The COVID-19 pandemic profoundly transformed the global epidemiology of infectious diseases. Beyond curbing viral transmission, public health interventions – including masking, social distancing, and lockdowns – were associated with substantial reductions in several bacterial infections.1,2 In their rigorous epidemiological study conducted in Navarra, Spain, Arregui García and colleagues provide compelling evidence of these shifts in the incidence of invasive pneumococcal disease (IPD).3 The study also yields significant insights into the evolving dynamics of pneumococcal serotypes, persistent challenges for vaccination strategies, and the growing value of genomic epidemiology in understanding IPD transmission and burden.
Their surveillance data from 2018 to 2024 document a dramatic reduction in IPD incidence during the COVID-19 pandemic, decreasing from 11.6 to 5.6 cases per 100,000 population across all age groups and affecting both vaccine-covered and non-vaccine serotypes. Notably, as public health restrictions were lifted, incidence rebounded to near pre-pandemic levels, reaching 13.0 cases per 100,000 in 2023–2024. This pattern of initial decline followed by a post-pandemic surge has been observed in other countries. In Brazil, pneumococcal isolates dropped sharply in 2020 but increased from 2021 to 2022, while in England, IPD incidence in children under 15 exceeded both 2020 and pre-pandemic averages once COVID-19 restrictions were eased.4,5 This rebound highlights the interconnectedness of respiratory pathogens and the profound influence of non-pharmaceutical interventions (NPIs) on their transmission dynamics.
A striking finding in the study by Arregui García and colleagues is the persistence and resurgence of serotype 3, which, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13), remains the most frequent serotype and exhibited a notable increase after NPIs were relaxed.3 Other serotypes, such as 19A and 6C, also remained prevalent during the pandemic in Brazil and were associated with reduced antimicrobial susceptibility.4 These trends highlight potential challenges in vaccine-induced immunity, including immune escape or clonal expansion. Importantly, the increasing circulation of serotypes targeted by newer vaccines, such as PCV15 and PCV20, underscores the relevance of next-generation vaccines in aligning immunization strategies with the evolving pneumococcal landscape and mitigating future disease burden.
Beyond epidemiological trends, the integration of genomic tools represents a paradigm shift in pneumococcal surveillance. By enabling precise serotyping alongside characterization of resistance determinants, virulence factors, and population structure, genomics provides a more nuanced understanding of pneumococcal evolution. The authors’ use of whole-genome sequencing (WGS) for serotyping represents a commendable advancement. This approach, increasingly adopted by leading national surveillance programs, has revealed remarkable serotype and genotype diversity and allowed identification of lineages linked to increased disease severity and antimicrobial resistance.6 Similar genomic studies have elucidated serotype re-emergence in post-vaccine contexts, exemplified by the recent serotype 4 outbreak in Canada, where phylogenetic analyses traced local transmission clusters among vulnerable populations.7 Collectively, these findings highlight the transformative potential of genomic surveillance in detecting evolutionary and epidemiological shifts that traditional phenotypic methods may miss. Although the study by Arregui García and colleagues focuses on Navarra, limiting national or global extrapolation, its adoption of WGS signals a forward-looking commitment to comprehensive and adaptive pneumococcal surveillance. The authors also acknowledge a limitation in serotyping methodology: WGS was introduced only in 2023 to overcome prior technical constraints. Nonetheless, this work exemplifies the critical need for continuous, high-quality surveillance systems capable of responding to evolving epidemiological patterns.
Looking ahead, several critical questions demand urgent investigation: understanding why serotype 3 persists despite vaccination; assessing the real-world impact of PCV15 and PCV20 as their use expands; and leveraging WGS to identify emerging strains with altered resistance or virulence profiles. Vaccine policy must remain dynamic, balancing serotype replacement risks, incorporating new valencies, and monitoring for emerging serotypes. History reminds us that bacterial coinfections can amplify pandemic disease burden: during the 1918 influenza pandemic, pneumococcal coinfections caused a substantial proportion of deaths, and in the COVID-19 pandemic, approximately 10% of severe cases involved pneumococcal coinfection.8 Experimental murine models of influenza- and SARS-CoV-2-pneumococcus coinfection show synergistic increases in bacterial burden and mortality, while combined vaccination provides full protection.9,10 These observations underscore the importance of sustaining – and even intensifying – pneumococcal vaccination during pandemics to mitigate concurrent bacterial complications and reduce post-pandemic morbidity.6
Ultimately, the pandemic's ripple effects on pneumococcal disease remind us that infectious disease control requires an integrative approach, vigilant to microbial adaptation, the evolving interplay between pathogens, and attentive to shifting human behaviours. The Navarra experience shows that the story of IPD is far from static; when “the masks came off,” incidence resurged, highlighting the fragile balance in disease dynamics. The road ahead demands continuous, data-driven vigilance, scientific innovation, and adaptive public health strategies to stay one step ahead of this versatile pathogen.
FundingThe authors have not received funding for this editorial commentary.
Conflicts of interestThe authors have no conflicts of interest.
