In 2017–2018, New South Wales (NSW), Australia, experienced a hepatitis A virus (HAV) outbreak predominantly affecting men who have sex with men (MSM). We aimed to estimate immunity and identify immunity gaps among MSM in NSW. We triangulated four data sources. We tested 409 residual sera collected from males undergoing syphilis testing between August and October 2017 for anti-HAV IgG. We surveyed all publicly funded sexual health clinics about HAV testing and vaccine provision for the preceding financial year. We conducted a convenience behavioural survey of 50 men at a sex-on-premises venue in October 2017, and we analysed community survey data from 2018 to 2019 (n = 5,924). Descriptive statistics and logistic regression ere used to examine associations with immunity and vaccination. Overall serological immunity was 62.8% (257/409) and increased with age, from 50.0% in those aged under 26 years to 79.0% in those over 45 years. Clinic immunity and community survey estimates were higher (74.5% and 76.8%). Immunity gaps were identified among bisexual men, those less connected to the gay community, and people born outside Australia. NSW Health implemented targeted vaccination and community engagement in response. Multisource assessment provided actionable evidence to guide targeted vaccination and outbreak response.

Care homes are vulnerable to respiratory syncytial virus (RSV) outbreaks, with residents at risk of severe disease outcomes, though surveillance studies are lacking. In September 2024, RSV vaccination was introduced for adults in England aged 75–79 years, excluding most residents (median age 86 years). Between October 2024 and March 2025, we prospectively extracted information on RSV outbreaks in English care homes reported to UK Health Security Agency (UKHSA). Enhanced surveillance questionnaires (ESQs) were completed for a sample of outbreaks, including information on symptomatic residents, testing, and outcomes. Acute respiratory infection (ARI) cases were defined symptomatically, RSV cases based on test-positive RSV (≤5 residents tested per home), and RSV outbreaks as ARI outbreaks including ≥1 RSV case. We described outbreak trends, attack rates, hospitalizations, and deaths. Of 2419 ARI outbreaks in care homes, 222 (9%) were RSV outbreaks, with additional respiratory viruses identified in 69 (31%). Among 48 (22%) RSV outbreaks completing ESQs, the median ARI attack rate was 15% (IQR 10%–24%). Of 350 ARI cases, 32% (112) were confirmed RSV cases on routine testing, 20% (71) were hospitalized, and 6% (20) died. These findings demonstrate the vulnerability of care home residents to RSV infection, hospitalization, and death, which are potentially preventable through vaccination.

On 17 October 2023, the County of San Diego (CoSD), California’s Epidemiology and Immunization Services Branch received reports of eight salmonellosis patients with illness onsets beginning in September 2023. CoSD disease investigators identified common exposure to Farm A-produced unpasteurized dairy products and performed epidemiologic and environmental investigations. Isolates were submitted for whole-genome sequencing. Cases were defined as persons with Salmonella infection with an isolation date on or after 15 September 2023. Twenty-five cases, including 23 confirmed and two probable, were identified among county residents, with 19 (76%) reporting exposure to Farm A unpasteurized dairy products. Median patient age was 12 years (range: 1–47 years). Three children (12%) were hospitalized. Environmental samples of unpasteurized milk collected from Farm A tested positive for S. Typhimurium, matching the outbreak strain by WGS. After Salmonella identification, CoSD released early advisories warning of Farm A-associated risks, likely preventing additional infections.

Cholera is associated with devastating outbreaks among forcibly displaced people. Insights into the relative contributions of the public (extra-household) and domestic (intra-household) domains to cholera spread in camps, as well as the circumstances under which each may drive transmission, can support the design of response strategies. However, these have yet to be systematically investigated. We developed an agent-based model of cholera transmission in camps informed by a rapid appraisal conducted in Northeast Nigeria, an expert consultation, and humanitarian minimum standards. We simulated outbreaks in a stylized camp that meets water quantity standards and compared this with conditions where water supply is overwhelmed or compromised following floods and population influxes. We found that domestic transmission can exclusively drive cholera outbreaks. However, unless hygiene conditions are extremely poor and water is not adequately chlorinated, these outbreaks appear to be small. Following shocks, outbreaks can be large and progress rapidly. Although they are initially shaped by the public domain, domestic domain transmission can sustain or exacerbate them. We recommend directing humanitarian and development activities towards mitigating the consequences of extreme weather events and unplanned population influxes, as well as developing adaptive preparedness and response strategies that explicitly and comprehensively address them.

