Bacterial mRNA Vaccines: Programming Immunity Against Antimicrobial Resistance

ABSTRACT

The relentless rise of antimicrobial resistance poses a critical threat to global health, urgently demanding the development of antibacterial vaccines. Messenger RNA (mRNA) technology, validated during the COVID‐19 pandemic, offers a powerful platform of fast development and flexibility. However, its application against bacterial pathogens remains an emerging frontier due to the structural complexity of bacterial antigens, challenges in achieving effective mucosal and cellular delivery, and the need to elicit balanced Th1/Th17‐dominated immune responses for durable protection. Progress in antigen design, mRNA engineering, and lipid nanoparticle (LNP) delivery has enabled early preclinical success against Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae. Yet, challenges such as complex antigen expression, mucosal targeting, and immune durability persist. This review provides a brief overview of recent advances in bacterial mRNA vaccine design, including antigen selection, mRNA engineering, and delivery platform optimization. Additionally, we summarize current preclinical progress across key bacterial pathogens and highlight emerging strategies that integrate AI‐guided antigen discovery, synthetic biology, and next‐generation delivery systems to accelerate clinical translation. Finally, we highlight the prospects of bacterial mRNA vaccines by integrating synthetic biology, AI‐driven antigen prediction, and advanced delivery systems. These cutting‐edge technologies hold the promise of overcoming existing barriers, ultimately establishing mRNA vaccines as a viable and powerful strategy to curb the tide of antibiotic‐resistant infections.

1. Introduction

Bacterial infections pose escalating threats to global health, primarily being fueled by the evolution and selection of antimicrobial resistance (AMR) mechanisms (Ventola 2015; Czaplewski et al. 2016). According to the World Health Organization (WHO), AMR is implicated in at least 1.27 million annual deaths globally, with projections indicating a potential surge to 10 million deaths per year by 2050 (Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis, 2019: a systematic analysis (2022)). Pathogens such as Mycobacterium tuberculosis (M. tuberculosis), Pseudomonas aeruginosa (P. aeruginosa), and Streptococcus pneumoniae (S. pneumoniae) are particularly concerning. These pathogens employ mechanisms such as biofilm formation (P. aeruginosa), drug target mutations (M. tuberculosis), and the production of antibiotic‐inactivating enzymes (e.g., β‐lactamase in S. pneumoniae), which have significantly reduced the efficacy of many first‐line drugs (Gygli et al. 2017; Sacks et al. 2018). In this context, vaccines represent a critical strategy for infection prevention, offering a promising solution to mitigate the burden of AMR (Micoli et al. 2021; Buchy et al. 2020; La Guidara et al. 2024).

However, the development of effective bacterial vaccines confronts numerous obstacles. The intricate nature of bacterial antigens, the variability of virulence factors, and the adeptness of certain pathogens in evading host immune responses collectively contribute to these challenges (Khlebnikova et al. 2024; Aernout et al. 2025). Traditional vaccine modalities, including live‐attenuated, inactivated, and subunit vaccines, have proven a certain degree of success against specific pathogens such as S. pneumoniae and Haemophilus influenzae (H. influenzae). Nevertheless, these approaches are limited in providing effective protection against intracellular pathogens (e.g., M. tuberculosis) and highly mutable antigens (e.g., the capsular polysaccharides of K. pneumoniae). Furthermore, the development cycle for such vaccines is often protracted and resource‐intensive. For instance, the Bacille Calmette‐Guérin (BCG) vaccine, the sole licensed vaccine for tuberculosis, confers less than 50% efficacy against adult pulmonary M. tuberculosis infection (Kleinnijenhuis et al. 2012). Similarly, pneumococcal polysaccharide conjugate vaccines, despite covering numerous serotypes, face challenges in keeping pace with the emergence of mutant strains.

The emergence of nucleic acid‐based vaccines, particularly mRNA vaccines, has heralded a transformative breakthrough in bacterial vaccine development. The success of mRNA vaccines against COVID‐19 has clearly established their capacity for rapid design, scalable manufacturing, and the induction of robust humoral and cellular immune responses. Distinct from traditional paradigms that require complex in vitro protein production and purification, the mRNA modality directly encodes the antigen of interest. Upon delivery via lipid nanoparticles (LNPs), host cells translate the mRNA, enabling endogenous antigen production that potently stimulates both humoral and cellular immunity (Meulewaeter et al. 2023). This attribute renders it exceptionally suited for combating bacterial infections that necessitate the concerted activation of both antibody‐mediated and T‐cell‐mediated immunity. For example, an mRNA vaccine targeting P. aeruginosa can encode outer membrane proteins Pseudomonas type III secretion tip protein and outer membrane protein F (PcrV and OprF), stimulating neutralizing antibodies while concurrently enhancing T helper 1 cells/T helper 17 cells (Th1/Th17) immune responses, thereby overcoming the pathogen's biofilm‐mediated defense mechanisms (Kawaguchi et al. 2025; Wang et al. 2023).

Notwithstanding their monumental success in virology, the application of mRNA vaccines against bacterial diseases presents unique hurdles: (1) The complexity and diversity of bacterial antigens often surpass that of viral antigens (Gergen and Petsch (2022)) (2) Immune polarization remains another challenge: intracellular pathogens such as Listeria require robust CD8⁺ T‐cell responses, whereas current mRNA vaccines often preferentially promote CD4⁺ T‐cell activation (Li et al. 2024; Shepherd and McLaren 2020); (3) The necessity for local mucosal immunity (e.g., in respiratory and intestinal tracts), whereas most LNP systems are optimized for systemic delivery, rendering mucosal immunization a formidable challenge (Lavelle and Ward 2022); (4) Safety considerations: the potential for mRNA vaccines to encode bacterial toxins (e.g., S. aureus α‐toxin) raises concerns regarding the induction of excessive inflammatory responses (Bergstrom et al. 2024). Consequently, meticulous optimization of antigen sequences as well as mRNA molecules is paramount to balancing immunogenicity and safety.

Despite these challenges, bacterial mRNA vaccines retain tremendous promise. They enable rapid production and can be tailored to encode specific antigens for a broad spectrum of bacterial pathogens, offering novel strategies to counteract bacterial infections. To fully realize the potential of bacterial mRNA vaccines, further refinements in antigen design, mRNA stability, and delivery systems are imperative. This review provides a comprehensive overview of the latest advancements in bacterial mRNA vaccines, with a particular emphasis on technological innovations, immunological mechanisms, and delivery strategies that are shaping the future of this field. We also discuss persistent obstacles hindering the widespread clinical implementation of mRNA vaccines for bacterial infections and propose strategic frameworks for overcoming these challenges. By integrating cutting‐edge technologies such as Artificial Intelligence (AI)‐driven antigen design and synthetic biology, bacterial mRNA vaccines harbor the potential to offer sustainable solutions for infection prevention and control in the impending post‐antibiotic era. This review aims to chart a preliminary sketch for realizing the potential of mRNA technology in combating AMR and preventing bacterial infections in the post‐antibiotic era.

2. Antigen Design and Screening

The breakthrough of lipid‐nanoparticle (LNP)‐encapsulated mRNA vaccines against SARS‐CoV‐2 proved cell‐free, sequence‐programmable platforms that can generate potent and safe immunity in humans within just a few months (Polack et al. 2020; Pardi et al. 2018a; Kon et al. 2023). Translating this success to bacterial pathogens is attractive (Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050 (2024)). However, bacteria differ profoundly from viruses: they possess complex cell walls, secrete immune‐modulating toxins, form biofilms, and display diverse polysaccharide capsules that mask epitopes (Gao et al. 2024; Ramírez‐Larrota and Eckhard 2022). Therefore, the development of bacterial mRNA vaccines first relies on the precise identification of protective antigens and the systematic optimization of antigen‐encoding constructs (Sacks et al. 2018; Pardi and Weissman 2017). Over the past 5 years, dozens of peer‐reviewed studies and several pre‐prints have contributed to refining these design principles, advancing candidates against M. tuberculosis, P. aeruginosa, Yersinia pestis (Y. pestis), Clostridioides difficile (C. difficile), Klebsiella pneumoniae (K. pneumoniae), and multi‐serotype S. pneumoniae (Larsen et al. 2023; Nahian et al. 2025). Based on these advances, the antigen design of bacterial mRNA vaccines has gradually shifted from empirical screening to a rational design model that combines pathogen biology, computational prediction, and construct optimization.

