Epidemiology and Infection

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.

Globally, Hepatitis C Virus (HCV) infection is a leading cause of chronic liver disease and remains a significant public health threat in Ghana. However, there is a paucity of data on the prevalence and awareness of HCV among market sellers and informal workers in Ghana. This study sought to determine the prevalence and awareness of HCV among this population. This was a cross-sectional study conducted among 397 sellers and workers at Kejetia market from December 2024 to January 2025. HCV was diagnosed using the One Test Hepatitis C Virus Test Strip (Qingdao Hightop) for the qualitative detection of HCV antibodies. Data were analysed using SPSS version 26 and GraphPad Prism version 8.0. A p < 0.05 was considered statistically significant for awareness of HCV. The prevalence of HCV in this study was 4 (1.0%). Awareness of HCV was low at 112 (28.2%). Residence (p=0.021) and age group (p=0.040) were significantly associated with HCV awareness. Age 41-50 years was almost three times more likely to be aware of Hepatitis C infection compared to [&le;] 30 years. Although the prevalence of HCV was low, awareness of the infection was also limited; this highlights the need for public health authorities to implement targeted HCV education programs in major markets to effectively reach informal sector workers who are often overlooked by conventional campaigns.

Genetic ancestry composition has been used extensively as a predictor of clinical outcomes, multiomic biomarkers, and endophenotypes, but the models have most often used untransformed ancestry fractions as explanatory variables. Under a simplex constraint results from this type of model can be uninterpretable and misleading. We demonstrate the use of multiple transformed log ratio coordinates of ancestral proportions as predictors in a study of excreted myeloperoxidase (MPO), a neutrophilic enzyme used as a fecal biomarker to measure intestinal inflammation and enteropathy. We show how to convert these difficult-to-interpret effects into association results for shifts between two ancestries under an isoancestry constraint (holding an ancestry fraction constant) using post-estimation average marginal effects and explain their geometric interpretation. We found that increasing proportion of African ancestry was associated with increased levels of excreted MPO in low-income household infants in three Northeastern Brazil studies, with a smaller negative secondary association of European ancestry, all under a tri-continental ancestry composition (African, European, Amerindian). While the maximum log(MPO) outcome variance explained by differences in genetic ancestry was modest at a few percent, we show evidence that these differences in heritability were context-dependent on measurement of MPO under active enteric infection. The results were attenuated by socio-economic status, but a signal remained. Overall, we found that African genomes carry additional alleles that enable a more intensive neutrophil response to enteric infection relative to European and Amerindian genomes, illuminating a possible host genetic background role in modulating immune response to enteric diseases and pathogens.

Background: Optimising sampling frames for genomic surveillance of E. coli and Klebsiella may support interventions to mitigate bloodstream infections (BSIs), but approaches to estimating sample size and how these relate to bacterial population diversity at multiple genetic levels (strain/plasmid/antimicrobial resistance genes [ARGs]) are lacking. Methods: Using systematically collected, regionally-stratified, whole genome sequencing data from a 6-month genomic survey of English E. coli/Klebsiella BSI isolates (n=1,939; NEKSUS), we used Bayesian approaches to estimate the sample sizes required to capture genetic diversity at strain- (MLST, fastBAPS clusters), plasmid- and ARG-levels, using two diversity measures: 'coverage' (i.e. proportion of the bacterial population/plasmids/ARGs represented by features observed in the sample), and the number/proportion of unique features observed at varying surveillance sample sizes. Our method is available as a user-friendly R Shiny application, EpiSENTRY (https://01a0c3dd-90d2-e597-58a5-51391a468387.share.connect.posit.cloud/). Findings: Randomly sampling 1,400 E. coli/Klebsiella BSI isolates each achieved [&ge;]80% coverage of bacterial lineages and ARGs (i.e. capture features constituting [&ge;]80% of the population) at 95% certainty, but captured lower proportions of unique features (28% MLSTs, 59% fastBAPS clusters, 19% plasmid subcommunities, and 57% ARGs for E. coli; 49%, 87%, 50% and 83% for Klebsiella, respectively). Sample sizes required for 80% coverage of E. coli plasmid populations were higher than MLSTs (1,928 [95% CrI: 1,837-2,025] vs 1,351 [1,230-1,472]), while for Klebsiella, estimates were lower for plasmids (1,115 [1,052-1,181] vs 1,422 [1,331-1,515] for MLSTs). Lower sample sizes adequately captured 80% coverage of fastBAPS clusters and ARGs (649 [575-727] and 27 [23-30], respectively, for E. coli; 113 [84-145] and 83 [72-96] for Klebsiella), due to feature-specific frequency distributions. Klebsiella BSIs were more diverse than E. coli, with sampling 10.9% vs 3.2% of total annual BSIs in England needed to reach 80% MLST coverage. Plasmid populations and Klebsiella MLSTs were region-specific, emphasising the need for regionally-representative sampling. Interpretation: Bayesian analysis facilitates estimates of context-specific genomic surveillance sample sizes. Cost-effective targets for coverage require further optimisation.

