Clinical Infectious Diseases
◐ Oxford University Press (OUP)
Preprints posted in the last 7 days, ranked by how well they match Clinical Infectious Diseases's content profile, based on 231 papers previously published here. The average preprint has a 0.20% match score for this journal, so anything above that is already an above-average fit.
Khan, P. Y.; Govender, I.; McCreesh, N.; Sithole, M.; Mkwanzai, E.; Sweeney, S.; Ording-Jespersen, G.; Wong, E. B.; Hanekom, W.; Houben, R. M. G. J.; White, R. G. M. G. J.; Smit, T.; Smith, M. J.; Fielding, K.; Grant, A. D.
Show abstract
Background Tuberculosis remains the leading infectious cause of death worldwide. In the WHO African region, declining incidence has coincided with antiretroviral therapy (ART) scale-up, though whether this reflects reduced progression to disease or reduced transmission is unclear. We evaluated how ART and symptom status influence within-household Mycobacterium tuberculosis complex (MTBC) transmission risk. Methods We conducted a case-contact household study in rural South Africa, enrolling index adults with bacteriologically-confirmed pulmonary tuberculosis. MTBC immunoreactivity was measured in all child household contacts (aged 2-14 years) as a proxy measure of within-household transmission. We assessed the influence of index person ART status and symptom status, and explored effect-measure modification of the association between index person HIV status and transmission risk by sex. Results Among 755 child contacts of 296 index persons, effective ART was not associated with within-household MTBC transmission risk (risk ratio [RR], 1.07; 95% CI, 0.66-1.74). Among PLHIV engaged in ART care, WHO TB four-symptom screen (WHO4SS) status was not associated with transmission risk (RR, 0.80; 95% CI, 0.43-1.47), although absence of reported cough reduced risk (RR, 0.61; 95% CI, 0.38-0.96). A pronounced interaction between sex and HIV status was observed: HIV-negative women had the highest within-household MTBC transmission risk (30.5% vs. 14.3% in women with HIV) whereas risks were similar between HIV-positive and HIV-negative men. Conclusions We found no evidence that effective ART or WHO4SS status influenced within-household MTBC transmission risk, though confidence intervals were wide. Absence of reported cough was associated with lower risk, and transmission risk was highest among child contacts of HIV-negative women. These findings suggest reported cough is a useful marker of transmission risk and that routine tuberculosis screening within ART care may reduce transmission from PLHIV; intensified efforts are nonetheless needed to achieve earlier tuberculosis detection in HIV-negative individuals.
Gupta, M.; Zoega, H.; Stopard, I. J.; Liu, B.; Macartney, K.; Wood, J. G.; Hogan, A. B.
Show abstract
Introduction: Respiratory infections are a leading cause of morbidity. Newly available vaccines to prevent respiratory syncytial virus (RSV) disease and encouraging clinical progress on vaccines for human metapneumovirus (hMPV) and parainfluenza (PIV) could reduce the disease burden beyond existing influenza and SARS-CoV-2 immunisation programs. However, evidence on the contribution of these viruses to respiratory disease burden across the lifespan remains limited. Methods: We reviewed studies from 01/2002-11/2025 reporting age-stratified, medically attended cases of influenza, and at least one of RSV, hMPV, or PIV, in high-income countries, excluding periods substantially overlapping with the COVID-19 pandemic. Using only studies that tested for all four viruses, we estimated the age-specific proportion of cases that were non-influenza (total across RSV, hMPV and PIV) compared to influenza using a mixed-effects logistic regression model. Results: Following exclusions and screening, 61 studies were included in the primary analysis comprising >500,000 detections of the four viruses. We found that a substantial proportion of medically attended respiratory illness in infants and young children was due to PIV, hMPV and RSV, rather than influenza, with a non-influenza virus proportion of 90.2% (95% CI 85.9-93.2%) in young infants aged 0-6 months. The converse was true for school-aged children, with a non-influenza virus proportion of 34.8% (95% CI 26.5-44.2%) in children aged 5-18 years. In adults aged 65+ years, non-influenza causes of medically attended disease were common at 60.2% (95% CI 50.0-69.5%). Restricting to studies reporting hospitalised cases (n=19) produced broadly similar age-specific trends in relative virus burden contributions. Discussion: We highlight the significant burden of medically attended illness due to PIV, hMPV and RSV across ages, particularly in infant and preschool-aged children and older adults, supporting the need for effective vaccines targeting this burden.
Mwenda, M.; Oliveira, R.; Mambwe, B.; Chiyesu, C.; Bohmeier, B.; Mosler, K.; Phiri, M.; Sinyoolo, A.; Chiposa, V.; Namonje, T.; Munsanje, M.; Ilunga, M.; Chirwa, C.; Mwape, I.; Mumba, D.; Coppee, R.; Stoica, M.-A.; Veiga, M. I.; Drakeley, C.; Pearson, R.; Verity, R.; Chirwa, J.; Mockenhaupt, F. P.; Vvn Loon, W.; Portugal, S.; Simulundu, E.; Bwalya, S.; Miller, J. M.; Chilengi, R.; Fanaka, C.; Bridges, D. J.; Hawela, M.; Hendry, J. A.
