Infection and Immunity

Background: Urinary tract infection (UTI) is the most common secondary condition among people with spinal cord injury/disease (SCI/D). Intravesical Lacticaseibacillus rhamnosus GG (LGG) is an antibiotic-sparing approach to managing urinary symptoms. Objective: Determine the optimal number of doses of intravesical LGG for urinary symptom reduction. Design: Prospective, randomized, two-arm dosing trial. Setting: National recruitment with a local subsample providing urine samples in Washington, DC, USA. Participants: Adults with SCI/D and neurogenic lower urinary tract dysfunction (NLUTD) who use intermittent catheterization (IC); 177 enrolled and randomized (intention-to-treat), with 76 compliant instillers (39 low-dose, 37 high-dose) in the per-protocol analytic sample. Interventions: Two (2 doses/24 hours) or four (4 doses/36 hours) intravesical LGG regimens, self-initiated in response to cloudier or malodorous urine per the Self-Management Protocol using Probiotics (SMP-Pro). Main Outcome Measures: Primary: proportion achieving [≥]20% reduction on the Urinary Symptom Questionnaire for Neurogenic Bladder-Intermittent Catheter version (USQNB-IC). Secondary: urinary biomarkers (leukocyte esterase, nitrite, white blood cells, urinary neutrophil gelatinase-associated lipocalin [uNGAL]) and standard urine culture (SUC) in a local subsample. Results: By Day 2, 57.9% (63.8% low-dose; 51.2% high-dose) achieved [≥]20% total symptom reduction; high-dose success rose to 70.0% by Day 4. Thirty percent of high-dose participants did not respond at either time point and could not be distinguished from responders by demographics or urine biomarkers. Urinary biomarkers and SUC were unchanged pre- to post-instillation. No serious adverse events were adjudicated as attributable to intravesical LGG by an independent Data Safety Monitoring Board (DSMB). Conclusions: A two-dose course of intravesical LGG yields clinically meaningful symptom improvement in the majority of people with SCI/D and NLUTD who use IC; four doses benefits a meaningful subgroup of two-day non-responders, while a small cohort remains nonresponsive. These results provide preliminary dosing guidance and support progression to a definitive trial.

We previously reported inherited RORgammaT deficiency in seven patients from three ancestries (Chilean, Palestinian, Saudi Arabian) with mycobacterial disease and chronic mucocutaneous candidiasis (CMC). We report here five additional patients from different ancestries (Afghan, Indian, Iranian, Japanese, Sri Lankan), each homozygous for a new loss-of-function RORC variant. All but one patient, the exception receiving early prophylaxis, developed mycobacterial disease due to a near-complete depletion of innate-like adaptive T cells, including MAIT and iNKT cells, low counts of adaptive TH1* and CD8+ T cells, and impaired Mycobacterium-induced IFN-gamma production by the remaining cells of these subsets, NK cells, conventional CD4+ T, Vdelta1, and Vdelta2 gamma-delta T cells. Most patients also displayed CMC due to their low counts of TH17 and TH1* cells. One patient died from disseminated Bacille Calmette-Guerin (BCG) vaccine infection, but, unexpectedly, all the other patients are still alive and clinically stable. RORgammaT is essential for protective immunity against mycobacteria and Candida in humans.

Males incur greater risk of tuberculosis (TB) than females, but the contribution of sex-associated immune differences remains unclear. We addressed this using sex-stratified transcriptomic analyses across four independent studies spanning active pulmonary TB, subclinical TB and latent infection, in peripheral blood, bronchoalveolar lavage (BAL) and by using the tuberculin skin test (TST) as a standardised in vivo antigenic challenge. In blood of active TB patients, expression of TNF- and type I interferon-regulated signatures, genome-wide gene expression, and performance of leading host-response biomarkers of TB were comparable between sexes. Similarly, blood transcriptomic biomarkers showed no meaningful sex-related differences for predicting asymptomatic or incident TB. In the TST of people with latent infection, bulk and single-cell RNA sequencing identified only limited differences, largely restricted to sex chromosome-linked transcripts, with no consistent evidence of dimorphism in immune-regulated pathways. Single-cell RNA sequencing of BAL samples identified reduced abundance of B cells in male TB patients, with gene expression differences again largely restricted to sex chromosome-linked transcripts. These findings suggest that canonical immune responses associated with TB are broadly similar between the sexes, and that increased TB risk among males more likely reflects differential exposure rather than intrinsic immunological susceptibility.