Background: The Central Brain Tumor Registry of the United States (CBTRUS) uses a histology grouping model based on the World Health Organization (WHO) to classify cancer registry records for clinically relevant statistical reporting. Methods: CBTRUS, together with its consulting neuropathologists, reviewed and aligned its histology groupings with the 2021 WHO Classification update. Obsolete histology nomenclature along with their International Classification of Diseases for Oncology 3rd edition (ICD-O-3) codes were identified, currently included histologies were reclassified as appropriate, and new codes found in 2021 WHO were incorporated. An evaluation was conducted of the frequency of histology codes affected in the reclassification process, as well as incidence and survival pre- and post- reclassification of CBTRUS Tumor Type Groupings. Results: After review of the CBTRUS grouping scheme, 205 codes were reclassified and 2 new codes were incorporated. Tumor type groups most affected were those classified as glioma. Reclassification resulted in 167,038 of 491,804 (34%) cases having a grouping reclassification or reporting change, indicating that the 2021 revision of the WHO Classification has significantly impacted the collection and reporting of primary b CNS tumors. Conclusion: This work demonstrates the need to be responsive to changes in classification and coding for statistics to reflect real-world clinical use. This will require collaboration from all parties to have the ability to reconcile clinical practices and surveillance requirements.

Background: Long-term mortality data among Brazilian police officers and firefighters are scarce. This study investigated the leading causes of death in Brazilian male military police officers and firefighters over three decades, comparing their mortality and mean age at death with those of the male population. Methods: We retrospectively analyzed death records of male military police officers and firefighters from Espirito Santo (ES), Brazil, from 1988 to 2019. Mortality was analyzed across three decades and the standardized mortality ratios (SMRs) for the three leading causes were calculated using the male populations of ES and Brazil as references. Results: Overall, 2,198 deaths were identified, with a mean age at death of 59 {+/-} 18.5 years, compared with 60.5 {+/-} 23.9 years among men in ES and 63.4 {+/-} 23.7 years among Brazilian men. Mean age at death was 36 {+/-} 9 years among active-duty and 68 {+/-} 13 years among inactive personnel. Across the study population, the leading causes of death were circulatory system diseases (32%), external causes (26%) and neoplasms (15%). Circulatory disease mortality was higher in the second and third decades compared with both reference populations, whereas external-cause mortality shifted from higher, in the first two decades, to lower than expected in the last decade. Neoplasm mortality was higher relative to Brazil only in the last decade. Conclusion: Mortality patterns differed by cause and over time. The younger mean age at death among active-duty personnel, together with cause-specific excess mortality, highlights the importance of long-term occupational health surveillance and preventive strategies.

Background Schistosomiasis is a parasitic disease caused by flatworms known as schistosomes. The infection cycle starts when people shed eggs through the stool or the urine. Larva infects freshwater snails to later infect humans through the skin during water based activities. Schistosomiasis is commonly associated with rural areas. In this study, we wanted to see if the schistosomiasis distribution is different in rural and urban areas, along with potential risk factors associated with schistosomiasis distribution. Methodology Fresh urine samples were collected from 1,699 school-aged children (5 - 15 years old) in urban and rural sites in the Kimpese health district. Prevalence of haematobium and mansoni schistosomiasis was determined using, respectively, the urine sedimentation and the Point-of-Care Circulating Cathodic Antigen test with a quantitative estimate of infection intensity obtained with an RDT-Reader. Collected risk factors were tested for association with schistosomiasis infection and its intensity. Results The overall prevalence of schistosomiasis found in urban and rural areas was 75% and 82% respectively, with higher prevalence of S. mansoni in rural schools, and higher S. haematobium prevalence in urban schools. The difference in total prevalence between schools in urban and rural areas was significant, X2 (1, N = 1699) = 13.03, p = .0003. S. mansoni intensity of infection was also higher in rural children (mean = 162 mV) compared to those in urban areas (mean = 76 mV) (p < 2e-16). Male gender, washing dishes in the river, and swimming were associated with schistosomiasis in urban areas. Age, Springs, and rivers were significant factors in rural sites. Age, river, and washing dishes in the river were factors associated with the intensity of infection. Conclusion Our results showed very high prevalence in both rural and urban areas, which implies that control programs should consider them with the same interest and also revise control strategies.