The infection fatality risk indicates the probability of death among infected individuals. The age-dependent heterogeneity of infection fatality risk is crucial for severity assessment and prioritization of countermeasures. However, infection fatality risk estimation requires infection data from a large-scale seroepidemiological survey combined with either direct ascertainment of deaths caused by infection or excess mortality estimates. To overcome the difficulty in ascertaining death, we propose an alternative approach to estimating the age-specific infection fatality risk for SARS-CoV-2 using medicolegal death investigation data in Tokyo with systematic post-mortem polymerase chain reaction testing. We integrated (i) polymerase chain reaction positivity among all deceased individuals at the Tokyo Medical Examiner’s Office, (ii) age-specific all-cause mortality risks from vital statistics, and (iii) age-stratified cumulative infection risks derived from seroepidemiological surveys. Infection fatality risk was computed using Bayes’ theorem. Results showed that infection fatality risk increased steeply with age. Our estimates (0.02% for ages 0–39 years, 0.30%–0.50% for ages 40–64 years, and 3.8%–4.2% for those aged ≥65 years) were consistent with published pre-vaccination meta-analytic estimates. Systematic testing within medicolegal death investigation systems can provide rapid, age-resolved severity assessments, improving the timeliness and comparability of infection fatality risk estimation across jurisdictions.

Observational vaccine effectiveness (VE) studies provide essential real-world evidence but are prone to bias. Valid synthesis relies on rigorous risk-of-bias (RoB) assessment in systematic reviews of VE studies. Following JBI guidance, we mapped and described RoB assessment methodologies in systematic reviews of VE studies. We searched MEDLINE, Embase, and Web of Science from 1 January 2013 to 17 May 2023 and the grey literature from 1 January 2018 to 15 August 2023. Of 367 identified reviews, 38 lacked any RoB assessment, yielding 203 systematic reviews. Of these, 190 used existing tools (NOS (85/190, 44.7%), ROBINS-I (46/190, 24.2%), and JBI (11/190, 5.8%)) and 13 used an author-developed tool (13/203, 6.4%). Tools were adapted in 16.7% (34/203) of reviews and 7.2% (14/203) used multiple tools. Reviews included 20 (±25.7) observational studies, commonly cohorts (175/203, 86.2%), with COVID-19 (66/203, 32.5%) and seasonal influenza (62/203, 30.5%) frequently studied. VE was reported descriptively in 25.1% (51/203) of reviews, while 74.9% (152/203) provided meta-analyzed estimates primarily based on laboratory-confirmed infection (137/203, 67.5%) and symptomatic disease (130/203, 64.0%). Our findings indicate heterogeneous RoB assessment, reflected by use of different/multiple tools, frequent adaptations, author-developed methods, and absence of RoB assessment, highlighting the need for clearer guidance or tailored tools.

Acute otitis media (AOM) is a major driver of paediatric antibiotic prescriptions. We assessed the impact of oral and topical antibiotics on middle ear, nasopharyngeal, and gut microbiome compositions, and the gut resistome, in children with AOM and ear discharge (AOMd). Fifty-eight children with AOMd and ear pain and/or fever were randomized to oral amoxicillin suspension (n = 31) or hydrocortisone-bacitracin-colistin eardrops (n = 27) for 7 days. From 57 out of 58 children, baseline, and Week-2 middle ear fluid (MEF) and nasopharyngeal (NP) samples were sequenced, along with baseline, Week-2, and Month-3 faecal samples. At baseline, the top 5 MEF genera were Streptococcus, Haemophilus, Turicella, Staphylococcus and Alloiococcus and NP genera Moraxella, Haemophilus, Streptococcus, Corynebacterium, and Dolosigranulum. At Week-2, the ear discharge had resolved in all but four children (oral n = 3, eardrops n = 1). In NP samples, the relative and absolute abundances of Streptococcus decreased to a greater extent after oral than eardrop treatment, but Moraxella and Haemophilus increased only following oral treatment. Neither treatment significantly altered the faecal microbiome or resistome at Week-2 and Month-3. Therefore, both treatments resolved the middle ear discharge in most children, but oral amoxicillin suspension may reduce NP Streptococcus more than hydrocortisone-bacitracin-colistin eardrops at the cost of potentially increasing other NP pathobionts.

