Clinical Infectious Diseases

Background: Reactivation of herpes simplex viruses (HSV) can occur in the early post-allogeneic hematopoietic cell transplant (aHCT) period despite antiviral prophylaxis. Few studies have assessed HSV infection in the modern era, in which acyclovir/valacyclovir is recommended for up to 1 year post aHCT. We evaluated the incidence and management of breakthrough HSV during the first 100 days post-aHCT over two decades. Methods: Patients who received their first aHCT at Fred Hutchinson Cancer Center between 2002-2022 were reviewed for breakthrough HSV infection within the first 100 days on prophylaxis (acyclovir 800 mg or valacyclovir 500 mg twice daily). Cases were identified via culture, polymerase chain reaction, and/or direct fluorescent antibody testing; clinical records were reviewed for symptoms, outcomes, and prophylaxis/treatment regimens. Refractory/resistant (R/R) infections were defined according to consensus guidelines. Results: We reviewed data from 4,357 aHCT recipients aged [≥]18 years, among whom 3,749 (86%) were HSV seropositive and 23 developed breakthrough HSV infection (observed probability = 0.6%). Among those who had an infection, the median time from transplant to first positive test was 46 days (IQR: 24.0-69.5). Oral and genital mucosa were the most common sites of infection. In total, 11 of 23 (47.8%) patients with breakthrough HSV developed R/R infection. Conclusions: Breakthrough HSV infections are rare in the first 100 days after aHCT among patients receiving antiviral prophylaxis. Refractory/resistant infections were uncommon but represented almost half of breakthrough cases. Our findings highlight the sustained effectiveness of universal prophylaxis in the early post-transplant period.

Background Community-based tuberculosis screening can identify asymptomatic tuberculosis, but microbiological confirmation has been sputum-dependent. We evaluated the diagnostic performance, yield, and operational characteristics of centralized qPCR testing of community-collected tongue swabs (TS). Methods We conducted a cross-sectional study among household contacts (HHCs; [≥]18 years) of individuals receiving treatment for pulmonary TB in South Africa. During household visits, health workers collected TS specimens and, where possible, sputum, which was tested in participants' homes using Xpert MTB/RIF Ultra. TSs were transported non-refrigerated in molecular transport medium to a distant central laboratory for manual qPCR assay. The primary outcome was diagnostic performance of TS qPCR compared with sputum Xpert Ultra using paired results. Secondary outcomes were diagnostic yield by TS and operational indicators of the centralized testing workflow. Findings 909 HHCs were enrolled; median age 39 years (IQR 28-55), 532 (58.5%) were asymptomatic, 617 (67.9%) were sputum scarce. TS were collected from 901/909 (99.1%) and sputum from 292/909 (32.1%) participants. Among 271 paired TS-sputum results, TS qPCR sensitivity was 60.9% (95% CI 38.5-80.3), specificity 95.2% (91.7-97.5), and overall agreement 92.3% (88.5-95.0). Yield increased from 1.8% (95% CI 1.0-2.8) with symptom-restricted sputum testing to 3.2% (2.1-4.5) with symptom-agnostic sputum testing and 5.9% (4.5-7.7) when TS testing was implemented among sputum-scarce individuals, identifying 25 additional HHCs with positive molecular test results (86.2% increase). Operational indicators demonstrated successful implementation, with 2.3% specimen loss and valid molecular results for 93.8% who provided a TS. Interpretation Despite lower per-test sensitivity than sputum testing, TS may provide a scalable strategy for expanding microbiological screening beyond sputum-dependent pathways, thereby substantially increasing tuberculosis detection among HHCs. Funding U.S. NIH; Australian Department of Foreign Affairs and Trade; UK Foreign, Commonwealth and Development Office

Pregnant women with late latent or latent of unknown duration syphilis are recommended to receive three doses of benzathine penicillin G each 9 or fewer days apart; data on interval variations are limited. We found no significant difference in risk of congenital syphilis between 9-day and 6-8 day dosing intervals.