Show abstract
Background Artemisinin derivatives are central to first-line treatment of both uncomplicated and severe Plasmodium falciparum malaria. Emerging artemisinin partial resistance in East Africa threatens to spread across the continent. Methods In two cross-sectional studies in Zambia in 2024, we genotyped the artemisinin resistance-associated gene Pfkelch13. In Kaoma, western Zambia, we evaluated the percentage of patients with day-3 parasite positivity following treatment with artemisinin-based combination therapy, and ex vivo parasite susceptibility to dihydroartemisinin (the active metabolite of artemisinin). We also assessed longitudinal changes in Pfkelch13 mutation prevalence in Kaoma using isolates collected from 2018 through 2026. Results We identified a novel mutation, Pfkelch13 A724E, in 52% (113 of 217) of isolates from Western Province, 51% (94 of 184) of isolates from North-Western Province, and 11.7% (229 of 1,949) of isolates country-wide. In Kaoma, 28% (21 of 75) of patients carrying Pfkelch13 A724E mutant parasites before treatment were parasite positive on day 3, compared with 0% (0 of 23) of patients with the wild-type allele (P=0.003). Within day-3 positive patients, the proportion of A724E mutant parasites increased significantly after treatment (P = 0.013). The prevalence of Pfkelch13 A724E in Kaoma increased steadily from 0% (95% confidence interval [CI], 0 to 22%) in 2018 to 79% (95% CI, 73 to 85%) in 2026. Conclusions A novel Pfkelch13 mutation conferring partial resistance to artemisinin is spreading in Zambia. Additional clinical evaluations are urgently needed in the region. (Funded by the Gates Foundation, INV-048316).
Jones, L.; Ergas, R.; Tibbs, A.; Russo, E. T.; Norville, J.; Bingay, B.; Brown, C. M.; Reich, N. G.; Pasco, R.
Show abstract
Background Pediatric immunizations for Respiratory Syncytial Virus (RSV), including monoclonal antibodies for infants and vaccines for pregnant people, have become broadly available and can prevent severe RSV outcomes in infants. However, quantifying the impact of RSV immunization in prevention of severe pediatric illness at the population-level is limited by lack of RSV case surveillance data. The Massachusetts Department of Public Health (DPH) conducted a modeling analysis using routine public health surveillance data to estimate the state-level impact of new RSV immunization products on Emergency Department (ED) visits and hospitalizations in Massachusetts for highest risk pediatric groups. Methods A scenario projection tool, called R.Scenario.Vax, was utilized to simulate RSV-associated ED hospital encounters by age group in the context of newly available immunizations. ED visit and hospitalization data from the National Syndromic Surveillance Program (NSSP) during the time period 10/08/2017--10/19/2024 were analyzed, scaled to account for changes in RSV testing practices over time and missing encounter volume in historic data, and utilized to inform model fit of a "typical" RSV season. RSV immunization data from the Massachusetts Immunization Information System (MIIS) for the 2023--2024 and 2024--2025 RSV seasons informed high and moderate pediatric RSV immunization coverage scenarios and their impact was compared to a counterfactual reference scenario of no new immunizations. Median projections were quantitatively and qualitatively compared to observed 2024--2025 season data. Percent reduction in hospital encounters and encounters averted per 10,000 population were calculated for each scenario as compared to the reference. Results Projections for the youngest at-risk age groups showed significantly lower RSV-associated ED visits and hospitalizations during the 2024--2025 season for both high and moderate immunization coverage scenarios. Median projections for infants under 6 months old in the highest coverage scenario, wherein nearly all infants were immunized, showed 72.6% lower ED visits and 73.4% lower hospitalizations when compared to the reference scenario, equating to 262 ED visits and 85 hospitalizations averted per 10,000 population. Conclusions Our results support the use of modeling methods for public health insights and suggest that RSV immunizations for infant populations result in significantly lower RSV-related ED encounters in Massachusetts.
Noviyanti, R.; Setya Utami, R. A.; Smith, L.; Trianty, L.; Ekawati, L.; Sutanto, E.; Amalia, R.; Amelia, A. R.; Hafidzah, M. A.; Fadila, N.; Puspitasari, A. M.; Nisa, F. A.; Hidar, H.; Kariodimedjo, P.; Farinisia, A.; Hutahaean, G.; Christian, M.; Kesuma, T. A.; Subekti, D.; Soebianto, S.; Wulandari, F.; Nuraeni, N.; Budiman, W.; Ertanto, Y.; Widiarta, M. D.; Furkan, F.; Nekkab, N.; Mazhari, R.; White, M.; Robinson, L.; Longley, R.; Baird, J. K.; Mueller, I.
