We analysed 15,982 quality-controlled SARS-CoV-2 genome sequences from Hong Kong, obtained from NCBI and GISAID between 2020 and 2023, to characterize lineage dynamics, mutational profiles, demographic distributions, and variant-specific viral entry. Genomic surveillance identified 543 lineages and 5,982 unique mutations. Lineages A, B, and B.4 dominated the initial epidemic waves, whereas Delta and Omicron emerged and predominated in later waves. Omicron BA.1 and BA.2 exhibited distinct distributions across gender and age groups, while JN.1 harboured several novel mutations. Molecular simulations comparing spike receptor-binding domain (SRBD)–ACE2 interactions revealed significant differences in binding affinity among variants (F = 4.404, p = 9.12 × 10⁻⁷). JN.1 demonstrated enhanced ACE2-binding affinity, suggesting increased viral entry and potential transmissibility. By integrating genomic, demographic, and molecular evidence, this study provides a comprehensive account of SARS-CoV-2 evolution in Hong Kong and highlights the public health relevance of emerging variants. These findings support sustained genomic surveillance and demographic monitoring to strengthen pandemic preparedness. Future research should evaluate public health strategies and adopt holistic frameworks integrating population characteristics with genomic evidence to mitigate the effects of future variants.

Sensitive and high-throughput testing for Neisseria gonorrhoeae (NG) is widely underpinned by automated commercial solutions using nucleic acid amplification tests. We outline our experience of using Roche Cobas 8800 CT/NG (Cobas NG) for primary testing of NG at scale. Over 360000 specimens were tested over a three-year period. A disproportionate number of ‘indeterminate’ oropharyngeal swabs (25%) tested positive by Cobas NG but failed to confirm by Xpert CT/NG, significantly higher than genital samples (4%) (chi-square p-value <0.05). Such samples are highly problematic, as they fail to provide a definitive result for the patient. To investigate this non-specificity, publicly available sequences for Cobas NG DR-9 targets were aligned with Neisseria genome databases. We found a strain of Neisseria lactamica (PubMLST 49718), isolated from a throat swab, which was predicted to cross-react with Cobas NG. We subsequently confirmed a Cobas NG false-positive result with this isolate. BLAST analysis showed the target gene NG DR-9 was rare among available non-NG Neisseria whole genome sequences. This may suggest the existence of an as-yet unknown and difficult to cultivate oral commensal that contains NG DR-9. Our findings further highlight the need for NG confirmatory testing of oropharyngeal samples screened with Cobas NG.

In this retrospective cohort study, we assessed the prevalence of post-COVID-19 condition (PCC) and its determinants among six ethnic groups in Amsterdam, the Netherlands. We analysed data from participants of the HELIUS cohort with SARS-CoV-2 infection who answered questions on the presence and duration of COVID-19-related symptoms between May and November 2022. We estimated the prevalence of PCC, defined as having ≥1 of 15 pre-determined COVID-19-related symptoms remaining for at least 3 months after infection, by ethnicity at several timepoints since infection adjusted for age and sex, and assessed determinants of PCC overall using logistic regression. Of 932 infected participants, 31% [95% confidence interval (95%CI): 27%–37%] developed PCC. At 3 months after infection the adjusted prevalence of PCC varied from 17% (95%CI: 13%–24%) in the Dutch-origin group to 41% (95%CI: 34%–48%) in the South-Asian Surinamese group, and was significantly higher among participants of South-Asian Surinamese, Turkish and Moroccan origin compared to those of Dutch origin (all P < 0.001). Participants who were of South-Asian Surinamese origin, older, female, without a vocational education or university degree, or obese were more likely to have PCC. Those of Ghanaian origin or infected during the period of Omicron predominance were less likely to have PCC. There were clear between-ethnic differences in the prevalence of PCC, which was more common in individuals of South-Asian Surinamese, Turkish, and Moroccan origin compared to those of Dutch origin. These differences mirror ethnic differences in SARS-CoV-2 infection and disease severity. Certain factors of PCC emerged, while consistent across ethnic groups.