Blood banks represent highly controlled healthcare environments where microbiological surveillance has traditionally focused on blood products rather than environmental microbial reservoirs. Despite their critical role in transfusion safety, the ecology of surface-associated microorganisms and the persistence traits that enable their long-term survival remain poorly understood. Here, we combined scanning electron microscopy, culture-based microbiology, phenotypic characterization, MALDI-TOF mass spectrometry, and whole-genome sequencing to investigate whether surfaces within a public blood bank facility constitute reservoirs of environmentally derived bacteria with enhanced persistence potential. Samples collected from a public blood bank in Tucuman, Argentina yielded 37 culturable bacterial isolates, predominantly Gram-positive environmental taxa together with a limited number of opportunistic Gram-negative species. More than 30% of the isolates exhibited multidrug resistance, while several strains displayed strong biofilm formation, amyloid-like fiber production, motility, and hemolytic activity, indicating multiple phenotypic strategies associated with long-term surface persistence. Whole-genome sequencing of six representative isolates confirmed species identity, identified genes related to antimicrobial resistance, adhesion, biofilm formation, stress adaptation, and cytotoxicity, and revealed frequent genotype-phenotype discordance, highlighting the importance of integrating genomic and phenotypic analyses. Notably, one isolate exhibited less than 92% average nucleotide identity with publicly available genomes, suggesting the presence of a previously undescribed environmental species. Thus, blood bank surfaces function as selective ecological niches favoring bacteria with persistence-associated traits rather than simply reflecting contamination from blood products. These microorganisms may constitute latent biosafety hazards if environmental barriers fail, particularly in facilities handling biological materials intended for vulnerable patients. Our results support the incorporation of integrated bioimaging, phenotypic characterization, and genome-resolved environmental surveillance into infection prevention strategies and transfusion biosafety programs within a One Health framework.

Background: Oral care is a critical nursing intervention for mechanically ventilated patients in intensive care units because it reduces oral microbial colonization and contributes to the prevention of ventilator-associated pneumonia, a major cause of morbidity, prolonged hospitalization, and increased healthcare costs among critically ill patients. Despite the availability of evidence-based guidelines, gaps in nurses knowledge and inconsistent implementation of oral care practices remain challenges, particularly in low- and middle-income settings. Objective: This study aimed to assess the level of knowledge among intensive care unit nurses regarding oral care for mechanically ventilated patients at Tenwek Hospital, Kenya, determine factors influencing knowledge, and examine the relationship between nurses knowledge and selected demographic and professional characteristics. Methods: An analytical cross-sectional study design was employed. The study was conducted among intensive care unit nurses at Tenwek Hospital. A sample of 38 nurses was selected from a target population of 60 intensive care unit nurses using simple random sampling. Data were collected using a structured self-administered questionnaire assessing socio-demographic characteristics, knowledge of evidence-based oral care practices, awareness of guidelines, and factors influencing knowledge. Data were analyzed using descriptive statistics, chi-square tests, Pearson correlation, and logistic regression, with statistical significance set at probability value less than 0.05. Results: Thirty-five nurses participated, yielding a response rate of 92.1 percent. The findings demonstrated generally high knowledge levels regarding oral care practices for mechanically ventilated patients. Most nurses correctly identified recommended oral care frequency (88.6 percent), oral assessment before care (91.4 percent), suctioning before and after oral care (94.3 percent), and the role of oral care in preventing ventilator-associated pneumonia (97.1 percent). However, knowledge gaps were identified in areas such as toothbrushing practices and documentation of oral care procedures. Training, continuing professional education, availability of guidelines, workload, resources, supervision, and teamwork were identified as important factors influencing knowledge. The findings revealed that professional qualification (probability value equal to 0.02), intensive care unit experience (probability value equal to 0.030) and formal oral care training (probability value equal to 0.021) were significantly associated with nurses knowledge of oral care practices. Conclusion: Intensive care unit nurses at Tenwek Hospital demonstrated adequate knowledge of evidence-based oral care practices for mechanically ventilated patients. However, targeted educational interventions are required to address identified gaps and strengthen standardized oral care delivery. Continuous professional development, consistent use of guidelines, supportive supervision, and adequate resource provision are recommended to enhance patient safety and reduce preventable intensive care unit complications such as ventilator-associated pneumonia. Keywords: Intensive care unit nurses; Oral care; Mechanically ventilated patients; Ventilator-associated pneumonia; Nursing knowledge; Evidence-based practice