While malaria transmission in coastal East Africa is strongly shaped by climatic variability, few studies examine long-term interactions in rapidly urbanizing settings. This study evaluated the impact of climate and seasonal trends on malaria incidence in Dar es Salaam, Tanzania (2014–2024). Monthly cases and meteorological data were analyzed using seasonal-trend decomposition (STL) and generalized additive models (GAMs) to quantify nonlinear and lagged climatic associations. Over the decade, malaria incidence declined sharply from >130 cases per 10,000 in 2014 to <30 by 2023. However, strong seasonal peaks persisted, with STL revealing consistent annual surges during April–June following the rainy season. GAM analysis identified rainfall as the dominant climatic driver, demonstrating significant 1- and 2-month lagged effects (p < 0.001). Daytime (1-month lag) and night-time (2-month lag) temperatures showed non-linear associations, peaking in incidence at optimal mosquito-development temperatures (~30–31°C). Despite substantial incidence declines, transmission remains highly climate-sensitive. Driven primarily by lagged rainfall and temperature effects rather than current-month conditions, these dynamics underscore the urgent need for climate-informed early warning systems and targeted seasonal interventions in coastal urban environments.

Aligned with the increasing trend observed across the EU/EEA, congenital syphilis (CS) cases have risen in Portugal, which has the third highest rate per 100000 live births in the EU/EEA. This study aimed to analyse CS cases reported in Portugal, focusing on pregnancy monitoring and antenatal screening to identify gaps in preventing vertical transmission of syphilis. We conducted a descriptive study, including confirmed CS cases reported in Portugal from 2015 to 2024. We calculated annual incidence per 100000 live births and the proportion of pregnancies monitored and antenatal screenings performed. During 2015–2024, 99 confirmed CS cases were reported, 64.6% in infants under 1 month of age. The incidence of CS increased eightfold from 2016 to 2024. Among mothers of CS cases, 67.7% had pregnancies classified as monitored; of these, 77.6% had a record of antenatal screening, and 88.5% of those screened tested positive. These findings highlight potential fragilities in antenatal care, diagnosis and treatment, contributing to the resurgence of CS in Portugal. Addressing missed opportunities for prevention requires improving maternal healthcare, strengthening surveillance systems, and ensuring the timely treatment of pregnant people and their partners, in order to reverse this trend and move towards the elimination of vertical transmission of syphilis.

We aimed to comprehensively assess Stenotrophomonas maltophilia infections, examining their incidence and clinical and microbiological characteristics in a tertiary hospital between 2021 and 2023. Primary outcomes were 30-day mortality and desirability-of-outcome ranking (DOOR). S. maltophilia incidence rose from 0.38 in 2017 to 2.66 cases/1000 patient-days in 2023, correlated with carbapenem consumption (rho = 0.90, p = 0.04). The cohort included 101 patients (median age of 61 years, IQR 43–71); 63% were male patients, 91% admitted in ICU, predominantly with lower respiratory tract infections (75%). Difficult-to-treat resistance (DTR) was identified in 14% of the isolates and associated with previous trimethoprim–sulfamethoxazole (TMP–SMX) use (aOR 23.15, 95% CI 3.67–145.77). Thirty-day mortality was 25% and associated with invasive mechanical ventilation (aOR 5.80, 95% CI 1.03–32.63), while appropriate definitive therapy was protective (aOR 0.01, 95% CI <0.01–0.16). Worse DOOR outcomes were associated with levofloxacin-resistant isolates (69.3%, CI 55.9%–80.9%) and inappropriate definitive treatment (81.1%, 95% CI 68.2%–90.8%). Overall, S. maltophilia has emerged as a relevant carbapenem-resistant gram-negative bacteria, with a high frequency of DTR phenotypes associated with previous TMP–SMX exposure. Appropriate therapy and levofloxacin susceptibility were linked to better outcomes.

We sought to assess predictive factors for SARS-CoV-2 infectiousness using a meta-analytic approach. We searched LitCovid, medRxiv, Google Scholar, and the WHO COVID-19 database until June 30 2025, including studies which cultured SARS-CoV-2, relating them to clinico-epidemiologic and laboratory variables and RT-PCR cycle threshold (Ct) values. Using linear mixed-effects regression models, we tested for independent associations with Ct values with 95%CIs and adjusted P-values in a multivariable model. We used a modified QUADAS criteria to assess risk-of-bias. We included 50 studies, with 39 in quantitative synthesis. The percentage of culture-positive specimens decreased with increasing Ct values (subgroup test difference Q = 96.71;P < 0.001) and time since the first PCR test (Q = 26.95;P = 0.0026). Presence of symptoms (Q = 20.1;P < 0.01), gene platform used (Q = 14.89;P = 0.002), being a cancer patient (Q = 24.9;P < 0.0001), and vaccination status (Q = 8.80;P = 0.012) were associated with increased culture-positivity, whereas a rising Ct (adjusted Ct change −6.58[95%CI] -5.30, −7.86;P < 0.001) was strongly associated with culture-negativity. Analysing 186 immunocompetent patients with 1,393 Ct values, 2 consecutive Cts ≥ 30 or a rising Ct value on serial testing demonstrated a sensitivity of 87.5% and specificity of 96.3% using culture positivity as the outcome. Serial Ct monitoring, integrated with clinico-epidemiologic data is a valuable tool for assessing infectiousness, providing objective criteria for discontinuing isolation and guiding clinical decisions.