Show abstract
Summary Background Persistent transmission from relapsing Plasmodium vivax infections threatens malaria elimination programs in the Asia-Pacific and Americas. Tools to identify people at risk of relapse are urgently required. We aimed to validate a panel of eight P. vivax serological biomarkers for predicting future relapses. Methods In this observational study, soldiers returning from malaria-endemic Papua to non-endemic East Java, Indonesia, were screened at enrolment using antibody measurement (Luminex) and trained random forest classification algorithms, then followed for 6 months. Active case detection was performed fortnightly by microscopy. Algorithms classified soldiers as recently infected (last nine months) and thus at risk of relapse, based on anti-vivax antibody measurements at enrolment. Findings Between December 2018 and July 2022, 592 soldiers were enrolled, with 553 completing follow-up; 119 experienced a P. vivax relapse. Of these, 102 were correctly classified as at risk of relapse at enrolment, corresponding to 86% sensitivity and 86% specificity, with an AUC of 0.92. Interpretation P. vivax serological biomarkers can identify people at risk of relapse with high sensitivity and specificity and could be used as a novel public health intervention, P. vivax serological testing and treatment (PvSeroTAT), to reduce relapse-driven transmission.
BEAVOGUI, A. H.; Doumbia, S.; Kieh, M.; Leigh, B.; Sow, S.; Lhomme, E.; Ben-Farhat, S.; Dubois Cauwelaert, N.; Roy, C.; Diouf, W.; Idrissa, S.; Diarra, S.; Millimouno, N. P.; Diallo, F. A.; Kamara, M.; Pratt, D.; Dicko, I.; Kennedy, S. B.; Esperou, H.; Choi, E. M.; Kpetigo, A.-M. D.; D'Ortenzio, E.; Diallo, A.; Lancrey-javal, S.; Hamze, B.; Schwimmer, C.; Wiedemann, A.; Ayouba, A.; Peeters, M.; Lane, H. C.; Higgs, E.; Watson-Jones, D.; Yazdanpanah, Y.; Greenwood, B.; RICHERT, L.; Levy, Y.; PREVAC study team,
Show abstract
Background: The World Health Organization has expanded its recommendations for prophylactic Ebola vaccination for at-risk populations. Durable vaccine-induced immunity is important for sustaining outbreak preparedness in regions with recurrent Ebola virus disease (EVD). We assessed five-year persistence of vaccine-induced immune responses in adults and children from the PREVAC trial. Methods: Two large randomised phase 2 trials (NCT02876328), in adults and children aged [≥]1 year, were conducted in four west African countries. Participants were randomly assigned to placebo or to one of three Ebola vaccine strategies: Ad26.ZEBOV followed by MVA-BN-Filo at 56 days; rVSV{Delta}G-ZEBOV-GP followed by placebo; or rVSV{Delta}G-ZEBOV-GP followed by a homologous booster dose at 56 days. After 12 months of follow-up, the primary results were published, participants unblinded to their vaccine assignment, and follow-up continued for 60 months. After Month 24, placebo group recipients were offered active vaccination. Anti Ebola virus glycoprotein Immunoglobulin G (IgG) concentrations were measured for 5 years. Findings: 1401 adults and 1401 children were initially randomized, and 1315 (93.9%) adults and 1322 (94.4%) children attended at least one long-term visit. Retention was high, with 95% followed beyond 1 year and 83% completion at 5-year follow-up. For the three vaccine strategies, antibody geometric mean concentrations (GMC) declined modestly between Months 12 and 24, followed by a stable plateau from Months 24 to 60. At Month 60, antibody GMC were higher in the rVSV-based groups (1099 and 1216 EU/ml for adults; 1982 and 2347 EU/ml for children) than in the Ad26.ZEBOV, MVA-BN-Filo group (252 adults and 645 EU/ml children). Antibody persistence at Month 60 was heterogeneous, varying by age, sex, country, and baseline IgG concentration. Interpretation: Licensed Ebola vaccines induced sustained antibody responses in adults and children for up to 5 years. While the protective antibody level is unknown, these data demonstrate long-lasting immune responses from currently employed vaccine strategies.
Li, K.; Perniciaro, S.; Kwon, J.; Grubaugh, N. D.; Weinberger, D. M.; Pitzer, V. E.
Show abstract
Human metapneumovirus (HMPV) causes acute lower respiratory infections, primarily affecting young children and older adults, with seasonal outbreaks peaking annually in March or April in the United States and other temperate regions in the Northern hemisphere. However, the factors driving HMPV seasonality in the United States remain poorly understood. We analyzed laboratory-confirmed HMPV cases and age-specific emergency department visits across 10 US regions, fitting an age-stratified dynamic transmission model to assess spatiotemporal patterns and investigate the influence of environmental variables and viral interference from RSV on HMPV transmission rates. We found that models incorporating climate variables into the transmission rate, including vapor pressure, precipitation, potential evapotranspiration, and minimum temperature, could not capture the timing of HMPV activity across all regions. Instead, HMPV timing was associated with RSV activity, with the HMPV transmission rate reduced in the presence of RSV. We showed that, unlike RSV, only models incorporating viral interference could reproduce the biennial pattern of HMPV observed in some regions, characterized by alternating late-small and early-large epidemics. Furthermore, our model successfully reproduced post-COVID-19 HMPV and RSV epidemics and predicted that RSV interventions are not likely to lead to a substantial increase in HMPV activity despite decreasing competition from RSV. Our work unravels the spatiotemporal dynamics of HMPV and its interaction with RSV, informing future seasonal forecasting and intervention strategies for HMPV.