To deal with the COVID-19 pandemic, Denmark implemented an aggressive program aimed at controlling the pandemic which included both testing and contact tracing programs. The large amount of data collected in Denmark on the pandemic and its integrated nature made it possible to investigate the effectiveness of the testing and contact tracing effort. The results of that investigation and a discussion of the effectiveness and limitations of the different control efforts are reported herein, as are lessons learned concerning possible improvements for the future. The analysis is limited to the period from the start of the COVID-19 pandemic in Denmark (late Feb. 2020) into May 2021, at which time the impact of vaccination intervention was already playing a role with ~25% of the Danish population at least partially vaccinated. From the available data sets we estimate the national Infection Detection Efficiency (IDE) starting around July 1, 2020, the time at which the national infection detection program started to be implemented in a more robust form. The results rely on daily COVID-19 hospital admissions, PCR test results, and anti-body prevalence values for the Danish population. We find that for the long-term average, the combined Danish national testing and contact tracing program identified on average about 55 to 60% of the infected individuals during the period from Sept. 1, 2020, into early May 2021. However, higher infection detection efficiencies were achieved in localized areas for short time intervals. Our investigations further indicate that the Danish testing and contact tracing program, which was among the most ambitious in the world, could have had a better balance between voluntary probing on the one hand and focused contact tracing and targeted testing on the other hand. As typically implemented, it proved to be largely ineffective in controlling the pandemic. However, in at least one case when it was implemented in an enhanced and focused mode, it was able to bring a large local outbreak that dominated the country's cases under control. We have compiled a list of lessons learned regarding the use of contact tracing procedures to control potential future pandemics before vaccinations become available.

Background: Pertussis has resurged in the post-COVID-19 era, yet diagnostic delay remains a barrier to timely treatment and transmission interruption, particularly among adults. Methods: Retrospective observational cohort study of 787 patients with confirmed pertussis from January 2016 through March 2026 across two South Carolina health systems. Electronic health record data from the 60 days preceding confirmation were used to characterize diagnostic timing (same-day vs. delayed), delay duration, and respiratory pathogen testing patterns including pertussis test modality. Results: Adults accounted for 48.4% of cases (median age 16 years [IQR 4-52]; 61.6% female). Same-day diagnosis was highest among children aged 1-4 years (75.4%) and lowest among adults aged 50 and older (approximately 50%). Among the 305 patients (38.8%) with delayed diagnosis, median delay ranged from 7-12 days in children to 22.5-26.5 days in adults aged 50 and older. Delay did not vary significantly by COVID-19 period, race, ethnicity, or insurance type. Testing breadth was greater in inpatient and emergency settings than outpatient. Pertussis testing was predominantly PCR-based in children but serologic in adults, potentially reflecting later clinical presentation relative to illness onset; however, the near-absence of PCR testing in older adults may contribute to missed diagnoses during the early illness window when PCR sensitivity is highest. Conclusions: Older adults experienced markedly delayed pertussis diagnoses compared with children. Earlier consideration of pertussis in adults with prolonged cough, including PCR testing early in illness before serologic conversion, may reduce diagnostic delay and facilitate timelier treatment and contact tracing.

