Microbial Biotechnology

Standard in vitro antimicrobial susceptibility testing (AST) using Mueller-Hinton broth (MHB) does not reflect infection-site conditions, and its results often do not correlate with therapeutic outcomes. Here, we compared the antibiotic susceptibility of methicillin-resistant Staphylococcus aureus (MRSA), a common chronic wound pathogen, in simulated wound fluid (SWF) resembling wound exudate versus MHB, revealing discordant AST results across six of nine tested antibiotic classes. The most significant were 128-fold increased resistance to tetracyclines and 256-fold sensitization to {beta}-lactams in SWF. Tetracycline resistance was mediated by MntC, an extracellular manganese-binding protein, whereas {beta}-lactam sensitization was driven by cell envelope remodelling in SWF. Galleria mellonella wound infection results matched the SWF susceptibility phenotypes, suggesting SWF better predicts in vivo wound infection therapeutic outcomes. These comprehensive phenotypic and mechanistic insights into MRSA antibiotic responses under wound-infection-mimetic conditions with direct in vivo validation identify a potential new antibiotic adjuvant target and may guide improved antibiotic therapy for MRSA wound infections.

Antimicrobial resistance (AMR) is a growing global public health threat that complicates the treatment and control of bacterial infections. Shigella spp., a leading cause of bacterial diarrhea worldwide, has increasingly exhibited resistance to multiple antimicrobial agents that are commonly recommended therapy for severe shigellosis. Although conventional antimicrobial susceptibility testing (AST) remains the reference standard, it is time-consuming and provides limited insight into the genetic mechanisms underlying resistance. Whole-genome sequencing (WGS) has emerged as a complementary approach for AMR detection by enabling direct identification of resistance genetic determinants encoded in bacterial genomes. Machine learning (ML) methods applied to genomic features such as k-mers have shown promise for predicting resistance phenotypes from WGS data; however, applications to Shigella remain limited. In this study, we developed and evaluated an interpretable ML framework for predicting ciprofloxacin resistance using k-mer features derived from WGS data of 1,424 Shigella isolates collected in Ontario, Canada, between 2018 and 2025. K-mers were extracted from known gene targets associated with ciprofloxacin resistance, including chromosomal quinoline resistance-determining regions (QRDRs: gyrA and parC) and plasmid-mediated determinants (qnr). Supervised ML approaches were trained and compared. We evaluated the influence of k-mer lengths (k=11, 15, 21 and 31) on predictive performance and model interpretability; and compared models based on chromosomal determinants alone and models incorporating both chromosomal and plasmid-mediated determinants. Randon Forest classifier achieved the most consistent performance across models. Inclusion of plasmid-mediated determinants improved predictive accuracy relative to chromosomal-only models. Although differences across k-mer lengths were modest, k = 11 produced the highest area under the receiver operating characteristic curve (AUC) and the lowest Brier score. SHAP analyses localized high-impact features within QRDRs of gyrA and parC, supporting biological interpretability. These findings demonstrate that biologically-informed k-mer-based ML models can accurately and transparently predict ciprofloxacin resistance in Shigella, supporting their potential integration into genomic AMR surveillance and digital public health frameworks. Author summaryIn this study, we used genome sequencing data to develop machine learning models that predict ciprofloxacin resistance for Shigella directly from bacterial DNA. We focused on small DNA fragments (k-mers) derived from known resistance genes and mutations. Among the approaches tested, a Random Forest model showed the most consistent performance. Combining chromosomal mutations with plasmid-mediated resistance genes improved prediction accuracy and helped identify key genetic regions associated with resistance. These findings demonstrate that machine learning applied to genomic data can accurately and interpretable predict antibiotic resistance, supporting its potential use in genomic surveillance and public health monitoring.

Mycetoma is a neglected tropical disease caused by various bacterial and fungal pathogens that has a significant health impact across a broad geographically defined "mycetoma belt" spanning South America, Africa and Asia. Histologically, mycetoma is characterised by invasive and destructive granuloma development in the skin, deep tissues and bone, leading to tissue destruction, deformities and high morbidity. The presence of macroscopic, highly compacted pathogen microcolonies, or "grains," is a key diagnostic feature, and the formation of grains supports pathogen persistence and disease chronicity. However, there is a paucity of information on immune responses in mycetoma patients and on the relative importance of phylogeny and/or grains in establishing the local immune landscape. Here, we used spatial proteomics to examine the distribution of 43 immune-related proteins in surgical biopsies from 11 patients with mycetoma of bacterial (Actinomycetoma; Actinomadura pelletierii and Streptomyces somaliensis; n=6) and fungal (Eumycetoma; Madurella mycetomatis; n=5) origin. Using mixed-effects modelling, an exploratory analysis across species and pathogen classes revealed few significant differences in immune marker expression. In contrast, and independently of pathogen class, the cellular infiltrate closest to grain boundaries had higher per-cell expression of CD66b+, ARG1, and VISTA. The preferential accumulation of CD66b+ARG1+VISTA+ cells at grain boundaries was confirmed by quantitative immunofluorescence analysis. Hence, the local tissue microenvironment surrounding the mycetoma grain represents a specialised immunosuppressive niche, with parallels to the tumour microenvironment.