Colosi, E.; Calmon, L.; Fässli, M.; Koch, K.; Bielicki, J. A.; Colizza, V.
Show abstract
Pooled testing programs were introduced during the COVID-19 pandemic to expand surveillance capacity while preserving testing resources, but evidence on their epidemiological impact in schools under real-world conditions remains limited. We analyzed data from the pooled testing program implemented in public primary schools of the canton of Basel-Landschaft, Switzerland, during the Fall-Winter 2021 Delta wave. We used an agent-based transmission model informed by pooled and individual testing results, school characteristics, contact networks, and community incidence. The model was fitted to pooled positivity ratios in four clusters of administrative areas with similar epidemic trajectories. We compared pooled testing with alternative protocols in terms of school transmission, testing volume, and student-days lost. During the study period, pooled testing was offered to 21'187 students across 62 public primary schools, with high and stable participation across clusters (mean 71-79%). The fitted model reproduced observed pool positivity trends well. Compared with pooled testing, reactive class closure, reactive screening, and symptomatic testing were associated with higher in-school transmission, with excess ranging from 50% to 87%, 63% to 104%, and 72% to 133% across clusters. Weekly individual screening achieved similar reductions in transmission but required 15-25 times more tests. Relaxing class closure after depooling substantially reduced student-days lost without increasing transmission. Under real-world conditions, pooled testing provided an effective and resource-efficient strategy to reduce SARS-CoV-2 transmission in primary schools. Combining early detection of asymptomatic infections with low testing demands, pooled testing offers a scalable approach to school surveillance and control for pandemic response in educational settings.
Saxe, G.; Shubov, A.; Smith, C. N.; Golshan, S.; Shekhtman, T.; Wilson, S.; Slater, D.; Bair, Z. J.; Beathard, C.; Davis, R. A.; MacElhern, L.; Kao, L. K.; Senowitz, P.; Gosnell, N.; Buchholz, D.; Aguilar-Carreno, H.
Show abstract
Use of fungal mycelia, which has antiviral properties, constitutes a novel strategy for addressing existing and newly emerging viral diseases. We evaluated safety and feasibility of fungal mycelia (Fomitopsis officinalis and Trametes versicolor, FoTv) for treatment of COVID-19 and assessed its antiviral effects and potential to reduce symptoms. In a randomized, double-blind, placebo-controlled, dual site (UCSD/UCLA medical centers) clinical trial we examined non-hospitalized patients who contracted mild-to-moderate COVID-19 [≤] 96 hours, and experienced symptom onset [≤] nine days, before enrollment. FoTv was safe, well-tolerated, and feasible for COVID-19 treatment. Minor differences in biochemical markers were observed between groups (26 FoTv, 24 Placebo). FoTv significantly reduced the number and severity of symptoms, particularly sore throat/cough, and in vitro SARS-CoV-2 (pseudovirus) cellular infection. In conclusion, FoTv was safe and reduced COVID-19 symptoms and cellular viral infection. Future studies should investigate therapeutic benefits of fungal mycelia for SARS-CoV-2 and other viruses. Clinicaltrials.gov registration:NCT04667247.
Cantrell, L.; Karampatsas, K.; Andrews, N.; Beach, S.; Bentley, E.; Berardi, A.; Bijlsma, M. W.; Cagil Kocana, C.; Daniel, O.; French, N.; Hall, T.; Izu, A.; Khalil, A.; Kwatra, G.; Kyohere, M.; Madhi, S. A.; Mboizi, R.; Miselli, F.; Nielsen, M.; Thorn, N.; van de Beek, D.; Walker, K.; Heath, P. T.; Le Doare, K.; Voysey, M.; PREPARE WP3 Study Group,
Show abstract
Vaccines to prevent infant group B streptococcus (GBS) disease are advancing, with licensure likely based on safety and immunologic endpoints rather than clinical efficacy data. This approach requires robust, generalisable serological thresholds of risk reduction (SToRRs). We combined data from six case-control studies in Europe and Africa to define SToRRs for early-onset (EOD) and late-onset (LOD) GBS disease. Across diverse epidemiological and healthcare settings, anti-capsular polysaccharide IgG concentrations were consistently higher in infants who remained disease free than in those who developed disease. Higher antibody concentrations were required to reduce the risk of EOD than LOD, and higher concentrations were required for serotype Ia than for serotype III. This study provides a quantitative framework to support correlates-based evaluation and potential licensure of maternal GBS vaccines.
Wong, A.; Lee, C. W.; Park, A.; Yin, L.; Choi, Y.