Background. Public-health use of influenza surveillance - situational awareness, planning for clinical surge, and issuing advisories or warnings - needs more than an accurate point estimate of next week's count. What matters operationally is whether a rise is caught early, whether the direction of change is right, and whether an alert threshold is about to be crossed, all with honest uncertainty. For such use a forecast must also respect reporting delay, later data revision, and the calibration of its prediction intervals. Using Japan's sentinel surveillance, we evaluated short-term probabilistic forecasts that respect the data release history, and we measured what adding other surveillance series contributes, focusing on the properties that matter for public-health decisions. Methods. The target was the number of influenza reports per sentinel site in each of the 47 prefectures. For each forecast we predicted, as quantiles, the value 1-4 weeks after the most recent observed week. We compared three models: a ridge regression trained jointly across prefectures; a gradient-boosting quantile regression (GBQR) that learns from many surveillance series; and their equal-weight combination on the log scale. Six seasons were used to develop the models. The 2025/26 season was held out as a temporal evaluation period after the specification was fixed; because its epidemic profile had already been seen, it is not a fully independent prospective test. We scored forecasts with the weighted interval score (WIS) and checked prediction-interval coverage. For the Japanese target series we used the value first published for each week; some auxiliary series were taken as retrieved and therefore include later revisions. Results. In 2025/26, the combination's WIS relative to a persistence forecast was 0.841, 0.811, 0.794 and 0.818 at horizons of 1-4 observed weeks - that is, 16-21% lower than persistence. Coverage of the 80% prediction interval was 79.7%, 77.1%, 74.5% and 75.1%, and of the 95% interval 94.3%, 93.4%, 92.6% and 91.8%. Adding auxiliary series improved the GBQR over the development period. However, on the original scale the combination's edge over ridge regression was not statistically clear, and in some low-level rising phases the combination did worse than ridge. Conclusions. Over the period studied, models that share information across regions scored better than a persistence forecast. For public-health use, however, the operative questions are the real lead time once reporting delay is accounted for, whether rises from low levels and threshold exceedances are caught in time, and whether the upper prediction intervals are wide enough; on these, the present evidence is not yet sufficient. The 2025 change to the sentinel system also means that pre-change advisory and warning thresholds cannot be read mechanically. A prospective evaluation with strictly controlled data availability is needed before such forecasts are used to support advisories or planning.

Background. Safely managed drinking-water monitoring under Sustainable Development Goal target 6.1 uses source-water quality, yet Escherichia coli is common in household drinking water in Bangladesh despite near-universal improved sources. We compared source and household point-of-use (POU) E. coli detection within households and estimated how the safely managed estimate changes if POU replaces source E. coli. Methods. Cross-sectional secondary analysis of the Bangladesh MICS 2025 water-quality subsample (February-June 2025; detection >=1 colony-forming unit/100 mL). We classified 5,944 households with readable paired results into four joint patterns and, exploratorily, examined POU detection among negative-source households and two-week diarrhoea in children under five with survey-weighted modified Poisson models. Results. E. coli was detected in 47.4% of source and 84.8% of POU samples; only 12.7% of households were negative at both. Among negative-source households, 75.8% had E. coli in household water, versus 94.7% with a detected source, persisting (33.3%) even direct from the source. The JMP-aligned safely managed estimate was 42.5% (95% CI 40.8-44.1); substituting POU for source E. coli gave 12.6% (11.4-13.8), not an SDG indicator estimate. The diarrhoea prevalence ratio for POU detection (1.04, 0.59-1.86) was too imprecise to interpret. In exploratory spatial analysis, POU detection clustered geographically (Moran's I 0.16 cluster level, 0.31 district level, both p<0.001) and was independently associated with lower elevation (odds ratio 0.62, 0.56-0.70) and longer travel time to healthcare (1.65, 1.29-2.12); five districts had complete detection among 84-94 households tested. Conclusions. Source and POU classifications differed substantially; the survey cannot show where or when contamination occurred. Contamination was spatially clustered, arguing against pure noise and pointing to districts for follow-up. The findings support evaluating standardised POU sampling as a complement to source-based monitoring, with targeted follow-up and cross-season, cross-country replication.