Spatial risk models for Lassa fever (LF) generally predict the primary reservoir, Mastomys natalensis, is restricted to rural landscapes. This study integrates multispecies biotic interactions and anthropogenic land-use into a high-resolution framework to evaluate LF’s urban potential. I implemented an integrated multispecies occupancy model to reconstruct the reservoir’s realized niche, accounting for sampling bias and invasive rodent competitors. A socio-economic filter, proxied by night-time lights, was introduced to model the dampening effect of urban infrastructure on spillover. Annual infections were estimated using a demographic compartmental model incorporating empirical seroreversion rates. Results indicate high biological hazard across the peri-urban fringes of major West African cities. However, an infrastructure-driven socio-economic shield decouples this hazard from human incidence in dense urban cores. Accounting for spatial shielding and antibody waning yields an estimated 2.6 million annual Lassa virus infections. Comparing predictions to clinical data reveals substantial surveillance gaps, identifying highly suitable silent districts in Nigeria, Benin, and Togo with zero reported cases. LF possesses the biological potential to become a peri-urban disease; addressing these surveillance gaps at the peri-urban interface is a critical public health priority.

In England, Lyme disease (LD) surveillance is based on laboratory-confirmed cases. However, clinical and epidemiological characteristics of these cases are limited; therefore, we conducted an enhanced surveillance study of acute LD in England. Enhanced data were collected through an online questionnaire sent to all laboratory-confirmed acute cases of LD resident in England, with specimen dates between 1 April 2023 and 31 March 2024. The analysis included data from 511/1086 cases. Respondents were representative of age, sex, and region of national LD trends. A total of 57.3% of the respondents reported that they did not realize that they had been bitten by a tick. Among those who remembered a tick bite, 66.1% reported bites close to their home and only 10.6% happened abroad, and 28.5% reported that the tick bite could have occurred in a garden. Most respondents were residents of areas of higher socioeconomic status. Erythema migrans was noted by 70.5% of the respondents. It is important to raise awareness among both patients and clinicians that ticks can be found in urban and suburban parks and gardens, as well as ensuring that wildlife initiatives to increase biodiversity include information on tick prevention and tick checks.

Commonly used components of health risk assessments and outbreak investigations are the proportion of the general population exposed to potential sources, often coming from national surveys collected with one reference period, such as 7 days. However, risk assessors may need this value for a different period of time (e.g. 1 day, a full year, etc.) and outbreak investigators may need a reference period that matches their case questionnaire. Use of these proportions is biased if the reference period does not match what is needed. Three surveys that collected exposure information with more than one reference group were used to fit six models that were developed to estimate the relationship between proportion and reference period length, and thus, convert proportions collected with one reference period to any desired reference period. A practical implementation of the best model is provided in a spreadsheet for health practitioners, such as those working in risk assessment or outbreaks who need to convert proportions to a new reference period. The conversion method can be used in any subject matter across the sciences, where surveys collect the proportion of respondents who experienced an event in a defined reference period.

Progress in reducing global malaria incidence has slowed in recent years, demonstrating the need for new vector control tools to complement existing interventions in reaching global malaria control targets. Spatial repellents (SRs) can reduce pathogen transmission by altering the behaviors of Anopheles spp. mosquito vectors. A recent cluster-randomized control trial in western Kenya found that SRs reduced first-time infections by 33.4% in a highly-endemic setting with substantial insecticide resistance and high coverage of insecticide treated nets. We modeled the likely impact of the SR intervention in this setting under different deployment strategies, with the goal of identifying the best overall and per-product strategies. Continuous monthly SR deployment with 100% coverage caused the greatest (45.1%) reduction in infections versus no SR, although some seasonal approaches averted more infections per SR product. Six months of SR use starting in October caused a 36.4% reduction in infections and eight months starting in September reduced infections by 44.7%. This study identified optimum and efficient SR use strategies and highlights the importance of SR protection during periods of low and increasing transmission. When resources are limited, the coverage, deployment strategy, and timing of SR deployment all play a key role in maximizing product impact.

