The missing link in combating antimicrobial resistance: leveraging vaccines for prevention

Abstract

Antimicrobial resistance (AMR) threatens to claim 10 million lives annually by 2050, yet vaccines—proven tools to prevent infections and reduce antibiotic use—remain underutilized in AMR strategies. Despite evidence that pediatric vaccination could prevent 181,500 AMR-associated deaths annually in low- and middle-income countries (LMICs) and that pneumococcal conjugate vaccines reduce nonsusceptible infections by 56.9%, vaccines are rarely integrated into National AMR Action Plans with explicit targets, financing mechanisms, or surveillance linkages. AMR and immunization programs operate as separate vertical structures with different champions, financing streams, and data systems. This siloed approach prevents operationalization of vaccine-AMR evidence into policy and limits coordinated action. National AMR Action Plans prioritize stewardship, surveillance, and drug discovery while overlooking vaccines’ role in reducing infection burden, limiting resistant pathogen circulation, and decreasing antibiotic consumption. This commentary argues that vaccines must be treated as core AMR infrastructure in LMICs, requiring five governance shifts: (1) institutionalized collaboration between immunization and AMR stakeholders; (2) vaccine coverage targets embedded in AMR action plans; (3) coordinated surveillance linking immunization registries with AMR data systems; (4) financing mechanisms recognizing vaccines as AMR infrastructure investments; and (5) research prioritizing next-generation vaccines against resistant pathogens. Drawing on efforts in the Philippines to convene physician societies, government agencies leading AMR and immunization efforts, and academic institutions, we demonstrate how these shifts can be piloted through a formal AMR-Vaccine Network, offering a testable model for operationalizing vaccine-AMR integration in LMICs. The challenge extends beyond establishing the evidence base to operationalizing that evidence through governance reform.

Summary box

• Vaccines are powerful yet underused tools to reduce infections, antibiotic use, and resistance, particularly in low- and middle-income countries (LMICs).

• Vaccines must be treated as core AMR infrastructure, integrating them into governance, financing, and surveillance systems of national action plans.

• Five governance shifts are proposed: institutionalized collaboration between immunization and AMR stakeholders, vaccine coverage targets embedded in AMR action plans, surveillance integration linking immunization and AMR data, dedicated budget lines for vaccines as AMR investments, and R&D prioritizing vaccines against resistant pathogens.

• The Philippines offers a testable pilot model for LMICs to establish a formal AMR-Vaccine network, considering the groundwork that has already been started.

• Success requires action from three sectors. Policymakers must embed vaccine targets in AMR action plans. Professional societies must champion integration through clinical guidelines. The global health community must support LMIC-led pilots through technical assistance and funding.

Introduction

In children, pneumonia is often viral, accounting for roughly 61% of radiographically confirmed cases requiring hospital admission, with the respiratory syncytial virus (RSV) contributing the largest fraction [1]. Despite this, bacteria remain more common in very severe pneumonia cases than in severe cases. The bacterium most likely responsible, and identified as the leading cause of lower respiratory tract infection mortality across all age groups, Streptococcus pneumoniae, is one we can already prevent [2]. Safe and effective vaccines, covering some but not all serotypes, exist, yet when coverage is inadequate or delayed, antibiotics become the default, making each unnecessary prescription feed the wider crisis of antimicrobial resistance (AMR).

Across many communities, children with vaccine-preventable diseases (VPDs) are prescribed antibiotics “just in case,” due to limited diagnostic capacity, insufficient provider training, unclear treatment guidelines, or pressure from caregivers demanding antibiotics. Adolescents or adults with influenza are also prescribed broad-spectrum antibiotics when vaccination could have prevented infection. There exist safe and effective vaccines against the three leading causative agents of lower respiratory tract infections, namely pneumococcus, H. influenzae type b, and the influenza virus [2], with many LMICs including the Philippines integrating these into their national immunization program. Vaccines could reduce illness burden, treatment costs, and antibiotic misuse. Meanwhile, RSV still lacks routine programmatic immunization in most places.

