D. M. et al. Phase 2b controlled trial of M72/AS01E vaccine to prevent tuberculosis. N. Engl. J. Med. 379, 1621–1634 (2018).

    Article  Google Scholar 

  13. Chen, W. Will the mRNA vaccine platform be the panacea for the development of vaccines against antimicrobial resistant (AMR) pathogens? Expert Rev. Vaccines 21, 155–157 (2022).

    Article  CAS  PubMed  Google Scholar 

  14. Mayer, R. L. & Impens, F. Immunopeptidomics for next-generation bacterial vaccine development. Trends Microbiol. 29, 1034–1045 (2021).

    Article  CAS  PubMed  Google Scholar 

  15. van der Woude, M. W. & Bäumler, A. J. Phase and antigenic variation in bacteria. Clin. Microbiol. Rev. 17, 581–611 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Tan, A., Atack, J. M., Jennings, M. P. & Seib, K. L. The capricious nature of bacterial pathogens: phasevarions and vaccine development. Front. Immunol. 7, 586 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Seib, K. L., Srikhanta, Y. N., Atack, J. M. & Jennings, M. P. Epigenetic regulation of virulence and immunoevasion by phase-variable restriction-modification systems in bacterial pathogens. Annu. Rev. Microbiol. 74, 655–671 (2020).

    Article  CAS  PubMed  Google Scholar 

  18. Trzilova, D., Anjuwon-Foster, B. R., Torres Rivera, D. & Tamayo, R. Rho factor mediates flagellum and toxin phase variation and impacts virulence in Clostridioides difficile. PLoS Pathog. 16, e1008708 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Georgieva, M., Kagedan, L., Ying-Jie, L., Thompson, C. M. & Lipsitch, M. Antigenic variation in Streptococcus pneumoniae PspC promotes immune escape in the presence of variant-specific immunity. mBio 9, e00264-18 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Vink, C., Rudenko, G. & Seifert, H. S. Microbial antigenic variation mediated by homologous DNA recombination. FEMS Microbiol. Rev. 36, 917–948 (2012).

    Article  CAS  PubMed  Google Scholar 

  21. Ernst, J. D. in Strain Variation in the Mycobacterium Tuberculosis Complex: Its Role in Biology, Epidemiology and Control (ed. Gagneux, S.) 171–190 (Springer, 2017).

  22. Rappuoli, R. Glycoconjugate vaccines: principles and mechanisms. Sci. Transl. Med. 10, eaat4615 (2018).

    Article  PubMed  Google Scholar 

  23. Rappuoli, R. Reverse vaccinology. Curr. Opin. Microbiol. 3, 445–450 (2000).

    Article  CAS  PubMed  Google Scholar 

  24. Sette, A. & Rappuoli, R. Reverse vaccinology: developing vaccines in the era of genomics. Immunity 33, 530–541 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Mayer, R. L. et al. Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes. Nat. Commun. 13, 6075 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Pardi, N. & Krammer, F. mRNA vaccines for infectious diseases—advances, challenges and opportunities. Nat. Rev. Drug Discov. 23, 838–861 (2024).

    Article  CAS  PubMed  Google Scholar 

  27. Nagata, T., Uchijima, M., Yoshida, A., Kawashima, M. & Koide, Y. Codon optimization effect on translational efficiency of DNA vaccine in mammalian cells: analysis of plasmid DNA encoding a CTL epitope derived from microorganisms. Biochem. Biophys. Res. Commun. 261, 445–451 (1999).

    Article  CAS  PubMed  Google Scholar 

  28. Maruggi, G. et al. Immunogenicity and protective efficacy induced by self-amplifying mRNA vaccines encoding bacterial antigens. Vaccine 35, 361–368 (2017).

    Article  CAS  PubMed  Google Scholar 

  29. Kawaguchi, K. et al. mRNA vaccine induces protective immunity against the type III secretory virulence of Pseudomonas aeruginosa. Preprint at https://www.biorxiv.org/content/10.1101/2023.06.09.544431v1.full.pdf (2023).