A cross-sectional study using point prevalence survey (PPS) methodology was conducted on May 20, 2024, at 18 tertiary care hospitals located in the 6 Gulf Cooperation Council (GCC) countries to assess the prevalence of healthcare-associated infections (HAIs) and associated pathogens. The measured outcome was the presence of active HAIs in different hospital units. During the PPS day, 651 HAI events were detected among 580 patients after reviewing the information of 6826 patients. The prevalence of patients with HAIs was 8.5% (95% CI 7.8%–9.2%). The prevalence was higher in older patients (11.8%, 95% CI 10.2%–13.4%), in intensive care units (24.6%, 95% CI 21.5%–27.8%), and in specialty care areas (12.7%, 95% CI 9.8%–15.7%). The most frequent type of HAIs was pneumonia (27.8%), followed by bloodstream infection (25.0%), urinary tract infection (10.9%), and skin infection (9.7%). Device-associated HAIs represented 15.4% of all HAIs, with ventilator-associated pneumonia, central line-associated bloodstream infection, and catheter-associated urinary tract infection being the main types. Approximately 61.9% of HAIs were microbiologically confirmed. Out of them, 65.3% were caused by Gram-negative bacteria and 31.8% were caused by multidrug-resistant pathogens. The findings confirm that the high HAI burden in GCC hospitals is higher in high-resource countries but lower in lower/middle-resource countries.

Salmonella Enteritidis is typically transmitted to humans via consumption of eggs or poultry meat. In July 2023, Denmark and Austria concurrently reported two outbreaks of genetically distinct S. Enteritidis sequence type (ST) 11. In both countries, cases were identified as part of the outbreaks using core-genome Multilocus Sequence Typing (cgMLST) between 1st of January and 1st of October, 2023. Outbreak investigations were conducted and included interviews with cases, food tracing, and, using cgMLST, comparisons of human, food, and environmental isolates. In the EU, 207 cases across 11 countries were found. Patient food histories pointed towards chicken, often sold as kebab meat. Extensive traceback investigations from affected restaurants and wholesalers in Austria and Denmark identified chicken meat produced in Poland as the vehicle of the outbreaks. Due to the death of one patient in Austria, the food safety authorities initiated more food safety controls for this food product, which led to food recalls. Recalls of specific chicken products from Poland were also conducted in Denmark. Despite national interventions and regulations targeting poultry producers, the EU remains collectively vulnerable to large-scale food contamination events originating in a single member state. Effective international and cross-sector collaboration was crucial to identifying the vehicle of these outbreaks.

We examined inequalities in weekly hospitalization rates related to COVID-19, influenza, and respiratory syncytial virus based on neighbourhood-level material deprivation, neighbourhood-level ethno-racial diversity, rurality, and sex. Hospitalization rates were measured as the weekly number of hospitalizations per 10 000 people. Local regression models were used to fit observed weekly hospitalization rates within each study year and each population subgroup, and statistical significance of between-subgroup differences in peak hospitalization rate was assessed based on the overlap of 95% confidence intervals. We also provided comparisons of pre-pandemic (July 2017–June 2020) versus post-pandemic (July 2020–June 2023) trends. More materially deprived neighbourhoods showed up to a 2.5-times increase in peak weekly hospitalization rates compared to less materially deprived neighbourhoods. Peak hospitalization rates were up to 2.3-times higher among more versus less diverse neighbourhoods. Some age groups showed peak hospitalization rates up to 2.8-times higher among urban residents. Peak hospitalization rates were up to 1.3-times higher in younger males versus younger females and up to 1.6-times higher in older females versus older males. Variations due to neighbourhood-level material deprivation, neighbourhood-level ethno-racial diversity, rurality, and sex should be considered when designing and implementing public health policies aiming to reduce respiratory virus burden.