Background: Pooled testing increases testing efficiency and reduces testing costs. This approach has been recently recommended by the World Health Organization for use with low-complexity nucleic acid amplification TB diagnostics to increase access to testing when resources are constrained. Pooled testing can also be used with novel near point of care tests, and evidence is needed on diagnostic performance of pooled testing in these more portable, lower cost tests. Methods: We evaluated pooled testing on the Pluslife MiniDock MTB assay with stored sputum collected from adults with presumptive TB. We assessed sensitivity and specificity against the reference standard of liquid culture and diagnostic agreement against Xpert MTB/RIF Ultra and individual MiniDock MTB; we also estimated pooled testing efficiency. Results: Swabs from sputum specimens were tested in 287 pools of 3 and on 861 individual tests. Against culture, sensitivity of testing was 88% (87/99, 95%CI, 80-93%) as compared to 89% (88/99, 95%CI, 81-94%) for individual MiniDock MTB testing, with pooled testing specificity of 99% (97-99%) as compared to 95% (94-97%) for individual testing. Pooled testing saved 32% of tests in this population that included 12% (100) people with culture-positive TB. Conclusions: Pooled testing with sputum swabs from three people had similar diagnostic accuracy against TB culture as individual sputum swab testing in this evaluation. These results provide evidence that pooled testing with near point of care tests could help to further reduce testing costs and help to expand access to molecular testing at the lowest levels of the health system.

Background: Vancomycin-resistant Enterococcus (VRE) species are common healthcare-associated pathogens that cause difficult-to-treat infections. Whole genome sequencing of patients has revealed a substantial burden of patient-to-patient VRE transmission in hospitals, with patients in intensive care units (ICUs) at particularly high risk of acquisition. However, few studies adequately characterize the pathways of VRE transmission between patients in acute care settings, a necessary step to identify current gaps in infection prevention practices. By harnessing genomic clustering analyses of whole genome sequences of VRE isolates from patients, environmental surfaces, and healthcare providers (HCP) in ICUs, we aim to reconstruct indirect pathways of pathogen movement to identify patterns of VRE spread and opportunities for transmission prevention. Methods and Findings: We collected daily samples (N = 6848) from ICUs in two hospitals over 13 weeks from four main sampling sources: patients, HCP hands, patient rooms, and shared surfaces. Samples were cultured on selective media and sent for whole genome sequencing (WGS). We used genomic thresholds to identify clusters of related VRE isolates and distinguish unrelated isolates. VRE was detected in samples from 20 out of 322 unique occupant-stays (6.22%). VRE isolates were detected from all sampling sources except for shared surfaces. A total of 44 unique VRE isolates were identified, 43 Enterococcus faecium (VREfm) and one Enterococcus faecalis (VREf). Two distinct patterns of VREfm spread were observed: 1) an outbreak setting with observed patient-to-patient transmission and low VRE diversity, and 2) high VRE diversity and pathogen movement between occupant-stays facilitated by persistent HCP and environmental contamination, but no observed transmission events. VRE detection probabilities were not significantly different between occupant-stays in outbreak and non-outbreak settings (OR = 0.63, 95% CI (0.23, 1.83), p = 0.32). However, inclusion of VRE isolated from non-patient samples increased the number of occupant-stays with VRE detection from 6 to 20, a 3.3-fold increase, as compared to patient samples alone. Inclusion of non-patient samples also increased the number of VRE multi-isolate genomic clusters detected by 7-fold. Our findings are limited because sampling was primarily conducted in ICUs. Due to the combination of short ICU stay durations and imperfect test sensitivity, VRE transmission events were probably underdetected. Conclusions: Our findings characterize the complex nature of VRE transmission pathways in ICU settings. Even without an ongoing outbreak, we found substantial evidence of VRE movement between occupant-stays, facilitated by a combination of HCP hands and environmental surfaces. This study highlights the importance of environmental sampling for understanding VRE transmission potential, which is likely to be underestimated using patient sampling alone. We recommend that future studies incorporate follow-up sampling after discharge to better understand the true burden of transmission.