BACKGROUND: Half of positive blood cultures in pediatric emergency departments (PEDs) represent contaminants, driving unnecessary hospitalization, antibiotic exposure, and repeat visits. A clinical decision rule derived at CHU Sainte-Justine showed 99% sensitivity and 60% specificity for distinguishing bacteremia from contaminants but had not been externally validated. We sought to validate this rule in an independent pediatric cohort. METHODS: This retrospective diagnostic study spanned from January 2015 to May 2025 at a tertiary PED in Switzerland, using positive blood cultures from patients younger than 16 years. The four predictors (Gram-negative organisms or Gram-positive cocci in pairs or chains; time to positivity <17 hours; indwelling device; suspected osteoarticular infection) classified each case as low, moderate, or high risk. The primary outcome was bacteremia, adjudicated by two independent reviewers, based on organism identity and infectious disease specialist's assessment. Diagnostic accuracy was assessed with 95% CIs. RESULTS: Of 130 children enrolled (median age 3.8 years [IQR 0.9-9.9]; 61.5% male), 78 (60.0%) had true bacteremia. The rule yielded a sensitivity of 97.4% (95% CI, 91.0-99.7), specificity of 69.2% (95% CI, 54.9-81.3), positive predictive value of 82.6% (95% CI, 73.3-89.7), and negative predictive value of 94.7% (95% CI, 82.3-99.4). Both false-negatives were immunocompetent children with methicillin-susceptible Staphylococcus aureus bacteremia without indwelling devices. Among contaminants, 71% received antibiotics under usual care versus 31% classified as moderate or high risk by the rule. CONCLUSIONS: This first external validation supports the Sainte-Justine rule in a distinct pediatric population, preserving sensitivity with higher specificity. Multicenter validation is warranted before adoption.

Background Oral care is a critical nursing intervention for mechanically ventilated patients in intensive care units (ICUs) and plays an important role in preventing ventilator-associated complications. However, variability in nurses' competency in oral care remains a concern, particularly in resource-limited settings. Objective To assess ICU nurses' competency in providing oral care to mechanically ventilated patients and determine factors associated with competency at Tenwek Hospital, Kenya. Methods An analytical cross-sectional study was conducted among ICU nurses at Tenwek Hospital. A total of 38 nurses were invited, and 35 participated, yielding a response rate of 92.1%. Data were collected using a structured questionnaire and an observational competency checklist. Descriptive statistics and inferential analysis, including chi-square tests and binary logistic regression, were performed using SPSS version 30. Statistical significance was set at p<0.05. Results ICU nurses demonstrated generally high competency in key oral care practices, including use of personal protective equipment (100%), suctioning before and after oral care (91.4%), and oral assessment (80.0%). However, gaps were identified in documentation of oral care (62.9%) and adherence to standardized protocols (65.7%). Formal oral care training was significantly associated with competency (OR=5.63, 95% CI: 1.78-17.81, p=0.002), as were professional qualification (p=0.030) and ICU experience (p=0.021). In multivariable analysis, oral care training (OR=3.01, p=0.006), ICU experience (OR=2.85, p=0.015), and availability of guidelines (OR=2.17, p=0.047) were independent predictors of competency. Conclusion ICU nurses at Tenwek Hospital demonstrate satisfactory competency in oral care for mechanically ventilated patients, although gaps remain in documentation and protocol adherence. Strengthening training, guideline availability, and institutional support systems is essential to improve consistency and quality of oral care practice. Keywords Intensive care unit; oral care; nursing competency; mechanically ventilated patients; ventilator-associated pneumonia; Kenya.