BackgroundIn long-term care facilities (LTCFs), close-contact identification often relies on staff recall and monitoring records because residents may be unable to self-report reliably. How these different record-generation processes relate to proximity-based sensor measurements in routine LTCF workflow remain unclear, and how such differences may influence contact-based decision-making in outbreak response is not well understood. MethodsWe conducted a five-day observational study in a Japanese LTCF using ultra-wideband (UWB) indoor positioning. Twenty-seven participants wore UWB tags, including 16 residents and 11 staff members; 10 staff members completed questionnaires. We compared UWB-derived proximity with questionnaire-derived contacts from staff self-report and monitoring-based proxy records, and assessed directional discrepancies under multiple distance-time thresholds. ResultsQuestionnaire-based records and UWB-derived proximity showed different patterns of discrepancy across contact types. Within this facility, resident-related monitoring-based proxy records showed relatively small directional discrepancies, whereas staff self-reports tended to identify additional resident-staff contacts under the baseline threshold ([≤]1.0 m for [≥]15 min). Several alternative thresholds were associated with discrepancies closer to zero than the baseline, although the apparent ranking varied by summary metric. ConclusionsIn this single-facility observational study, different contact-list generation processes were associated with different patterns of discrepancy relative to a proximity-based operational measure. These findings support interpretation in terms of workflow-specific contact-list generation rather than a single universally optimal threshold and may help inform facility-level review of contact identification practices in LTCFs. These findings support aligning contact identification strategies with facility-specific workflows to improve the feasibility and effectiveness of IPC practices in LTCFs.

Acinetobacter baumannii is a major cause of severe hospital-acquired infections, with a steadily increasing global prevalence driven by a few clinically adapted lineages. Animals and natural environments also harbor A. baumannii populations, but assessing their connections to clinical lineages is limited by sparse genomic data and a lack of integrated sampling. We conducted a local One Health genomic epidemiology study, sampling, isolating, sequencing, and characterizing several hundred A. baumannii isolates from clinical, animal, and environmental contexts. Within a geographically restricted area, we recovered several globally distributed clinical lineages (international clones, ICs), as well as livestock- and environment-associated lineages shared across Europe, highlighting widespread dissemination beyond clinical settings. Isolates closely related to the emerging clinical lineage IC11 were found in livestock, but no other clinically associated lineages were detected outside clinical contexts. Among these, the epidemic superlineage IC2 was identified in both human and veterinary clinical settings, indicating that similar practices in human and animal medicine select for closely related opportunistic pathogens. We found that hospitals host distinct, antibiotic-sensitive endemic populations capable of causing infection. These populations belong to a diversifying clade spanning clinical and environmental contexts and carry a high load of insertion sequences. Strong plasmid conservation further suggests frequent horizontal gene transfer across ecological compartments. Overall, A. baumannii comprises diverse, context-adapted lineages with a high potential for global spread. Although intercontext transmission appears limited, plasmids may overcome these ecological barriers. Our findings underscore the need for integrated One Health surveillance to better understand transmission pathways and limit the emergence of clinically adapted strains.

Background: Metronidazole (MTZ) is a first-line antibiotic for several enteric infections. Its use is common in low-income countries, where most primary-care consultations are conducted by nurses. However, increasing resistance among some enteric pathogens is a growing concern. Using WHO guidelines, we conducted a register-based cross-sectional study to assess MTZ prescribing practices and their determinants in public and private primary healthcare facilities in South Benin. Methods: We performed a register-based cross-sectional study covering the year 2020 in 11 primary healthcare facilities (5 public and 6 private) in Abomey-Calavi, South Benin, following WHO recommendations. In total, 200 visits per facility were selected using systematic random sampling. The primary outcome was the prevalence of MTZ prescription. Determinants of MTZ prescription were identified using multivariable logistic regression analysis. Results: In total, 2,200 medical visits were analyzed. The median age of patients was 19 years, and 57% were female. Antimalarials were prescribed in 52% of visits. Antibacterial agents were prescribed in the majority of visits, with MTZ being the second most frequently prescribed antibiotic (18%), after aminopenicillins (27%). In multivariable analysis, digestive symptoms (adjusted odds ratio [aOR], 8.65; 95% confidence interval [CI], 6.49-11.6), genitourinary symptoms (aOR, 6.84; 95% CI, 3.18-15.0), and skin lesions (aOR, 2.39; 95% CI, 1.58-3.60) were independently associated with increased odds of MTZ prescription. In contrast, fever (aOR, 0.66; 95% CI, 0.49-0.87), respiratory symptoms (aOR, 0.44; 95% CI, 0.26-0.71), and malaria (aOR, 0.21; 95% CI, 0.15-0.28) were associated with decreased odds. Visits in the private sector were also associated with higher odds of MTZ prescription compared with the public sector (aOR, 2.31; 95% CI, 1.78-3.02). Conclusion: MTZ is the second most commonly prescribed antibiotic in primary care in the study area, with its use largely driven by digestive symptoms. Further studies are needed to assess the appropriateness of this prescription. Additionally, research is warranted to understand better the determinants of higher antimicrobial prescribing in the private healthcare sector.