Show abstract
Background. Tobacco smoke exposure, quantified by serum cotinine, is associated with cardiovascular, metabolic, and sleep-related health risks. The relationship between biomarker-verified tobacco smoke exposure and objectively measured, free-living wrist-worn ambient light patterns has not been examined in a nationally representative U.S. adult sample. Methods. We analyzed NHANES 2011-2014 cross-sectional data from 6,937 adults aged >20 years with valid serum cotinine and wrist-worn Physical Activity Monitor (PAM) ambient light data. Seven light outcomes were modeled using survey-weighted linear regression with log2(cotinine+1) as the continuous exposure across four covariate adjustment levels. Benjamini-Hochberg false discovery rate (FDR) correction was applied across the 7 outcomes within each model. Results. In Model 2 (adjusted for age, sex, race/ethnicity, education, poverty-income ratio, BMI, and survey cycle; N = 6,350), higher serum cotinine was associated with significantly higher nighttime light (beta = +0.024, 95% CI: 0.010, 0.038; p-FDR = 0.014) and lower evening light (beta = -0.031, 95% CI: -0.055, -0.008; p-FDR = 0.042). In exploratory behavioral models without alcohol (Model 3a; N = 5,766), both nighttime and evening associations remained FDR-significant. After additional adjustment for alcohol, which substantially reduced the sample due to 37.6% missingness (Model 3b; N = 3,866), the nighttime association attenuated below the FDR threshold, while the evening association remained FDR-significant. Categorical analyses showed progressively higher nighttime light across cotinine groups, and a hypothesis-generating sex interaction was identified (p-interaction = 0.001). Conclusions. Higher serum cotinine concentrations were associated with higher nighttime and lower evening ambient light after sociodemographic adjustment. Attenuation after behavioral adjustment and the cross-sectional design preclude causal inference. Longitudinal studies with formal mediation analyses are needed to clarify the temporal ordering and mechanisms linking tobacco smoke exposure, smoking-related behaviors, and personal light-dark cycle patterns.
Kim, D.; Pasco, R.; Johnson, K. E.; Fox, S. J.; Reich, N. G.; Meyers, L. A.
Show abstract
Accurate outbreak forecasts are critical for timely and effective public health response. In the United States, however, most forecasts are produced at the state level, which can mask substantial sub-state heterogeneity and limit their utility for local planning. We generated and evaluated forecasts of the percentage of Emergency Department visits attributable to influenza across 173 large metropolitan Health Service Areas (HSAs) using a gradient boosting quantile regression (GBQR) model, and compared their accuracy to forecasts derived from state-level data alone. At a one-week, two-week and three-week horizon, local forecasts outperformed state-based forecasts in 98.8%, 90.8%, and 78.6% of HSAs, respectively, achieving mean weighted interval scores that were on average a 39.2% lower (95% range: 5.9% to 76.7%), 19.6% lower (-6.3% to 59.5%) , and 11.4% lower (-11.7% to 44.9%), respectively. The performance advantage of local forecasting was strongest in HSAs representing a smaller share of their state's population and increased with the proportion of the HSA population living in urban areas and the number of metropolitan areas within a state. These results, based on an analysis of HSAs with populations greater than 250,000, demonstrate that fine-scale modeling can substantially improve forecast accuracy and highlight the potential value of local forecasts for outbreak preparedness and response.
Hines, A. G.; Mathis, S. M.; Johansson, M. A.; Biggerstaff, M.; Reed, C.; Borchering, R.
Show abstract
Since the U.S. 2013/14 influenza season, the CDC's FluSight Challenge has provided a platform for evaluating influenza forecasting models and fostering collaboration across institutions. The Challenge aims to improve the science and enhance the utility of infectious disease forecasts for public health decision making. We analyzed ten years of submitted forecasts (2014/15-2019/20 (influenza-like illness seasons) and 2021/22-2024/25 (hospital admissions seasons)) across a range of model types, including statistical, mechanistic, machine learning, and hybrid models. Influenza-like illness (ILI) forecasts were evaluated using the exponentiated logarithmic score (skill metric) while hospital admissions forecasts were evaluated using the log transformed relative Weighted Interval Score. Corresponding potential performance differences were assessed using Wilcoxon rank-sum tests, and associations with team participation history were evaluated using Spearman's rank correlation. Model performance varied by season, and no single model type consistently outperformed others. In ILI seasons, statistical models generally performed better than mechanistic and machine learning models, though consistent differences were not observed in more recent hospital admissions seasons. Ensemble forecasts showed better overall performance across seasons, and the CDC's FluSight ensemble ranked among the top-performing forecasts every year. We also found a positive correlation between forecast accuracy and the number of years a team participated in the Challenge, with statistically significant associations in four seasons. These findings highlight the benefits of ensemble approaches and sustained engagement in improving forecasting performance, while also underscoring the continued value of forecast evaluation before and following the COVID-19 pandemic. Insights from the FluSight Challenge can guide future infectious disease forecasting efforts and support more effective public health preparedness.