Fracture nonunion remains a major cause of morbidity, yet patient-specific factors associated with impaired healing remain incompletely characterized. Anemia has been associated with adverse orthopaedic outcomes, but its relationship with fracture nonunion is poorly understood. We examined whether pre-fracture anemia, anemia burden, and clinically relevant anemia subtypes were associated with nonunion following tibial or femoral fractures. Using commercial and Medicare fee-for-service claims from 2016 through 2023, we identified adults aged 19 years or older with a tibial or femoral fracture, continuous enrollment during the preceding year and for at least six months after fracture, and no baseline cancer. Pre-fracture anemia was evaluated as any anemia, the number of distinct anemia diagnoses, and nutritional, hemolytic, aplastic, and other anemia subgroups. Nonunion occurring six to eighteen months after fracture was assessed using incidence rates and multivariable-adjusted hazard models. Among 326,673 adults, 149,704 had pre-fracture anemia and 176,969 did not. The crude incidence of nonunion was 42% higher among individuals with anemia than among those without anemia (incidence rate ratio, 1.42; 95% confidence interval, 1.32 to 1.53) and increased with greater anemia burden. After adjustment for demographic and clinical characteristics, including prior fractures at other anatomical sites, pre-fracture anemia remained associated with nonunion following tibial and femoral fractures, with hazard ratios of 1.83 (95% confidence interval, 1.54 to 2.18) and 1.38 (95% confidence interval, 1.26 to 1.50), respectively. Associations were also observed for nutritional and other anemias, whereas estimates for hemolytic and aplastic anemias were limited by few nonunion events. Within the femur, the association was strongest for distal fractures. These findings demonstrate that pre-fracture anemia is independently associated with nonunion. The increase in risk with greater anemia burden and findings across evaluable subgroups suggest that pre-fracture anemia may help identify patients at increased risk of impaired fracture healing.

Background and objectives Spontaneous bacterial peritonitis (SBP) is a life-threatening complication of cirrhosis with ascites, carrying one- and two-year mortality rates exceeding 70% and 80%, respectively. Fluoroquinolone prophylaxis is the cornerstone of SBP prevention. Real-world longitudinal data on prescribing practices and clinical outcomes from Indian tertiary care centers are sparse. We aimed to evaluate fluoroquinolone prescribing patterns, guideline adherence, and six-month clinical outcomes in SBP patients at a tertiary academic center in North India. Methods This was a pre-specified sub-analysis of a 15-month analytical longitudinal study at AIIMS Rishikesh. Adults (age >/=18 years) admitted with SBP and initiated on fluoroquinolone prophylaxis were enrolled consecutively and followed for six months. Prescribing practices were compared against EASL and AASLD recommendations. The primary outcome was the rate of guideline-directed prescribing. Secondary outcomes included clinical cure at discharge, six-month cure, relapse, regimen modification, adverse drug reactions, and treatment compliance. Categorical variables were compared by Fisher's exact test or chi-squared test (SPSS). Results Forty-eight SBP patients were included (mean age 44.75 +/- 11.94 years; 85.4% male). Guideline-directed fluoroquinolone prophylaxis was prescribed to all patients (100%). Norfloxacin 400 mg once daily was predominant (85.4%), followed by levofloxacin (10.4%) and moxifloxacin (4.2%). Cure at discharge was 85.4%. At six months, 64.6% maintained sustained cure and 22.9% relapsed. Regimen modification occurred in 22.9%, most commonly antimicrobial substitution. Nausea was the only adverse drug reaction (4.8%). Treatment compliance was 73.8%. No patient underwent therapeutic drug monitoring. Conclusions Fluoroquinolone prescribing for SBP prophylaxis at AIIMS Rishikesh was fully concordant with standard guidelines. Despite complete adherence, a relapse rate of 22.9% and frequent regimen modification underscore the limitations of long-term fluoroquinolone prophylaxis, likely reflecting emerging quinolone resistance. Strengthening antimicrobial stewardship is essential to sustain prophylaxis effectiveness in Indian tertiary care settings.

