Shifting epidemiology and prevalence of methicillin-resistant Staphylococcus aureus in Indonesia: a systematic review and meta-analysis

1 Introduction

Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the most clinically significant antimicrobial-resistant (AMR) pathogens worldwide, contributing substantially to morbidity, mortality, and healthcare expenditures (1–3). According to the Global Research on Antimicrobial Resistance (GRAM) Study published in The Lancet (2022), MRSA was responsible for an estimated 121,000 deaths directly attributable to antimicrobial resistance in 2019 and was associated with approximately 345,000 deaths globally, making it the leading pathogen–drug combination contributing to AMR mortality worldwide (4). Invasive MRSA infections, including bacteremia, pneumonia, and endocarditis, are associated with significantly higher case-fatality rates compared to methicillin-susceptible strains, with reported mortality ranging from 20% to 40% depending on clinical severity and healthcare setting (5, 6). The expanding distribution of both hospital-associated (HA-MRSA) and community-associated (CA-MRSA) lineages further underscores the urgent need for robust epidemiological surveillance and region-specific burden assessments (7, 8).

Despite advances in infection prevention and antimicrobial stewardship, the burden of resistant bacterial infections continues to increase in many regions, particularly in low- and middle-income countries, where surveillance systems and access to effective treatment remain limited (9). Among priority bacterial pathogens, MRSA remains a major cause of healthcare-associated infections because of its resistance to β-lactam antibiotics, association with prolonged hospitalization, increased healthcare costs, and higher morbidity and mortality (10, 11). Recognizing its substantial clinical and public health impact, the World Health Organization (WHO) continues to identify antibiotic-resistant S. aureus as a high-priority bacterial pathogen requiring strengthened surveillance, infection prevention, and research efforts (12).

The epidemiology of MRSA has evolved considerably over recent decades, with variations observed across geographical regions, healthcare settings, affected populations, and molecular characteristics. In Asia, MRSA continues to be an important cause of healthcare-associated infections, although reported prevalence varies substantially across countries due to differences in surveillance systems, infection prevention practices, antimicrobial stewardship, and diagnostic approaches (11, 13). MRSA also remains a major public health concern across Southeast Asia, where healthcare-associated infections and antimicrobial resistance continue to pose substantial challenges (14). Several countries in the region, including Thailand, Malaysia, Vietnam, and Singapore, have reported persistently high MRSA prevalence in both hospital- and community-associated settings despite ongoing infection prevention and antimicrobial stewardship efforts (15). Differences in healthcare infrastructure, antimicrobial prescribing practices, laboratory diagnostic capacity, and surveillance systems contribute to considerable regional variation in MRSA epidemiology (8, 16). As the largest archipelagic country in Southeast Asia, Indonesia faces additional challenges related to its diverse geography, unequal healthcare access, and fragmented antimicrobial resistance surveillance, underscoring the need for comprehensive national epidemiological evidence (14, 16, 17).

The epidemiology of MRSA in Indonesia remains incompletely characterized, with available data largely derived from single-center studies and limited regional reports. A study conducted at Dr. Soetomo Hospital, Surabaya, reported an MRSA prevalence of 8.1% among patients upon hospital admission (18). Subsequent clinical isolate analyses from the same tertiary center identified MRSA in approximately 28% of S. aureus isolates, particularly from wound and intensive care unit (ICU) specimens (19). Despite these findings, Indonesia lacks a comprehensive national synthesis of MRSA prevalence data, limiting the ability to evaluate temporal shifts in epidemiology, regional distribution patterns, and the overall public health burden. Furthermore, the potential transition from predominantly hospital-associated strains toward increased community dissemination has not been systematically assessed at the national level.

As the epidemiology of MRSA varies across time, settings, and patient populations in Indonesia, interpretation of these patterns may also benefit from consideration of the healthcare delivery context in which MRSA is identified and managed. Differences in burden and distribution can affect care processes such as coordination across services, continuity of care, and the organization of care pathways, which are relevant to hospital care quality (20, 21). In this regard, discussion of shifting MRSA epidemiology may be complemented by a patient-centered care (PCC) perspective, particularly when considering how healthcare providers maintain coordinated and responsive care across the patient pathway.