Background: The relationship between recent viral infection and subsequent susceptibility to, or protection against, other viruses remains unclear, particularly across ages and symptom status. Methods: A prospective cohort study enrolled participants aged 6 months to 49 years in Washington and Oregon, USA, 2022-2024. Weekly nasal swabs were tested for SARS-CoV-2, respiratory syncytial virus (RSV), and influenza A/B; additional swabs were collected during symptomatic illness and were also tested for parainfluenza (PIV) 1-4, endemic human coronaviruses (hCOV), adenovirus, human metapneumovirus, human rhinovirus (hRV), and enteroviruses. Proportional hazards regression models were used to characterize associations between incident symptomatic infection (illness) and history of recent illness due to other viruses (within 1-7, 8-14, 15-30, 31-60, 61-90, 91-180 days), adjusted for geographic region, age, sex, daycare/school/work attendance, household size, and number of children in the household. For SARS-CoV-2, influenza, and RSV, these analyses were repeated to study incidence of infection (including asymptomatic cases). Findings: Of 3,560 participants, 2,969 (83%) had [≥]1 illness over 4,299 person-years. Adjusted hazard ratios (aHRs) in the short term ([≤]2 weeks) after an illness were predominantly below 1, indicating that recent viral illness was often associated with lower risk of subsequent illness with other viruses. Across age groups, recent hRV illness was associated with lower risk of hCOV, PIV, and RSV illness (aHRs 0.07-0.27). SARS-CoV-2 illness was associated with a higher short-term risk of adenovirus and PIV illness (aHRs 3.20-3.33). In children aged 6 months-4 years, recent influenza illness was associated with higher short-term risk of SARS-CoV-2 illness. Including asymptomatic infections generally attenuated these associations. Interpretation: Some viral illnesses may alter short-term susceptibility to subsequent viral illnesses. Interactions may differ by age and symptom status. Funding: US Centers for Disease Control and Prevention; Washington State Department of Health.

To characterize anti-nucleocapsid (anti-N) IgG binding antibody responses following first PCR-confirmed SARS-CoV-2 infections in a highly vaccinated population, we evaluated antibody boosting and durability in a longitudinal cohort in Michigan. Among 113 participants with paired pre- and post-infection serum specimens tested using a multiplex electrochemiluminescence assay, SARS-CoV-2 infection induced substantial boosting of anti-N IgG concentrations; approximately 80% of participants becoming anti-N seropositive following infection, and 81% of participants demonstrating at least a 4-fold rise in antibody concentrations following infection. Population-level analyses of 66 participants with post-infection serum specimens collected 52-120 days after infection demonstrated sustained anti-N IgG concentrations over time, with no evidence of substantial decline. These findings demonstrate robust boosting and sustained infection-induced anti-N IgG responses in a highly vaccinated population through four months following SARS-CoV-2 infection. This supports the use of anti-N antibodies for longitudinal serosurveillance, including those who are vaccinated.

Background: The HIV reservoir is established within days of infection and persists despite antiretroviral therapy (ART). However, data describing early reservoir decay dynamics and the host immune responses associated with this process remain limited. Methods: We analyzed more than 500 longitudinal blood samples from 67 individuals treated during acute HIV infection. Plasma cytokines and HIV reservoir size (intact and defective DNA) were quantified. Associations between immune markers and reservoir decay following ART initiation were assessed using unsupervised clustering, mixed-effects linear spline models, and nonlinear modeling. Results: Higher levels of IFN-{gamma}, IL-10, IL-18, and TNF- during weeks 24-52 of ART were associated with significantly faster decay of both intact and defective HIV DNA. These relationships were independent of ART initiation timing (days since infection), baseline viremia, initial CD4+ T cell count, and longitudinal CD4:CD8 ratio. Among these cytokines, IL-10 demonstrated the strongest association with accelerated reservoir decay, despite prior evidence linking it to larger reservoirs in SIV models. Discussion: These findings highlight the pleiotropic and stage-dependent roles of cytokines across acute to later stages of HIV, suggesting that a coordinated balance between immune activation and regulation of inflammation may promote early HIV reservoir decay.

In this test-negative study, the effectiveness of the maternal RSVpreF vaccine among infants <6 months was 73.9% against medically attended respiratory syncytial virus (RSV) infection and 86.3% against RSV-associated hospitalization. Maternal RSVpreF and nirsevimab had comparable initial effectiveness, but effectiveness of RSVpreF waned approximately 1.7 times more rapidly.