  30. Messou, M.-A. A. Harnessing a mRNA Platform Against Salmonellae (Harvard Univ. Press, 2018).

  31. Kon, E. et al. A single-dose F1-based mRNA-LNP vaccine provides protection against the lethal plague bacterium. Sci. Adv. 9, eadg1036 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ozdilek, A. & Avci, F. Y. Glycosylation as a key parameter in the design of nucleic acid vaccines. Curr. Opin. Struct. Biol. 73, 102348 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gupta, R. & Brunak, S. Prediction of glycosylation across the human proteome and the correlation to protein function. In Proc. Pacific Symposium on Biocomputing 2002 (eds Altman, R. B. et al.) 310–322 (World Scientific, 2002).

  34. Ozdilek, A., Paschall, A. V., Dookwah, M., Tiemeyer, M. & Avci, F. Y. Host protein glycosylation in nucleic acid vaccines as a potential hurdle in vaccine design for nonviral pathogens. Proc. Natl Acad. Sci. USA 117, 1280–1282 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Tameris, M. D. et al. Safety and efficacy of MVA85A, a new tuberculosis vaccine, in infants previously vaccinated with BCG: a randomised, placebo-controlled phase 2b trial. Lancet 381, 1021–1028 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Ndiaye, B. P. et al. Safety, immunogenicity, and efficacy of the candidate tuberculosis vaccine MVA85A in healthy adults infected with HIV-1: a randomised, placebo-controlled, phase 2 trial. Lancet Respir. Med. 3, 190–200 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Tameris, M. et al. A double-blind, randomised, placebo-controlled, dose-finding trial of the novel tuberculosis vaccine AERAS-402, an adenovirus-vectored fusion protein, in healthy, BCG-vaccinated infants. Vaccine 33, 2944–2954 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Muir, E. et al. Trafficking and processing of bacterial proteins by mammalian cells: insights from chondroitinase ABC. PLoS ONE 12, e0186759 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Rabouille, C. Pathways of unconventional protein secretion. Trends Cell Biol. 27, 230–240 (2017).

    Article  CAS  PubMed  Google Scholar 

  40. Lin, P. L. & Flynn, J. A. L. CD8 T cells and Mycobacterium tuberculosis infection. Semin. Immunopathol. 37, 239–249 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Grant, N. L. et al. Mycobacterium tuberculosis-specific CD4 T cells expressing transcription factors T-Bet or RORγT associate with bacterial control in granulomas. mBio 14, e00477-23 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Tian, L. et al. CTLs: killers of intracellular bacteria. Front. Cell. Infect. Microbiol. 12, 967679 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Osterloh, A. Vaccination against bacterial infections: challenges, progress and new approaches with a focus on intracellular bacteria. Vaccines 10, 751 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Shanmuganathan, G. et al. Role of interferons in Mycobacterium tuberculosis infection. Clin. Pract. 12, 788–796 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Baker, H. A. & Bernardini, J. P. It’s not just a phase; ubiquitination in cytosolic protein quality control. Biochem. Soc. Trans. 49, 365–377 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Weigele, B. A., Orchard, R. C., Jimenez, A., Cox, G. W. & Alto, N. M. A systematic exploration of the interactions between bacterial effector proteins and host cell membranes. Nat. Commun. 8, 532 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Dersh, D., Hollý, J. & Yewdell, J. W. A few good peptides: MHC class I-based cancer immunosurveillance and immunoevasion. Nat. Rev. Immunol. 21, 116–128 (2021).

    Article  CAS  PubMed  Google Scholar 

  48. Ruiz Cuevas, M. V. et al. Most non-canonical proteins uniquely populate the proteome or immunopeptidome. Cell Rep. 34, 108815 (2021).

    Article  CAS  PubMed  Google Scholar 

  49. Yewdell, J. W. Hide and seek in the peptidome. Science 301, 1334–1335 (2003).

    Article  CAS  PubMed  Google Scholar 

  50. Pamer, E. G. Immune responses to Listeria monocytogenes. Nat. Rev. Immunol. 4, 812–823 (2004).

    Article  CAS  PubMed  Google Scholar 

  51. Delogu, G., Howard, A., Collins, F. M. & Morris, S. L. DNA vaccination against tuberculosis: expression of a ubiquitin-conjugated tuberculosis protein enhances antimycobacterial immunity. Infect. Immun. 68, 3097–3102 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Pishesha, N., Harmand, T. J. & Ploegh, H. L. A guide to antigen processing and presentation. Nat. Rev. Immunol. 22, 751–764 (2022).