To address these knowledge gaps, the present study aimed to estimate the pooled prevalence and characterize the evolving epidemiological patterns of MRSA in Indonesia through a systematic review and meta-analysis. Specifically, this review synthesized available evidence on MRSA prevalence across different geographical regions, study periods, healthcare settings, clinical specimen types, and laboratory identification methods to provide a comprehensive national overview of its epidemiological distribution. The study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (22, 23), using a systematic and reproducible approach to identify, appraise, and quantitatively synthesize published observational studies conducted in Indonesia. By integrating fragmented evidence into a robust national estimate, this study aims to improve the understanding of MRSA epidemiology in Indonesia, identify important sources of epidemiological variation, and provide evidence to support infection prevention and control (IPC) strategies, antimicrobial stewardship (AMS) programs, national antimicrobial resistance (AMR) surveillance, and evidence-based public health policy.

2 Materials and methods

This study was conducted as a systematic review and meta-analysis to comprehensively synthesize the available evidence on the prevalence and epidemiological trends of methicillin-resistant Staphylococcus aureus (MRSA) in Indonesia. The primary objective was to estimate the pooled prevalence of MRSA among clinical isolates and to evaluate temporal and regional variations across healthcare settings. The review protocol was prospectively registered in PROSPERO under the registration number CRD420261300013. The study was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines (23).

2.1 Literature search

Electronic databases including PubMed, Scopus, Cochrane Library, and Garuda (Garba Rujukan Digital - Indonesian national database) were systematically searched for studies published between 1 January 2000 and 20 January 2026 reporting the frequency or prevalence of MRSA in healthcare settings of Indonesia. The search strategy was developed using a structured PICO framework and combined controlled vocabulary terms (MeSH) and free-text keywords with Boolean operators (AND/OR). Core search terms included “Staphylococcus aureus,” “MRSA,” “methicillin-resistant Staphylococcus aureus,” “methicillin resistance,” and epidemiological descriptors such as “prevalence,” “epidemiology,” “incidence,” “frequency,” and “distribution,” together with geographic identifiers “Indonesia” or “Indonesian.” Searches were restricted to human studies where applicable.

Database-specific search strings were tailored according to indexing systems and field tags (e.g., MeSH terms in PubMed, TITLE-ABS-KEY in Scopus, and exploded descriptors in the Cochrane Library). The full reproducible search strategies for each database are provided in the Supplementary Materials. In addition to electronic searches, a manual hand-search screening of reference lists from all included articles and relevant reviews was conducted to identify additional eligible studies. Grey literature available within the Garuda database was also screened to minimize publication bias and ensure comprehensive coverage of Indonesian studies.

2.2 Inclusion and exclusion criteria

Original articles were included if they met all of the following criteria: (i) observational study investigating the prevalence, frequency, or proportion of methicillin-resistant Staphylococcus aureus (MRSA) in human populations in Indonesia; (ii) study population derived from healthcare-associated or community settings, including both clinical infections and asymptomatic colonization; (iii) study conducted between 1 January 2000 and 20 January 2026; (iv) study published in English or Indonesian language; and (v) MRSA identified using recognized phenotypic or genotypic laboratory methods in accordance with established standards (e.g., cefoxitin disk diffusion, oxacillin screening, broth microdilution, E-test, or PCR detection of mecA/mecC).

Case reports, small case series, narrative reviews, systematic reviews, conference abstracts without full text, editorials, and interventional studies were excluded. Studies with a total sample size of fewer than 30 cases were also excluded because very small study populations may produce unstable prevalence estimates and reduce the reliability of pooled prevalence analysis. Studies involving non-human subjects, environmental or food isolates, populations outside Indonesia, or those not clearly distinguishing MRSA from methicillin-susceptible Staphylococcus aureus (MSSA) were also excluded. When duplicate or overlapping datasets were identified, the study with the largest sample size or longest study period was retained for analysis.