The integration of vaccination and AMR agendas, especially within LMIC health priorities, is yet to be fully realized. Stewardship, surveillance, and drug-discovery dominate National Action Plans on AMR, while the role of vaccines in reducing infections, limiting resistant pathogen circulation, curbing secondary bacterial infections, and decreasing selective pressure remains underrecognized [3–6]. Without integration, we overlook one of the most effective tools to reduce resistance. The new frontier of AMR also looms with Gram-negative infections, such as Klebsiella pneumoniae [7] and Pseudomonas aeruginosa [8], alongside viral threats like RSV [9]. By 2050, drug-resistant infections could claim 10 million lives annually and cost USD$ 100 trillion of economic output [10]. Vaccine programs have long been vertical structures with dedicated staff, and financing streams, whereas AMR National Action Plans (NAPs), driven only after the 2016 WHO Global Action Plan, still face resource constraints [11]. Only 11% of countries finance their NAPs through national budgets [12] with many lagging in budgeted, multisectoral implementation [13]. This funding and structural imbalance is especially problematic in LMICs, where the double burden of VPDs and drug-resistant infections is greatest [14]. Applying an “AMR lens” to immunization offers a practical route to link vaccination and AMR agendas for maximal public health impact.

Vaccines must be treated as core AMR infrastructure by leveraging on established immunization programs and embedding an AMR lens into vaccination priorities, targets, financing, and data systems. This commentary argues that national AMR strategies in LMICs must treat vaccines as core preventive infrastructure, with dedicated targets, financing mechanisms, and integrated data systems that explicitly measure and value their contribution to reducing antibiotic use and resistant infections. Integration requires five governance shifts in the LMIC health sector: (1) stronger collaboration between vaccine and AMR stakeholders across clinical, public health, academia, and private sector; (2) target-setting to measure vaccine contributions to AMR reduction; (3) coordinated epidemiological surveillance to break siloed systems, and enhance laboratory surveillance; (4) advocacy for greater financing allocation for using new vaccines, life-course immunization, and high risk group immunization; and (5) sustained research and innovation on vaccines targeting resistant pathogens and their AMR impact. Drawing on the integration efforts being done in the Philippines, we demonstrate how these shifts can be piloted, offering a replicable model for other LMICs [15].

Added value of vaccines as AMR prevention tools

The impact of vaccines is often measured through reductions in infection severity and incidence, yet rarely measured by the antibiotic prescriptions avoided. The value of vaccines can also be seen in reductions in the incidence and prevalence of resistant infections, fewer hospitalizations and deaths linked to AMR, and even decreases in resistant organisms circulating in the environment.

Quantitative evidence demonstrates substantial potential of vaccines to mitigate AMR. In terms of mortality, a recent modeling study estimated that pediatric vaccination in LMICs could prevent approximately 181,500 AMR-associated deaths each year [16]. In terms of morbidity, pneumococcal conjugate vaccines reduce nonsusceptible pneumococcal infections by 56.9% and carriage of nonsusceptible pneumococci by 28.1% [17]. Additionally, projection studies done in China reveal AMR-related cost reductions of US$371 million, as steadily-increasing PCV coverage could reduce antibiotic resistance to penicillin by 6.6%, amoxicillin by 10.9%, and third-generation cephalosporins by 9.8% over five years [18]. Influenza vaccination was also found to reduce antibiotic courses by 28.1% among healthy adults [19].

To make this value visible, health systems should track antibiotic courses averted for common respiratory and diarrheal diseases, resistant cases prevented, and the hospital and household costs avoided. Though exploratory at first, such measures demonstrate to policymakers that vaccines are life-saving and prevent infections, making them integral to national AMR strategies [5, 7].

Five governance shifts to operationalize the vaccine-AMR link

Shift 1: strengthen collaboration between immunization and AMR stakeholders

AMR and immunization programs have traditionally developed separately, and would operate with different champions, financing streams, and data systems. This practice has prevented communication between the two, limiting opportunities for collaboration and coordination.

AMR and immunization governance should be institutionally linked through cross-representation across decision-making bodies and by establishing a joint technical working group or network that meets regularly to review shared indicators, align key messages, and deliver coordinated policy recommendations. Membership should reflect the multisectoral nature of AMR and include representatives from National AMR and immunization programs, professional medical societies, academic institutions, local government units, veterinary and agricultural sectors, and civil society organizations. In the Philippines, groundwork for institutionalized collaboration has begun, as evidenced by a recent stakeholder meeting convening department representatives overseeing AMR and vaccination programs, along with physician societies as champions to chart initial steps toward integration, bringing AMR surveillance and immunization program managers together to identify opportunities for data linkage and joint advocacy [15].

Breaking the siloed systems requires shared efforts to measure vaccine impact on resistance, link immunization and AMR datasets, establish joint dashboards to track progress, and build analytic capacity to act on gathered data. Embedding vaccines into AMR policy dialogues and aligning them with national surveillance will demonstrate that vaccines are essential AMR infrastructure, strengthening national responses and providing a model for other countries in the region.