Sajib, M. S.; Tanmoy, A. M.; Kanon, N.; Jui, A. B.; Islam, M. S.; Dola, N. Z.; Hossain, M. M.; Mobarak, R.; Shahidullah, M.; Hoque, M.; Ahmed, A. N. U.; Holmes, A. H.; Saha, S. K.; Saha, S.; Wan, Y.; Hooda, Y.
Show abstract
Background Healthcare-associated infections pose a major burden to neonatal health worldwide and remain difficult to track in low-resource hospitals because patient movement data and pathogen genomic data are rarely integrated into actionable transmission models. Existing approaches are often restricted to specific settings, highly structured electronic health records (EHRs), or analyses focused on either patient movements or pathogen characteristics alone. To address this gap, we developed PathoPath, an open-source integrative modelling platform, and evaluated its utility in a high burden paediatric hospital in Dhaka, Bangladesh. Methods PathoPath is an open-source R package that combines electronic health records with whole genome sequencing data to generate contact networks from direct and indirect contacts using minimal structured inputs. We retrospectively applied PathoPath to 373 cases of Klebsiella pneumoniae species complex (KpSC) infection identified in 2021 at the largest paediatric referral hospital in Dhaka, Bangladesh. Ward level patient movement trajectories were used to reconstruct contact networks, and genomic data from isolates from children <60 days were integrated to identify probable dissemination of bacterial clones and antimicrobial resistance plasmids. Findings PathoPath identified 750 direct contacts among 317 patients, forming 25 connected components, with the largest including 93 patients. KpSC infections were identified across 21 of 37 wards, with the neonatal intensive care unit accounting for 77.9% of all cases. Integration of genomic and network data distinguished sustained clustering of ST147 from multiple probable inter-clonal dissemination events involving IncFII plasmids carrying blaNDM-5 and/or blaOXA-181 within ST16. Four dominant sequence types accounted for 65.6% of sequenced isolates, and carbapenemase genes were detected in 95.8%. Interpretation PathoPath reconstructs hospital-wide contact networks and integrates them with pathogen genomics to map probable dissemination of pathogens and antimicrobial resistance using minimal structured clinical data. It could support more targeted infection prevention and control in hospitals where granular digital records are not available.
Herrera-Diestra, J. L.; Bi, K.; Ptak, S.; Ertem, Z.; Al-amery, A.; Harris, M.; Meyers, L. A.
Show abstract
Background. The 2026 FIFA World Cup will bring an estimated 1--5~million international visitors to 11~US host cities between June~11 and July~19, 2026---the largest tournament in history. Large-scale international gatherings accelerate importation of infectious diseases from diverse source populations. Advance estimation of importation risk is essential for public health preparedness and surveillance prioritization. Methods. We developed a Poisson importation framework applied to five diseases (dengue fever, influenza, malaria, measles, and pertussis) across the 11~US venue cities. Three nested travel models of increasing resolution were constructed: a baseline model using routine June~2024 arrival data; a World Cup--adjusted model incorporating projected visitor growth factors; and a schedule-driven model routing WC fans to specific cities based on match assignments. WHO incidence and BTS T-100 routing fractions were combined with Monte Carlo uncertainty propagation (5,000 Uniform draws on under-reporting and travel-while-infectious parameters) to yield median importation estimates with 95\% uncertainty intervals. Results. Dengue posed the highest importation risk at most venue cities under the schedule-driven model (median $\Lambda > 10$ expected importations from Brazil alone; 95\% uncertainty interval 5.9--33.1), robust across the full literature-supported parameter range; Atlanta was the exception, where malaria probability exceeded dengue, driven by direct travel from West and Central African nations. Influenza ranked second at most cities, coinciding with the Southern Hemisphere winter peak. Pertussis showed broad geographic spread but carries the widest relative uncertainty, as the assumed detection rate sits at the upper bound of the literature range. Background tourism accounted for the dominant share of total importation risk; the World Cup fan increment contributed approximately 8.3\% of projected arrivals for WC-qualified nations. Conclusions. This Poisson importation framework, built entirely from publicly available data, provides reproducible importation risk estimates for mass gathering events. The framework extends to additional diseases, cities, and gatherings, offering a transparent baseline complementary to proprietary modeling systems.
Wagner, A. P.; Risebro, H.; Clark, A.; Stirling, S.; Sims, E.; Bion, V.; Blacklock, J.; Birt, L.; Bryant, R.; Cook, L.; Dean, T.; Wyn Griffiths, A.; Guillard, C.; Holland, R.; Jones, A. P.; Jones, L.; Katangwe-Chigamba, T.; Pitcher, J.; Scott, S.; Wright, D.; Patel, A.