2.3 Data extraction and definitions

The following data were extracted from each included study: author name, publication year, study period, geographic location, study setting, total sample size, number of Staphylococcus aureus and MRSA isolates, reported MRSA prevalence, specimen source, and diagnostic methods. MRSA was defined based on recognized phenotypic or genotypic identification methods (e.g., cefoxitin or oxacillin testing and/or mecA/mecC detection). Data extraction was conducted independently by two reviewers, and discrepancies were resolved by consensus.

2.4 Quality assessment

The methodological quality of eligible studies was assessed using the Joanna Briggs Institute (JBI) Critical Appraisal Checklist for Studies Reporting Prevalence Data (24). This tool evaluates key methodological domains, including sample representativeness, sampling methods, adequacy of sample size, reliability of outcome measurement, and appropriateness of statistical analysis. The checklist consists of nine items, with each item scored as 1 (yes) or 0 (no/unclear). Studies with a total score of ≥7 were considered to have a low risk of bias. Quality assessment was performed independently by two reviewers, and disagreements were resolved through discussion and consultation with a third reviewer to achieve consensus.

2.5 Meta-analysis

Meta-analysis was performed using the Jamovi software (version 2.3.28). A random-effects model was applied to estimate the pooled prevalence of MRSA, accounting for between-study variability. Statistical heterogeneity was assessed using Cochran’s Q test and the I² statistic. To evaluate potential publication bias, Egger’s weighted regression test was conducted. A P-value of <0.05 was considered statistically significant for publication bias.

3 Results

3.1 Characteristics of included studies

A total of 342 records were identified through database searching and manual hand-searching. After removal of duplicates (n = 38), 300 studies were screened based on title and abstract, of which 257 were excluded. Forty-three full-text articles were assessed for eligibility, and 17 studies were excluded according to the predefined eligibility criteria, including small sample size (n = 4), abstract-only publications (n = 2), duplicate reports identified during full-text assessment (n = 2), inappropriate patient populations (n = 4), and irrelevant outcomes (n = 5). Consequently, 24 studies were included in the final quantitative synthesis (Figure 1). Among the included studies, four were identified through manual hand-searching of the reference lists of relevant articles because they were not indexed in the predefined electronic databases (PubMed, Scopus, Cochrane Library, and Garuda) but fulfilled all predefined inclusion criteria and provided extractable data on MRSA prevalence among Indonesian populations. To ensure methodological consistency and minimize selection bias, these studies underwent the same screening, eligibility assessment, and methodological quality appraisal as records identified through database searches before being included in the final quantitative synthesis (Figure 1).

The main characteristics of the included studies are summarized in Table 1. The studies were conducted between 2001 and 2025 and covered diverse geographic regions across Indonesia, including Jakarta, West Java, Central Java, East Java, North Sumatra, Bali, South Sulawesi, Jambi, Central Kalimantan, and West Sumatra. Most studies were hospital-based, although community-associated populations were also represented. MRSA isolates were obtained from various clinical specimens, including respiratory tract specimens (encompassing nasal and nasopharyngeal swabs), blood, wound and pus samples, urine, tissue, and other body fluids. All included studies applied recognized phenotypic and/or genotypic methods for MRSA identification, such as disk diffusion, agar dilution, automated systems (e.g., VITEK 2), agglutination assays, and PCR-based detection.

Table 1. Characteristics of studies included in the meta-analysis.

MRSA, methicillin-resistant Staphylococcus aureus; DD, disk diffusion; AM, automatic machine; GS, gram stain; PCR, polymerase chain reaction; NA, not applicable; MLST, multilocus sequence typing; AT, agglutination test; AC, agar culture; MLVA, multilocus variable-number tandem-repeat analysis; AD, agar dilution.

3.2 Risk of bias assessment

Risk of bias was assessed using the Joana Briggs Institute (JBI). Of the 24 included studies, 19 were classified as low risk of bias (score ≥7) and five as moderate risk, with no study rated as high risk overall. Most studies demonstrated appropriate sampling frames, valid MRSA identification methods, and adequate statistical analyses, while moderate ratings were mainly related to sampling procedures or response rate reporting. The study-level and domain-level risk of bias assessments are presented in Figures 2a, b, respectively, generated using the robvis tool.