Shift 2: establish AMR-related vaccine targets and metrics

Current AMR NAPs account for vaccination only to the extent as an infection prevention and control measure, but rarely is it integrated into its strategic objectives or implementation plans [20]. This includes targets for vaccine coverage or contributions to AMR reduction. Without explicit targets, the preventive value of vaccines remains invisible to policymakers and funders.

To address this, vaccine coverage indicators should be embedded into AMR priorities, budgets, and accountability frameworks. Monitoring should use up-to-date population registries for coverage denominators and routinely report the estimated antibiotic courses and resistant infections averted through immunization.

In Pakistan, its AMR NAP 2017–2022 identified typhoid conjugate vaccine (TCV) introduction as a priority response to drug-resistant typhoid, and after the 2016–2019 XDR typhoid outbreak in Sindh, TCV was added to routine immunization in 2019 and incorporated into provincial AMR monitoring [21]. By 2022, TCV coverage reportedly reached 89% in Sindh, alongside a 78% decline in XDR typhoid cases [22].

Embedding vaccination metrics within AMR monitoring frameworks makes prevention visible. Clear targets create accountability and help steer financing. When vaccine performance is written into AMR plans, immunization is recognized as an essential AMR infrastructure.

Shift 3: coordinate epidemiological surveillance linking immunization and AMR data systems

Immunization coverage data and AMR surveillance operate in parallel and rarely intersect, facing challenges to implementation such as data fragmentation, incompatible platforms, and limited laboratory capacity. However, linking these data streams is essential to demonstrate vaccine impact on resistance and guide evidence-based policy.

National surveillance systems should integrate five data streams at facility, subnational, and national levels: (1) vaccination coverage (by vaccine, age, gender, location); (2) disease incidence from sentinel surveillance and notifiable disease reporting; (3) antimicrobial susceptibility testing results and serotype data; (4) antibiotic consumption from pharmaceutical sales and prescription records; and (5) health outcomes including hospitalizations, Disability-Adjusted Life Years, and AMR-attributable mortality rates.

The Philippines Department of Health Antimicrobial Resistance Surveillance Program operates 24 surveillance sites providing pathogen serotype and susceptibility profiles [23]. Linking this laboratory surveillance with immunization registry data through the Field Health Services Information Systems (FHSIS), which tracks the immunization rates in children, would enable quantifying vaccine impact on resistant infections over time [24]. Italy provides a proof-of-concept: a 20-year ecological analysis found negative correlations between influenza vaccination coverage and AMR proportions in E. coli and K. pneumoniae, demonstrating population-level associations between vaccination and reduced resistance [25]. Implementation requires joint dashboards visualizing these linked streams for real-time monitoring, analytic capacity within ministries of health to translate findings into policy, and regional networks to facilitate data sharing and harmonize methods.

Shift 4: advocate for greater financing allocation for vaccination as AMR infrastructure

Vaccines should be financed as AMR infrastructure, in a tiered approach, recognizing that LMICs vary in fiscal capacity, health system maturity, and eligibility for external support. As countries advance toward universal health coverage, vaccination, particularly life-course immunization for elderly and adults with comorbidities, should be included into primary-care insurance benefit packages, positioning them as core primary care entitlements.

Insights from the Philippines’ roundtable on linking AMR and vaccination revealed that supply chain dysfunction is the most pressing barrier to vaccination coverage. Adopting pooled multi-year procurement to secure volume and lower prices, and prioritising vaccines with greatest AMR impact is essential to ensure a continuous and steady supply, such as pneumococcal conjugate vaccine (PCV) and Hib for children, and PCV and influenza for adults with comorbidities, where even partial protection reduces secondary bacterial infections and inappropriate antibiotic use [26].

AMR NAPs should include dedicated budget lines for vaccines with clear evidence against drug-resistant infections and prioritize these as prevention investments. This does not necessarily require new allocations but reorienting existing measures for infection prevention and control toward vaccines with AMR co-benefits can occur within current budget lines while making the AMR rationale justifiable to government spending.

Economic evidence can also guide these decisions. Modeling data suggests TCV introduction is cost-effective at USD$890 per Disability-Adjusted Life Year (DALY) averted into non-outbreak settings, and about USD$ 140 per DALY averted following an outbreak [27]. For Gavi-eligible countries, co-financing arrangements for vaccines offer a practical entry point that aligns immunization with AMR goals [28], thus the need to leverage external financing strategically.