The aim of this study was to evaluate the impact of the vaccination programme with 23-valent pneumococcal polysaccharide vaccine (PPV23) on non-invasive pneumococcal pneumonia (NIPP) in adults above 60 years old during the first three post-implementation years. For this retrospective impact study with a regression discontinuity design, we included patients aged 56 to 85 years who presented with NIPP at the hospital between November 1, 2016 and September 30, 2023. NIPP was defined as a positive pneumococcal urinary antigen test without meeting criteria for invasive pneumococcal disease (blood and/or cerebrospinal fluid culture positive for Streptococcus pneumoniae). We estimated the overall impact and the impact stratified by time since eligibility for vaccination for each birth cohort. Data were obtained from 14 laboratories throughout the Netherlands, which were estimated to cover 34.9% of the Dutch population. We observed 3821 NIPP patients, of whom 634 were eligible for vaccination. The overall impact was 19.7% (95% confidence interval 8.5, 29.7). Impact estimates decreased over time since eligibility, although non-significantly with overlapping confidence intervals. These insights contribute to the existing body of evidence about PPV23 impact on NIPP, informing future vaccination policy.

Encephalitis lethargica (EL), also known as the ‘European Sleeping Sickness’, emerged in Europe around 1916, with Sweden reporting the highest global incidence rate in 1921. This study investigates regional variations in EL incidence across Sweden between 1920 and 1930, with a particular focus on the major outbreak in 1921. Using data from Public Health in Sweden, incidence rates were calculated for all Swedish regions, revealing a disproportionate concentration of cases in central and northern areas, especially in the parish of Vilhelmina in Västerbotten. To contextualize this outbreak, monthly disease data from the Annual Reports of the Chief Provincial Doctor in Västerbotten were analysed to compare the local disease panorama. Notably, preceding the first EL cases in Vilhelmina, influenza/H1N1 and mumps were frequently reported. Although the aetiology of EL remains unresolved, the presence of a preceding influenza and mumps epidemic is consistent with the dual-pathogen hypothesis, suggesting that interactions between infectious agents may have contributed to the emergence of EL in local hotspots.

In this proof-of-concept study, we explored the potential of structured general practice data for early signal detection, to enhance pandemic preparedness. We used electronic health record data from the Family Medicine Network (FaMe-Net) in the Netherlands between 2014 and 2024. Descriptive evaluation with surveillance attributes was performed, and the Farrington flexible method was used to construct an alert threshold for respiratory, gastroenteritis, rash, infectious conjunctivitis, and fever syndromes. Alert signals were generated, indicating when the observed weekly count exceeded the threshold. This data registry performed adequately for most surveillance attributes. We analysed 634708 diagnostic codes and 9 infectious disease syndromes in the data registry. In 154 weeks, the number of alert signals ranged from 3 to 20. We found similarities and variations in the number of alert signals between infectious syndrome definitions within the different data types. Structured general practice data showed potential for surveillance and early signal detection of infectious diseases because it performed well on most surveillance attributes and weekly counts of infectious disease syndromes led to the generation of alert signals. Further validation of these alert signals is needed, to underpin their early warning potential for timely public health action.

Bat rabies in mainland France is mainly caused by European bat lyssavirus 1 (EBLV-1; Lyssavirus hamburg), which is almost exclusively associated with the common serotine bat, Cnephaeus (Eptesicus) serotinus. Two variants, EBLV-1a and EBLV-1b, circulate in France and display largely distinct, parapatric distributions. Because bats are highly sensitive to climatic conditions due to their physiological characteristics, including heterothermy, we investigated the relationship between climate and the geographical distribution of these two variants. Using generalized linear models and species distribution models, we assessed the influence of temperature and precipitation on EBLV-1 occurrence. The distribution of EBLV-1 cases was significantly associated with climatic variables, particularly minimum temperatures during the coldest month, maximum temperatures during the warmest month, and precipitation during the driest period. EBLV-1a was more frequently associated with areas characterized by milder winters and warmer, more humid conditions, whereas EBLV-1b was linked to colder and drier environments. Habitat suitability models predicted limited overlap between the two variants, supporting the existence of distinct climatic niches. These findings suggest that climatic factors contribute to shaping the spatial distribution of EBLV-1 variants and highlight the need for broader scale studies to better understand their ecology and potential response to future climate change.