3.3 Prevalence of methicillin-resistant Staphylococcus aureus strains in clinical samples

The pooled prevalence of MRSA among confirmed Staphylococcus aureus isolates in Indonesia was 41% (95% CI: 27%–56%), based on 24 studies including 1,650 MRSA cases out of 4,920 isolates (Table 2). Temporal subgroup analysis demonstrated notable variation, with prevalence estimates increasing from 6% (2001–2010) to 59% (2019–2024), although substantial heterogeneity was observed across all periods (I² >96%, P < 0.001). Specimen-based analysis (Table 3) showed an overall pooled prevalence of 39% (95% CI: 24%–53%), with respiratory tract specimens exhibiting the highest prevalence (44%), followed by blood (37%) and wound samples (25%). Geographical stratification (Table 4) revealed marked regional disparities, with the highest pooled prevalence observed in North Sumatra and several provinces outside Java, whereas lower estimates were reported in Jakarta and Bali. The spatial distribution of MRSA across provinces is illustrated in Figure 3.

Table 2. Meta-analysis of the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infections in Indonesia.

CI, confidence interval.

Weighted mean of prevalence.

n, number of events (MRSA isolates); N, total number of Staphylococcus aureus.

Table 3. Meta-analysis of the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infections in blood, wound and respiratory tract samples in Indonesia.

CI, confidence interval.

Weighted mean of prevalence.

n, number of events (MRSA isolates); N, total number of Staphylococcus aureus.

Table 4. Meta-analysis of the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infections in different parts of Indonesia.

CI, confidence interval.

Weighted mean of prevalence.

n, number of events (MRSA isolates); N, total number of Staphylococcus aureus.

Subgroup analysis according to laboratory identification method (Table 5) included 22 studies, comprising 11 studies that identified MRSA using phenotypic methods alone and 11 studies that employed phenotypic methods with molecular confirmation. Phenotypic identification included conventional antimicrobial susceptibility testing methods such as cefoxitin or oxacillin disk diffusion, automated susceptibility testing systems (e.g., VITEK 2 Compact and BD Phoenix M50), agar dilution, agglutination assays, and related phenotypic approaches. Studies with molecular confirmation primarily used PCR, with several studies additionally performing molecular typing techniques such as multilocus sequence typing (MLST) and multiple-locus variable-number tandem-repeat analysis (MLVA). The pooled prevalence of MRSA was 41% (95% CI: 20%–61%) among studies using phenotypic methods only and 41% (95% CI: 17%–66%) among studies using phenotypic methods with molecular confirmation.

Table 5. Subgroup meta-analysis of MRSA prevalence according to laboratory identification method.

CI, confidence interval.

Weighted mean of prevalence.

n, number of events (MRSA isolates); N, total number of Staphylococcus aureus.

The forest plot (Figure 4) demonstrates considerable variability in prevalence estimates across individual studies, with wide confidence intervals supporting the application of a random-effects model. Consistent with statistical findings, heterogeneity was high in most subgroup analyses. The funnel plot (Figure 5) appeared relatively symmetrical, and Begg’s and Egger’s tests did not indicate significant publication bias in the overall analysis (P >0.05), suggesting that small-study effects were unlikely to substantially influence the pooled prevalence estimate.

4 Discussion

This systematic review and meta-analysis provides the first comprehensive national synthesis of MRSA prevalence in Indonesia. The pooled prevalence of MRSA among confirmed Staphylococcus aureus isolates was 41% (95% CI: 27%–56%) (Table 2), indicating that nearly two out of five S. aureus infections in Indonesia are methicillin-resistant. This substantial burden places Indonesia within the higher endemic range reported in Southeast Asia, where hospital-based MRSA prevalence has frequently exceeded 30%, particularly in tertiary-care centers in countries such as Thailand, Vietnam, and Malaysia (25–27). A multicenter surveillance analysis from the Asia-Pacific region similarly demonstrated persistently high MRSA proportions among invasive S. aureus isolates (28). Considering that MRSA was responsible for approximately 121,000 deaths directly attributable to antimicrobial resistance globally in 2019 (4), the continued high prevalence observed in Indonesia represents a clinically and epidemiologically significant concern.