    Article  CAS  PubMed  Google Scholar 

  53. Lizée, G., Basha, G. & Jefferies, W. A. Tails of wonder: endocytic-sorting motifs key for exogenous antigen presentation. Trends Immunol. 26, 141–149 (2005).

    Article  PubMed  Google Scholar 

  54. Lotteau, V. et al. Intracellular transport of class II MHC molecules directed by invariant chain. Nature 348, 600–605 (1990).

    Article  CAS  PubMed  Google Scholar 

  55. Rowell, J. F. et al. Lysosome-associated membrane protein-1-mediated targeting of the HIV-1 envelope protein to an endosomal/lysosomal compartment enhances its presentation to MHC class II-restricted T cells. J. Immunol. 155, 1818–1828 (1995).

    Article  CAS  PubMed  Google Scholar 

  56. Wu, T. C. et al. Engineering an intracellular pathway for major histocompatibility complex class II presentation of antigens. Proc. Natl Acad. Sci. USA 92, 11671–11675 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Kreiter, S. et al. Increased antigen presentation efficiency by coupling antigens to MHC class I trafficking signals. J. Immunol. 180, 309–318 (2008).

    Article  CAS  PubMed  Google Scholar 

  58. Lizée, G. et al. Control of dendritic cell cross-presentation by the major histocompatibility complex class I cytoplasmic domain. Nat. Immunol. 4, 1065–1073 (2003).

    Article  PubMed  Google Scholar 

  59. Diken, M., Kranz, L. M., Kreiter, S. & Sahin, U. mRNA: a versatile molecule for cancer vaccines. Curr. Issues Mol. Biol. 22, 113–128 (2017).

    Article  PubMed  Google Scholar 

  60. Sahin, U. et al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 547, 222–226 (2017).

    Article  CAS  PubMed  Google Scholar 

  61. Rojas, L. A. et al. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature 618, 144–150 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. You, Z. et al. Induction of vigorous helper and cytotoxic T cell as well as B cell responses by dendritic cells expressing a modified antigen targeting receptor-mediated internalization pathway1. J. Immunol. 165, 4581–4591 (2000).

    Article  CAS  PubMed  Google Scholar 

  63. Noy-Porat, T. et al. Acetylcholinesterase-Fc fusion protein (AChE-Fc): a novel potential organophosphate bioscavenger with extended plasma half-life. Bioconjug. Chem. 26, 1753–1758 (2015).

    Article  CAS  PubMed  Google Scholar 

  64. Elia, U. et al. Design of SARS-CoV-2 hFc-conjugated receptor-binding domain mRNA vaccine delivered via lipid nanoparticles. ACS Nano 15, 9627–9637 (2021).

    Article  CAS  PubMed  Google Scholar 

  65. Shattock, R. J. et al. A self-amplifying RNA vaccine provides protection in a murine model of bubonic plague. Front. Microbiol. 14, 1247041 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Meulewaeter, S. et al. Alpha-galactosylceramide improves the potency of mRNA LNP vaccines against cancer and intracellular bacteria. J. Controlled Release 370, 379–391 (2024).

    Article  CAS  Google Scholar 

  67. Wang, X. et al. Strong immune responses and protection of PcrV and OprF-I mRNA vaccine candidates against Pseudomonas aeruginosa. NPJ Vaccines 8, 76 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Mead, P. Epidemiology of Lyme disease. Infect. Dis. Clin. North Am. 36, 495–521 (2022).

    Article  PubMed  Google Scholar 

  69. Moderna announces clinical and program updates at 4th vaccines day. Moderna https://www.accesswire.com/748485/Moderna-Announces-Clinical-and-Program-Updates-at-4th-Vaccines-Day (2023).

  70. Pine, M. et al. Development of an mRNA-lipid nanoparticle vaccine against Lyme disease. Mol. Ther. 31, 2702–2714 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Gross, D. M. et al. Identification of LFA-1 as a candidate autoantigen in treatment-resistant Lyme arthritis. Science 281, 703–706 (1998).