Importance Tuberculosis preventive therapy is central to reducing tuberculosis, and foreign-born individuals account for most US tuberculosis cases. Current US Preventive Services Task Force guidance recommends testing and treating all foreign-born individuals regardless of age or time since immigration, yet the risks of disease progression and of treatment-related harm are not uniform across these groups. Objective To evaluate the cost-effectiveness and health outcomes of tuberculosis infection treatment strategies among immigrants from high-burden settings, stratified by age and time since immigration. Design Decision analytical model using individual-level microsimulation (Markov model) over a 30-year horizon, with deterministic and probabilistic (second-order Monte Carlo) sensitivity analyses. Costs and outcomes were discounted at 3%. Setting US federally funded tuberculosis clinic care (healthcare-sector perspective), using observed data from the Boston Medical Center/Boston Public Health Commission tuberculosis clinic and published literature. Participants A simulated cohort of 10000 IGRA-positive, foreign-born adults from high tuberculosis incidence settings (excluding immunosuppressed individuals), modeled as recent or remote (immigrated 25 years earlier) immigrants at ages 35 and 65 years. Interventions Rifampin daily for 4 months, isoniazid daily for 9 months, or no preventive therapy. Main Outcomes and Measures Costs, disability-adjusted life-years (DALYs), incident tuberculosis cases and deaths, treatment completion, and incremental cost-effectiveness ratios (ICERs), with the proportion of simulations in which each strategy was optimal at a willingness-to-pay threshold of $50000 per DALY averted. Results Among recent immigrants, rifampin was the dominant strategy at ages 35 and 65 years (optimal in 88.5% and 93.9% of simulations), yielding the fewest tuberculosis cases (119.44 and 82.31 per 10 000) and the highest treatment completion (71.4% and 67.7%). Among remote immigrants, rifampin remained the dominant strategy (optimal in 53.41% of simulations), followed by no treatment. In older remote immigrants, no treatment was optimal in 94.7% of simulations. ICERs for treatment vs no treatment were unfavorable ($193 600 and $412 857 per DALY averted for rifampin and isoniazid, respectively, at age 65). Conclusions and Relevance In this decision analytical model, rifampin was cost-effective for recent immigrants, whereas no treatment was optimal for older remote immigrants. Age and time since immigration may help risk-stratify tuberculosis infection treatment and reduce unnecessary treatment in lower-risk populations.

Background: Monoclonal antibodies have emerged as a prophylactic strategy to prevent symptomatic SARS-CoV-2 infection in immunocompromised individuals. However, the evolutionary and clinical implications of breakthrough infections under this regime remain unclear. Methods: A male in their 80s with a haematological/oncological diagnosis received a 2000 mg intravenous infusion of sotrovimab in March 2023 and was diagnosed with COVID-19 by RT-qPCR from a nasopharyngeal swab in August 2023. Weekly samples (n=24) were collected through February 2024 (171 days). All samples underwent whole-genome sequencing, with select mutations subjected to functional assessment. Findings: Sequencing identified the GE.1 lineage at all timepoints. An intra-host recombination event in ORF1ab (positions 8942-12458) was detected prior to 23 weeks post-detection, followed by a 14-fold increase in viral load (7.42e+06 to 1.00e+08 RNA copies/mL) and a marked shift in the viral population. E340D, a sotrovimab resistance mutation, was detected at low abundance (46%) within the first week post-infection, fluctuated over time, and was nearly fixed by week 15 (107 days) post-detection. We assessed five spike mutations - V36M, S98F, and V213G in the N-terminal domain, Y505P in the receptor-binding domain, and P681Q near the S1/S2 cleavage site - and additionally evaluated the impact of E340D. V36M conferred the highest infectivity across all cell lines, with the most significant effect in low-TMPRSS2 cells. While all mutations showed enhanced infectivity with the addition of E340D, the effect was most pronounced in mutations with lower baseline infectivity. The addition of E340D significantly decreased relative neutralizing titres for V36M, S98F, and V213G, enabling escape from neutralizing antibodies in XBB-responsive individuals, illustrating an enhanced phenotypic advantage. Patient neutralizing activity was absent pre-sotrovimab, and sotrovimab-induced neutralization was further compromised by selection of E340D. Interpretation: Sotrovimab pre-exposure prophylaxis in an immunocompromised patient did not prevent SARS-CoV-2 infection, and selected for resistant mutation E340D, with unexpected fitness consequences across non-receptor binding domain spike regions.