The subgroup analyses performed in this study indicate that the epidemiological patterns of MRSA in Indonesia have changed over time and vary across multiple epidemiological dimensions. This interpretation is supported by several findings from the present meta-analysis. First, subgroup analyses demonstrated temporal variation in MRSA prevalence across different study periods, indicating that the epidemiological burden of MRSA in Indonesia has evolved over time rather than remaining constant. Second, substantial geographic variation was observed, with MRSA reported across multiple provinces and healthcare institutions, suggesting a broader distribution beyond isolated healthcare facilities. Third, marked differences in MRSA prevalence among clinical specimen types and healthcare settings reflect the heterogeneous nature of MRSA transmission and its occurrence across diverse patient populations. Furthermore, subgroup analyses according to laboratory diagnostic methods demonstrated differences in prevalence estimates between studies using phenotypic methods alone and those incorporating molecular confirmation, underscoring the influence of diagnostic approaches on epidemiological estimates. Taken together, these findings indicate that the epidemiology of MRSA in Indonesia is dynamic and increasingly heterogeneous, supporting the concept of evolving epidemiological patterns rather than a uniform nationwide distribution. Globally, MRSA epidemiology has evolved from primarily hospital-acquired outbreaks to widespread dissemination of both hospital-associated (HA-MRSA) and community-associated (CA-MRSA) lineages (7, 8). Molecular epidemiology studies from Indonesia have demonstrated circulation of mecA-positive strains and PVL-associated clones in both healthcare and community settings (29–31), supporting the possibility of cross-transmission dynamics. The specimen-specific subgroup analysis further demonstrated marked variation in MRSA prevalence, with respiratory tract specimens showing the highest pooled prevalence, followed by blood and wound specimens. The higher prevalence observed in respiratory and colonization-associated specimens aligns with evidence that nasal and upper respiratory carriage serve as important reservoirs for transmission and subsequent invasive infection (32, 33). In contrast, bloodstream and wound specimens are more likely to represent invasive infections occurring in hospitalized patients, reflecting differences in patient populations, clinical severity, and healthcare exposure. These variations across specimen types may also be influenced by specimen collection practices and laboratory diagnostic approaches, which could partly contribute to the heterogeneity observed among the included studies. Furthermore, regional disparities across provinces (Table 4; Figure 3) may reflect heterogeneity in referral patterns, healthcare density, local prescribing behavior, and infection control compliance rather than purely microbiological differences.

Despite substantial heterogeneity across studies, the methodological quality was generally acceptable, with most studies classified as low risk of bias (Figure 2). The dispersion of effect sizes in the forest plot (Figure 4) supports the appropriateness of a random-effects model, while the symmetrical appearance of the funnel plot (Figure 5) and non-significant Begg’s and Egger’s tests suggest minimal publication bias. Nevertheless, the very high heterogeneity (I² >96%) suggests substantial variability among the included studies and should be considered when interpreting the pooled prevalence estimates. This variability likely reflects differences in study populations, healthcare settings, geographical regions, specimen types, laboratory diagnostic methods, and study periods rather than methodological shortcomings alone. The use of a random-effects model and subgroup analyses was intended to account for these differences and to provide a more comprehensive understanding of the epidemiological diversity of MRSA across Indonesia. Several limitations should be considered. The substantial heterogeneity across studies indicates variability in design, sampling methods, and laboratory diagnostics that may influence pooled estimates. Most included studies were hospital-based, potentially overestimating the national burden and limiting generalizability to community settings. In addition, several Indonesian regions remain underrepresented, restricting the ability to fully describe nationwide epidemiological trends. The included studies also varied in laboratory diagnostic approaches, with some relying solely on phenotypic methods and others incorporating molecular confirmation, which may have influenced MRSA prevalence estimates. Furthermore, insufficient reporting of molecular epidemiological characteristics and the inconsistent classification of hospital-associated and community-associated MRSA limited our ability to perform more detailed subgroup analyses according to MRSA lineage or transmission setting.