This study aimed to evaluate the efficacy of DHP as an alternative to SP for the prevention of malaria and malaria-related complications during pregnancy. A systematic review and meta-analysis were conducted using pooled effect sizes extracted from published studies. Compared to SP, DHP significantly reduced maternal malaria infection by 78% (RR 0.22, 95% CI: 0.09–0.55), placental malaria infection by 73% (RR 0.27, 95% CI: 0.08–0.98), and maternal anaemia by 16% (RR = 0.84, 95% CI: 0.79–0.89). Women randomized to the DHP arm had a 28% lower risk of foetal loss (RR 0.72, 95% CI: 0.40–1.31), a 4% lower risk of low birth weight (RR 0.96, 95% CI: 0.69–1.32), and a 17% lower risk of preterm births compared with those receiving SP (RR 0.83, 95% CI: 0.61–1.13), though the reduction was not statistically significant. Therefore, DHP appears to be more effective than SP as IPTp therapy for reducing maternal malaria infection, placental malaria infection, and maternal anaemia. However, this study does not significant advantage of DHP over SP in reducing adverse birth outcomes.

Between 2023 and 2025, four outbreaks of zoonotic Cryptosporidium parvum infection involving 39 laboratory-confirmed cases occurred at a single animal-contact visitor attraction in South West England. A retrospective outbreak investigation, incorporating elements of a descriptive case series, was undertaken to identify factors associated with repeated transmission and to draw insights for infection prevention and control. The study integrated epidemiological, veterinary, environmental, and molecular data, including exposure questionnaires, animal faecal testing, environmental sampling, observational assessments, and genotyping of human and animal isolates. Zoonotic gp60 subtype IIaA15G2R1 predominated across outbreaks. In the fourth outbreak, identical gp60 subtypes and shared multiple-locus variable-number tandem-repeat analysis alleles in lamb and human samples supported zoonotic transmission. Environmental sampling identified faecal indicator organisms and Shiga toxin-producing E.coli on high-touch surfaces. An observational assessment identified frequent opportunities for faecal–oral exposure during close contact with young ruminants. Despite compliance with industry standards, persistent environmental contamination, in-pen contact, and child behavioural factors were identified as plausible contributors to transmission. These findings highlight the challenges of preventing zoonotic infection in this setting and support refinement of existing guidance.

The World Health Organization (WHO) has set global goals to eliminate AIDS and viral hepatitis as public health threats. To better target testing, intelligence on missed opportunities for early diagnosis is needed. We determined hospital and emergency department (ED) attendance before late diagnosis of blood-borne viruses (BBVs) in Scotland 5 years to 2 months prior to diagnosis. Late diagnoses were defined as: CD4 count <350 cells/cmm within 90 days of HIV diagnosis; presentation/death from cirrhosis or hepatocellular carcinoma within 1 year of hepatitis C (HCV)/hepatitis B (HBV) diagnosis. Associations were assessed using logistic regression. Among 543 people diagnosed with HIV 37% were late and 2% of people diagnosed with HCV (4,379) and HBV (1,608) were late. Among late diagnoses: 44.1% of HIV, 60.6% of HCV, and 50% of HBV cases previously attended ED and 27.0% of HIV, 46.5% of HCV, and >30% of HBV cases were previously admitted to hospital. The majority were admitted to hospital or attended ED multiple times. Among people newly diagnosed with HIV, those diagnosed late were more likely to have previously attended ED (aOR: 1.41, CI: 0.99–2.02). Further effort is warranted to address the frequent missed opportunities for earlier BBV diagnosis in secondary care.

Mpox has evolved into a global public health concern following rapid geographic expansion and altered clinical and epidemiological characteristics. The 2022 outbreak of monkeypox virus (MPXV) marked the first widespread expansion to non-endemic regions, particularly among men who have sex with men (MSM). In the Democratic Republic of the Congo (DRC), where Clade I MPXV is endemic, data on urban exposures are limited. We evaluated serologic evidence of exposure using a four-plex MPXV assay among 1,823 participants from two major DRC cities, Kinshasa and Goma, between April and June 2024. Of these participants, 523 (28.7%) self-identified as MSM, 498 (27.3%) as professional sex workers (SW), 107 (5.9%) as MSM and SW, and 695 (38.1%) as other at-risk individuals. Overall, 2.9% of participants were seroreactive. By subpopulation, 4.8%, 2.1%, and 1.7% of at-risk, MSM, and SW participants were seroreactive (p = 0.0086). Classification tree modelling identified age as the strongest predictor of reactivity, with higher MPXV seroreactivity in older participants. These data provide evidence of mpox seroreactivity prior to sustained human-to-human transmission in urban settings. Understanding exposure dynamics is critical for anticipating re-emergence of mpox in global cities where interpersonal networks may sustain transmission even in the absence of zoonotic spillover.