Show abstract
Introduction Care home (CH) influenza vaccination of staff improves resident health, yet uptake remains low at just over 11% (England, 2025/2026). We report an economic evaluation (EE) of "FluCare", an intervention to increase staff influenza vaccination through: vaccination clinics at CHs; promotional materials; and CH financial incentives. Method Seventy-five CHs were randomised to FluCare or control. A cost-consequence analysis took the influenza vaccination programme funder perspective, but also extended to the National Health Service (NHS) and CH perspective. Costs included: influenza vaccination; administration fee; FluCare components; CH resident NHS utilisation. Outcomes were: staff influenza vaccination rates; staff sickness; and resident mortality. Sensitivity analyses excluded intervention CHs that did not host vaccination clinics. Results Compared to control CHs, adjusted analysis found intervention homes with a mean absolute increase in vaccination rates of 1.8% (95% CI: -6.0%, 10.8%; p=0.572) at an increased cost of {pound}451 (95% CI: {pound}239, {pound}675; p<0.001) to the vaccination programme funders: {pound}249 per additional percentage point (PAPP) per CH. Vaccination clinics were delivered late in the influenza season, with 80% taking place from February 2023. Including only intervention CHs that hosted staff flu vaccination clinics (23/35), increases the mean difference to 10.1% (95% CI: 0.9%, 21.9%; p=0.018) and costs to {pound}805 (95% CI: {pound}603, {pound}1,079; p<0.001): {pound}79 PAPP per CH. Differences between trial arms in other costs and outcomes were marginal and generally non-significant. Conclusions FluCare delivered little improvement when staff flu vaccination clinics did not occur and had little impact on other costs/outcomes. Cost-effectiveness depends on willingness-to-pay for increased staff vaccination, but cost PAPP per CH improved from {pound}249 to {pound}79 when only CHs hosting clinics were considered. Late implementation, likely reduced impact by limiting clinic delivery, as reflected in sensitivity analysis. Future evaluations should implement FluCare earlier in the season.
Morris, H.; Pritt, B. S.
Show abstract
Effective filtration and concentration of stool specimens is an essential pre-analytical step for reducing fecal debris and improving organism recovery using microscopy-based ova and parasite (O&P) examination. This study evaluated three commercially available fecal sedimentation-based filtration/concentration systems, ParaPak SpinCon (Meridian Bioscience), Mini Parasep SF (Apacor), and the newly-available ParadeviceReingenuity), for qualitative parasite detection and workflow logistics using conventional and artificial intelligence (AI)-assisted microscopy. Forty clinical stool specimens (20 parasite-positive and 20 parasite-negative) were processed with the 3 devices, and the resultant 120 wet mount and 120 trichrome stained smear preparations were examined using conventional microscopy. Trichrome-stained slides were also scanned at 40x magnification using a Hamamatsu NanoZoomerS360 flatbed digital slide scanner and images were analyzed using the Techcyte Fusion Human Fecal Trichrome AI algorithm. Positive and indeterminate digital findings were confirmed by conventional glass slide microscopy. Slides and digital images were reviewed in a blinded manner. Concordance was assessed among the 360 initial evaluations (microscopy and AI-assisted), and discrepant parasitology results were resolved through re-review and specimen reprocessing as needed. Final qualitative agreement across slide/image evaluations using all three concentration systems was 100%. Minor discrepancies in protozoan and white/red blood cell detection/identification were noted in 5 and 7 cases, respectively, and likely reflected sampling and observer variability. While the three concentration systems produced equivalent qualitative results, the Paradevice and Mini Parasep SF offered the most streamlined workflows. These findings support the Paradevice and Mini Parasep SF as efficient, analytically equivalent systems that are compatible with traditional and AI-assisted O&P workflows.
Moe, A. B.; Haverty, C.; Lee, M.; Hahn, S. E.; McElrath, T. F.; Jain, M.; Rasmussen, M.; Corso, A.; Larson, M. L.; Morrison, H.; Melroy, L. M.; Roofeh, J.; Phelps-Sandall, B.; Kiefer, D.; Biggio, J. R.
Show abstract
Introduction: Preeclampsia (PE) is a leading cause of maternal and neonatal morbidity and mortality, and low-dose aspirin (LDA) prophylaxis is the cornerstone of evidence-based prevention. Despite guideline recommendations, LDA adherence remains poor, with 10-25% of moderate-risk patients taking aspirin. Objective personalized risk stratification using biomarkers has been shown to motivate behavior change in other disease contexts. Survey data suggest that patients are more motivated to take aspirin if informed by an objective predictive test. Here, we report real-world LDA adherence among patients who received a high-risk result from a cell-free RNA (cfRNA) PE risk prediction test. Methods: This retrospective, observational survey study included asymptomatic patients of advanced maternal age (AMA; [≥] 35 years at delivery) with singleton pregnancies without USPSTF-defined preexisting high-risk conditions for PE who received the cfRNA PE risk prediction test. Patients who opted in to receive text message surveys were asked about LDA use following receipt of test results. High adherence was defined as reporting LDA use on at least 6 of 7 days per week at least 85% of the time surveyed. The primary analysis included patients with a high-risk test result and at least one LDA frequency survey response following receipt of test result. The observed proportion of adherent patients was compared to a baseline estimate of 25% using an exact binomial test. Results: Of 166 patients who received a cfRNA PE risk prediction test result, 48 (28.9%) received a high-risk result. Of these, 29 (60%) opted in and responded to at least one survey, constituting the primary analysis population. Twenty-seven of the 29 (93.1%; 95% CI: 78.0-98.1%) were classified as highly adherent, significantly higher than the 25% baseline adherence estimate for moderate-risk patients (p < 0.0001). Conclusion: Among surveyed patients who received a high-risk cfRNA PE test result, the proportion classified as highly adherent to LDA (93%) substantially exceeded published estimates of adherence in a similar patient population and met the clinically meaningful threshold of [≥] 80% associated with reduced risk of preterm preeclampsia. These findings indicate that objective and personalized biomarker risk testing may be a powerful driver of behavior change that current guidelines have failed to produce.