Sepsis is a substantial contributor to neonatal mortality in Africa, with Klebsiella pneumoniae as the leading causative pathogen. Incorporating molecular tools such as whole genome sequencing (WGS) into routine surveillance of important bacterial pathogens, including those causing neonatal sepsis, can support targeted deployment of infection prevention and control measures and treatment interventions. This study aimed to understand the current practices and capacity for culture, identification and genomic analysis of bacterial pathogens in Africa, with a particular focus on K. pneumoniae, to support standardised genomic surveillance. A cross-sectional online survey was distributed to various clinician and scientist networks across Africa. All respondents completed a demographics section, while sections on laboratory test capacity, blood culture practices, WGS, and bioinformatics analysis were completed based on experience in these aspects. Responses were received from 52 institutions in 25 African countries. Among 51 institutions completing the laboratory test capacity section, 61% reported performing blood cultures, with the majority using manual commercial biochemical systems for species identification (71%) and manual disk diffusion for antibiotic susceptibility testing (82%). Participating institutions reported near-universal access to a -80{degrees}C freezer, centrifuge and thermocycler, but shaking incubators were less commonly available (67%). More than half of respondents (54%) indicated that they perform the entire WGS workflow (including DNA extraction, library preparation and WGS) internally, with most performing DNA extraction internally (88%) using column-based kits (70%). Outsourcing was progressively more common at later workflow stages. Infrastructure challenges that limit bioinformatics analysis capabilities were reported by all 23 respondents who completed this question, including limited access to high-performance computing and data storage space. This survey found sufficient capacity to support genomic surveillance of neonatal sepsis pathogens across participating African institutions. However, investments in blood culture, supply chains, sequencing, bioinformatics, and data dissemination capacity are needed to realise its full potential. These findings will support the development of standardised genomic surveillance protocols tailored to the diverse capacities of African laboratories.

ABSTRACT Background: Poliomyelitis remains a major public health concern where population immunity is incomplete and circulating vaccine-derived poliovirus (cVDPV) persists. Although Nigeria interrupted wild poliovirus (WPV) transmission in 2020, cVDPV cases continue to pose challenges, particularly in parts of northern Nigeria. Modern control strategies require a synergy of routine immunization, supplementary campaigns, disease surveillance, and community trust. Methods: This multicentre descriptive cross-sectional study evaluated community knowledge and attitudes towards polio immunization across 37 Local Government Areas (LGAs) in 20 states and the Federal Capital Territory (FCT). A multistage sampling strategy was utilized to select 1,850 adult respondents (50 per LGA) spanning rural, semi-urban, and urban settlements. Results: Overall, 40.4% (n = 747) of respondents demonstrated good knowledge, while 58.4% (n = 1,080) displayed positive attitudes towards polio immunization. A striking disparity was observed across residence classifications: respondents in urban/semi-urban LGAs exhibited significantly higher levels of good knowledge (51.7%, 569/1,100) compared to those in rural LGAs (23.7%, 178/750; {chi} = 144.00, df = 1, p < 0.001). Main sources of information were Questionnaire responses (53.6%) and community and Traditional leaders(17.2%). Conclusion & Recommendations: Substantial knowledge deficits persist in rural northern Nigerian communities despite generally favorable attitudes. Interventions must prioritize localized risk communication, involvement of traditional/religious leaders, strengthening routine primary healthcare integration, and targeting zero-dose children in hard-to-reach areas. Keywords: Poliomyelitis, Oral Polio Vaccine, Vaccine Hesitancy, Northern Nigeria, Community Health, Routine Immunization.

Background: Shotgun metagenomic pipelines routinely discard host-derived reads, which can exceed 90% of reads in low-biomass clinical samples. Whether these reads support mitochondrial heteroplasmy detection, and at what allele fraction, has not been established. Methods: Shotgun metagenomic data from 47 upper respiratory tract swabs from healthy adults in Nagpur, India, were analysed. Human Reads were recruited against the rCRS and realigned competitively to GRCh38 to remove nuclear mitochondrial segments (NUMTs). Kraken2 was used as a microbial control. Heteroplasmy was called against a pooled, substitution-specific beta-binomial error model and a leave-one-out panel of normals. The detection limit was evaluated from the substitution spectrum against gnomAD v3.1. Results: Complete mitochondrial genomes were recovered from all samples (mean depth 433X, range 9-3,029X). Competitive realignment relocated 3.22% of recruited reads to nuclear loci; microbial cross-mapping removed 0.045%. Error rates varied 12.8-fold across substitution classes, with T>A being the highest. The 134 calls had a Ti/Tv of 0.43, compared with 3.51 in gnomAD, and T>A accounted for 42.5% of calls. T>A allele fractions never exceeded 4.72%, whereas transitions reached 90.81%. At a 5% threshold, T>A calls disappeared, and Ti/Tv rose to 2.20 before plateauing; 16 calls exceeded this limit. Macrohaplogroups were assigned in 46 of 47 samples (M 22, R 23, N 1). Conclusions: Metagenomic host reads support complete mitochondrial recovery, haplogroup typing, and heteroplasmy detection for allele fractions > 5%. Below this, a T>A-dominated error process persists after NUMT removal that background-fitted models do not capture.