2.1. Biological Basis for Antigen Selection

Bacterial antigens are typically proteins; however, some pathogens also critically rely on surface polysaccharides or complex virulence factors, which present formidable challenges for conventional mRNA vaccine platforms. For instance, developing an mRNA vaccine against P. aeruginosa, a Gram‐negative bacterium, necessitates the screening of proteins expressed on the bacterial surface or secreted into the extracellular milieu as potential antigens. Commonly targeted antigens include: (1) Adhesins, which facilitate bacterial attachment to host cells, a pivotal initial step in infection; (2) Toxins, which often exhibit high immunogenicity and can induce potent neutralizing antibodies; and (3) Outer membrane proteins (OMPs), which are integral to maintaining bacterial structural integrity and mediating substance exchange (Sacks et al. 2018). The selection of appropriate antigens is crucial for inducing effective humoral and cellular immune responses, particularly against pathogens that employ immune evasion strategies like biofilm formation or antigenic variation (Asadinezhad et al. 2023). For this reason, relying solely on experience or traditional step‐by‐step verification methods often has limited efficiency, and there is an urgent need for more systematic prediction and optimization strategies.

2.2. Computational and AI‐Assisted Antigen Screening

Given the complexity of bacterial antigens, especially those involving polysaccharides and multi‐component virulence factors, rational antigen selection mandates an in‐depth understanding of the pathogen's biology. For example, antigen selection of P. aeruginosa typically involves prioritizing protein antigens with specific subcellular localizations. However, conventional approaches have limitations, and accurately identifying the most efficacious targets from a vast pool of potential antigens remains non‐trivial (Di Salvatore et al. 2023). Advances in computational biology and AI have provided powerful new strategies for antigen screening. Computational biology leverages whole‐genome sequencing data to predict potential antigenic targets based on parameters such as surface accessibility, hydrophilicity, and antigenic index. Furthermore, protein structure prediction tools (e.g., AlphaFold2) can evaluate potential binding interactions between antigens and immune receptors (e.g., MHC molecules) (Jumper et al. 2021; Hashemi et al. 2023). In parallel, AI employs machine learning algorithms (e.g., support vector machines, neural networks) to analyze extensive antigen datasets, automatically extracting complex sequence features (Sacks et al. 2018). By incorporating knowledge of bacterial pathogenic mechanisms and infection processes, AI can more precisely identify antigens with high immunogenicity and protective potential (Oli et al. 2020).

2.3. mRNA Construct Optimization Following Antigen Selection

Upon identification of a suitable antigen, optimization of the antigen coding sequence for the host expression system becomes critical to enhance vaccine efficacy. As codon usage preferences vary across organisms, codon optimization—replacing rare codons in the bacterial gene with those frequently used by the host cell—can significantly augment mRNA translation efficiency and antigen yield (Sacks et al. 2018; Williams 2014). Strategic utilization of 5′ and 3′ untranslated regions (UTRs) is also vital for enhancing vaccine performance. The 5′ UTR contains ribosome binding sites that regulate translation initiation, while cis‐acting elements in the 3′ UTR influence mRNA stability and translational efficiency (Sacks et al. 2018; Trepotec et al. 2019). Additionally, structural modifications to the antigen can enhance immunogenicity (Wang et al. 2025). Incorporating an N‐terminal signal peptide can facilitate directed protein secretion, enhancing immune recognition. Similarly, the rational introduction or optimization of T‐cell and B‐cell epitopes can significantly bolster immune cell recognition and response, thereby improving the overall immunogenicity of the vaccine construct. Together, these strategies establish a rational design framework linking antigen structure to immunological outcomes (Pardi and Weissman 2017) (Table 1).

Table 1.

Summary of the Design Principles Linking Antigen Features to Translational Immunogenicity.

Design step	Key advances	Illustrative examples
In‐silico antigen triage	Whole‐proteome reverse‐vaccinology pipelines now couple de novo structural modeling with AI classifiers that learn “protective signatures” (surface accessibility, epitope density, HLA coverage, essentiality).	Evaxion's EDEN platform and Baseimmune's variational‐autoencoder pipeline have reduced candidate lists for Pseudomonas, Klebsiella and C. difficile from > 3000 ORFs to < 50 high‐value targets.
Multi‐antigen/epitope strings	Concatemers or bicistronic cassettes broaden serotype coverage and limit escape; flexible linkers prevent mis‐folding.	PcrV–OprF/I fusion protects 90% of mice in burn‐sepsis models (Fakoor et al. 2020); Ag85B–CysD tri‐fusion (CysVac2) exceeds BCG boost in murine TB (Counoupas et al. 2016).
Non‐protein targets	Co‐delivery of glyco‐toolbox mRNAs (oligosaccharyl‐transferases, glycosyl‐hydrolases) enables in situ expression of capsular polysaccharide mimetics—first shown for K. pneumoniae O‐antigen (Harada et al. 2019).	n/a
Codon & structure tuning	High‐throughput screening of 5′/3′‐UTRs, Kozak contexts and GC content (40–65%) boosts translation 5‐ to 20‐fold while maintaining innate‐sensing balance.	Self‐amplifying RNA (saRNA) scaffolds cut effective dose 10‐fold in plague F1 vaccine (Sacks et al. 2018; Shattock et al. 2023).
Trafficking motifs & secretion signals	tPA or IL‐2 signal peptides drive extracellular release; lipoylation motifs anchor antigens to host membranes, enhancing MHC‐II loading.	tPA‐tagged Omp‐based construct cleared Klebsiella pneumoniae within 72 h in lungs of mice (Liao et al. 2024).

Abbreviation: n/a, Not Available.

Collectively, rational antigen selection and mRNA construct optimization provide the molecular foundation of bacterial mRNA vaccines, but their protective efficacy ultimately depends on how effectively these designs are translated into host immune activation in vivo. In addition to the identity and expression efficiency of the encoded antigen, vaccine performance is shaped by how antigens are processed and presented, how innate immune pathways are engaged, and how efficiently the mRNA is delivered to relevant cellular and tissue compartments. Antigen design, immune programming, and delivery engineering should therefore be viewed as interdependent determinants of vaccine efficacy rather than isolated modules. In the following sections, we discuss the immune mechanisms and delivery platforms that translate molecular design into durable antibacterial protection.

3. Immune Mechanisms of Bacterial mRNA Vaccines

Bacterial mRNA vaccines elicit a coordinated immune response by leveraging the host's cellular machinery to produce antigens in situ, thereby initiating a coordinated cascade of innate and adaptive immune responses (Pardi and Weissman 2017). A cornerstone of durable protection is the generation of long‐lived memory T and B cells, capable of mounting a rapid anamnestic response upon pathogen re‐exposure (Goel et al. 2021). Therefore, the protective efficacy of bacterial mRNA vaccines depends on efficient antigen presentation, balanced T helper cell polarization, and sustained immune memory formation (Figure 1).

Figure 1.