    Article  CAS  PubMed  Google Scholar 

  72. Bobe, J. R. et al. Recent progress in Lyme disease and remaining challenges. Front. Med. 8, 666554 (2021).

    Article  Google Scholar 

  73. Wolf, M. A. et al. Multivalent mRNA-DTP vaccines are immunogenic and provide protection from Bordetella pertussis challenge in mice. NPJ Vaccines 9, 103 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Global Tuberculosis Report 2023 (World Health Organization, 2023).

  75. Mangtani, P. et al. Protection by BCG vaccine against tuberculosis: a systematic review of randomized controlled trials. Clin. Infect. Dis. 58, 470–480 (2014).

    Article  PubMed  Google Scholar 

  76. Larsen, S. E. et al. An RNA-based vaccine platform for use against Mycobacterium tuberculosis. Vaccines 11, 130 (2023).

  77. Neha, A., Albrecht, S. S., Mustafa, D., Annette, V. & Ugur, S (2024). RNA for preventing or treating tuberculosis. WIPO patent WO2024028445A1 (2023).

  78. Polack, F. P. et al. Safety and efficacy of the BNT162b2 mRNA COVID-19 vaccine. N. Engl. J. Med. 383, 2603–2615 (2020).

    Article  CAS  PubMed  Google Scholar 

  79. Verbeke, R., Hogan, M. J., Loré, K. & Pardi, N. Innate immune mechanisms of mRNA vaccines. Immunity 55, 1993–2005 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Morais, P., Adachi, H. & Yu, Y.-T. The critical contribution of pseudouridine to mRNA COVID-19 vaccines. Front. Cell. Dev. Biol. 9, 789427 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Mulroney, T. E. et al. N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting. Nature 625, 189–194 (2024).

    Article  CAS  PubMed  Google Scholar 

  82. Rappuoli, R., Alter, G. & Pulendran, B. Transforming vaccinology. Cell 187, 5171–5194 (2024).

    Article  CAS  PubMed  Google Scholar 

  83. Petit, T. J. P. & Lebreton, A. Adaptations of intracellular bacteria to vacuolar or cytosolic niches. Trends Microbiol. 30, 736–748 (2022).

    Article  CAS  PubMed  Google Scholar 

  84. Leddy, O., White, F. M. & Bryson, B. D. Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I. eLife 12, e84070 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Panda, S. et al. Identification of differentially recognized T cell epitopes in the spectrum of tuberculosis infection. Nat. Commun. 15, 765 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Sette, A. & Crotty, S. Immunological memory to SARS-CoV-2 infection and COVID-19 vaccines. Immunol. Rev. 310, 27–46 (2022).

    Article  CAS  PubMed  Google Scholar 

  87. Arunachalam, P. S. et al. Durability of immune responses to mRNA booster vaccination against COVID-19. J. Clin. Invest. 133, e167955 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Fedele, G., Palmieri, A. & Onder, G. The immune response to SARS-CoV-2 vaccination in older people. Lancet Healthy Longev. 4, e177–e178 (2023).

    Article  PubMed  Google Scholar 

  89. Kamar, N. et al. Three doses of an mRNA COVID-19 vaccine in solid-organ transplant recipients. N. Engl. J. Med. 385, 661–662 (2021).

    Article  PubMed  Google Scholar 

  90. Walsh, E. E. et al. Efficacy and safety of a bivalent RSV prefusion F vaccine in older adults. N. Engl. J. Med. 388, 1465–1477 (2023).

    Article  CAS  PubMed  Google Scholar 

  91. Pennington, S. H. et al. Nonspecific effects of oral vaccination with live-attenuated Salmonella Typhi strain Ty21a. Sci. Adv. 5, eaau6849 (2024).

    Article  Google Scholar 

  92. Kleinnijenhuis, J. et al. Bacille Calmette-Guérin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc. Natl Acad. Sci. USA 109, 17537–17542 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Ziogas, A., Bruno, M., van der Meel, R., Mulder, W. J. M. & Netea, M. G. Trained immunity: target for prophylaxis and therapy. Cell Host Microbe 31, 1776–1791 (2023).

    Article  CAS  PubMed  Google Scholar 

  94. Arunachalam, P. S. et al. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature 596, 410–416 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Yamaguchi, Y. et al. Consecutive BNT162b2 mRNA vaccination induces short-term epigenetic memory in innate immune cells. JCI Insight 7, e163347 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Benn, C. S., Schaltz-Buchholzer, F., Nielsen, S., Netea, M. G. & Aaby, P. Randomized clinical trials of COVID-19 vaccines: do adenovirus-vector vaccines have beneficial non-specific effects? iScience 26, 106733 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Föhse, K. et al. The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses. Clin. Immunol. 255, 109762 (2023).