The findings of this review indicate that MRSA in Indonesia should be considered not only as an antimicrobial resistance and infection prevention issue, but also in relation to how care is organized and delivered in tertiary healthcare settings, such as hospitals. From a patient-centered care (PCC) perspective, MRSA management often involves multiple care steps, including diagnosis, infection-control precautions, treatment decisions, inter-unit coordination, and discharge planning. The quality of care depends not only on technical correctness but also on continuity and coordination across the patient pathway. This perspective is consistent with the PCC paradigm, which emphasizes integrated care pathways, patient involvement, and organizational alignment rather than isolated provider actions (20, 21).

A practical implication is that MRSA can serve as a tracer condition for assessing PCC functioning in routine hospital care. Hospitals may be technically compliant with infection-control procedures yet still experience gaps in patient-facing care if transitions, education, and coordination are fragmented. Recent evidence on multidrug-resistant organism (MDRO) patient experiences and infection prevention communication also supports the importance of clear education and context-appropriate communication in infection-related care pathways (34, 35).

At the systems level, MRSA surveillance findings may be more useful when linked to hospital decision-making and service improvement, rather than interpreted only as aggregate epidemiological indicators (36, 37). For Indonesian healthcare providers and hospitals, this supports a pathway-based approach in which Infection Prevention and Control (IPC), Antimicrobial Stewardship (AMS), and hospital quality teams are aligned to maintain both technical quality and patient-centered care in MRSA management (20, 21, 36).

The findings of this study indicate that changes in MRSA epidemiology in Indonesia are reflected by temporal variation in prevalence, differences in geographic distribution, variation across clinical specimen types, diversity of healthcare settings, and differences in laboratory detection approaches. Together, these findings suggest that the epidemiological patterns of MRSA are becoming increasingly heterogeneous rather than remaining confined to a single healthcare setting or population. Antimicrobial resistance should therefore be interpreted not only as a microbiological surveillance problem, but also as a healthcare delivery and quality improvement problem. MRSA burden varies across settings and clinical pathways. Hospitals may face increasing demands on care coordination, continuity of care, patient education, and cross-unit communication, all of which are central to PCC and integrated clinical pathway implementation. In this sense, MRSA can be viewed as a tracer of how well healthcare providers, such as hospitals, are able to leverage epidemiology and antimicrobial resistance data into service redesign and hospital quality improvement (20, 21, 37).

Overall, these findings indicate that MRSA continues to represent a persistent and potentially expanding antimicrobial resistance challenge in Indonesia. Strengthening national AMR surveillance systems, harmonizing laboratory diagnostic standards, implementing routine admission screening in high-risk units, and reinforcing antimicrobial stewardship programs are critical strategies to reduce transmission and mitigate clinical impact. Continued molecular surveillance will also be essential to monitor clonal evolution and guide targeted infection control policies. Greater standardization of surveillance methodologies and reporting practices would improve the comparability of future studies and strengthen epidemiological monitoring in Indonesia.

5 Conclusion

This systematic review and meta-analysis demonstrate that MRSA remains highly prevalent in Indonesia, with nearly two out of five Staphylococcus aureus isolates exhibiting methicillin resistance. The findings indicate sustained endemic transmission, regional disparities, and substantial heterogeneity across clinical settings. Despite acceptable methodological quality and minimal publication bias, gaps in nationwide surveillance persist. Strengthening antimicrobial stewardship, standardizing laboratory diagnostics, expanding regional surveillance coverage, and integrating molecular epidemiological monitoring into national AMR programs are essential to mitigate the ongoing and potentially expanding burden of MRSA in Indonesia.

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Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fitd.2026.1847829/full#supplementary-material

Supplementary material Supplementary material at the source

Footnotes

Edited by: Dushyant Dudhagara, Bhakta Kavi Narsinh Mehta University, India

Reviewed by: Adhi Kristianto Sugianli, Padjadjaran University, Indonesia

Raquel Nunes, Federal University of Rio de Janeiro, Brazil