Shiga toxin-producing Escherichia coli (STEC) O157 is a foodborne pathogen causing gastrointestinal illness. In August 2025, multiple nursing homes (NHs) in Belgium reported gastroenteritis cases among residents, which were later confirmed as STEC O157. A national outbreak investigation team was established to identify the source and implement control measures. Regional health authorities conducted field investigations, including NH visits, interviews, and exposure assessment. Microbiological and food chain investigations were coordinated nationally. We compared menus and initiated traceback investigations for high-risk food items for STEC. Using a retrospective case–control design, we calculated food-specific odds ratios and 95% confidence intervals. Additionally, we ranked exposures according to their permutation importance in a random forest prediction model. Investigations pointed to filet américain, consumed on 13 August, as the most plausible source. No leftovers were available for microbiological confirmation. We identified a batch of raw minced beef distributed to 104 institutions, including affected NHs, and found STEC-positive samples linked to it. With 71 cases and 10 deaths, this was among the largest STEC outbreaks in Belgium, prompting authorities to publish communications advising at-risk populations against the consumption of raw meat and underscoring the need to review existing recommendations on high-risk food items for foodborne infections.

Evidence describing paediatric COVID-19 and influenza co-infection is limited because influenza circulation was minimal during the early COVID-19 pandemic. We used the National Clinical Cohort Collaborative, a multicentre electronic health record repository, to describe the characteristics and clinical outcomes of paediatric COVID-19 and influenza co-infections in the United States from March 2020–April 2024. We defined co-infection as COVID-19 and influenza identified <7 days apart. We reported demographics, pre-existing diagnoses, and clinical outcomes and used generalized estimating equation models. We defined clinical outcomes as Severe/Moderate disease (hospitalization, critical care, or death) versus emergency department/outpatient encounters. We repeated analyses using varying co-infection definitions to assess robustness of findings. Among 1.53 million patients, 10,277 were co-infected, and 647 (6%) were hospitalized. Co-infections occurred predominantly among children aged <12 years. The most common pre-existing diagnoses were obesity (24%), asthma (10%), and congenital/genetic conditions (5%). The risk for Severe/Moderate disease was greatest among persons aged 0–4 years (adjusted risk ratio (aRR) 3.05; 95% confidence interval (CI): 2.35–3.97) and those with ≥2 pre-existing diagnoses (aRR 2.89; 95% CI: 2.43–3.43). Similar distributions of disease severity were observed across varying co-infection definitions. This study provides a large-scale epidemiological characterization of paediatric COVID-19 and influenza co-infection and successfully implemented a practical EHR-based co-infection case definition for future analyses.

Maternal syphilis and congenital syphilis (CS) have been increasing globally, but there are limited data from Fiji. We performed secondary analysis of clinical trial data of intrapartum azithromycin given to pregnant women to determine the prevalence of maternal syphilis and estimate the incidence of probable CS. Healthy, pregnant women at a tertiary hospital were routinely tested for syphilis, and their infants, were enrolled between July 2019 and January 2022. World Health Organisation case definitions for maternal and CS were used. Of the 2112 women enrolled, 2073 (98.2%) were tested for syphilis; 82.7% (n = 1715) were iTaukei (indigenous Fijians), and the median age was 27 years (interquartile range [IQR] 23–32). The maternal syphilis prevalence was 6.6% (n = 137). The majority (85.4%, n = 117) of women with positive serological result received at least one dose of benzathine penicillin 30 days prior to delivery. There were 139 infants born to mothers with positive serological results. The 2.5-year pooled incidence of probable CS was 212 per 100000 livebirths. Confirmation of CS was not possible as results of polymerase chain reaction test of cerebrospinal fluid were not available. Fiji has a substantial burden of maternal and CS. To eliminate mother-to-child transmission, improvements in testing and follow-up are needed, along with comprehensive data and confirmatory testing to accurately determine disease burden.