BackgroundDelayed tuberculosis (TB) treatment remains a major challenge to TB control and is associated with increased mortality, drug resistance, and onward transmission. Food insecurity may contribute to delayed TB treatment through economic, physical, and psychosocial pathways. Depression and anxiety are also associated with delayed TB treatment and may mediate the relationship between food insecurity and delayed TB treatment. This study examined the association between food insecurity and delayed TB treatment initiation and assessed the mediation roles of depression and anxiety for this relationship among people newly diagnosed with TB. MethodsWe recruited 180 participants newly diagnosed with TB in Gaborone, Botswana. Food insecurity, depression, and anxiety were measured using the Household Food Insecurity Access Scale, PHQ-9, and Zung Self-Rating Anxiety Scale, respectively. Delayed TB treatment was defined as > 2 months since first TB symptoms. Logistic regression was used to examine the association between food insecurity and delayed TB treatment. Causal mediation analysis was conducted to assess the mediating roles of depression and anxiety. ResultsAmong the 180 participants, 45 (25%) experienced delayed TB treatment initiation. Participants with delayed TB treatment had slightly higher median scores for food insecurity (2 vs. 1, p = 0.11), depression (9 vs. 6, p = 0.001), and anxiety (37 vs. 34, p = 0.05). There was insufficient evidence of an overall association between food insecurity and delayed TB treatment initiation (OR = 1.04, 95% CI 0.98-1.11, p = 0.20). Mediation analysis found insufficient evidence of total and direct effects through depression and anxiety. However, there was evidence of significant indirect effect through depression (OR = 1.04, 95% CI 1.01-1.08, p < 0.001) and a borderline indirect effect through anxiety (OR = 1.02, 95% CI 1.00-1.04, p = 0.05). ConclusionMediation analysis revealed associations between food insecurity and delayed TB treatment initiation mediated by depression and anxiety which were not evident in total effects analysis. These findings highlight the importance of considering both socioeconomic and psychological factors in addressing delayed TB treatment. Further studies are needed to confirm these pathways.

Wastewater surveillance (WWS) is established as a vital tool for monitoring polio and SARS-CoV-2 with potential to improve surveillance for many other infectious diseases. This study evaluated the feasibility of detecting measles virus (MeV) RNA in wastewater as part of a national WS preparedness trial in Brisbane, Australia, from March to June 2025. Composite and passive sampling methods were employed in parallel at three wastewater treatment plants serving populations between 230,000 and 584,000. Nucleic acids were extracted and analyzed using RT-qPCR targeting MeV N and M genes to distinguish wild-type and vaccine strains. MeV RNA were detected in both 24-hour composite and passive samples on May 26 to 27, 2025 from the largest catchment of 584,000 which also included an international airport. No measles cases were reported in this city or region within 4 weeks of the WS detections. These were confirmed as vaccine-derived measles virus (MeVV) strain via specific RT-qPCR assay. Extraction recoveries varied (11.5% to 70.5%), with passive sampling showing higher efficiency. This is the first report of use of passive samples for detection of MeV. These findings are consistent with other studies reporting WWS results of both MeVV genotype A and wild type genotype B and/or D. It demonstrates the potential for sensitive MeV WWS with rapid differentiation of MeVV from wild type MeV shedding, including in airport transport hubs and with different sample types. Use of WWS could strengthen measles surveillance by enabling rapid detection of MeV RNA and supporting outbreak preparedness and response. This requires optimised methods which are specific to or differentiate wild-type MeV from MeVV. Furthermore, the successful detection of MeV using passive sampling in this study highlights its potential for deployment in diverse global contexts which may include non-sewered settings.

BackgroundThe World Health Organization has developed several global template protocols for epidemiological investigations, including for household transmission investigations (HHTIs). These investigations facilitate rapid characterisation of novel or re-emerging respiratory pathogens and support evidence-based public health actions. Beyond technical readiness, community buy-in is central to the feasibility and acceptability of HHTIs. Research is needed to determine the perceived legitimacy among the community to inform local protocol adaptation and development of implementation plans that consider community attitudes and needs. MethodsIn 2025, we conducted a convenience survey of community members living in Victoria, Australia to explore: their understanding of emerging respiratory diseases; their willingness to take part in public health surveillance activities such as HHTIs; the acceptability of clinical and epidemiological data collection and respiratory/blood sample collection as main components of HHTIs, and; participant comfort towards including their companion animals in HHTIs. ResultsWe received 282 survey responses, of which 235 were included in the analysis dataset. Compared to the general Victorian population, our participants included a higher proportion of participants who reported being female, tertiary-educated, of Aboriginal and/or Torres Strait Islander heritage, born in Australia and speaking only English at home. Participants indicated overall high levels of comfort and acceptability towards participation in HHTIs, particularly in relation to clinical and epidemiological data collection, with lesser but still high levels of comfort with providing multiple respiratory specimens in a 14-day period. Participants were least comfortable with other specimens such as urine and blood. Involving companion animals in HHTIs was similarly acceptable as human-focused components. ConclusionsDespite our survey population being non-representative of the general Victorian population, our findings provide valuable descriptive insights into the acceptability of HHTIs in Victoria, Australia from which to benchmark future local and international surveys and community engagement activities.