The WHO has recommended tongue swabs (TS) as alternative samples for microbiological diagnosis of tuberculosis. We evaluated the effects of oral hygiene and food/drink intake on TS performance in South Africa. Food/drink intake prior to sampling marginally decreased Mycobacterium tuberculosis DNA signal strength, but neither behavior decreased diagnostic sensitivity.

Background: Ensitrelvir reduced symptomatic COVID-19 after household exposure in the SCORPIO-PEP trial, but its economic value as post-exposure prophylaxis is unknown. Objective: To estimate the cost-effectiveness of ensitrelvir post-exposure prophylaxis for high-risk household contacts in Japan. Methods: We developed a decision-analytic cost-utility model from the Japanese public healthcare payer perspective. Trial risks of symptomatic COVID-19 through day 10 were linked to Japanese evidence on hospitalization, mortality, costs, quality of life, and life expectancy. Because the trial observed no COVID-19-related hospitalization or death, downstream outcomes were modeled only through prevention of symptomatic disease. We performed deterministic, probabilistic, structural, subgroup, and threshold analyses. Results: Ensitrelvir increased costs by JPY 54,945 and gained 0.003267 QALYs per exposed contact, yielding an ICER of JPY 16.82 million/QALY. None of 10,000 simulations was cost-effective at JPY 5 million/QALY. Applying the overall-trial relative risk to the high-risk baseline yielded JPY 19.24 million/QALY. Restricting post-acute utility loss to 6 months, halving it, or excluding it yielded ICERs of JPY 23.62 million, JPY 26.76 million, and JPY 65.51 million/QALY, respectively. The drug acquisition-cost threshold was JPY 11,021 per course. Conclusions: At current Japanese costs, ensitrelvir post-exposure prophylaxis for high-risk household contacts was unlikely to be cost-effective at JPY 5 million/QALY. This conclusion remained unfavorable under conservative efficacy, post-acute utility, hospitalization-attribution, and mortality assumptions. Severe-outcome benefits remain model-based extrapolations rather than trial-observed effects.

Background: Influenza vaccine effectiveness (VE) is assessed annually through prospective enrollment of patients presenting with acute respiratory symptoms in a test-negative study design. Influenza VE has also been estimated from electronic health record (EHR) databases by linking medical diagnoses, laboratory test results, and patient influenza vaccination. There are limited data on agreement between influenza VE estimates from prospective enrollment versus EHR databases. Methods: The US Influenza Vaccine Effectiveness Network prospectively enrolled outpatients meeting clinical screening criteria and collected respiratory specimens to determine influenza virus infection. Seven study sites also identified EHR databases that included diagnostic codes for outpatient encounters associated with medically attended acute respiratory illness (MAARI), clinical respiratory virus testing, and influenza vaccination status. Effectiveness of influenza vaccination against laboratory-confirmed influenza was estimated from both data sources using logistic regression models including patient age, study site, and month of illness as 100(%) x (1 - adjusted odds ratio), comparing influenza vaccination among laboratory-confirmed influenza-positive patients versus laboratory-confirmed influenza-negative patients. Results: From October 2024--April 2025, 2,016 (30%) of 6,793 prospectively enrolled patients and 75,885 (24%) of 282,444 EHR MAARI encounters had laboratory-confirmed influenza virus infection. Effectiveness of vaccination against laboratory-confirmed influenza was 36% (95% confidence interval [CI]: 26-44) among prospectively enrolled patients and 38% (95% CI: 36-39) among EHR MAARI encounters. Comparing influenza VE estimates from the two data sources, confidence intervals overlapped for all age groups except for adults aged [&ge;]65 years: -3% (95% CI: -53-30) among prospective enrollment versus 35% (95% CI: 32-39) VE from EHR MAARI encounters. Conclusion: Overall, influenza VE estimates from retrospective EHR data were similar to VE estimates using the test-negative design with prospective enrollment. The age group-specific differences in estimated VE observed in US adults aged [&ge;]65 years compared with younger age groups merit further investigation.