Purpose: Nonresponse to routinely collected patient-reported outcome measures (PROMs) threatens the representativeness of aggregated data. We characterized patient-, provider-, and clinic-level factors associated with PROMIS Global-10 nonresponse in routine radiation oncology care. Methods: In this retrospective cohort study, all adults seen at five Mass General Brigham radiation oncology clinics over one year were included. The primary outcome was patient-level nonresponse, defined as never completing the portal-administered Global-10 versus completing it at least once. Using iterative mixed-effects logistic regression, we modeled patient-, provider-, and clinic-level factors. Results: Among 12,214 patients, 71 providers, and five clinics, patient- and appointment-level response rates were 35.4% and 10.9%, with patient-level response ranging nearly fivefold across clinics (12.8% to 66.2%). In Model 1, male sex, lower education, not working, and recent surgery had higher odds of nonresponse, and longer time since diagnosis lower odds. After provider- and clinic-level factors were added, patient sex, education, and employment became nonsignificant, whereas recent surgery (adjusted odds ratio [aOR] 1.97) and longer time since diagnosis (aOR 0.46 for >12 months) persisted. A provider's historical collection rate was protective but attenuated at the clinic level. There, a later program launch (aOR 0.29) and higher historical collection rate (aOR 0.79) correlated with lower nonresponse, whereas academic versus community setting did not. Conclusions: Nonresponse to routinely collected PROMs is a multilevel phenomenon driven substantially by clinic-level implementation factors, not patient characteristics alone. Because response rate is only a proxy for representativeness, PROMs programs and PRO-based performance measures should prioritize representative collection over volume.

Controlled human infection models (CHIMs) are increasingly used in infectious disease research to study pathogen dynamics and evaluate interventions under controlled conditions. However, these studies are resource-intensive and involve ethical and safety constraints, making efficient study design critical. Dose-finding is a key early component in CHIMs, where the aim is to identify a challenge dose that achieves a target infection probability. Traditional rule-based designs are commonly used but can be inefficient, motivating the use of model-based adaptive approaches such as the Bayesian Continual Reassessment Method (CRM). Although CRM has been extensively studied and widely adopted in Phase I oncology trials for identifying the maximum tolerated dose of therapeutics, its application in CHIM settings remains limited, particularly when the endpoint of interest is infection. This tutorial provides step-by-step guidance for implementing a Bayesian CRM in dose-finding CHIMs, using an oropharyngeal Neisseria gonorrhoeae challenge as a motivating case study. The framework outlines key design components, including dose-grid specification, dose-response model, prior elicitation, Bayesian updating, decision rules, and stopping criteria, with particular emphasis on a clinically interpretable parameterisation. Trial operating characteristics are evaluated through simulation studies under multiple dose-response scenarios and prior-predictive analyses, and compared with a commonly used '3+3' type rule-based design. This work highlights the advantages of Bayesian model-based designs for dose-finding in CHIMs over classic rule-based designs and provides a structured, reproducible framework for implementing CRM, supporting their application in future CHIM studies.

Background and Aims The optimal treatment for first episodes and first recurrences of Clostridioides difficile infections (CDI) is unknown and there is emerging evidence for pulse and taper (P-T) regimens. Therefore, we sought to estimate the relative efficacy of treatment options. Methods MEDLINE and CENTRAL were searched from database inception to May 21, 2025 and unpublished conference abstracts were searched from recent infectious disease conferences. RCTs on the treatment of first episodes or first recurrences of CDI comparing fixed-dose or P-T regimens of fidaxomicin or vancomycin were included. The primary and secondary outcomes were 40- and 56-day CDI recurrence, respectively. A random-effects network meta-analysis on the risk ratio (RR) scale was conducted using a standard regimen (10-14 days) of vancomycin as the comparator. Treatments were ranked using the surface under the cumulative ranking curve (SUCRA). Results 8 RCTs were included comprising a total of 2181 patients. For 40-day recurrence, fidaxomicin P-T had the highest probability of ranking best (RR=0.10, 95%Confidence Interval [95%CI]=0.10-0.49, SUCRA=1.00), followed by vancomycin P-T (RR=0.49, 95%CI=0.32-0.76, SUCRA=0.61), fixed-dose fidaxomicin (RR=0.61, 95%CI=0.49-0.76, SUCRA=0.39), and, finally, fixed-dose of vancomycin (SUCRA=0.00). The treatments ranked in the same order for 56-day recurrence, though only 3 RCTs reported on this timepoint. Conclusion Vancomycin P-T, fidaxomicin P-T, and fixed-dose fidaxomicin were all superior to a fixed-dose vancomycin. Head-to-head comparative effectiveness RCTs are needed to quantify their relative effect sizes of and impact on long-term prevention of recurrent CDI.