Immune Mechanisms of Bacterial mRNA Vaccines. Lipid nanoparticle (LNP)‐encapsulated bacterial antigen mRNA is taken up by antigen‐presenting cells (APCs), translated in the cytosol, and processed into peptide antigens for presentation on major histocompatibility complex class I (MHC I) and class II (MHC II) molecules. MHC I presentation activates CD8⁺ cytotoxic T cells, whereas MHC II presentation promotes CD4⁺ T‐cell differentiation into T helper cells (Th) such as Th1 and Th17 subsets. Th1‐derived interferon‐γ (IFN‐γ) and Th17‐derived interleukin‐17 (IL‐17) and IL‐22 support macrophage activation, neutrophil recruitment, and antibacterial effector function. In parallel, B cells internalize antigen, receive CD4⁺ T‐cell help, and differentiate into plasma cells and memory B cells, leading to antibody production and durable humoral immunity. LNP‐encapsulating mRNA may also triggers innate immune sensing through endosomal and cytosolic pattern recognition receptors, including Toll‐like receptors (TLRs) and melanoma differentiation‐associated protein 5 (MDA5), resulting in type I interferon and cytokine production. Together, these processes coordinate innate activation, cellular immunity, humoral responses, and immune memory following bacterial mRNA vaccination.

3.1. Cellular Immune Activation

Following delivery, host ribosomes translate the mRNA into bacterial antigens within the cytosol. These antigens undergo proteasomal degradation into peptides that bind to major histocompatibility complex class I (MHC I) molecules and are subsequently displayed on the cell surface, where they are recognized by CD8⁺ cytotoxic T lymphocytes (CTLs) (Dersh et al. 2021). Activated CTLs target and eliminate infected or antigen‐expressing cells and are therefore particularly important for protection against intracellular bacterial pathogens (Chaudhary et al. 2021).

Simultaneously, antigen‐presenting cells (APCs), particularly dendritic cells (DCs), may internalize mRNA vaccines through endocytosis or membrane fusion. A portion of the translated antigen is redirected from endosomal compartments to the cytosol via the cross‐presentation pathway, enabling MHC I loading even in non‐infected cells (Iavarone et al. 2017; Roche and Furuta 2015). This mechanism is crucial for eliciting robust CD8⁺ T‐cell immunity against intracellular pathogens such as Listeria monocytogenes and Mycobacterium tuberculosis.

Other antigen fragments are processed in endosomal vesicles and presented via MHC II molecules to CD4⁺ T helper (Th) cells. Cytokine cues derived from innate immune sensors, particularly type I interferons, IL‐12, and IL‐23—drive Th1 and Th17 differentiation. Th1 cells release interferon‐γ (IFN‐γ) to activate macrophages and enhance cellular antimicrobial activity, while Th17 cells secrete interleukin‐17 (IL‐17) to recruit neutrophils and fortify mucosal barrier defense. The polarization balance between Th1 and Th17 responses is critical, as it tailors immunity to different bacterial niches: Th1‐dominated responses are essential for controlling intracellular pathogens (e.g., M. tuberculosis), while Th17 responses are pivotal for clearing extracellular bacteria at mucosal surfaces (e.g., S. pneumoniae) (Cooper and Khader 2008; Domingo‐Gonzalez et al. 2016; Andrade et al. 2025).

3.2. Humoral and Mucosal Immune Activation (B Cell and Antibody Response)

Activated B cells, aided by Th cell–derived cytokines (IL‐21, IFN‐γ), differentiate into plasma cells that secrete antigen‐specific antibodies. These antibodies neutralize bacterial toxins, prevent adhesion to epithelial surfaces, and promote opsonophagocytosis. Importantly, a subset of germinal center B cells develops into long‐lived memory B cells and bone marrow plasma cells, ensuring durable antibody production (Crotty 2019; Pardi et al. 2018b; Lederer et al. 2020).

In parallel, memory CD8⁺ and CD4⁺ T cells—including resident memory (T_RM) subsets within mucosal tissues—maintain rapid recall capacity upon secondary bacterial exposure. The induction of such tissue‐resident memory populations is a key target for next‐generation bacterial mRNA vaccines, particularly those delivered via inhaled or mucosal routes (Reina‐Campos et al. 2025; Amsen et al. 2018). Secretory immunoglobulin A (sIgA) serves as the primary antibody class and a key effector of the mucosal immune system. It is uniquely transported across epithelial into mucosal secretions as a dimer complexed with a secretory component, which confers stability (Siggins et al. 2021). sIgA functions as the first line of specific immune defense by neutralizing pathogens and toxins, excluding them from the epithelial surface (“immune exclusion”), and shaping the commensal microbiota. The generation of high‐affinity, antigen‐specific sIgA is a T‐cell‐dependent process, traditionally attributed to follicular helper T cells (Tfh) within organized mucosal lymphoid tissues, which direct B cell class‐switch recombination to IgA (Mantis et al. 2011; Pabst 2012). Recent research has significantly refined our understanding of the long‐term maintenance of mucosal humoral immunity by highlighting the critical role of tissue‐resident memory T cells (T_RM) (Takamura 2018; Zheng and Wakim 2022). T_RM cells are nonrecirculating lymphocytes that persist long‐term at barrier sites such as the intestinal and respiratory tracts. Beyond their established role in rapid cellular recall responses, CD4 + T_RM cells are now recognized as essential local regulators of secondary sIgA production (Shenoy et al. 2020). Upon re‐encountering cognate antigen, mucosal T_RM cells are swiftly reactivated to provide immediate helper signals, including CD40L and cytokines such as IL‐4, IL‐10, and IL‐21 (Cheng and Becattini 2024). These signals directly support the reactivation and differentiation of nearby mucosal memory B cells and plasma blasts, driving a rapid and robust anamnestic sIgA response entirely within the effector tissue, without the delay of recruiting circulating lymphocytes (Laidlaw and Cyster 2021). This T_RM‐sIgA axis represents a sophisticated adaptation for mucosal defense, ensuring immediate, localized humoral protection at the precise sites of pathogen entry. Understanding this interplay is crucial for developing next‐generation mucosal vaccines aimed at eliciting sustained sterilizing immunity.

3.3. Innate Immune Activation and Adjuvant Effects

The adjuvant activity of bacterial mRNA vaccines arises both from the intrinsic immunostimulatory properties of mRNA and from its delivery vehicles. LNPs enhance endosomal escape and trigger pattern recognition receptors (PRRs) such as Toll–like receptors (TLR3, TLR7, TLR8) and RIG‐I‐like receptors (RLRs) (Arya et al. 2020). Controlled activation of these sensors induces type I interferons and pro‐inflammatory cytokines, which prime APCs and shape adaptive polarization toward Th1/Th17 profiles (Pardi et al. 2018a; Corbett et al. 2020; Lavelle and McEntee 2024).

Excessive activation, however, may lead to systemic inflammation; thus, fine‐tuning the balance between innate stimulation and antigen translation efficiency remains pivotal (Figure 2). Rational mRNA modification (e.g., pseudouridine incorporation) and delivery optimization can minimize reactogenicity while preserving adjuvanticity (Sacks et al. 2018; Mochida and Uchida 2024). Together, these processes establish a robust, self‐adjuvanted immune response that links early innate sensing to the formation of durable adaptive and memory immunity.

Figure 2.

Integration of molecular design, immune mechanisms, and delivery system in bacterial mRNA vaccines. Molecular design defines the immunological blueprint through codon optimization, untranslated region (UTR) tuning, and chemical modification of mRNA constructs. Immune mechanisms encompass antigen presentation, Th1/Th17 polarization, memory formation, and innate pattern recognition receptor (PRR) activation. Delivery systems—including lipid nanoparticles (LNPs), polymers, and hybrid carriers—serve as the operational interface that enables precise cellular targeting and cytosolic mRNA release. Together, molecular design determines what is encoded and how efficiently it can be expressed, delivery engineering governs where and how the mRNA reaches target cells, and immune mechanisms translate these inputs into coordinated antibacterial immunity.