    Article  PubMed  Google Scholar 

  98. Stevens, N. E. et al. No evidence of durable trained immunity after two doses of adenovirus-vectored or mRNA COVID-19 vaccines. J. Clin. Invest. 133, e171742 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hellgren, F. et al. Modulation of innate immune response to mRNA vaccination after SARS-CoV-2 infection or sequential vaccination in humans. JCI Insight 9, e175401 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Han, X. et al. Adjuvant lipidoid-substituted lipid nanoparticles augment the immunogenicity of SARS-CoV-2 mRNA vaccines. Nat. Nanotechnol. 18, 1105–1114 (2023).

    Article  CAS  PubMed  Google Scholar 

  101. Hayashizaki, K., Kamii, Y. & Kinjo, Y. Glycolipid antigen recognition by invariant natural killer T cells and its role in homeostasis and antimicrobial responses. Front. Immunol. 15, 1402412 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Pifferi, C., Fuentes, R. & Fernández-Tejada, A. Natural and synthetic carbohydrate-based vaccine adjuvants and their mechanisms of action. Nat. Rev. Chem. 5, 197–216 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Gozzi, N. et al. Estimating the impact of COVID-19 vaccine inequities: a modeling study. Nat. Commun. 14, 3272 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Leppek, K. et al. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. Nat. Commun. 13, 1536 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Meulewaeter, S. et al. Continuous freeze-drying of messenger RNA lipid nanoparticles enables storage at higher temperatures. J. Control. Release 357, 149–160 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Muramatsu, H. et al. Lyophilization provides long-term stability for a lipid nanoparticle-formulated, nucleoside-modified mRNA vaccine. Mol. Ther. 30, 1941–1951 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Saied, A. A. Building Africa’s first mRNA vaccine facility. Lancet 402, 287–288 (2023).

    Article  PubMed  Google Scholar 

  108. Xue, T. et al. RNA encoding the MPT83 antigen induces protective immune responses against Mycobacterium tuberculosis infection. Infect. Immun. 72, 6324–6329 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Lorenzi, J. C. C. et al. Intranasal vaccination with messenger RNA as a new approach in gene therapy: use against tuberculosis. BMC Biotechnol. 10, 77 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  110. Blakney, A. K. et al. Effects of cationic adjuvant formulation particle type, fluidity and immunomodulators on delivery and immunogenicity of saRNA. J. Control. Release 304, 65–74 (2019).

    Article  CAS  PubMed  Google Scholar 

  111. Arya, S., Lin, Q., Zhou, N., Gao, X. & Huang, J. D. Strong immune responses induced by direct local injections of modified mRNA-lipid nanocomplexes. Mol. Ther. Nucleic Acids 19, 1098–1109 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Sajid, A. et al. mRNA vaccination induces tick resistance and prevents transmission of the Lyme disease agent. Sci. Transl. Med. 13, 9827 (2021).

    Article  Google Scholar 

  113. Rais, M. et al. Immunogenicity and protection against Mycobacterium avium with a heterologous RNA prime and protein boost vaccine regimen. Tuberculosis 138, 102302 (2023).

    Article  CAS  PubMed  Google Scholar 

  114. Legere, R. M. et al. Intramuscular but not nebulized administration of a mRNA vaccine against Rhodococcus equi stimulated humoral immune responses in neonatal foals. Am. J. Vet. Res. 85, ajvr.23.09.0208 (2023).

    PubMed  Google Scholar 

  115. Alameh, M.-G. et al. A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection. Science 386, 69–75 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Leddy, O., White, F. & Bryson, B. Leveraging immunopeptidomics to study and combat infectious disease. mSystems 6, 10–21 (2021).

    Article  Google Scholar 

  117. Leddy, O. et al. Immunopeptidomics informs discovery and delivery of Mycobacterium tuberculosis MHC-II antigens for vaccine design. Preprint at https://www.biorxiv.org/content/10.1101/2024.10.02.616386v1.full (2024).