Accurate discrimination between viral, bacterial, and inflammatory diseases in febrile children remains a major clinical challenge that contributes to diagnostic uncertainty, inappropriate antimicrobial use, and suboptimal clinical management. Host blood transcriptomics offer a promising strategy to improve diagnostic precision. The present study represents the largest integrative multi-cohort pediatric study of transcriptomic biomarker discovery, validation, and confirmation reported to date, integrating harmonized public transcriptomic datasets with an independent confirmation cohort comprising well-phenotyped patients to identify parsimonious host-response signatures for differentiating viral, bacterial, and inflammatory diseases. Transcriptomic signatures were derived from an integrated retrospective microarray multi-cohort (n=1,683), independently validated in a retrospective RNA-seq cohort (n=767), and confirmed by digital PCR in an independent cohort (n=29), demonstrating reproducibility across patient populations, transcriptomic technologies, and analytical platforms. The analysis identified binary signatures and a unified multiclass classifier that consistently achieved high diagnostic accuracy across all three study phases and outperformed more than 30 published host transcriptomic signatures. Decision curve analysis showed substantially greater clinical net benefit than C-reactive protein across clinically relevant decision thresholds. These findings provide a strong foundation for clinically deployable molecular diagnostics to improve patient triage, antimicrobial stewardship, and precision medicine in childhood infections.

Importance: Maternal vaccination and long-acting monoclonal antibodies are now available in the U.S. to prevent RSV. Long-acting monoclonal antibody administration in the U.S. commonly occurs after hospital discharge in outpatient settings, leaving some infants unprotected early in life when severe RSV risk is highest. Comparative effectiveness between the two interventions and whether delays affect effectiveness estimates have not been quantified. Objective: To evaluate the effectiveness of infant long-acting monoclonal antibody strategies and a maternal vaccination strategy, each compared to no intervention, and the comparative effectiveness of intervention strategies when accounting for real-world delays in monoclonal antibody receipt. Design: Cohort study using target trial emulation to compare four strategies for prevention of RSV-related outcomes. Setting: The U.S. between 2023 and 2025 using a nationwide database of employer-sponsored commercial insurance claims. Participants: 120,586 commercially insured mother-infants, whose infants were born in the U.S. during the 2023-2024 or 2024-2025 RSV season. Infants who could not be paired with their mother's record, did not enroll in commercial insurance within 75 days from birth, received palivizumab, and had an implausible birth date were excluded. Interventions: Comparison of four RSV prevention strategies: (i) maternal RSVpreF; (ii) long-acting monoclonal antibody given within the first week of life (mAb as intended); (iii) long-acting monoclonal antibody given within a six-month grace period from birth (mAb within grace period); and (iv) a control. Main outcomes and measures: Effectiveness against first RSV-associated hospitalization and medically-attended RSV illness was summarized using adjusted hazard ratios (aHR) and estimated using an inverse propensity weighting approach, with weights accounting for maternal age, maternal comorbidities affecting pregnancy, obstetric and newborn complications, season, region, and birth timing relative to October 1. A weighted Kaplan Meier estimator was used to estimate strategy-specific cumulative incidence of RSV outcomes over time. Results: In the first five weeks of life, the mAb within grace period strategy doubled the hazard of RSV hospitalization (aHR: 2.0 [95% CI: 1.0-4.9]) and increased the hazard of medically-attended RSV (aHR: 1.6 [95% CI: 1.0-2.7]) compared to the maternal RSVpreF strategy. The hazard for RSV hospitalization was similar for the mAb as intended strategy compared to the maternal RSVpreF strategy (aHR = 0.9 [95% CI: 0.3-1.9]). Conclusions and relevance: RSVpreF and monoclonal antibodies were similarly effective when monoclonal antibodies were administered close to birth, but when accounting for real-world delays in monoclonal antibody receipt, the maternal RSVpreF strategy was more effective than the mAb within grace period strategy.