Background The 2022-2023 global mpox outbreak highlighted the critical need for robust genomic surveillance capabilities to track mpox virus (MPXV) evolution and transmission dynamics. Methods Building upon our established SARS-CoV-2 sequencing infrastructure, we implemented a Molecular Loop probe-based long-read sequencing approach using Pacific Biosciences Sequel II technology for comprehensive MPXV genomic surveillance across the United States (US). From August 2024 to June 2025, we generated 326 high-quality whole genome sequences from residual mpox-positive clinical specimens collected by Labcorp across all 10 US Department of Health and Human Services regions. Results Our analysis identified two samples containing clade Ib MPXV in January and June 2025 and captured shifting trends in clade IIb diversity, with 13 distinct lineages observed. We also identified multiple instances of large (~1.6-17.6kb) deletions proximal to the inverted terminal repeats in clade IIb genomes. APOBEC3 mutation analysis indicated substantial evidence of human-to-human transmission among both clades. Further, we observed significantly higher APOBEC3-associated SNPs per kilobase (P<0.001) in clade IIb genomic variable regions relative to their central conserved region. Our assay exhibited strong reproducibility across biological replicates from individual patients and accuracy was confirmed via parallel sequencing of select specimens by US Centers for Disease Control and Prevention (CDC) using metagenomic sequencing. We also demonstrated via custom simulation that our assay discriminates all known MPXV clades and lineages, including those we have not observed in the US. Conclusions Our integrated nationwide surveillance system facilitates real-time genomic tracking of outbreak evolution, with demonstrated capacity across SARS-CoV-2 and MPXV, positioning this platform for rapid deployment during future pathogen emergence.

Estimating dengue force of infection (FOI) is essential for understanding transmission dynamics and targeting intervention programmes, yet surveillance data in endemic settings required for estimations are often incomplete, with varying formats. We developed a Bayesian hierarchical catalytic model that jointly fits age-stratified case data, aggregate case data, and seroprevalence surveys within a single framework, incorporating external covariates to improve parameter identifiability. Synthetic validation showed that covariates alone recovered accurate FOI point estimates even when most districts contributed only aggregate data, but did so with poorly calibrated uncertainty; anchoring the model with a single seroprevalence survey was necessary to bring credible interval coverage close to nominal. Applied to 128 districts across Java and Bali, Indonesia (2016-2024), the model revealed substantial spatial heterogeneity in FOI and reporting rates. Many districts in Java exceeded the WHO-suggested seroprevalence threshold for vaccine introduction, yet were classified as low-priority when using reported incidence as prioritisation criterion, particularly in areas with weak surveillance. Model-based seroprevalence estimation, integrating multiple data sources, offers a more consistent basis for identifying high-priority districts for vaccine introduction, and is less susceptible to surveillance bias than reported incidence.

Background: Opioid use disorder (OUD) is heritable, yet most genome-wide association studies (GWAS) have focused on European populations, leaving the genetic architecture of OUD in non-European populations underexplored. Methods: We conducted GWAS of OUD across three ancestries using electronic health records and genomic data from 52,357 All of Us Research Program participants (8,912 cases; 43,445 matched opioid-exposed controls; 48.5% female). Participants were stratified into European (EUR), African (AFR), and Admixed American (AMR) ancestry groups for logistic regression GWAS, with independent replication in the Million Veteran Program. We then applied the deep-learning model AlphaGenome to predict the tissue-specific transcriptomic and splicing consequences of top risk variants across 13 reward-pathway brain regions. Results: We identified and replicated a novel DDX6 risk locus, alongside established OPRM1 and FURIN signals. AlphaGenome predicted the DDX6 regulatory allele downregulates the stress-resistance gene FOXR1 in the nucleus accumbens, while the protective OPRM1 variant (rs1799971) upregulates OPRM1 expression across reward networks. Other signals of interest included IL6R and SHISA9 (EUR); GHR (AFR); and ASTN2 (AMR). Conclusions: This study identifies DDX6 as a novel OUD risk locus, replicates associations with OPRM1 and FURIN, and highlights biologically plausible ancestry-specific signals in AFR and AMR populations. We also replicated top variants in an independent population. Finally, integrating GWAS with deep-learning annotations provides specific, localized biological hypotheses to guide future experimental validation and targeted therapeutics.