Background: COVID-19 vaccination uptake is influenced by various sociodemographic and psychological factors. Previous studies have suggested that the relationship between personality traits and vaccination is context-dependent. However, this association has not been investigated in Japan, a unique sociocultural context characterized by historically low vaccine confidence but exceptionally high COVID-19 vaccine uptake. We examined the association between the Big Five personality traits and completion of the primary COVID-19 vaccination series, exploring potential gender-personality interactions. Methods: A web-based, cross-sectional survey was conducted among 7,210 Japanese adults (aged 20-85 years) in December 2021. Personality was assessed using the Japanese version of the Ten-Item Personality Inventory. Multivariable Poisson generalized estimating equations were used to calculate adjusted prevalence ratios (PRs) and assess gender-personality interactions. Results: Higher extraversion and lower openness were significantly associated with vaccination completion across genders. A significant gender-agreeableness interaction was observed: agreeableness (PR = 1.016, 95% CI: 1.008-1.024) was positively associated with vaccination completion among men but not women. A similar, though only marginally significant, interaction pattern was observed for neuroticism (PR = 1.011, 95% CI: 1.004-1.019 among men). Conclusions: Personality traits act as modest but meaningful, gender-specific psychological modifiers of vaccination behavior in Japan. Public health campaigns should transition from traditional "one-size-fits-all" messages to personality-tailored and gender-responsive communication strategies to optimize vaccine uptake and bolster psychological resilience in future pandemics.

Introduction: In temperate regions, influenza and respiratory syncytial virus (RSV) typically exhibit seasonal epidemics during the winter months, often concurrently with SARS-CoV-2 epidemics. Monitoring past and real-time trends in infection dynamics is important for informing public health situational awareness, including identifying and characterising unusual epidemic activity. However, data used to monitor these trends can exhibit substantial noise including strong day-of-the-week variation in reporting. In addition, case data for influenza can obscure distinct trends in influenza subtypes if not combined with virological data. Aim: By quantifying trends in respiratory virus activity using statistical methods, the Australia-Aotearoa Consortium for Epidemic Forecasting and Analytics (ACEFA) aims to provide government partners with comprehensive epidemic intelligence. Methods: Analyses were performed on daily case time series data for SARS-CoV-2, RSV and influenza across Australia's eight jurisdictions. Past and real-time trends were inferred for each pathogen and each influenza subtype using Bayesian p-spline models. Results: The 2025 Winter Situational Assessment Program provided weekly reports throughout the winter season and during the out-of-season influenza A H3N2 epidemic, driven by the emergence of the novel influenza subclade ('subclade K'). Despite limited subtyping data, our analysis provided an early signal of increasing influenza A H3N2 during a period in which overall influenza cases were decreasing; increases in influenza A H3N2 activity were first detected in July, and by mid-August, increasing H3N2 activity was estimated across all jurisdictions. Discussion: Our analysis highlights the benefits of incorporating statistical methods into real-time epidemic situational assessment and in consolidating reporting across jurisdictions.

Introduction: Tuberculosis (TB) care is typically organised around biomedical and public health priorities, including diagnosis, infection control, treatment adherence, and prevention of transmission. Although qualitative research has described the burden of TB, lived experience is often treated as descriptive rather than as knowledge that can inform care. We examined how Aboriginal people in remote northern Australia experienced TB, and what these experiences reveal about how TB care can be strengthened in practice. Methods: We conducted an inductive qualitative study involving in-depth interviews with Aboriginal people with lived experience of TB. Interviews were supported by Aboriginal community health workers. Data were analysed using reflexive thematic analysis, with Aboriginal contributors involved in interpretive workshops to refine themes and guide culturally safe representation. Results: Twenty-one Aboriginal people contributed across 13 interviews. Three interrelated themes described the TB journey. Illness often challenged dominant biomedical expectations: symptoms were commonly normalised, which fear, ambivalence, and endurance were shaped by experiences of compromised health and cumulative loss. Distance from family, community, and Country was experienced as both protection and sacrifice; separation was endured to protect others but carried substantial costs, particularly when its purpose and duration were unclear. Recovery involved rebuilding strength, connection, and identity. Clear explanation, continuity, and opportunities for choice supported engagement in care, while survivors and community health workers provided important sources of trust, support, and shared responsibility. Conclusion: Lived experience is practice-relevant knowledge for TB programmes. Care should minimise avoidable harms of separation, support continuity and choice, and recognise survivors, Aboriginal health workers, and communities as partners in the design and delivery of care.