Background: Individuals living with HIV have been under-represented in operational research and trials of all-oral regimens for multidrug- and rifampicin-resistant tuberculosis (MDR/RR-TB) treatment. We report outcomes from a prospective observational cohort study of a nine-month regimen comprised of bedaquiline, linezolid, a fluoroquinolone, delamanid, and clofazimine, in Lesotho, a setting with a high prevalence of HIV infection. Methods: We analyzed patients who initiated the regimen between 2020 and 2023. Overall, and by HIV status, we characterized treatment safety by summarizing the frequency and timing of clinically relevant adverse events. We described treatment effectiveness at the end of treatment and sustained treatment success eighteen months after treatment initiation. Results: Two hundred and fifty-five patients who initiated the shortened all-oral regimen were included in the analysis, of whom 161 (63.1%) were living with HIV. Regardless of HIV status, the most frequent clinically relevant adverse event was peripheral neuropathy, followed by myelosuppression. The estimated unadjusted rates of sustained treatment success at 18 months post-treatment initiation were 86.4% (95% confidence interval (CI): 81.4%, 90.5%) overall, 85.0% (95% CI: 78.2%, 90.4%) among patients living with HIV, and 88.8% (95% CI: 80.3%, 94.5%) among people without HIV. Conclusions: The effectiveness of the nine-month all-oral regimen was excellent. Although adverse events were common, they were manageable and did not appear to substantially impact treatment success. Results were similar regardless of HIV status, supporting the use of this regimen in this population.

Evidence on vaccine effectiveness (VE) of 2025-26 COVID-19 vaccines is limited. We estimated VE of BNT162b2 LP.8.1-adapted vaccine among non-immunocompromised adults [&ge;]65 years through December 2025 using linked claims and immunization registry data from two U.S. states. VE against COVID-19-related ED/UC encounters was 48% (95% CI:19, 66).

Seasonal influenza remains a major cause of morbidity and mortality worldwide. Although neuraminidase inhibitors improve outcomes, influenza-related deaths persist. We evaluated the impact of early aspirin (ASA) and non-aspirin nonsteroidal anti-inflammatory drug (NSAID) use on outcomes in adults hospitalized with influenza. This retrospective study included adults admitted to the University of Minnesota Medical Center from 2016 to 2018. Continuous variables were summarized as medians with interquartile ranges (IQRs) and categorical variables as counts and percentages. Group comparisons used Wilcoxon rank-sum, Chi-square, or Fishers exact tests. Analyses included case-control comparisons, assessments by vaccination status, and subgroup analyses by early ASA or NSAID use. Among 2,816 patients, 320 had laboratory-confirmed influenza, with vaccination less common among cases. Unvaccinated patients had higher rates of intensive care unit (ICU) admission (23.6% vs. 11.1%; P = 0.003) and ventilatory support (15.0% vs. 6.1%; P = 0.009). In vaccinated patients, early ASA use was associated with older age and higher in-hospital mortality, whereas early NSAID use was associated with no in-hospital deaths, better one- and three-year survival (P < 0.001), and fewer, though not statistically significant, cardiovascular complications. In unvaccinated patients, ASA use was associated with lower three-year survival (59.1% vs. 79.2%; P = 0.013), while NSAID use was associated with fewer ICU admissions and no cardiovascular or renal complications. In both vaccinated and unvaccinated adults hospitalized with influenza, early NSAID use was associated with improved survival and fewer complications, whereas ASA use was associated with worse outcomes.