Stochastic epidemic models are a cornerstone of infectious disease epidemiology and are often used to study intervention scenarios. However, large run-to-run variability can make intervention effects difficult to estimate precisely. We revisit the epidemic Sellke construction, which assigns each individual an infection threshold for the cumulative infection hazard such that, conditional on the thresholds, the epidemic trajectory becomes deterministic. This enables coupling of simulations with and without an intervention, yielding low-variance effect estimates even when outcomes such as final size or peak incidence vary widely between runs. We develop an exact, event-driven implementation that maintains infection and recovery events in priority queues. Cumulative infection-hazard updates require O(log N) time per event, yielding overall complexity O(Elog N) for E events in a population of size N. The implementation achieves computational performance comparable to the classical Gillespie algorithm while naturally accommodating non-Markovian infectious periods and complex infectiousness profiles. We illustrate the approach using distance-dependent spread of avian influenza between poultry farms in the Netherlands and a multilayer population with households, schools, and workplaces. In both examples, coupling enables efficient within-run comparisons of intervention scenarios across stochastic realisations.

Patients and caregivers seek informational and emotional support throughout medical care, especially when interpreting unfamiliar laboratory test results. Although resources such as patient portals and online health communities (OHCs) help address questions, gaps remain. The emergence of large language models (LLMs) offers the potential to be a complementary source of support to assist patients and caregivers in understanding and using their test results. The objective of our study is to empirically compare LLM responses to patients online questions containing their laboratory test results to responses written by peers in an OHC. We compared the 519 peer replies to 122 laboratory test-related posts from an OHC to 488 responses generated from four LLMs using mixed computational and qualitative methods. LLMs frequently provided clear explanations of medical terminology and structured interpretations of numeric results but were longer and less readable. Peers offered more personalized, context-specific emotional support. Overall, LLMs have the potential to complement peer responses in OHCs, but require greater emotional depth, reasoning transparency, and alignment with community norms.

Background: Children born prematurely (before 37 weeks) or admitted to the neonatal unit (NNU) are at increased risk of adverse long-term physical health outcomes. It is also recognised that there is an association with later academic performance and special educational needs, however it is not clear whether these broad risk factors could be used as stand-alone heuristics to identify children who may benefit from additional support in educational settings. We aimed to examine the associations between neonatal unit (NNU) admission and educational attainment in mid-childhood. Methods and Findings: Pregnancy data from a prospective birth cohort (Pregnancy Outcome Prediction Study, Cambridge, United Kingdom, 2008-2012) were linked to national educational outcomes (Department for Education, United Kingdom). Multivariable regression models adjusted for maternal, child, and socioeconomic factors were used to evaluate associations between (i) all NNU admissions, (ii) at term NNU admissions >48 hours, (iii) preterm birth without ongoing physical health needs, and educational outcomes at ages 5-11 years. Children who required any NNU care were more likely not to meet expected educational standards across multiple ages and domains in early and mid-childhood: age 5 early year foundation (aOR 1.64, 95% CI 1.19-2.27, p=0.003), phonics at age 6 (aOR 2.43, 95% CI 1.72-3.57, p<0.001), and at age 7 (here assessments were divided into multiple domains): reading (aOR 1.67, 95% CI 1.18-2.38, p=0.004), writing (aOR 1.72, 95% CI 1.25-2.38, p<0.001), mathematics (aOR 1.56, 95% CI 1.09-2.22, p=0.020), and science (aOR 1.85, 95% CI 1.22-2.78, p=0.003). Similar patterns were observed among both at term-born infants who stayed >48hrs in NNU (phonics assessment at age 6 aOR 2.26, 95% CI 1.51-3.36, p<0.001) and in children born preterm without long-term physical health sequelae (phonics assessment at age 6 aOR 3.07, 95% CI 1.96-4.81, p<0.001). These associations were robust to adjustment for demographic, perinatal, and socio-economic factors. By age 11, differences in academic attainment were attenuated and no longer clearly distinguishable across all exposure groups. However, there was an increased likelihood of special educational needs (SEN) at age 11 associated with any NNU admission (aOR 1.78, 95% CI 1.15-2.73, p=0.009), at term NNU admission for >48hrs (aOR 1.88, 95% CI 1.19-3.00, p=0.007), and children born preterm without long-term physical health sequelae (aOR 1.50, 95% CI 1.00-2.25, p=0.049). Predictive performance of any NNU admission for SEN at age 11 was moderate (AUC 0.70, 95% CI: 1.14-2.65, p=0.010), with balanced sensitivity and specificity and high negative predictive value. Conclusions: NNU admission, for both term and preterm infants, is associated with poorer educational outcomes and an increased likelihood of special educational needs in mid-childhood.