These approaches are complementary to one another, with a phased strategy that might begin with external support for vaccine introduction, transitioning to dedicated AMR NAP budget lines, and ultimately integrating vaccine costs into UHC benefit packages as health systems strengthen. The key principle is that vaccines must be financed as core AMR infrastructure, with the same budgetary visibility and policy priority afforded to antimicrobial stewardship, diagnostics, and surveillance.

Shift 5: invest in research and innovation for next-generation vaccines against resistant pathogens

Even as we leverage existing vaccines, we must also prepare for the next wave of resistant infections. Gram-negative bacteria are already at the heart of the crisis. Klebsiella pneumoniae causes life-threatening intra-abdominal infections often resistant to nearly every available drug, while Escherichia coli, behind most recurrent urinary tract infections, drives repeated cycles of antibiotics, relapse, and rising resistance. Other pathogens such as Neisseria gonorrhoeae and drug-resistant M. tuberculosis increasingly evade available antibiotics [29]. To operationalize vaccines as AMR infrastructure, vaccine development must be framed as part of AMR infrastructure, not as a separate research silo, through the following steps: (1) incorporate resistance burden, and antibiotic consumption into vaccine target selection criteria; (2) establish advance market commitments for vaccines targeting WHO priority pathogens (K. pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa); (3) include AMR-related outcomes (antibiotic courses averted, resistant infection incidence) as secondary endpoints in clinical trials; (4) strengthen capacity in LMIC institutions to conduct vaccine-AMR research; and (5) streamline regulatory approval processes for vaccines with demonstrated AMR benefits. Typhoid conjugate vaccine (TCV) development offers a model, accelerated through Gavi support in response to rising drug-resistant typhoid, post-introduction studies in Pakistan and Zimbabwe are now quantifying TCV’s real-world impact on resistant cases, providing real-world evidence to inform decisions [21, 30]. The WHO estimates that scaling up existing and pipeline vaccines across 23 priority pathogens could reduce antibiotic use by 2.5 billion doses annually [31]. Investment in next-generation vaccines particularly against these Gram-negative bacteria must be recognized as essential AMR infrastructure, with dedicated funding streams, streamlined regulatory pathways, and mechanisms to ensure affordability in LMICs where resistance burdens are highest.

Conclusion

We discuss AMR as an impending crisis while overlooking a practical tool we already have: vaccines. Though vaccines alone will not eliminate AMR, they represent an underutilized prevention strategy with demonstrated efficacy. Each infection averted reduces selection pressure for resistance and decreases population-level antibiotic consumption. The challenge is more than just establishing the evidence base; it is operationalizing that evidence through governance reform.

National AMR action plans must embed vaccine coverage targets alongside antibiotic stewardship metrics. Surveillance systems must link immunization registries with antimicrobial resistance and consumption data to enable population-level impact assessment. Financing mechanisms must recognize vaccines as AMR infrastructure investments deserving dedicated budget allocations.

The Philippines offers a proof-of-concept, with recent efforts [15, 32], that brought together physician societies, government agencies, and academic institutions, demonstrating collective readiness to pilot these shifts through a formal AMR-Vaccine Network. With established AMR surveillance infrastructure and documented policy gaps, the Philippines can generate replicable lessons for other LMICs. Success requires three commitments: policymakers must embed vaccine targets in AMR action plans and create dedicated budget lines; professional medical societies must champion integration through clinical guidelines and advocacy; and the global health community must support LMIC-led pilots through technical assistance and funding.

As resistance continues to erode our therapeutic options, particularly in LMICs where both infectious disease burden and AMR prevalence are highest, vaccines must transition from peripheral considerations to foundational components of comprehensive AMR prevention strategies.

Author contributions

PEL, GA, and JJ conceptualised the commentary. PEL and LEC drafted the initial manuscript and conducted the literature synthesis. PEL, LEC, LP, CFV, NS, MJODL, and JJ contributed to manuscript revisions. All authors reviewed, refined, and approved the final version of the manuscript. PEL is responsible for the overall content as guarantor.

Funding

This work was supported by the International Centre for Antimicrobial Resistance Solutions (ICARS) under the project Advancing Vaccine Uptake to Mitigate Antimicrobial Resistance in Low- and Middle-Income Countries of South- or South-East Asia (Project ID 100049), and by the International Vaccine Institute Europe Regional Office through investment from the Swedish Ministry for Foreign Affairs Grant UD2022/000123.

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.