Background Clostridioides difficile infections (CDI) continue to cause substantial morbidity and mortality, with increasing incidence in some countries post-COVID-19. Recurrence affects 10-20% of CDI patients: whether risk factors have changed over time is unclear, particularly post-COVID-19. Methods Using electronic health records from hospitals in Oxfordshire, UK, including results from community samples, we estimated the incidence of CDI recurrence across different calendar periods between 2000-2025. To investigate whether risk factors had changed over time, we used interaction tests within multivariable Fine-Gray regression models (modelling death as a competing risk), using backwards elimination, starting from 39 risk factors identified from the literature. Results Recurrence occurred within 1-year in 12.6%, 12.5%, 10.8% and 13.1% of CDI cases in "high virulence" 2003-2008 (n=527), "post-high virulence" 2008-2012 (n=252), "pre-pandemic" 2012-2020 (n=143) and "post-pandemic" 2020-2025 (n=110) periods respectively. The only factor with evidence of variation in its association with recurrence over time was surveillance classification (heterogeneity p=0.019; others p>0.05). Compared with hospital-onset cases, community-onset community-associated cases had increasing recurrence risks over time (subdistribution hazard ratios (SHRs)=2.05 (95% CI 1.27-3.31) in "post-pandemic" and 1.86 (1.16-2.98) in "pre-pandemic"), especially compared to the "high virulence" era of the early 2000s (SHR=0.81 (0.56-1.16)). This heterogeneity persisted after adjusting for baseline blood tests as a marker of severity (heterogeneity p=0.022). Conclusions Compared with hospital-onset hospital-associated cases, recurrence risks increased for community-onset community-associated CDI cases over time. Recurrence is a key contributor to overall CDI incidence and the underlying causes of increasing risks with community-onset community-associated cases should be explored further.

Background Otitis media is a leading cause of childhood morbidity and presents a significant healthcare burden worldwide. Streptococcus pneumoniae is a major aetiological agent of OM, and the introduction of pneumococcal conjugate vaccines into the Malaysian National Immunisation Programme in 2020 would have altered pneumococcal carriage and serotype distribution. This study aimed to determine pneumococcal carriage, serotype distribution, and associated risk factors among children with OM in the early post-PCV era in Peninsular Malaysia. Methods and Findings A total of 360 children with OM were recruited from hospitals on the east and west coasts of Peninsular Malaysia between 2023 and 2025. Nasopharyngeal and middle ear fluid samples were collected for Spn isolation by culture, followed by serotyping using multiplex PCR. Sociodemographic, environmental, and medical history data were analysed for associations with pneumococcal carriage using chi-square, Fishers exact tests, and logistic regression. Pneumococcal carriage was detected in 26.7% of children in either NP or MEF samples, with carriage rates of 25.6% and 1.9% in NP and MEF samples, respectively. The most prevalent serotypes were 23A, 15B/15C, non-typable strains, 19F, and 11A/11D. Daycare attendance (p = 0.012, aOR [95% CI]: 2.177 [1.186 - 3.995] and residence in rural areas (p = 0.019, aOR [95% CI]: 2.476 [1.159 - 5.292] were significantly associated with pneumococcal carriage. The main limitation of the study was the reliance on self-reported questionnaire data, which may have introduced recall bias and reporting errors. Conclusions The predominance of non-vaccine serotypes and non-typable Spn indicates ongoing serotype replacement and the emergence of phase-variant strains in the early post-PCV era. Continued surveillance is essential to monitor these changes and inform the development of next-generation pneumococcal vaccines. This study was registered under clinical trial registration number NCT05429541.

Autoantibodies neutralizing type I IFNs (AAN-IFN-I) have been found in significant proportions of cases of severe, critical, and fatal COVID-19 pneumonia. We performed a systematic review of 54 studies reporting auto-Abs against type I IFNs and a meta-analysis of 20 studies reporting auto-Abs neutralizing type I IFNs published between 2020 and 2026. The meta-analysis included data for 11,380 SARS-CoV-2-infected individuals from Europe, North America, South America, Asia, the Middle East, North Africa and international multicenter cohorts, including 7,814 with severe or critical disease (69%). The pooled prevalence of AAN-IFN-I was estimated at 7.9% (95% CI, 6.0-10.4). Disease severity was strongly associated with AAN-IFN-I prevalence (OR, 11.7; 95%CI, 7.6-17.9; P=5x10^-29). The pooled prevalence of AAN-IFN-I reached 11.4% (95% CI, 10.2-12.7%) in patients with severe or critical COVID-19 and 15.3% (95% CI, 12.1-19.2%) in those who died. The prevalence of AAN-IFN-I increased with age in patients with severe, critical, or fatal COVID-19. AAN-IFN-I probably accounted for about 1.1 million of the 7.1 million deaths from COVID-19. AAN-IFN-I are strong, common, global determinants of life-threatening COVID-19 pneumonia.