Savic, L.; Dias, P.; Vairale, J.; Begum, S.; Khan, K.; Fowler, A. J.; Kaura, V.; Watson, S.-L.; Littlejohns, A.; Pearse, R. M.; Abbott, T. E. F.
Show abstract
Background One in four surgical patients carries a drug allergy label, of which an estimated 90% are incorrect. Avoidance of first-choice drug therapies may lead to worse postoperative outcomes. We sought to determine the nature and extent of any association between drug allergy labels and postoperative complications. Methods A multicentre observational study in 21 NHS hospitals. Eligible patients were 18 years or older, undergoing common surgical procedures: primary hip or knee replacement; internal fixation of closed long bone fracture; colorectal resection; trans-urethral resection of prostate or bladder tumour; caesarean section; hysterectomy. Exclusion criteria: use of antibiotics in the two weeks prior to surgery, previous participation in the study. Primary outcome was postoperative complications within 30 days following surgery, a composite outcome comprising: all postoperative infections, anastomotic leak, acute respiratory distress syndrome, myocardial infarction, postoperative bleed, pulmonary embolism, stroke, antimicrobial side effects, death. Results Among 13,646 patients, 3924 (29%) carried greater than or equal to1 drug allergy labels. Labelled patients were more likely to develop postoperative complications (989/3924 (25%) vs 1926/9722 (20%); OR 1.21 [1.10-1.34]; p<0.001). They were more likely to develop surgical site infections (337/3924 (9%) vs 760/9722 (8%); OR 1.19 [1.03 -1.38]; p<0.018), and any postoperative infection (750/3924 (19%) vs 1472/9722 (15%); OR 1.24 [1.11-1.38] p<0.001). Labelled patients experienced increased risk of allergic drug reactions (31/3924 (0.01%) vs 29/9722 (<0.01%); OR 3.00 [1.77-5.09]; p<0.001), but no increase in mortality. Conclusions Drug allergy labels are common, but often incorrect. Labelled patients experience worse postoperative outcomes, including infective and non-infective complications and increased risk of allergic drug reactions. Trial registration Registered with ISRCTN registry, ISRCTN15775657.
Sevilla-Parra, G.; Bravo-Garcia, F.; Mier y Teran Guevara, M.; Montes-Garcia, A.; Schäfer, A.; Ochoa-Rodriguez, N.; Bienvenu Caballero, M.; Gonzalez Zenteno, S. G.; Pena-Ayala, A.; Tinajero-Nieto, L.; Torres-Valdez, E.; Martinez, D.; Hernandez-Ledesma, A. L.; Medina-Rivera, A.; Alpizar-Rodriguez, D.
Show abstract
Objective: To characterize pregnancy outcomes and menstrual irregularities in Mexican women with systemic lupus erythematosus (SLE) and identify clinical factors associated with adverse pregnancy outcomes and early-onset menopause. Methods: We conducted a cross-sectional study of women with SLE enrolled in the Mexican Lupus Registry (LupusRGMX) between May 2021 and September 2024. Clinical and reproductive data were collected using standardized questionnaires. Menopause was defined as the absence of menstruation for [≥]12 consecutive months, and early menopause as onset before age 40. Univariable and multivariable logistic regression analyses were used to identify factors associated with pregnancy complications and early menopause. Results: A total of 210 women were included. Median age was 38 years (IQR 29-46) and median disease duration was 4 years (IQR 1-10). Among women with a history of pregnancy (47%), full-term delivery predominated (61%), while pregnancy loss occurred in 26% and preterm delivery in 13%. Pregnancy complications were reported in 9.6%, most commonly preeclampsia (6.7%). Younger maternal age was independently associated with pregnancy complications (OR 0.89, 95% CI 0.83-0.95) and adverse outcomes (OR 0.95, 95% CI 0.92-0.98). Higher disease activity was associated with complications in univariable analysis. Most pregnancies (68.3%) occurred before diagnosis. Early menopause was observed in 6.2% and independently associated with longer disease duration and older age. Conclusion: Younger maternal age was independently associated with adverse pregnancy outcomes, whereas disease activity showed an association in univariable analysis. Most pregnancies occurred prior to SLE diagnosis. Early menopause was associated with longer disease duration, suggesting impact of cumulative disease burden on ovarian function.