Background. Nigeria's reported Lassa fever case fatality ratio (CFR) rose from 18.9% at week 23 of 2025 to 25.0% in 2026, prompting concerns over failing clinical care. Because surveillance artefacts can also alter CFRs, candidate mechanisms that published data can resolve were identified and evaluated. Methods. This ecological study extracted weekly state-level counts from 474 Nigeria Centre for Disease Control and Prevention situation reports (2017-2026). Per a pre-specified plan, years were compared at phase-matched points, year-on-year CFR changes were decomposed into within-state and between-state components, and tipping-point ascertainment shifts calculated. Weekly incident and cumulative published totals were compared post hoc. Findings. Of 11 candidate mechanisms, 2 could be evaluated fully and 5 in part. On weekly incident counts, 2026 did not differ from 2025 at the phase-matched midpoint (+0.3 percentage points, 95% CI -5.0 to 7.6); within-state (-1.1, 95% CI -4.7 to 3.0) and between-state (+0.5, -2.0 to 2.9) components spanned zero. Conversely, the published cumulative CFR was 5.4 to 6.2 percentage points higher because 70 deaths were added retrospectively by week 36 outside weekly reports. Reconciling cumulative figures would require 279 missed survivors (6% of suspected cases not confirmed). Interpretation. The 2026 CFR rise came from deaths added to cumulative totals outside the weekly counts, and published data cannot attribute it to care. Endemic zoonotic CFRs cannot serve as clinical outcome measures unless testing volumes, deaths added late, and post-mortem sampling are published alongside case counts. Funding. US NSF-NIH-NIFA EEID; UK BBSRC; Birgitta Sintring Fellowship (Uppsala University).

In systematic review, the measures reported by the primary studies may not always be the measures sought by the systematic review investigators. Motivated by an systematic review of interventions to reduce meat consumption, we discuss here methods to infer relative risks and confidence intervals from randomized controlled trials that reported differences, possibly in the presence of repeated measures or multiple interventions.

Background: Excess mortality estimates depend on an expected baseline, an unobservable quantity typically derived from models with prescribed functional forms and short reference periods that exclude exceptional events. Singular Spectrum Analysis (SSA) offers a nonparametric alternative but requires subjective component selection and is sensitive to outliers. We combined SSA with automated component selection and outlier interpolation to estimate long-term baselines and compile a catalog of excess mortality events (EMEs). Methods: We analyzed weekly all-cause mortality (2015-2024) for six metropolitan areas with contrasting climatic, demographic, and epidemiological contexts: Brussels, Antwerp, and Liege (Belgium), and Athens, Thessaloniki, and Larisa (Greece). SSA was applied to standardized log-mortality rates; components were selected using Monte Carlo SSA, and COVID-19 periods were interpolated iteratively. EMEs were defined as weeks exceeding a quasi-Poisson two-z-score threshold, then screened for coincidence with heat waves, cold waves, COVID-19 periods, and influenza epidemics. Results: Baselines were consistent within countries: annual cycles in Belgium, with an additional significant semiannual cycle in Greece reflecting summer mortality. We cataloged 170 EMEs spanning 456 weeks and 14,210 excess deaths. Pandemic weeks accounted for 77% of excess mortality, and 96 weeks coincided with temperature extremes; 56 EMEs, representing 3.7% of excess mortality, remained unmatched. Conclusions: SSA yields reproducible, low-assumption baselines that capture country-specific seasonality. Because flexible baselines can absorb recurrent seasonal mortality, component selection is a substantive choice that should be reported explicitly, together with its sensitivity.