Over a ten-year surveillance period, we documented a marked and statistically significant decline in methicillin-resistant Staphylococcus aureus within our institution. MRSA accounted for approximately 38% of S. aureus isolates at its peak in late 2017 but declined steadily to less than 10% by June 2025. Using the non-parametric Theil–Sen estimator, we observed a median weekly reduction of 0.00056 in MRSA proportion—equivalent to an average annual decrease of approximately 2.9 percentage points. This downward monotonic trend was confirmed by the Mann–Kendall test (z = − 9.72, p < 0.001).
Weekly case counts also exhibited a consistent seasonal pattern. Total S. aureus isolations increased predictably from April through July each year, forming a broad mid-year peak. A similar annual harmonic was observed in the MRSA subset, although the effect did not reach conventional statistical significance, likely due to the smaller number of resistant isolates.
The timeline additionally revealed a perturbation associated with the COVID-19 pandemic. During the period of intense viral transmission (March 2020 to February 2022), overall S. aureus incidence increased, primarily driven by methicillin-susceptible strains. Notably, MRSA did not exhibit the surge reported in many high-income settings. Instead, following the peak associated with the Omicron wave, MRSA incidence declined more rapidly (post-peak slope: −0.418 cases per month, p = 0.007), suggesting that pandemic-related pressures did not reverse—and may have even accelerated—the pre-existing downward trend.
These aggregate trends masked substantial clinical heterogeneity. At the departmental level, MRSA accounted for 40% of isolates in General Surgery, compared to only 12% in Nephrology. At the syndromic level, MRSA prevalence ranged from 29% in surgical site infections to 18% in bloodstream infections—the two most frequently observed infectious syndromes. Throughout the decade, male patients contributed the majority of cases and consistently exhibited higher resistance rates than females. Together, these findings depict a hospital where MRSA is broadly in decline, yet persists within specific high-risk departments and clinical syndromes, necessitating targeted infection-control strategies even as the overall trend remains favorable.
Published reports indicate that, prior to the COVID-19 pandemic, MRSA incidence in hospital settings was either stable or declining, but during 2020–2021 many institutions experienced divergent trends—some documenting reductions of 28–41% associated with intensified hand hygiene and PPE use, while others reported increases in MRSA detection, reflecting heterogeneous pandemic impacts [16, 18, 29, 30]. In contrast, our ten-year surveillance at a Mexican university hospital revealed a consistent decline in MRSA prevalence, with no significant surge during the COVID-19 period. Notably, following the Omicron peak, MRSA incidence entered a markedly accelerated decline (βpost-peak = − 0.418 cases·month⁻¹; p = 0.007). These findings underscore a sustained post-pandemic decline in MRSA incidence within a resource-limited Latin American setting.
The progressive decline of MRSA may be multifactorial, involving both epidemiological and microbiological mechanisms. A primary driver is the implementation and intensification of infection control measures in healthcare settings [15, 31, 32]. These include improved hand hygiene, contact precautions, active surveillance, decolonization protocols, and enhanced environmental cleaning [32, 33]. Such interventions have been temporally associated with marked reductions in hospital-onset MRSA infections, particularly in intensive care units, and have been shown to reduce transmission of healthcare-associated MRSA clones such as USA100 in the United States and ST228-I in Europe [31, 33].
Clonal replacement is another important mechanism. Over time, certain epidemic MRSA clones have been supplanted by others with different fitness characteristics [34, 35]. For example, in several European and North American hospitals, older clones (e.g., ST228-I, CC45-MRSA-IV) have been replaced by more successful clones (e.g., CC22-MRSA-IV, CC5-MRSA-II, CC8-IV), which may have altered virulence, transmissibility, or antimicrobial susceptibility profiles [33, 34]. Some of these newer clones exhibit lower levels of antimicrobial resistance, possibly reflecting a fitness advantage in the absence of strong antibiotic selection pressure [36, 37].
Microevolutionary changes within MRSA lineages may also play a role. There is evidence that the maintenance of methicillin resistance, conferred by the mecA gene, imposes a fitness cost on S. aureus in the absence of selective antibiotic pressure [38, 39]. Loss of resistance determinants (e.g., mecA or SCCmec elements) has been observed in certain lineages, leading to the re-emergence of methicillin-susceptible S. aureus (MSSA) from previously resistant backgrounds, particularly when the selective advantage of resistance diminishes due to reduced antibiotic use or effective infection control [38].
The absence of a pronounced MRSA spike may reflect the influence of several mitigating factors. Broad antibiotic de-escalation guidelines implemented during the pandemic likely helped limit unnecessary use of broad-spectrum antibiotics [2, 40]. Additionally, the early adoption of SARS-CoV-2–specific therapeutics may have reduced empiric antibiotic prescribing [41]. Continued MRSA admission screening for patients with severe pneumonia, alongside the sustained implementation of contact precautions, may also have contributed to the stable MRSA proportion during this period [40, 42]. This combination of measures likely preserved previous gains in antimicrobial resistance control and facilitated the accelerated decline in MRSA incidence observed after 2022.
This study has several limitations inherent to its retrospective, single-center design. First, as data were obtained exclusively from laboratory records and clinical registries, the findings may not be generalizable to other institutions, which may differ in epidemiological profiles, diagnostic capacities, or infection control practices. Second, although robust time-series analytical methods and microbiological quality control protocols were employed, no molecular characterization or clonal typing of MRSA strains was conducted, limiting insights into the genetic dynamics underlying the observed decline. Third, case classification was based on electronic medical records, which may introduce misclassification bias or non-systematic data loss. Moreover, although isolates deemed colonizing were excluded, distinguishing colonization from active infection remains inherently challenging in complex clinical contexts. Finally, although significant shifts associated with the COVID-19 pandemic were identified, the potential influence of concurrent external factors—such as changes in clinical workflows, antimicrobial pressure, or hospital occupancy patterns—could not be fully accounted for and may have independently influenced MRSA incidence.
Future research should integrate high-resolution genomic and epidemiologic approaches to deepen our understanding of MRSA dynamics. Whole-genome sequencing of archived isolates will elucidate post-2022 clonal shifts, including potential USA300 incursions, while a multicenter network spanning Western Mexico can validate our seasonal and secular trends across diverse climates. Incorporating antimicrobial-use density metrics into interrupted-time-series analyses will quantify the precise impact of stewardship policies, and patient-level modeling—leveraging variables such as length of stay, device days, and immunosuppression—can refine risk-stratified prevention bundles. Finally, targeted qualitative audits of infection-control practices during surge versus baseline periods will contextualize pandemic-related resilience and inform adaptive strategies for future healthcare crises.