We used 2492 whole genome sequences from Laos to investigate the molecular epidemiology of SARS-CoV-2 from 2021 through 2024, covering the major waves of COVID-19 disease in Laos including time periods of travel restrictions and after relaxation of travel across international borders. We identify successive waves of COVID-19 caused by shifts in the dominant lineage, beginning with the Alpha variant in April 2021 and continuing through the Delta and Omicron variants. We quantify a shift from a small number of viral introductions responsible for widespread transmission in early waves to a larger number of introductions for each variant after travel restrictions were lifted, and identify potential routes of introduction into the country. Our study underscores the importance of genomic surveillance to public health responses to characterize viral transmission dynamics during pandemics.

BackgroundTimely cancer diagnosis in children and adolescents is critical to improving outcomes, yet substantial variation in diagnostic intervals persists across cancer types and care settings. We aimed to quantify time to diagnosis and assess variations by patient, demographic, and system-level factors. MethodsWe conducted a retrospective population-based study of children and adolescents aged 0-19 years diagnosed with one of 12 common cancers between 2010 and 2022 in Quebec, Canada. The diagnostic interval was defined as the time from first cancer-related healthcare encounter to diagnosis. We calculated medians and interquartile ranges (IQR) overall and by cancer type and used multivariable quantile regression to identify factors associated with time to diagnosis at the 25th, 50th, and 75th percentiles. ResultsAmong 2,927 individuals with cancer, diagnostic intervals varied by cancer type and age. Median intervals were longest for carcinomas (100 days; IQR 33-192) and shortest for leukemias (8 days; IQR 3-44). Compared with children living in Montreal, living in regional areas and other large urban centres was associated with longer 50th and 75th percentiles of time to diagnosis for hepatic and central nervous system (CNS) tumours. Diagnostic intervals were shorter in the post-pandemic period (2020-2022) across several cancer sites, with CNS tumours showing reductions across all quantiles. InterpretationDiagnostic timeliness differed by cancer type, age, and rurality, but not by sex, material, or social deprivation. The shorter diagnostic intervals observed in the post-pandemic period suggest that pandemic-related changes in care pathways may have expedited diagnosis for some cancers.

BackgroundThe rapid growth of the worlds urban population has contributed to the expansion of informal urban settlements in many cities across the world. In these settings, lack of safe sanitation combined with high population density and poverty contributes to heightened health risks for often vulnerable populations. The aim of this study was to evaluate the effect of a shared, onsite sanitation intervention on the nutritional status of children in Maputo, Mozambique. MethodsThe Maputo Sanitation (MapSan) trial was a controlled before-and-after study to evaluate the effect of a shared, onsite sanitation intervention on child health in Maputo, Mozambique. Here, we report the effects on childhood stunting, wasting and underweight, and height-for-age, weight-for-height and weight-for-age z-scores. Children were enrolled aged 1-48 months at baseline and outcomes were measured before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. The primary analysis was intention-to-treat. The trial was registered at ClinicalTrials.gov, number NCT02362932. ResultsWe enrolled 757 and 852 children in the intervention and control groups respectively. There was no evidence for an effect of the intervention on any outcome at 12 or 24 months of follow-up except for wasting where there was very weak evidence for an effect (adjusted prevalence ratio: 0.497; 95% CI: 0.22-1.11; p=0.09). In two exploratory analyses - one including only those children born into compounds post-intervention and a second excluding children in control compounds which had independently improved their sanitation facilities during follow-up - we found that stunting increased in the intervention group whilst wasting decreased. ConclusionsThis study contributes to the growing evidence on the role of sanitation in shaping child health outcomes in informal urban settlements. We found no evidence for an effect on stunting and weak evidence for an effect on wasting. More research is needed to understand how sanitation can reduce childhood undernutrition in complex urban environments.

Wearable-derived physiological features have been associated with disease risk, but most current studies focus on single conditions, limiting understanding of cross-disease patterns. This study adopts a trans-diagnostic approach to examine whether wearable data capture shared and condition-specific physiological signatures across multiple chronic conditions spanning physical and mental health, and then evaluates the utility of these features for disease classification. A total of 9,301 patients with at least 21 days of consecutive FitBit data from the All of Us Controlled Tier Dataset version 8 were analyzed. Disease subcohorts included cardiovascular disease (CVD), diabetes, obstructive sleep apnea (OSA), major depressive disorder (MDD), anxiety, bipolar disorder, and attention-deficit/ hyperactivity disorder (ADHD), chosen based on prevalence and relevance. Logistic regression and XGBoost models were fitted for each disease subcohort versus the control cohort. We found that compared to using just baseline demographic and lifestyle features, incorporating wearable-derived features enabled improved classification performance in all subcohorts for both models, except for ADHD where improvement was mainly observed for ROC-AUC in logistic regression model likely due to the smaller sample size in ADHD subcohort. The largest performance gains were observed in MDD (increase in ROC-AUC of 0.077 for Logistic regression, 0.071 for XGBoost; p < 0.001) and anxiety (increase in ROC-AUC of 0.077 for logistic regression, 0.108 for XGBoost; p < 0.001). This study provides one of the first comprehensive transdiagnostic evaluations of wearable-derived features for disease classification, highlighting their potential to enhance risk stratification in the real-world setting as a practical complement to clinical assessments and providing a foundation to explore more fine-grained wearable data. Author summaryWearable devices such as fitness trackers and smartwatches are becoming increasingly popular and affordable, providing continuous measurements of heart rate, physical activity, and sleep. Alongside the growing digitization of health records, this creates new opportunities for large-scale, real-world health studies. In this study, we analyzed wearable-derived physiological patterns across a range of chronic conditions spanning both physical and mental health to better understand how these signals relate to disease risk. We found that incorporating wearable-derived heart rate, activity and sleep features improved disease risk classification across several conditions, with particularly strong gains for major depressive disorder and anxiety. By examining how individual features contributed to model predictions, we also identified meaningful associations between physiological signals and disease risk. For example, both duration and day-to-day variation of deep and rapid eye movement (REM) sleep were associated with increased risk in certain conditions. Our study supports the development of real-time, automated tools to assess disease risk alongside clinical care.

Childhood socioeconomic position (SEP) can have lifelong effects on health. Many studies have used adult height as a surrogate marker for early-life conditions. In this study, we derived the non-genetic component of height, calculated as the residual from sex-specific standardized height regressed on genetically predicted height, as a surrogate for childhood SEP, using data from the Hispanic Community Healthy Study/Study of Latinos (2008-2011). A positive residual would indicate favorable early-life conditions promoting growth, while a negative residual indicates early-life adversity that may stunt the development. The height residual was associated with early-life variables such as parental education, year of birth, US nativity and age at first migration to the US (50 states/DC), supporting the validity of height residual as a surrogate for early-life conditions. Furthermore, a height residual was positively associated with better cardiovascular health (CVH) and cognitive function among middle-aged and older adults. Interestingly, among <35 years old, the height residual was negatively associated with the "Lifes Essential 8" clinical CVH scores. These results suggest the non-genetic component of height as a surrogate for childhood environment, with predictive value for CVH and cognitive function.

BackgroundAccelerometer-derived behavioral phenotype captures multidimensional aspects of human behavior extending well beyond physical activity, encompassing light exposure, step counts, physical activity patterns, sleep, and circadian rhythms. Whether these five domains constitute a unified behavioral architecture underlying cancer risk and whether circadian organization and light exposure confer incremental predictive value beyond movement volume alone remains to be comprehensively established. MethodsWe conducted an accelerometer-wide association study (AWAS) encompassing the complete accelerometer-derived behavioral exposome across five behavioral domains in UK Biobank participants with valid wrist accelerometry data. Incident solid cancers were designated as the primary endpoint, with prespecified site-specific solid cancers and hematological malignancy as secondary outcomes. Cox proportional hazards models with age as the timescale were used. The minimal covariate set served as the primary reporting tier, followed by sensitivity analyses additionally adjusting for adiposity/metabolic factors, independent activity patterns, shift work history, and accelerometry measurement quality. Nominal statistical significance was defined as two-sided P < 0.05 ResultsAmong 89,080 participants, 6,598 incident solid cancer events were observed over a median follow-up of 8.39 years. In the minimally adjusted model, the pan-solid-tumor association atlas was dominated by signals from activity volume, inactivity fragmentation, and circadian rhythm. Higher overall acceleration (HR per SD: 0.91, 95% CI: 0.89-0.94) and higher daily step counts (HR: 0.93, 95% CI: 0.90-0.95) were independently associated with reduced solid cancer risk, while inactivity fragmentation metrics were consistently linked to higher risk. Notably, circadian rhythms, most prominently cosinor mesor (Midline Estimating Statistic of Rhythm under cosinor model), emerged as leading inverse risk signals, underscoring the independent contribution of circadian behavioral architecture. Site-specific analyses revealed pronounced heterogeneity across tumor sites. Lung cancer exhibited a robust inverse activity-risk gradient, while breast cancer showed reproducible associations with MVPA. Most strikingly, nocturnal light exposure demonstrated a tumor-site-specific association confined to pancreatic cancer, a signal absent across all other sites examined. Associations for uterine cancer were predominantly inactivity-related and substantially attenuated following adjustment for adiposity and metabolic factors. ConclusionsAcross five accelerometer-derived behavioral domains, solid cancers as a whole were most consistently associated with a high-movement, low-fragmentation, and circadian-coherent behavioral profile. While site-specific heterogeneity exists, the broad cancer risk landscape is dominated by movement volume, inactivity fragmentation, and circadian rhythmicity. Light exposure, although more localized in its contribution, demonstrates a potentially novel and specific association with pancreatic cancer risk. These findings support a five-domain behavioral exposome framework for cancer epidemiology and, importantly, position circadian rhythm integrity and nocturnal light exposure as critically understudied dimensions warranting dedicated mechanistic investigation.

Background: Dengue is rapidly emerging in parts of Europe. How households value vector control attributes, and whether inferences depend on decision models or message framing, is unclear. Methods: We conducted a split-ballot online experiment among adults in Italy and France, as well as a hotspot subsample from Marche, Italy. National samples included 1,505 respondents in Italy and 1,501 in France; 183 respondents were recruited in Marche. Participants were randomised to a discrete choice experiment (random utility maximisation) or a regret-based choice experiment (random regret minimisation) and to one of three pre-task messages (control, loss aversion, community values). Each respondent completed 12 choice tasks comparing two dengue control programmes and an opt-out. We estimated mixed logit and mixed random-regret models with random parameters and treatment effects. Results: Across frameworks, nearby cases and high mosquito prevalence were the dominant drivers of programme uptake, whereas cost and operational burden were secondary. In pooled analyses, loss-aversion messaging increased the weight on high mosquito prevalence in both models (from 0.483 to 0.547 in the utility model; from 0.478 to 0.557 in the regret model). Cost effects were small nationally but larger in the hotspot subsample. Conclusions: Risk salience dominates preferences for dengue vector control in these European settings. Random utility and random regret models yield consistent rankings of attributes but differ in behavioural interpretation and some secondary effects; messaging effects were modest and context dependent.

BackgroundFamily-based HIV index case testing identifies family members with unknown HIV status and links them to care. Data are limited in southern Ethiopia. MethodsA facility-based cross-sectional study was conducted among 377 adults on antiretroviral therapy (ART) in Wolaita Zone, Southern Ethiopia, from November 2022 to May 2023. Participants were selected using systematic random sampling. Data were collected via interviewer-administered semi-structured questionnaire. Multivariable logistic regression identified factors associated with index case family testing. Adjusted odds ratios (AOR) with 95% confidence intervals (CI) were calculated, and statistical significance was declared at p < 0.05. ResultsThe proportion of index case family testing for HIV was 84.9% (95% CI: 81.2- 88.6). In multivariable analysis, urban residence (AOR = 2.8; 95% CI: 1.16-6.75), duration on ART greater than 12 months (AOR = 13.0; 95% CI: 4.6-36.9), disclosure of HIV status to family members (AOR = 5.6; 95% CI: 1.9-16.5), discussion of HIV status with family members (AOR = 6.6; 95% CI: 1.9-23.2), and being counselled by health professionals to bring families for testing (AOR = 6.3; 95% CI: 2.1-19.0) were significantly associated with index case family testing. ConclusionThe prevalence of family-based HIV index case testing in Wolaita Zone was 84.9%, below the national 95% target. Health professionals should strengthen counselling on ART adherence, status disclosure, family discussion, and active referral to improve testing uptake among family members of people living with HIV.

Study questionWhat are the characteristics and treatment outcomes of women who undertook planned egg freezing (PEF) in Australia and New Zealand between 2009 and 2023? Summary answerThere has been an average yearly increase in the uptake of PEF of 35%, with most women undergoing a single PEF procedure in their mid-thirties. Given ten years follow-up a little over one in four women return, with nearly half of those using donor sperm and one-third achieving a live birth. What is known alreadyPEF, where women freeze their eggs as a strategy to preserve fertility, has increased dramatically in high income countries in the last decade. Despite the rapid uptake of PEF, there remains limited information to guide women, clinicians and policy makers regarding the characteristics of women undertaking this procedure and treatment outcomes. Study design, size, durationA retrospective population-based cohort study of all women who undertook PEF in Australia and New Zealand between 2009 and 2023, including their subsequent return to thaw their eggs and treatment outcomes. Where women returned to utilise their eggs, all subsequent embryo transfer procedures were linked enabling calculation of live birth rates per woman. Participants/materials, setting, methods20,209 women who undertook PEF in Australia and New Zealand between 2009 and 2023 including 1,657 women who returned to thaw their eggs. Main results and the role of chanceThere has been a huge increase in uptake of PEF, from 55 women in 2009 to 4,919 in 2023. Women who freeze their eggs are typically aged 34-38 years (interquartile range) and nulliparous (98.6%). For women with at least 10 years follow-up (i.e. undertook PEF in 2009-13; N=514), 27.9% returned and thawed their frozen eggs (average time to return: 4.9 years). This reduced to 22.1% in those with at least 5 years follow-up (i.e. undertook PEF in 2009-2018; N=4,288). Of those who used their frozen eggs, 47% used donor sperm. After at least two years follow up, 33.9% had a live birth, rising over time to 37.8% for eggs thawed between 2019-2021. Limitations, reasons for cautionIn the timeframe 2009-2019 we did not have information on whether egg freezing occurred because of a cancer diagnosis, a cohort we wished to exclude from the study. As a result, for this timeframe we weighted observations by the probability that egg freezing occurred due to cancer, with the prediction model developed on the years 2020-2023. Wider implications of the findingsThis study provides recent and comprehensive data on PEF to guide prospective patients and clinicians and inform policy. The exponential growth in PEF in Australia and New Zealand mirrors trends in other high-income countries, suggesting a doubling time of 2-3 years. Study findings highlight the need for setting realistic expectations about the likelihood of returning to use frozen eggs and live birth rates. Study funding/competing interest(s)2020-2025 MRFF Emerging Priorities and Consumer Driven Research initiative: EPCD000014

1.Study questionDo singletons conceived by medically assisted reproduction (MAR) experience an elevated incidence of childhood cancers and are they at a greater risk of such cancers compared to naturally-conceived singletons? Summary answerWe found no strong evidence the adjusted risk of childhood cancers is increased for MAR-conceived singletons. What is known alreadyThere is longstanding concern children conceived via MAR may be at increased risk of childhood cancer. Current epidemiological evidence does not support such a relationship. Study design, size, durationWe conducted a retrospective population-based cohort study of 5,104,121 singletons born in Australia between 1991 and 2019. Median follow-up time varied from 4 to 10 years depending on mode of conception. Participants/materials, setting, methodsWe linked birth records to public medical insurance data of the mother to ascertain MAR conception. We classified treatment as ovulation induction/intrauterine insemination (OI/IUI) or assisted reproductive technology (ART; IVF/ICSI), with ART coded as either fresh embryo transfer or frozen embryo transfer. The cohort included 4,924,354 naturally-conceived singletons and 179,767 singletons conceived via MAR. We calculated standardised incidence ratios (SIRs) to ascertain differences in population incidence of childhood cancer, and generated hazard ratios (HRs) using flexible parametric survival models controlling for key confounders. We report absolute incidence and risk differences for both statistical approaches. Main results and the role of chanceThere was no increase in the incidence or risk of all childhood cancers combined for singletons conceived via MAR, either any MAR or specific MAR types. There was some evidence the incidence of leukemias, myeloproliferative diseases, and myelodysplastic diseases was increased after ART compared to the general population (SIR: 1.32, 95% CI 1.02-1.68; equating to 2.09, 95% CI 0.13-4.44 extra cancers per 100,000 person-years), but no increased risk after adjusting for available confounders (HR: 1.04, 95% CI 0.73-1.46). These cancers showed increased incidence and risk for those conceived via IVF (SIR: 1.54, 95% CI 1.01-2.26; HR: 1.77, 95% CI 1.06-2.95), but not ICSI (SIR: 1.27, 95% CI 0.83-1.85; HR: 0.76, 95% CI 0.48-1.22). Incidence of renal tumours was elevated after IVF (SIR: 2.37, 95% CI 1.02-4.67; equating to 1.83, 95% CI 0.03-3.99 extra cancers per 100,000 person-years) and frozen transfer ART (SIR: 2.52, 95% CI 1.09-4.97; equating to 2.12, 95%CI 0.12-5.53 extra cancers per 100,000 person-years), however risk was not elevated after adjusting for available confounders (HR: 1.06, 95% CI 0.47-2.38; and HR: 1.63, 95% CI 0.73-3.61 respectively). Limitations, reasons for cautionWe did not have information on parental cause of infertility, which could be a confounder for childhood cancer, although we did adjust for parental history of cancer. For many specific cancer types, fewer than 50 cases were observed in total. Given the number of comparisons reported and closeness of the lower-bound confidence interval to 1, we cannot exclude that a significant association between conception via IVF and leukemias, myeloproliferative diseases, and myelodysplastic diseases reflects a type I error. Wider implications of the findingsOur findings align generally with published meta-analyses on the risk of childhood cancers following MAR conception and reinforce the need for very large studies to increase confidence. Parents who have conceived via MAR and their offspring can be reassured there is not strong evidence the treatments increase the overall incidence or risk of childhood cancer. Study funding/competing interest(s)This work was funded by the National Health and Medical Research Council (NHMRC: APP1164852). Dr ARW declares that their involvement in this work was supported by employment at UNSW Sydney. Prof CMV declares payment to their institution from the National Health and Medical Research Council (APP1164852). Prof NH declares payment to their institution from the National Health and Medical Research Council (APP1164852); royalties and licenses for Berek and Hackets Gynecologic Oncology (Walters Kluwer); royalties and licenses for Hacker and Moores Essentials of Obstetrics and Gynecology (Elsevier); consulting fees from Darwin Hospital and Gold Coast University Hospital; support for attending the British Gynaecological Cancer Society meeting in Aberdeen, UK, Jun 2023; support for attending the Symposium on Gynaecological Cancer in Budapest, Hungary, Nov 2023; support for attending the International conference of the Rajiv Gandhi Cancer Centre in Delhi, India, Mar 2025; and membership of the Medical Advisory Committee for TruScreen (Australia and New Zealand). A/Prof SO declares that they received payment to their institution from the National Health and Medical Research Council (APP1164852); they received a grant from the European Society for Human Reproduction and Embryology (Open call 2022) including payment to their institution; and that they are a member of the Advisory Board of the Cervical Screening Program in Norway through The Norwegian Institute of Public Health (NIPH), for which they were reimbursed travel expenses to their institution. Prof MC declares support for Theramex European Society for Human Reproduction and Embryology registration and Fertility Society of Australia and New Zealand registration and accommodation. A/Prof USD declares that her involvement in this work was supported via an Early Career Fellowship from the Cancer Institute NSW (ID: 2020/ECF1163) and employment at UNSW Sydney. A/Prof USD also declares payment to their institution from the National Health and Medical Research Council (APP2035240) and the Medical Research Future Fund (APP2032214; APP2038377), and the Australian Research Council (DP240100072) as well as current grants from NSW Health, Prince of Wales Hospital Foundation, and unpaid involvement as an Associate Editor for the "Journal of Psycho-Oncology Research and Practice". Prof LJ declares payment to their institution from the National Health and Medical Research Council (APP1164852). Prof RJN declares they are the Chair of the Clinical Advisory Committee, Westmead Fertility; External mentor at VinMec hospital; Editorial Editor at the journal "Fertility and Sterility"; and has received funding from the National Health and Medical Research Council (NHMRC) for the NHMRC Centre for Research Excellence in Womens Health in Reproductive Life (CRE WHiRL). A/Prof CS declares stock or stock options associated with CSL Ltd, Sigma Healthcare Ltd, Resmed Inc, Medical Developments International Ltd, Vitrafy Life Sciences Ltd, Intuitive Surgical, and Steris PLC. Prof GMC declares payment to their institution from the National Health and Medical Research Council (APP1164852). Prof CV declares payment to their institution from the National Health and Medical Research Council (APP1164852); research grants receive from Merck KGaA and Ferring; payments for honoraria from Merk Ltd, Merk Sharpe & Dohme, Ferring, Organon, Gedeon-Richter for being an invited lecturer in scientific meetings/conferences on multiple occasions as well as member of advisory boards for these companies who have a commercial portfolio in the field of assisted reproduction technology (ART); and speaking fees from IBSA, Vianex, Sonapharm; travel support for their participation in scientific meetings/conferences both nationally and internationally, usually as an invited speaker for the following companies - Merck Ltd, Merck Sharpe & Dohme, Ferring, Organon, Gedeon-Richter; unpaid involvement as a Board member of the Hellenic Society of Fertility and Sterility, Member of the Editorial Board of the journal "Human Reproduction", Senior Deputy of the Coordination Committee of the Special Interest Group "Reproductive Endocrinology" of the European Society for Human Reproduction and Embryology, Member of the Editorial Board of the journal "F&S Reviews", Member of the Editorial Board of the journal "RBM Online", Member of the Editorial Board of the journal "Reproductive Biology & Endocrinology", Member of the Editorial Board of the journal "Frontiers in Endocrinology", and Member of the Editorial Board of the journal "Reproductive Sciences". SubjectReproductive epidemiology

Background: The enterotype concept proposed that gut microbiomes cluster into discrete types, but subsequent critiques demonstrated that such clustering depends on methodological choices, that the number of clusters is not fixed, and that faecal samples cannot capture spatial heterogeneity along the gastrointestinal tract. The stomach remains particularly understudied, and no systematic classification exists for gastric microbial community types. Methods: We assembled a multi-cohort dataset of 566 gastric mucosal samples spanning healthy controls to gastric cancer, with both Helicobacter pylori (HP)-negative and HP-positive individuals. Critically, we applied the key methodological lessons of the enterotype debate: we used a variational autoencoder (VAE) for dimensionality reduction to learn a continuous latent representation without forcing discrete structure, determined the optimal number of clusters using the Silhouette index (an absolute validation measure) across K=2 to K=10 rather than arbitrarily selecting a cluster number, and performed transparent evaluation of multiple clustering solutions. This VAE-plus-silhouette workflow directly addresses the critiques leveled against the original enterotype analysis. Results: Four gastotypes were identified, with K=4 achieving the highest mean silhouette score, indicating good cluster cohesion and separation. Two gastotypes (Variovorax-type and Trabulsiella-type) were significantly enriched in HP-positive samples, while two gastotypes (Bacteroides-type and Streptococcus-type) were significantly enriched in HP-negative samples. Random Forest and Gradient Boosting achieved excellent baseline performance for predicting HP infection (AUC = 0.990 and 0.993). Conclusions: The VAE-plus-silhouette workflow provides a robust, data-driven approach for identifying gastotypes without forcing discrete structure or arbitrarily fixing cluster numbers. Using this framework, we identified four gastotypes with significantly different HP infection rates. Variovorax-type and Trabulsiella-type showed strong HP-positive enrichment, while Bacteroides-type and Streptococcus-type showed strong HP-negative enrichment. These findings demonstrate that methodological advances from the enterotype controversy can be successfully transferred to the stomach, offering a reproducible taxonomy for stratifying HP infection status with potential clinical utility.