  118. Leddy, O., Yuki, Y., Carrington, M., Bryson, B. D. & White, F. M. PathMHC: a workflow to selectively target pathogen-derived MHC peptides in discovery immunopeptidomics experiments for vaccine target identification. Preprint at https://www.biorxiv.org/content/10.1101/2024.09.11.612454v1.full.pdf (2024).

  119. Gul, A. et al. Immunopeptidomics mapping of Listeria monocytogenes T cell epitopes in mice. Mol. Cell. Proteom. 23, 100829 (2024).

    Article  CAS  Google Scholar 

  120. Rodríguez-Ortega, M. J. et al. Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat. Biotechnol. 24, 191–197 (2006).

    Article  PubMed  Google Scholar 

  121. Montemari, A. L. et al. A shaving proteomic approach to unveil surface proteins modulation of multi-drug resistant Pseudomonas aeruginosa strains isolated from cystic fibrosis patients. Front. Med. 9, 818669 (2022).

    Article  Google Scholar 

  122. Menikou, S. et al. A proteomics-based method for identifying antigens within immune complexes. PLoS ONE 15, e0244157 (2021).

    Article  Google Scholar 

  123. Joglekar, A. V. & Li, G. T cell antigen discovery. Nat. Methods 18, 873–880 (2021).

    Article  CAS  PubMed  Google Scholar 

  124. Musvosvi, M. et al. T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection. Nat. Med. 29, 258–269 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Huang, H., Wang, C., Rubelt, F., Scriba, T. J. & Davis, M. M. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat. Biotechnol. 38, 1194–1202 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Mora, M., Donati, C., Medini, D., Covacci, A. & Rappuoli, R. Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach. Curr. Opin. Microbiol. 9, 532–536 (2006).

    Article  CAS  PubMed  Google Scholar 

  127. He, Y., Xiang, Z. & Mobley, H. L. T. Vaxign: The first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J. Biomed. Biotechnol. 2010, 297505 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  128. Vivona, S., Bernante, F. & Filippini, F. NERVE: New Enhanced Reverse Vaccinology Environment. BMC Biotechnol. 6, 35 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  129. Rawal, K. et al. Vaxi-DL: a web-based deep learning server to identify potential vaccine candidates. Comput. Biol. Med. 145, 105401 (2022).

    Article  CAS  PubMed  Google Scholar 

  130. Ong, E. et al. Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinformatics 36, 3185–3191 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Peters, B., Nielsen, M. & Sette, A. T cell epitope predictions. Annu. Rev. Immunol. 38, 123–145 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Sanchez-Trincado, J. L., Gomez-Perosanz, M. & Reche, P. A. Fundamentals and methods for T- and B-cell epitope prediction. J. Immunol. Res. 2017, 2680160 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  133. De Groot, A. S. et al. Better epitope discovery, precision immune engineering, and accelerated vaccine design using Immunoinformatics tools. Front. Immunol. 11, 442 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  134. Lindestam Arlehamn, C. S. et al. Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3 + CCR6 + Th1 subset. PLoS Pathog. 9, e1003130 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  135. da Silva Antunes, R. et al. T cell reactivity to Bordetella pertussis is highly diverse regardless of childhood vaccination. Cell Host Microbe 31, 1404–1416.e4 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  136. Mubarak, A. S., Ameen, Z. S., Hassan, A. S. & Ozsahin, D. U. Enhancing tuberculosis vaccine development: a deconvolution neural network approach for multi-epitope prediction. Sci. Rep. 14, 10375 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Shi, J. et al. In silico designed novel multi-epitope mRNA vaccines against Brucella by targeting extracellular protein BtuB and LptD. Sci. Rep. 14, 7278 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Prachar, M. et al. Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools. Sci. Rep. 10, 20465 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Buckley, P. R. et al. Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens. Brief. Bioinform. 23, bbac141 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  140. Conev, A., Fasoulis, R., Hall-Swan, S., Ferreira, R. & Kavraki, L. E. HLAEquity: examining biases in pan-allele peptide-HLA binding predictors. iScience 27, 108613 (2024).

    Article  CAS  PubMed  Google Scholar 

  141. Gonzalez-Galarza, F. F., Christmas, S., Middleton, D. & Jones, A. R. Allele Frequency Net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res. 39, D913–D919 (2011).