Prisons are high-risk environments for the spread of tuberculosis (TB). We investigated an ongoing prison-associated TB cluster to identify common exposures. We defined cases as residents in England with laboratory-confirmed TB belonging to the genetic cluster. We extracted records from the National TB Surveillance System, linked to prison operational data, and conducted descriptive analysis of demographic, clinical, and phylogenetic data. Years were masked for anonymity. Over six years, 12 individuals were identified, predominantly male (83%) and median age 34 years, in London, East Midlands, and East of England. Prison history was noted for 7/12 (58%) at 13 prisons. Everyone without prison history completed treatment, but 2/7 with prison history were lost to follow-up and 5/7 were still in treatment or outcome not evaluated. We identified frequent prison transfers and concurrent stays of four individuals at Prison B, and two at Prison G. Phylogenetic analysis indicated distinct sub-clusters with and without prison history, suggesting expansion of the cluster from community into prisons. Prisons continue to play a role in TB in England. Factors such as frequency of transfers could hinder treatment completion and control of transmission. Combining phylogenetic, epidemiological, and prison operational data facilitated investigation of transmission pathways.

Syphilis remains a significant transfusion-transmitted infection. In Colombia, routine epidemiological surveillance primarily targets pregnant women, leaving the burden of infection among the apparently healthy population. This study determined the incidence of Treponema pallidum and its associated factors in donors at a blood centre in Colombia between 2012 and 2024. A retrospective cohort study was conducted, analyzing 64,166 repeat blood donors. Incidence was calculated using 95% confidence intervals. Associations with demographic and donation-related variables were assessed using Chi-square test and potential confounders were adjusted using a multivariable regression model. The overall incidence of syphilis was 5.1 per 1,000 donors. The associated factors included age, sex, occupation, collection site, and donor type. Higher incidence proportions were observed in male donors (RR = 1.76), individuals aged between 60 and 65 years (RR = 2.43), unemployed individuals (RR = 3), donors collected at the centre (RR = 1.45), and replacement donors (RR = 3.51). These incidences indicate ongoing transmission within a low-risk population. The highest incidence in some groups enabled the generation of hypotheses about differential exposure patterns, guiding subsequent aetiological studies, and optimizing donor selection. Understanding local epidemiology is essential for designing public health interventions tailored to the specific epidemiological profile.

Rabies is a fatal zoonotic disease causing an estimated 59000 annual human deaths globally and approximately 523 in Kenya, with children disproportionately affected. Despite evidence that school-based educational interventions effectively increase rabies awareness and prevention among children, its implementation in Kenya is limited. This study aimed at utilizing an education programme to increase rabies awareness among primary school learners and evaluate their knowledge uptake. A quasi-experimental study was conducted among 210 learners from four primary schools (two urban, two rural). Pre-tested questionnaires assessed rabies awareness before and after rabies training sessions. Differences between urban and rural schools were assessed using χ2 tests, while Wilcoxon signed-rank test was used for pre- and post-training scores. Post-training, overall knowledge scores improved from 6.14 to 7.61(p < 0.001), with significant increase in learners’ knowledge on rabies transmission, zoonosis, and the importance of annual dog vaccination. Attitudes and perceptions improved from 3.23 to 4.03 (p < 0.001), particularly health-seeking behaviour and reporting post dog bite. In conclusion, school-based rabies education significantly improved learners’ awareness. Being the first report of such intervention in Kenya, it could serve as a model for other zoonoses.

Late HIV diagnosis increases morbidity and mortality. In this retrospective cohort study on the national HIV register, we analysed risk factors for late HIV diagnosis among newly registered people living with HIV (PLWH) between 2008 and 2023, using the updated definition. Of 2683 PLWH registered, 1813 (67.6%) were newly diagnosed with CD4+ T-cell count available ≤90 days for 1572 (86.7%). Eighty-seven of the 609 (14.3%) individuals with CD4+ T-cell count <350/μL had recent infections and were reclassified as non-late. Of the newly diagnosed, 50.3% were diagnosed late. Multivariable analysis identified higher age as an independent risk factor for late diagnosis (adjusted OR 1.42 per ten years, 95% CI 1.30–1.56). Of the Finnish-born, females had lower odds than males (aOR 0.59, 95% CI 0.39–0.88). Asian-born (aOR 6.83, 95% CI 3.49–13.35) and African-born females (aOR 3.26, 95% CI 1.58–6.73) had significantly higher odds than Finnish-born females. In urban municipalities, men who have sex with men had lower odds than individuals with heterosexual transmission (aOR 0.55, 95% CI 0.40–0.76). Higher age was the most important factor for increasing the proportion of late diagnoses. We recommend enhanced testing and risk awareness for older adults and migrants from high-prevalence countries.