4. Delivery Platforms for Bacterial mRNA Vaccines

Efficient mRNA delivery is fundamental to achieving robust antigen expression, stability, and immunogenicity—key prerequisites for combating bacterial infections that demand both cellular and humoral immunity. Unlike viral mRNA vaccines, which typically encode extracellular spike proteins, bacterial mRNA vaccines must express complex intracellular or surface‐associated antigens. These unique demands necessitate specialized delivery systems capable of precise tissue targeting, cytosolic delivery, and controlled innate immune activation (Aernout et al. 2025).

Recent progress in non‐viral platforms—especially LNPs, polymeric nanoparticles, and peptide‐based carriers—has expanded the toolkit available for bacterial mRNA vaccine development (Table 2). Each system offers distinct physicochemical and immunological advantages, and their optimization increasingly reflects lessons learned from viral mRNA vaccines while incorporating bacterial‐specific immune requirements (Hou et al. 2021a; Pardi et al. 2018b).

Table 2.

Comparison of Major Non‐viral Delivery Platforms for Bacterial mRNA Vaccines.

Platform	Representative materials	Advantages	Limitations	Notable applications/examples
Lipid nanoparticles (LNPs)	Ionizable lipids, cholesterol, DSPC, PEG‐lipids	High encapsulation efficiency; efficient cytosolic release; scalable GMP production	Limited mucosal penetration; potential reactogenicity	Pseudomonas aeruginosa PcrV mRNA vaccine (Wang et al. (2023)
Polymeric nanoparticles (PNPs)	PEI, chitosan, PBAE derivatives	Tunable charge and degradability; enhanced endosomal escape	Variable cytotoxicity; batch heterogeneity	Mycobacterium tuberculosis Ag85B/ESAT‐6 mRNA (Touray et al. (2023)
Peptide‐based carriers	CPPs (TAT, R9), amphiphilic peptides	Biocompatible; enable mucosal and intracellular delivery	Lower encapsulation efficiency; instability in serum	Streptococcus pneumoniae PsaA mRNA
Hybrid delivery systems	Lipid‐polymer hybrids, peptide‐polymer hybrids, or engineered exosomes	Enhanced targeting and immune modulation; natural tropism	Complex synthesis; scalability challenges	Early‐stage research (Chen et al. 2024; Mondal et al. 2023)

4.1. Non‐Viral Delivery Platforms

4.1.1. Lipid Nanoparticles (LNPs) As a Leading Delivery Platform

Table 2 compares the core design features, advantages, limitations, and representative applications of major non‐viral platforms used for bacterial mRNA delivery. LNPs represent the most advanced and clinically validated platform for in vitro transcribed mRNA delivery. Their core structure comprises four key components: an ionizable lipid (critical for endosomal escape via the proton sponge effect), phospholipids (contributing to bilayer structure), cholesterol (enhancing membrane stability and fluidity), and PEG‐lipids (modulating particle size, stability, and pharmacokinetics). This composition collectively ensures high mRNA encapsulation efficiency, protection from ribonucleases, and efficient cytosolic delivery into APCs (Hou et al. 2021b).

For bacterial mRNA vaccines, LNPs have been refined to favor Th1/Th17‐biased immunity—a critical axis for antibacterial protection. For example, an LNP‐formulated Pseudomonas aeruginosa mRNA vaccine encoding PcrV demonstrated enhanced dendritic cell activation and T‐cell priming, markedly reducing bacterial colonization in murine models (Wang et al. 2023).

Ongoing innovations include ionizable lipid diversification and charge‐modulated PEG architectures that balance translation efficiency with controlled pattern recognition receptor (PRR) stimulation, minimizing reactogenicity while maintaining immunostimulation.

4.1.2. Polymeric Nanoparticles and Peptide‐Based Delivery Systems

Polymeric and peptide‐based vectors offer complementary solutions to LNPs, providing modularity, biodegradability, and tunable charge densities. (1) Polymeric nanoparticles (e.g., polyethyleneimine [PEI], chitosan derivatives, and poly (β‐amino esters)) are being engineered for enhanced buffering capacity and endosomal escape efficiency (Rizwan et al. 2025). Their adjustable molecular weight and surface functionalization enable selective APC targeting (Zielińska et al. 2020). (2) Peptide‐based carriers, including cationic cell‐penetrating peptides (CPPs) and amphiphilic sequences, facilitate direct membrane translocation and cytosolic release of mRNA. Rational sequence engineering—guided by computational modeling—has yielded designs with reduced cytotoxicity and improved stability (Touray et al. 2023).

Although their transfection efficiency remains lower than optimized LNPs, polymeric and peptide‐based systems are emerging as promising adjuvant‐compatible or mucosal‐delivery–adaptable alternatives for bacterial vaccine applications. Compared with clinically validated LNP formulations, these platforms offer greater structural modularity and may be particularly attractive in settings where barrier traversal, local delivery, or cargo‐specific tuning is required (Guan et al. 2019).

However, these systems remain less mature than LNPs in terms of translational standardization. Polymeric and peptide‐based formulations often display greater variability in formulation reproducibility, lower encapsulation efficiency, more complex structure–function relationships, and less established large‐scale manufacturing workflows. Their immunological effects may also be more context‐dependent, especially when mucosal delivery, local reactogenicity, and formulation stability must be balanced simultaneously.

The selection of an optimal delivery platform should therefore align with antigen type, target tissue, and desired immune polarization. Pulmonary pathogens, such as Mycobacterium tuberculosis and Streptococcus pneumoniae may benefit from inhalable or aerosol‐compatible formulations capable of promoting local antigen expression and tissue‐resident immune responses, whereas enteric pathogens may require oral or protected delivery systems that can withstand gastrointestinal degradation and enable intestinal release. Future translational progress will likely depend on rational integration of the strengths of different carrier classes, rather than on any single universal platform (Cardoso et al. 2024; Huang et al. 2025).

Future translational efforts will rely on multimodal delivery integration—combining LNP precision with polymeric versatility and peptide adaptability—to achieve programmable biodistribution and tunable immune engagement (Figure 3). Future bacterial mRNA vaccine platforms will likely require closer integration of delivery engineering and immunological design to improve the prospects for safe, potent, and durable antibacterial protection.

Figure 3.

Core Non‐viral Delivery Platforms for Bacterial mRNA Vaccines. Schematic illustration of three major mRNA delivery systems: LNPs composed of ionizable lipids, cholesterol, phospholipids, and PEG‐lipids that encapsulate and release mRNA into antigen‐presenting cells (APCs); Polymeric nanoparticles, such as chitosan or poly (β‐amino ester) (PBAE) carriers, which complex with mRNA via electrostatic interactions and promote tunable endosomal escape; Peptide‐based carriers, including cationic or amphiphilic peptides that mediate direct membrane penetration and cytosolic mRNA delivery. Each platform elicits distinct immune activation profiles, with LNPs favoring efficient in vivo mRNA transfection, polymer systems enabling customizable charge and degradation, and peptide carriers offering biocompatibility and mucosal adaptability.

4.2. Route‐Specific and Tissue‐Targeted Delivery Strategies

The therapeutic success of bacterial mRNA vaccines ultimately hinges on the spatial precision of delivery—that is, the ability to deposit mRNA constructs at the anatomical sites where bacterial colonization and immune activation occur (Aernout et al. 2025). Because bacteria infect distinct mucosal or systemic niches, route‐specific delivery strategies have emerged to tailor antigen expression and immune responses to disease‐relevant tissues (Table 3) (Lu et al. 2025).

Table 3.

Route‐Specific mRNA Delivery Strategies Against Bacterial Infections.

Target tissue/infection	Representative pathogens	Delivery platform	Mechanism of targeting	Immune characteristics
Pulmonary (inhalable/aerosolized)	M. tuberculosis, S. pneumoniae	Dry‐powder LNPs, polymer–lipid hybrids	Aerodynamic particle deposition in alveoli; uptake by alveolar macrophages and DCs	Induces Th1/Th17 and tissue‐resident TRM cells
Gastrointestinal (oral)	H. pylori, E. coli	Chitosan–PBAE polymers, bacteria‐based carriers	pH‐sensitive release; mucus penetration	sIgA and Th17 mucosal responses
Lymphatic/systemic	K. pneumoniae, Listeria monocytogenes	Targeted LNPs, exosome‐like vesicles	Drainage to cervical/mesenteric lymph nodes	Balanced systemic and mucosal memory responses
Intranasal (upper airway)	Bordetella pertussis, S. aureus	Mucoadhesive peptide–LNP hybrids	Nasal mucosa absorption, APC targeting	Local IgA + IL‐17–mediated defense

For pulmonary infections caused by pathogens, such as Mycobacterium tuberculosis and Streptococcus pneumoniae, aerosolized or inhalable mRNA formulations have shown substantial promise (Lamont et al. 2026; Rezk and McClean 2025). Dry‐powder LNP‐mRNA formulations achieve efficient pulmonary deposition and induce robust mucosal and T_RM responses while maintaining stability at ambient temperature. Recent reports demonstrated that pulmonary delivery enhances antigen uptake by alveolar macrophages and dendritic cells, promoting localized Th1/Th17 polarization (Roh et al. 2022; Zhang et al. 2020).

For gastrointestinal pathogens such as Helicobacter pylori and enteropathogenic Escherichia coli, oral delivery systems leveraging polymeric or bioengineered bacterial vectors have been developed (Farris et al. 2018). These platforms use pH‐sensitive polymer coatings or biomimetic carriers to protect mRNA from enzymatic degradation in the gastric environment and enable site‐specific release in the intestinal mucosa. In a representative study, chitosan–poly (β‐amino ester) nanoparticles successfully mediated intestinal mRNA translation and antigen presentation, eliciting mucosal sIgA and Th17 responses (Kim et al. 2023).

Beyond the lung and gut, other tissue‐targeted strategies are under exploration, including intranasal immunization for upper‐airway defense and lymphatic‐targeted formulations to induce systemic memory via cervical or mesenteric nodes (Liu et al. 2024). Collectively, these delivery route optimizations represent a critical step toward achieving organ‐specific immunity against diverse bacterial pathogens (Figure 4).

Figure 4.

Multi‐Route Administration of mRNA‐LNP Therapeutics for Bacterial Infections. Schematic illustration of major administration routes and targeting strategies used for bacterial mRNA vaccines. Inhalation employs aerosolized or dry‐powder mRNA‐loaded lipid nanoparticles (LNPs) for delivery to the respiratory tract, with potential utility against pulmonary pathogens. Intranasal administration uses mucoadhesive mRNA‐LNPs to target the nasal mucosa and upper airways, supporting local immune protection against upper‐airway pathogens such as Bordetella pertussis and Staphylococcus aureus. Oral delivery leverages bioengineered bacteria or pH‐sensitive polymer‐based systems to protect mRNA cargo during gastrointestinal transit and enable intestinal release. Lymphatic targeting uses exosome‐like vesicles to promote lymph node delivery and systemic immune priming. Together, these route‐specific strategies illustrate how anatomical targeting can shape the localization and quality of antibacterial immune responses.

These advances aim to overcome the challenges posed by harsh environmental conditions and ensure localized immune activation. The design of targeted delivery systems must account for pathogen tropism, host mucosal architecture, and desired immune compartmentalization. The convergence of LNP, polymer, and peptide technologies has enabled increasingly precise modulation of biodistribution and immune activation kinetics.

While these developments show great promise, future research must focus on further refining delivery systems to achieve precise targeting and sustained immune activation. Overcoming these hurdles will be key to advancing bacterial mRNA vaccines into clinical applications, offering a scalable solution for combating antibiotic‐resistant infections. Besides, future innovations—such as AI‐guided formulation optimization, bioresponsive polymers, and multi‐route delivery frameworks—are expected to transform bacterial mRNA vaccines from localized prototypes into clinically translatable immunotherapies capable of organ‐specific protection.

5. Recent Advances in Bacterial mRNA Vaccines

Recent progress in bacterial mRNA vaccine research has provided important proof‐of‐concept evidence that nucleic acid platforms can be adapted to antibacterial indications. Across studies targeting Mycobacterium tuberculosis, Pseudomonas aeruginosa, Streptococcus pneumoniae, and other priority pathogens (Table 4 and Figure 5), encouraging preclinical signals have been reported, including improved antigen‐specific T‐cell responses, reduced tissue bacterial burden, and protection in challenge models. These advances collectively suggest that lessons from antiviral mRNA vaccinology can be partially translated to bacterial pathogens, particularly when combined with multi‐antigen design and delivery optimization.

Table 4.

Recent Advancements in Bacterial mRNA Vaccines Development.

Bacterial Pathogen	Vaccine Antigen (s)	Vaccine Platform	Key Findings	Preclinical/Clinical Status
Mycobacterium tuberculosis	Ag85B, ESAT‐6, CFP‐10	Self‐amplifying mRNA (saRNA)	Induced strong Th1 and Th17 responses, reduced bacterial load, improved survival in murine models (Blakney et al. 2019).	Preclinical
Pseudomonas aeruginosa	PcrV, OprF‐I	LNPs	Elicited mixed Th1/Th2 responses, reduced lung colonization and improved survival in mice.	Preclinical
Streptococcus pneumoniae	PsaA, PhtD	LNP‐mRNA	Induced broad immune responses, reduced pneumococcal colonization, enhanced bacterial clearance in mice.	Preclinical
Escherichia coli	FimH, OmpA	LNPs	Enhanced mucosal immunity, showed protection against intestinal E. coli infections in animal models.	Preclinical
Yersinia pestis	F1 antigen	LNP‐mRNA	Induced both humoral and cellular immune responses, provided protection against Y. pestis in mouse models.	Preclinical
Staphylococcus aureus	MntC, SEB, HLA, FnBPA, IsdB	LNP‐mRNA	The multivalent mRNA‐LNP vaccine against Staphylococcus aureus infection in mouse models demonstrates its great potential in inducing strong humoral and cellular immune responses (Gao et al. 2025).	Preclinical

Figure 5.

Cross‐pathogen principles of bacterial mRNA vaccine development. Schematic illustration summarizing shared design and immunological principles among bacterial mRNA vaccine models targeting Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae. Each pathogen module integrates multi‐antigen fusion constructs (e.g., Mycobacterium tuberculosis: Ag85B/ESAT‐6/CFP‐10; Pseudomonas aeruginosa: PcrV/OprF; Streptococcus pneumoniae: PsaA/PhtD), self‐amplifying or LNP‐formulated mRNA platforms, and induction of Th1/Th17‐biased immune responses. The figure highlights convergent strategies—including multi‐antigen design, saRNA/LNP delivery optimization, and cellular‐mediated immunity—that collectively reduce bacterial load and enhance protective efficacy across diverse infection models. These examples are intended to illustrate emerging design principles rather than direct indicators of clinical readiness.

At the same time, this literature should be interpreted with appropriate caution. Most currently available datasets remain confined to murine models, often under highly controlled challenge conditions, and efficacy readouts such as survival or log‐scale reductions in colony‐forming units do not necessarily predict durability, mucosal protection, or clinical benefit in humans. Differences in host susceptibility, infection kinetics, tissue tropism, and Th1/Th17 immune programming may substantially influence how well these preclinical findings translate across species. The studies discussed below should therefore be viewed primarily as early‐stage demonstrations of feasibility rather than as definitive indicators of clinical readiness.

5.1. mRNA Vaccines Against Mycobacterium Tuberculosis

Recent studies employing self‐amplifying mRNA (saRNA) or conventional mRNA encoding immunodominant antigens, such as Ag85 family proteins, ESAT‐6, and CFP‐10 have demonstrated potent Th1/Th17 activation in preclinical models (Musvosvi et al. 2023; Huang et al. 2020). In particular, an LNP‐mRNA vaccine encoding the CysVac2 fusion antigen (mRNA‐CV2) induced polyfunctional Th1 CD4⁺ responses and conferred ~0.7–0.9 log10 CFU reductions in lung bacterial burden compared with controls; when used as a BCG booster, it further enhanced pulmonary protection and innate/adaptive cell trafficking, supporting its utility in heterologous prime–boost regimens (Gause et al. 2017; Lukeman et al. 2025).

Design refinements at the RNA level also matter. A cap‐optimized multiepitope ESAT‐6 mRNA formulation elicited stronger cellular and humoral responses than BCG in head‐to‐head murine comparisons, underscoring how transcript engineering can translate into superior immunogenicity even against difficult antigens (Kozlova et al. 2024; Vanderschueren et al. 1994).

Beyond single constructs, multivalent/fusion designs and heterologous schedules show additive benefits. Reviews and comparative studies indicate that combining mRNA with protein subunits can improve protection—for example, mRNA‐prime/protein‐boost strategies achieved ≈0.85 log10 additional reductions in lung CFU over single‐modality vaccination, aligning with the field's shift toward modular, programmable regimens (Rezk and McClean 2025).

Formulation advances remain pivotal: LNP optimization (ionizable lipids/PEG architecture) and dose‐sparing saRNA platforms are being leveraged to prolong antigen expression while tempering reactogenicity—principles now recurrent across TB mRNA pipelines and increasingly validated in multi‐center preclinical reports (De Voss et al. 2025).

Despite these encouraging findings, important translational uncertainties remain. Protective readouts in murine tuberculosis models may be strongly influenced by strain background, vaccination schedule, infectious dose, and the specific challenge system used. Moreover, a reduction in lung bacterial burden, while informative, does not fully capture the complexity of human tuberculosis, including granuloma heterogeneity, latent infection dynamics, and long‐term immune containment. As a result, current TB mRNA vaccine studies are valuable for mechanistic prioritization, but they should not yet be overinterpreted as direct surrogates of human efficacy.

5.2. mRNA Vaccines Targeting Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major opportunistic pathogen responsible for severe hospital‐acquired infections, especially in immunocompromised and cystic fibrosis patients (Montemari et al. 2022). Its intrinsic multidrug resistance, quorum sensing, and biofilm formation make it particularly refractory to traditional vaccine approaches.

Recent efforts have centered on mRNA vaccines encoding components of the type III secretion system (T3SS)—a conserved virulence apparatus essential for epithelial invasion and immune evasion (Asif et al. 2025). Among these, LNP‐formulated mRNAs encoding the T3SS tip protein PcrV or the outer membrane protein OprF‐I elicited robust humoral and cellular immune responses in BALB/c mice. Two intramuscular doses (5 or 25 µg, 2 weeks apart) generated high titers of antigen‐specific total IgG, IgG1, and IgG2a, with a modest Th1 bias (IgG2a > IgG1). The geometric mean titers (GMTs) of anti‐PcrV and anti‐OprF‐I IgG exceeded those of protein‐based counterparts by approximately 4–6 fold, and sera exhibited strong opsonophagocytic killing (OPK) activity against multiple P. aeruginosa strains (Kawaguchi et al. 2023).

In functional protection models, these immune responses translated into striking efficacy. In a burn‐wound infection model challenged with 10× LD₅₀ of P. aeruginosa PAO1 or PA257, both mRNA vaccines achieved 100% survival, whereas protein vaccines achieved 70–80%. Even under a 50× LD₅₀ challenge, PcrV‐mRNA–LNP immunization (5 µg or 25 µg) maintained complete survival, while OprF‐I‐mRNA protected 50–75% of animals. In a systemic infection model, co‐formulated dual‐antigen mRNA vaccines (PcrV + OprF‐I) provided 85% survival, surpassing either single‐antigen mRNA (50–75%) and protein combinations (~50%). Quantitative bacterial enumeration further showed 1–2 log₁₀ reductions in CFU across lungs, liver, spleen, and kidneys, with PcrV‐mRNA consistently yielding the lowest bacterial loads (Wang et al. 2023).

Taken together, these studies support the feasibility of multi‐antigen mRNA vaccination against P. aeruginosa and highlight the value of combining rational antigen selection with optimized LNP delivery. Nevertheless, the apparent magnitude of protection should be interpreted carefully. Burn‐wound and acute systemic challenge models are useful for establishing biological activity, but they do not fully reproduce the chronic airway colonization, biofilm‐associated persistence, host heterogeneity, and inflammatory microenvironments that characterize human P. aeruginosa disease, particularly in cystic fibrosis or ventilator‐associated settings. Thus, while these data are encouraging, they define an important preclinical milestone rather than a resolved translational pathway.

5.3. mRNA Vaccines Against Streptococcus pneumoniae

Streptococcal infections, including pneumonia, meningitis, and sepsis, continue to impose a major global burden. A critical limitation of conventional polysaccharide‐protein conjugate vaccines is their restriction to serotype‐specific protection, necessitating frequent reformulation to cover non‐vaccine serotypes (Rodríguez‐Ortega et al. 2006). mRNA‐based strategies have emerged as a powerful alternative by targeting highly conserved pneumococcal proteins, such as pneumococcal surface adhesin A (PsaA) and pneumococcal histidine triad protein D (PhtD), to elicit broad‐spectrum immunity (Moyer et al. 2016).

A key advancement in this area involves the rational design of multi‐antigen mRNA constructs. For instance, a study by Moyer et al. (2020) demonstrated that encoding a fusion protein of PsaA and PhtD, linked by a flexible (GGGGS) × 3 linker, resulted in superior immunogenicity compared to single antigens or a simple mixture (Bahadori et al. 2024). This linker strategy enhances antigen persistence and promotes proper folding of individual domains, leading to broader B and T cell recognition (Storni et al. 2005). The mRNA‐LNP vaccine encoding this fusion antigen (mRNA‐PA) induced remarkably high and balanced IgG antibody titers (endpoint titers > 10 ^ 6 against both PsaA and PhtD) in mice. More importantly, it elicited a potent Th1‐biased T cell response, evidenced by a significant increase in antigen‐specific IFN‐γ and IL‐2 producing splenocytes (Shafaghi et al. 2023).

This robust systemic and mucosal immunity translated into strong protection in challenge models. In a murine model of pneumococcal colonization, immunization with the fusion antigen mRNA vaccine reduced nasopharyngeal bacterial load by over 100‐fold (2‐log reduction) compared to the control group (Anthi et al. 2025). Furthermore, in a lethal sepsis model, the vaccine provided complete protection against challenge with a highly virulent strain, whereas all control animals succumbed to infection. These findings suggest that rationally designed multi‐antigen mRNA constructs may help address some of the serotype‐related limitations associated with conventional pneumococcal vaccine strategies. However, this possibility remains provisional, as most evidence is still derived from murine colonization or sepsis models that incompletely capture the diversity of human pneumococcal carriage, transmission, age‐dependent susceptibility, and mucosal immune memory. Broader validation in more predictive preclinical systems will be needed before concluding that mRNA platforms can meaningfully overcome serotype replacement or provide durable cross‐serotype protection in humans.

5.4. Other Bacterial mRNA Vaccines

Plague, caused by Yersinia pestis, remains a global health concern. While recombinant subunit vaccines targeting the F1 capsule and LcrV (V) antigens are promising, they can provide incomplete protection against pneumonic plague and often elicit a Th2‐biased response. mRNA vaccines offer a path to enhance immunogenicity and response quality. A direct comparison by Kon et al. (2023) underscores this advantage. They developed an mRNA‐LNP vaccine encoding the Y. pestis V antigen. In murine models, a single 2 μg dose of the mRNA‐V vaccine induced neutralizing antibody titers more than 10‐fold higher than those elicited by an equivalent dose of recombinant V protein adjuvanted with Alum. This enhanced immunogenicity translated to superior protection: in a lethal pneumonic plague challenge, the mRNA‐V vaccine conferred 100% survival, significantly outperforming the partial protection (approx. 60%) offered by the protein subunit vaccine. This study confirms that the mRNA platform not only delivers conserved antigens more effectively but also drives a more favorable Th1‐biased immune response, which is critical for intracellular pathogens.

Staphylococcus aureus, particularly methicillin‐resistant strains (MRSA), is a formidable pathogen whose vaccine development has been plagued by clinical failures, partly due to its extensive immune evasion mechanisms (Gao et al. 2025). A landmark study by Chen et al. presented a breakthrough using a rational multivalent mRNA approach (Gao et al. 2025). The researchers designed a pentavalent mRNA‐LNP vaccine encoding five conserved antigens pivotal to different virulence mechanisms: the detoxified alpha‐hemolysin (HlaH35L), IsaA, MntC, Csa1A, and SdrD. This strategy aimed to neutralize multiple virulence factors simultaneously, disrupt biofilm formation, and promote opsonophagocytosis. In a murine sepsis model, the pentavalent vaccine provided broad protection, achieving 80% to 100% survival against challenges with diverse clinical MRSA isolates, drastically outperforming any single‐antigen formulation. Furthermore, the vaccine demonstrated efficacy in a renal abscess model, reducing bacterial burden in the kidneys by over 1000‐fold (3 log units) compared with controls. The vaccine potently induced antigen‐specific Th1 cells, which are crucial for combating persistent intracellular reservoirs of the bacterium.

Overall, these studies illustrate the breadth and adaptability of the mRNA platform across diverse bacterial pathogens, ranging from single‐antigen constructs to multicomponent cocktails targeting distinct virulence mechanisms. They also reinforce several recurring design principles, including antigen combination, delivery optimization, and the need to engage cellular as well as humoral immunity. At the same time, the field remains early. Most candidates have been evaluated only in small‐animal systems, often with short follow‐up and endpoint‐focused efficacy metrics. Consequently, the major value of these reports lies in establishing conceptual and mechanistic plausibility, while the extent to which these approaches will translate into reproducible, durable, and clinically meaningful protection remains to be determined.

6. Challenges and Future Perspectives of Bacterial mRNA Vaccine Development

Despite the transformative success of mRNA technology in viral vaccinology, its translation to bacterial infections remains both scientifically and clinically challenging. Compared with viruses, bacterial pathogens exhibit far greater antigenic complexity, immune diversity, and more diverse tissue tropisms, all of which complicate vaccine design and evaluation. As a result, the development of bacterial mRNA vaccines must address interconnected challenges spanning antigen selection, immune programming, delivery precision, manufacturability, and translational validation. At the same time, these barriers also create opportunities to reshape antibacterial vaccinology through the convergence of immunology, RNA engineering, materials science, and translational medicine.

6.1. Antigenic Complexity and Rational Target Selection

Bacteria possess multilayered structural and virulence architectures—including surface polysaccharides, secreted toxins, and intracellular effectors—that complicate the selection of protective antigens. Unlike viral spike proteins, which often display relatively clear immunodominance, bacterial antigens are frequently strain‐variable and may require multi‐antigen, fusion‐antigen, or epitope‐combination strategies to ensure broad coverage.

Emerging computational and AI‐guided antigen discovery pipelines are accelerating this process by integrating reverse vaccinology, structural modeling, and immunogenicity prediction (Buckley et al. 2022). Platforms such as AlphaFold2 and variational autoencoder networks enable the rational prioritization of epitopes with cross‐strain conservation, optimized MHC presentation, and minimal immune interference. Accordingly, antigenic diversity is increasingly being approached not merely as a biological obstacle, but as a design variable that can be systematically addressed through data‐driven selection frameworks.

6.2. Immune Polarization and Controlled Innate Activation

Bacterial immunity requires a balanced orchestration of Th1 and Th17 cellular responses alongside humoral protection. The mRNA‐LNP platform has demonstrated the capacity to induce balanced adaptive immunity in viral settings; the immunological requirements for bacterial protection are often more pathogen‐specific and compartment‐dependent. For optimal protection against intracellular pathogens like P. aeruginosa, strategies to further augment its cell‐mediated immunity (CMI) and drive robust Th1‐type responses are highly desirable.

Recent progress includes nucleoside modification (e.g., N1‐methylpseudouridine) to reduce excessive innate activation, self‐amplifying RNA (saRNA) for prolonged antigen expression, and LNP charge tuning to modulate pattern recognition receptor (PRR) signaling (Casmil et al. 2025). Together, these approaches support a more programmable form of innate immune engagement, in which inflammatory tone, antigen persistence, and downstream T‐cell polarization can be more precisely tuned to the needs of antibacterial protection.

6.3. Delivery Precision and Mucosal Targeting

Efficient delivery remains one of the most pressing challenges in bacterial mRNA vaccinology (Gu et al. 2024). Many bacterial infections initiate at mucosal barriers—lungs, gut, or nasopharynx—where conventional intramuscular delivery is insufficient to generate local immunity.

Advances in aerosolized and oral mRNA formulations have enabled site‐specific delivery and activation of tissue‐resident memory (T_RM) responses. Hybrid LNP–polymer systems and peptide‐based mucosal carriers now achieve stable transfection in epithelial and antigen‐presenting cells, as demonstrated in inhalable Mycobacterium tuberculosis and oral H. pylori models. In parallel, lymphatic‐targeted nanocarriers are being designed to coordinate systemic and mucosal immune memory. These developments suggest that the delivery route is no longer merely a pharmacological variable, but an immunological determinant that shapes the anatomical distribution, persistence, and quality of vaccine‐induced protection.

6.4. Manufacturing, Regulatory Translation, and Global Deployment

As bacterial mRNA vaccines move closer to translational consideration, manufacturing and quality control are becoming limiting determinants rather than downstream technical details. This challenge is especially pronounced for multicomponent formulations, including multi‐antigen mRNA cocktails, hybrid nanocarriers, and mucosal delivery systems, all of which introduce additional layers of physicochemical and analytical complexity beyond those encountered in simpler single‐antigen injectable products (Figure 6) (Whitley et al. 2022; Rosa et al. 2021).

Figure 6.

Bacterial mRNA Vaccine Development. Schematic overview illustrating four interrelated dimensions that govern the development of bacterial mRNA vaccines. Antigen Complexity highlights the challenge of selecting protective targets from multilayered bacterial antigens and the role of computational target discovery in improving antigen prioritization. Immune Modulation emphasizes controlled innate activation and the induction of Th1/Th17‐polarized immunity, which are central to effective antibacterial protection. Delivery Precision focuses on mucosal targeting and lipid nanoparticle (LNP) optimization to improve site‐specific mRNA delivery. Manufacturing & Regulation encompasses scalable production and the challenges associated with complex formulation, quality control, and regulatory translation. The central bacterial and pulmonary icons represent the linkage between pathogen‐specific antigen design and anatomically targeted delivery. Circular arrows labeled optimization loop indicate the iterative feedback among antigen design, immune programming, delivery engineering, and translational development. Together, the figure summarizes the major bottlenecks and optimization axes discussed in Section 6, including antigen complexity, immune modulation, delivery precision, and regulatory readiness.

One underappreciated bottleneck is analytical quality control for lipid‐rich nanoparticle formulations. Standard pyrogen and endotoxin testing workflows may be complicated by matrix interference from lipid excipients, surfactants, or complex nanoparticle assemblies, potentially affecting assay accuracy or interpretability.

In this context, reliance on a single conventional assay may be insufficient. Instead, orthogonal strategies incorporating traditional Limulus Amebocyte Lysate (LAL) testing together with newer approaches such as recombinant Factor C (rFC) assays or Monocyte Activation Tests (MAT) may be necessary, with formulation‐specific validation to confirm assay suitability. For bacterial mRNA vaccines, this issue is particularly relevant because product positioning at the interface of bacterial antigens, inflammatory adjuvanticity, and nanoparticle delivery raises the regulatory importance of robust pyrogen assessment (Huang et al. 2023; Leppek et al. 2022).

Batch‐to‐batch consistency also becomes more difficult when multiple mRNA species are co‐formulated. In such settings, regulatory quality cannot be reduced to average particle size or encapsulation efficiency alone. It must also account for the identity, integrity, ratio consistency, and potency of each RNA component, as well as potential drift in lipid composition, encapsulation bias among transcripts, and changes in storage stability over time. These challenges are amplified for formulations encoding detoxified toxins, secreted virulence factors, or structurally complex antigen combinations, where product comparability may depend not only on RNA quality attributes but also on downstream expression behavior and biological potency.

From a regulatory perspective, bacterial mRNA vaccines are unlikely to be evaluated simply as extensions of antiviral mRNA platforms. Although prior experience with prophylactic mRNA vaccines provides a valuable foundation, bacterial applications introduce additional questions regarding antigen complexity, mucosal indication claims, duration of local immunity, toxicity associated with encoded bacterial products, and the establishment of fit‐for‐purpose potency assays. Accordingly, successful translation will require not only scalable manufacturing workflows but also indication‐specific analytical frameworks that integrate chemistry, manufacturing, and controls (CMC) with immunological function and safety evaluation.

Recent industry pipelines help to make these translational challenges more concrete. According to Moderna's official pipeline, two mRNA Lyme disease vaccine programs (mRNA‐1975 and mRNA‐1982) are in Phase 2 development, illustrating that bacterial mRNA vaccination has already advanced beyond conceptual discussion into mid‐stage clinical evaluation. In parallel, CureVac has disclosed a proprietary prophylactic vaccine program against uropathogenic Escherichia coli (UPEC), together with preclinical data and continued development of tailored mRNA‐LNP technologies. These industrial examples indicate that the field is moving toward pathogen‐specific bacterial applications, but they also underscore that successful translation will require not only reusable mRNA backbones but also indication‐specific antigen validation, potency assays, formulation control, and scalable manufacturing workflows.

6.5. Translational Limitations of Current Preclinical Models

A major challenge in the field is that most bacterial mRNA vaccine candidates are still evaluated in preclinical systems with limited predictive value for human efficacy. Murine models remain indispensable for early immunogenicity and challenge studies, but they incompletely recapitulate human mucosal architecture, epithelial barrier biology, innate sensing thresholds, and Th1/Th17 polarization dynamics. As a consequence, outcomes such as survival, bacterial burden reduction, or splenic cytokine readouts—although informative—may overestimate the translational robustness of candidate vaccines.

This limitation is especially relevant for pathogens that colonize mucosal surfaces or establish chronic, compartmentalized infection. In these settings, clinically meaningful protection depends not only on systemic immune activation but also on epithelial transport, local antigen persistence, tissue‐resident memory formation, reactogenicity at barrier tissues, and the balance between protective inflammation and immunopathology. Many of these features are only partially represented in conventional mouse models. Moreover, standardized challenge designs often fail to capture the heterogeneity of human exposure routes, comorbid states, age‐dependent susceptibility, microbiome context, and prior immune history.

To narrow this translational gap, the field will likely need a more diversified preclinical toolbox. Human organoid systems may help model epithelial barrier responses, local antigen expression, and tissue‐specific inflammatory programs. Organ‐on‐a‐chip platforms may further enable dynamic interrogation of mucosal transport, nanoparticle–barrier interactions, leukocyte recruitment, and formulation‐associated toxicity under more physiologically relevant conditions. Although these systems cannot replace in vivo studies, they may serve as valuable intermediate platforms for formulation prioritization, de‐risking of mucosal delivery strategies, and improvement of the predictive validity of preclinical development prior to clinical testing.

6.6. Public Health Integration and Equitable Implementation

Beyond technological feasibility, bacterial mRNA vaccines should also be considered within the broader global strategy for antimicrobial resistance (AMR) control. The WHO Global Action Plan on AMR frames infection prevention as a core pillar of AMR mitigation, and the WHO has highlighted that both wider use of existing vaccines and development of new vaccines against priority pathogens could substantially reduce AMR‐associated mortality and antibiotic consumption. In this context, bacterial mRNA vaccines are potentially valuable not only as novel immunization tools but also as adaptable platform technologies capable of accelerating responses to emerging resistant pathogens.

However, the public‐health value of such vaccines will depend on equitable implementation, especially in low‐ and middle‐income countries (LMICs), where the burden of AMR is greatest. Key barriers include manufacturing cost, cold‐chain and fill‐finish requirements, uneven regulatory capacity, and limited access to technology transfer. WHO has noted that LMICs are disproportionately affected by AMR and that countries seeking local production often face constraints in regulatory systems and technology absorption. These challenges suggest that future bacterial mRNA vaccine strategies should be linked not only to antigen and delivery innovation, but also to access‐oriented manufacturing models, regional production networks, and regulatory strengthening.

These realities suggest that future bacterial mRNA vaccine strategies should be linked not only to advances in antigen design and delivery technology but also to access‐oriented manufacturing models, regional production networks, and regulatory strengthening efforts that enable broader and more equitable deployment.

7. Conclusion

In summary, bacterial mRNA vaccines mark a pivotal frontier in next‐generation immunology and the global fight against antimicrobial resistance (AMR). This technology transcends conventional vaccinology through programmable design, rapid adaptability, and scalable manufacturing—core attributes urgently needed in the post‐antibiotic era. The convergence of synthetic biology, artificial intelligence, and nanotechnology is reshaping the developmental paradigm of bacterial mRNA vaccines (Figure 7). Synthetic biology enables modular antigen engineering beyond protein targets; AI accelerates antigen discovery and mRNA optimization; and advanced delivery systems translate these designs into robust immunity and protection.

Figure 7.

Strategic roadmap for bacterial mRNA vaccines. The convergence of synthetic biology, artificial intelligence, and nanotechnology in advancing bacterial mRNA vaccine development. The central hub represents bacterial mRNA vaccines, while the surrounding domains highlighting key innovation pillars: synthetic biology for modular antigen and non‐protein target engineering; artificial intelligence for antigen prediction and mRNA optimization; and nanotechnology for advanced LNP/polymer delivery and mucosal targeting. The roadmap underscores how these disciplines may converge to support future pathogen‐specific and tissue‐targeted antibacterial vaccine development.

Future innovation will depend on co‐engineering these domains to create multi‐antigen, self‐amplifying, and tissue‐targeted vaccine architectures capable of eliciting durable Th1/Th17 and mucosal immune memory. As the scientific, regulatory, and manufacturing frameworks mature, bacterial mRNA vaccines may become an important component of future infectious disease prevention and biosecurity strategies, particularly for emerging and drug‐resistant pathogens.

Author Contributions

Rui Liao and Mingxing Luo contributed equally to this work. Rui Liao, Mingxing Luo, and Yang Li wrote the manuscript; Qian Wang, Shan Guan, Lifeng Xu, Weijun Zhang, Ping Luo, Ping Cheng, Jingjing Zhang and Jing Yang critically revised all versions of the article. All authors have read and agreed to the submitted version of the manuscript.

Conflicts of Interest

The authors declare no conflicts of interest.

Liao, R. , Luo M., Yang F., et al. 2026. “Bacterial mRNA Vaccines: Programming Immunity Against Antimicrobial Resistance.” Drug Development Research 87: e70335. 10.1002/ddr.70335.

Data Availability Statement

Data sharing is not applicable to this article as no data sets were generated or analyzed during the current study.