    Article  CAS  PubMed  Google Scholar 

  142. Zimmermann, P. The immunological interplay between vaccination and the intestinal microbiota. NPJ Vaccines 8, 24 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by a Research Foundation-Flanders (FWO-Vlaanderen) PhD fellowship for strategic basic research to I.A. (1S40923N) and postdoctoral fellowships to R.V. (1275023N), F.T. (12AN524N) and P.W. (12T1722N). D.P. acknowledges support from the European Research Council (ERC adv. grant no. 101055029), The EXPERT project (European Union’s Horizon 2020 Research and Innovation Programme under grant no. 825828), ISF grant 2012/20 and the Shmunis Family Foundation. F.I. and I.L. acknowledge support from Ghent University Concerted Research Action grant BOF21/GOA/033 and from European Union’s Horizon Europe research and from the Horizon Europe Project BAXERNA 2.0 (101080544). F.I. is further supported by starting grant BOF/STA/202209/011 from Ghent University.

Author information

Author notes

  1. These authors contributed equally: Ilke Aernout, Rein Verbeke, Francis Impens, Ine Lentacker.

Authors and Affiliations

  1. Ghent Research Group on Nanomedicines, Ghent University, Ghent, Belgium

    Ilke Aernout, Rein Verbeke, Stefaan C. De Smedt & Ine Lentacker

  2. VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium

    Fabien Thery, Patrick Willems & Francis Impens

  3. Department of Biomolecular Medicine, Ghent University, Ghent, Belgium

    Fabien Thery, Patrick Willems & Francis Impens

  4. Center for Plant Systems Biology, VIB-UGent, Ghent, Belgium

    Patrick Willems

  5. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Patrick Willems

  6. Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

    Uri Elia & Dan Peer

  7. Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel

    Uri Elia & Dan Peer

  8. Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel

    Uri Elia & Dan Peer

  9. Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel

    Uri Elia & Dan Peer

  10. Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel

    Uri Elia

  11. Fondazione Biotecnopolo di Siena, Siena, Italy

    Rino Rappuoli

  12. VIB Proteomics Core, VIB, Ghent, Belgium

    Francis Impens

Authors
  1. Ilke Aernout
    View author publications

    Search author on:PubMed Google Scholar

  2. Rein Verbeke
    View author publications

    Search author on:PubMed Google Scholar

  3. Fabien Thery
    View author publications

    Search author on:PubMed Google Scholar

  4. Patrick Willems
    View author publications

    Search author on:PubMed Google Scholar

  5. Uri Elia
    View author publications

    Search author on:PubMed Google Scholar

  6. Stefaan C. De Smedt
    View author publications

    Search author on:PubMed Google Scholar

  7. Rino Rappuoli
    View author publications

    Search author on:PubMed Google Scholar

  8. Dan Peer
    View author publications

    Search author on:PubMed Google Scholar

  9. Francis Impens
    View author publications

    Search author on:PubMed Google Scholar

  10. Ine Lentacker
    View author publications

    Search author on:PubMed Google Scholar

Contributions

I.A., R.V., P.W., F.T., F.I. and I.L.: conceptualization, visualization, drafting and review of the manuscript. U.E., S.C.D.S., R.R. and D.P.: review and editing.

Corresponding authors

Correspondence to Francis Impens or Ine Lentacker.

Ethics declarations

Competing interests

D.P. receives licensing fees (to patents on which he was an inventor), has invested in, consults for (or is on scientific advisory boards or boards of directors) or is a founder and hold shares or conducts sponsored research at Tel Aviv University for the following entities: ART Biosciences, BioNTech SE, Earli Inc., Geneditor Biologics Inc. Kernal Biologics, Merck, Newphase Ltd, NeoVac Ltd, RiboX Therapeutics, Roche, SirTLabs Corporation and Teva Pharmaceuticals Inc. R.R. holds shares in the GSK and Novartis group of companies. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Microbiology thanks Timothy Keys and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Aernout, I., Verbeke, R., Thery, F. et al. Challenges and opportunities in mRNA vaccine development against bacteria. Nat Microbiol 10, 1816–1828 (2025). https://doi.org/10.1038/s41564-025-02070-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41564-025-02070-z

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology