Acute gastrointestinal infections (AGIs) can lead to significant morbidity and mortality. In diagnosing AGI, culture-independent diagnostic tests offer advantages over traditional methods and increase the chance of detecting multiple pathogens (co-detection). A retrospective analysis of data from a tertiary pediatric hospital was conducted to characterize occurrence of AGI co-detections and compare outcomes with patients who had only one AGI pathogen detected. Medical records were obtained for patients with stool samples tested using BioFire FilmArray GI Panel between 1 January 2016 and 31 December 2020. Data were described using descriptive statistics, correlation analysis, and logistic regression to identify risk factors and estimate co-detection rates. During the study period, 12,753 patients had a total of 17,159 stool samples tested. Of these, 8,212(47.9%) tested positive, with 6,040(73.6%) being single detections and 2,172(26.4%) being co-detections. Patients with single detection experienced higher hospitalization rates than patients with co-detection. Patients 1–4 years old exhibited the highest co-detection rate relative to other age groups, while Hispanic/Latino individuals were 1.75 times more likely to have co-detection than other races. This study emphasizes the significance of understanding pathogen interactions concerning clinical characteristics and epidemiology of AGI, and the necessity for effective diagnostic strategies and optimal healthcare resource allocation.

Carbapenem-resistant Enterobacterales were isolated from the outlet of a wastewater treatment plant in Kristianstad in southern Sweden, during spring and summer of the year 2024. MALDI-ToF MS identification and subsequent whole-genome sequencing identified eight Klebsiella pneumoniae strains belonging to ST437 and ST873 and 10 Escherichia coli strains belonging to ST167, ST648, ST1284, and ST8346. All strains, except K. pneumoniae ST873, were NDM-5 positive. K. pneumaniae ST437 and E. coli ST8346 carried two carbapenemase genes, blaNDM-5 and blaOXA-181, as well as the extended-spectrum-β-lactamases (ESBL) gene blaCTX-M-15. These two multi-drug-resistant ST variants that are widespread globally, that have previously not been detected in clinical settings in Sweden, are now detected in treated wastewater in a Swedish middle-sized town.

COVID-19 led to a pandemic in 2020, which officially arrived in Colombia on 6 March 2020. As in other parts of the world, the spread of the virus was underestimated due to the lack of diagnostic tests and follow-up protocols. The present study estimates the number of daily cases of COVID-19 infection compatible with theoretical knowledge of the disease, seroprevalence studies, and records of daily deaths due to the disease. To this end, the REMEDID (Retrospective Methodology to Estimate Daily Infections from Deaths) algorithm was applied in nine Colombian cities. On average, official records detected only around 13% of the maximum number of infected persons in the first wave, which they dated with a delay of 25 days. In addition, there was an average delay of 30 days in detecting the first cases. In particular, in Bogotá, the city with the highest number of infections in Colombia, it was observed that (1) the first infected person arrived on 26 January 2020, 40 days before the official registration; (2) the maximum peak of infections was around 6 times higher than that recorded in the official statistics; and (3) this peak was reached on 08 July 2020, 39 days before the official registration date.

Powassan virus (POWV), a tick-borne flavivirus, is an emerging public health threat in the United States. In New York State (NYS), incidence of human POWV infection has increased in recent years. We describe the epidemiology of confirmed and probable POWV infection cases reported in NYS from 2013 to 2023. A total of 44 human cases were reported over the study period, with the highest incidence rates in Columbia and Putnam counties. Most cases occurred in White, non-Hispanic males over age 50. Hospitalization was reported in 91% of cases, and 11% were fatal. Human case data and tick surveillance results were analysed to assess spatiotemporal patterns of disease emergence. Spatial analysis revealed clustering of human cases in the Capital and Metropolitan regions of NYS. The prevalence of POWV in adult tick populations increased significantly statewide, and entomological risk was positively but modestly correlated to disease incidence at the ZIP code level. These findings suggest that POWV infection is emerging in geographically concentrated areas of NYS, highlighting the need for enhanced surveillance and targeted prevention efforts in high-risk regions.

We developed a dynamic COVID-19 Vaccination Barrier Index (CVBI) at the census-tract level in Clark County, Nevada and assessed its geographic disparities and relationship with COVID-19 vaccination rates over time. Using monthly census-tract data from December 2020 to June 2022, the CVBI integrated demographic, socioeconomic, environmental, housing, and transportation variables, alongside surrogates for vaccination accessibility and vaccine hesitancy. Lagged weighted quantile sum regression was applied to construct monthly indices, while a Besag-York-Mollié model assessed associations with vaccination rates. The results revealed consistent vaccination barriers such as living in group quarters, housing inadequacy, and population density across all vaccination statuses (partial, full, booster). Rural and northern Clark County, especially northeastern Las Vegas, exhibited higher CVBI scores that correlated negatively with vaccination rates. Booster vaccination patterns differed, displaying fewer significantly vulnerable tracts. The dynamic nature of barriers is evident, highlighting temporal shifts in the significance of variables like driving distance to vaccine sites. This study emphasizes the importance of dynamic, localized assessments in identifying vaccination barriers, guiding public health interventions, and informing resource allocation to enhance vaccine accessibility during pandemics.

West Nile virus (WNV) is a zoonotic mosquito-borne Flavivirus, with bird populations reservoirs. Although often asymptomatic, infection in humans can cause febrile symptoms and, more rarely, severe neurological symptoms. Previous studies assessed environmental drivers of WNV infections, but most overlooked areas with potential WNV circulation despite no reported human case, and mixed mechanisms affecting hosts vs. vectors. Our objective was to generate a WNV Bird Risk Index (BRI) mapping the potential of WNV circulation in bird communities across Europe. We first used a bird traits-based model to estimate WNV seroprevalence in European wild bird species and identify eco-ethological characteristics associated with it. This allowed us to build a map of the WNV BRI that showed a strong spatial heterogeneity across Europe. To validate this metric, using a Besag-York-Mollie 2 spatial model in a Bayesian framework, we showed a positive association between the BRI and the number of years with notified WNV human cases between 2016 and 2023, at the NUTS administrative region scale. To conclude, we provide a map quantifying the suitability for WNV to circulate in the bird reservoir. This allows to target surveillance efforts in areas at risk for WNV zoonotic infections in the future.

In France, HIV prevention measures including HIV testing, treatment, and uptake of pre-exposure prophylaxis (PrEP), have increased throughout the last decade. To analyse their impact, we performed a time series analysis of monthly HIV diagnoses reported via the national HIV surveillance database. In addition, we compared the timing of HIV promotional campaigns with monthly trends in HIV testing and PrEP initiation. From January 2012 to December 2022, new HIV diagnoses steadily decreased among men who have sex with men (MSM) born in France and heterosexuals born in France, whereas HIV diagnoses increased among MSM born abroad. HIV testing activity and PrEP use in France both steadily increased from 2014 to 2020, during which multiple campaigns targeting HIV testing and prevention occurred. The decline in HIV diagnoses among MSM born in France preceded the introduction of PrEP in 2016 and continued post-2016 without any acceleration in the rate of decline. Increased awareness of, access to and uptake of HIV prevention measures remain essential to progress towards HIV elimination in France, especially among MSM born abroad.

Hyderabad, the fourth-most populous city in India, accounts for the majority of people living with human immunodeficiency virus (HIV) (PLWH) in Telangana, likely comprised of two populations with a disproportionately high national HIV prevalence: gay, bisexual, and other men who have sex with men (MSM) and those who engage in sex work (SW). Research has shown that engaging in SW increases vulnerability to HIV transmission risk for both women and MSM, but less is known about contributors to non-optimal (ART) adherence. We analyzed data from 45 MSM and 49 women living with HIV who were enrolled in the first year of data collection from an mHealth education study in Hyderabad. Modified Poisson regression was used to measure factors associated with ART adherence measured with a visual analogue scale (VAS) (model 1) and pill count (model 2). Less than half (40.9%) reported ever engaging in SW, including 13 women and 25 MSM. The prevalence of non-optimal ART adherence was 14.9% with VAS and 42.4% with pill count. Engaging in SW was not associated with non-optimal ART adherence. Differences in non-optimal ART adherence measured by VAS and pill count suggest that future studies should utilize both methods to better distinguish the measures.

Accidental escapes of pathogens from laboratories continue to cause outbreaks in the community today, posing significant risks to the general public, animal communities and the environment. These incidents, as well as the uncertainties surrounding the origins of the COVID-19 pandemic, highlight the need to consider unnatural origins as part of emerging outbreak surveillance and detection. Identifying recurring patterns and distinctive factors of laboratory-associated disease outbreaks can aid in successfully preventing and mitigating these occurrences. Seventy incidents of laboratory-associated leaks that led to outbreaks in the wider public have been reported (Supplementary Appendix S1). Seven renowned cases that have been comprehensively studied were selected for review: (i) 1955 Polio vaccine incident in western USA, (ii) 1977 H1N1 influenza virus re-emergence in China and the Soviet Union, (iii) 1979 Anthrax release in Sverdlovsk, Soviet Union, (iv) 1995 Venezuelan equine encephalitis epidemics in Venezuela and Colombia, (v) 2003–4 SARS-CoV-1 escapes from Singapore, Taiwan and China, (vi) 2007 Foot-and-Mouth disease virus outbreak in Pirbright, England and (vii) 2019 Brucella leak in Lanzhou, China. These outbreaks were selected because data on their geographical spread, genetics, phylogeny, epidemiological factors (including attack rates, infectious dose, time, location and season of spread) and governmental and institutional responses to the incidents had been previously analysed and published. Thematic analysis of these lines of evidence revealed seven recurring insights described in historically confirmed laboratory-associated outbreaks: unusual strain characteristics, peculiar clinical manifestations or affected demographics, unusual geographical features, atypical epidemiological patterns, delayed government action and communication to the public, misinformation and disinformation spread to the public and biosafety concerns/incidents predating the event. The outbreaks exhibited between 13 and 19 retrospectively identified indicators. These indicators were used to develop preliminary risk criteria intended to support structured, hypothesis-generating assessment of outbreaks, rather than to establish origin.

Community-acquired pneumonia (CAP) remains an important public-health problem, and the COVID-19 pandemic and non-pharmaceutical interventions (NPIs) may have altered its burden. This study aimed to provide updated CAP burden among adults in Shanghai from 2016–2023.We analysed 61,230 participants aged 20–74 years from the Shanghai Suburban Adult Cohort and Biobank. CAP episodes were ascertained via ICD codes and clinical diagnoses. We calculated incidence rates before, during, and after NPIs, conducted subgroup analyses by age, sex, comorbidity and lifestyle. We used Poisson regression to compare stages, and Cox models to identify risk factors. The Overall CAP incidence was 42.1 per 1,000 person–years (95% CI 41.3–42.8). Incidence declined during NPIs (24.2/1,000 py) and rose after NPIs (95.9/1,000 py). The inpatient-to-outpatient ratio increased to 10.1% during NPIs and fell to 5.7% post–NPI. Among those without underlying conditions, rates were 40.1, 20.1 and 73.6/1,000 py before, during and after NPIs. Incidence was higher in participants ≥60 years and in those with multiple comorbidities, especially respiratory diseases. CAP burden temporarily fell during NPIs but resurged post–NPI, notably among high–risk groups. These findings highlight the need for targeted preventive strategies and continued CAP surveillance in the post-pandemic era.

Orientia tsutsugamushi, the causative agent of scrub typhus, is endemic to the Asia–Pacific region. In South Korea, the Boryong strain is considered dominant; however, nationwide phylogeographic distribution and genetic diversity based on clinical isolates remain incompletely characterized. In this study, 121 O. tsutsugamushi clinical isolates were collected from scrub typhus patients at 11 hospitals across South Korea between 2015 and 2024. Isolates were genotyped using 56-kDa gene sequencing and multilocus sequence typing (MLST) of seven housekeeping genes. Sequence analysis and phylogenetic reconstruction were performed using BLAST, PubMLST, BURST, MEGA11, DnaSP6, and R-based tools. Five 56-kDa genotypes were identified: Boryong (93.4%), Ikeda, Je-cheon, Young-worl, and Yeo-joo. MLST revealed 11 sequence types (STs), including five novel STs. While the Boryong strain and related STs were distributed nationwide, minor strains showed restricted distribution in northern regions. Several isolates sharing the same 56-kDa genotype exhibited different MLST STs, indicating possible recombination or local microevolution. This study provides the first nationwide MLST-based characterization of O. tsutsugamushi in South Korea and demonstrates the dominance of the Boryong strain alongside localized diversity. Our findings underscore the utility of MLST for higher-resolution typing and support the need for continued molecular surveillance to inform regional epidemiology and disease management.

We analysed weekly influenza A intensive care unit (ICU) or high dependency unit (HDU) admissions reported by age group and subtype by NHS trusts in England through mandatory surveillance during the 2023–2024 influenza season. We investigated whether subtype reporting varied with patient age group, NHS trust type and region. We estimated the subtype ratio and explored whether this estimate varied among subsets of trusts grouped by the regularity of subtype reporting. Our aim was to explore factors relating to subtype reporting and investigate how these affect subtype ratio estimates. 112 NHS trusts reported data, with 86 trusts reporting influenza A cases and 28 trusts reporting subtyped influenza A cases. The proportion of subtype reporting trusts varied with region and trust type, but not patient age group. The estimated ratio of influenza A(H1N1)pdm09 to influenza A(H3N2) was 3.13 (95% CI: 2.17, 4.51), indicating that influenza A(H1N1)pdm09 was dominant; this was approximately similar across levels of regularity of trust subtype reporting. The accuracy of subtype ratio estimates depends on the availability of influenza A subtype information and data representativeness. We identified low levels of subtype reporting, which likely limits early recognition of new influenza strains and informing of the prescription of antivirals in influenza outbreaks.

Shiga toxin-producing Escherichia coli (STEC) are zoonotic, foodborne pathogens that cause outbreaks of infectious gastrointestinal disease, including haemolytic uraemic syndrome (HUS) which can be fatal. In November 2023, a foodborne outbreak of STEC serotype O26:H11 stx2a/eae, involving 40 cases (54% female and 76% aged 0–9 years old), including 19 children with HUS. Whole-genome sequencing analysis revealed the outbreak strain was multidrug resistant and likely originated from outside the United Kingdom. Epidemiological analysis showed greatest odds of exposure among cases for consumption of a dried fruit product, predominantly in multi-packs. Batch numbers of the packs consumed by cases were rarely available, and where recorded, other packs in the same the batch were unavailable for testing; therefore, targeted microbiological testing was not possible. Fruit for drying can become contaminated when the crop is exposed to irrigation water or rainwater run off containing animal faeces. For STEC, where detection of the causative agent in food is challenging, we recommend establishing multi-source weight of evidence frameworks that promote the application of epidemiological and food chain evidence for public health action and the expansion of global surveillance networks to enhance the detection of foodborne threats at home and abroad.

Nationwide screening for parvovirus B19 among blood donors in Hungary has been conducted since 2019. Although B19 is primarily transmitted via the respiratory route, transfusion-related transmission also occurs. This study investigated the impact of COVID-19–related restrictions on B19 incidence. Between January 1 2019 and December 31 2024, a total of 2,043,119 blood donations were screened for B19 DNA using PCR, and the study period was divided into six epidemiological phases.

During the pre-restriction period (Phase I), B19 incidence was relatively low (0.87/10,000 donations). Following the introduction of COVID-19 restrictions (Phase II), highly viremic donations were not detected. Incidence gradually returned in Phase III (0.22/10000) and increased in Phase IV (1.96/10000), suggesting a minor outbreak. A marked surge in December 2023 (23.03/10000) initiated a nationwide epidemic, peaking in March–April 2024 (46.01/10000), before declining by August (Phase VI; 0.54/10000).

COVID-19 restrictions substantially reduced B19 transmission and may have led to increased population susceptibility. This likely contributed to the unusually intense B19 epidemic observed in 2024, which was considerably more severe than contemporaneous outbreaks reported in other countries.

We estimated the vaccine effectiveness (VE) of second monovalent and bivalent booster vaccines containing Omicron BA.1 or BA.4/BA.5 and the protection conferred by natural immunity against SARS-CoV-2 infection in Luxembourg. We conducted a test-negative case–control study among residents aged 60 years or older by integrating national socio-demographic, COVID-19 vaccination, and testing data, achieving full population coverage. Using conditional logistic regression, we estimated absolute and relative VE of monovalent and bivalent boosters and natural immunity from prior infection. Our analysis included 5,390 test-positive cases and 11,048 test-negative controls matched by week of testing between September 2022 and April 2023. Absolute VE for monovalent and bivalent boosters decreased from 64.8% and 66.6% in the first month to 1.5% and 16.5% after 5–6 months, respectively. The bivalent was superior to the monovalent booster only in individuals without natural immunity (relative VE 25.7%, 95% confidence interval 11.4%; 37.7%). Natural immunity lasted longer than vaccine-induced immunity with 80.7% protected at 4–8 months and 44.9% at 15–25 months post-infection. Both second booster vaccines provided temporary protection against SARS-CoV-2 infection; bivalent boosters offered a slight benefit over monovalent boosters. Natural immunity appears to confer longer-lasting protection.

We aimed to describe the evolution of gonorrhea infection and its antimicrobial resistance patterns in the Prairie provinces compared to Canada between 1980 and 2022. Data was collected from publicly available sexually transmitted infection reports in Canada, Alberta, Saskatchewan, and Manitoba. We extracted the number and rates of gonorrhea cases; percentage of cases by sex, age, ethnicity, sexual orientation; and data on cases diagnosed by culture and antimicrobial resistance. Descriptive statistics and age–period–cohort effect analysis were used. Gonorrhea cases in Canada rose from 32.4 per 100 000 in 1992 to 92.3 in 2022. In 2020, 36.9% of gonorrhea cases in Canada were females, compared to 42.8% in Alberta, 55.3% in Saskatchewan and 56% in Manitoba. People aged ≥30 years represented 22.5% of cases in 1980, and 54.1% in 2022. By 2022, the proportion of Canadian cases detected by culture declined to less than 10%, and azithromycin resistance of N. gonorrhoeae isolates was 8.1%. Alberta, Manitoba, and Saskatchewan reported higher rates of gonorrhea compared to Canada, with a higher proportion of female cases in Manitoba and Saskatchewan. Rising antimicrobial resistance rates and decreased culture testing present significant concerns for gonorrhea control and surveillance.

This cross-sectional study investigated how care home size influences COVID-19 transmission dynamics, focusing on outbreaks in England during the second wave of COVID-19 (Wave 2; December 2020 to March 2021) and the Omicron wave (December 2021 to February 2022). Using data from the UK Health Security Agency and the Care Quality Commission, positive SARS-CoV-2 test results were matched to care home registration and occupancy data, examining outbreak trajectories in homes of varying sizes and resident age groups. The study included over 90,000 positive cases across the two waves. Small care homes (SCHs, with 10 or fewer beds), predominantly housing younger adults, showed significantly higher early positivity rates: 42% of residents were positive at outbreak detection, rising to 61% by day 7. In contrast, larger homes had early positivity rates of only 3–6%. These findings suggest that SCHs, often designed for communal living, facilitate rapid within-home transmission similar to household settings. The study concludes that outbreak control strategies in SCHs should differ from those in larger care homes, emphasizing proportionate, individualized approaches that consider resident vulnerability and minimize disruption to social support systems. These results have broader implications for managing future infectious disease outbreaks and support the development of tailored guidance based on care home size and resident demographics.

Despite efforts by the Volta River Authority (VRA) to provide services for schistosomiasis control in communities along Ghana’s Volta Basin, high rates of transmission and re-infection persist in the region. To strengthen intervention effectiveness, the VRA partnered with the University of Health and Allied Sciences to conduct implementation research aimed at developing context-specific, evidence-based quality improvement strategies. This mixed-method study evaluates the reach, effectiveness, adoption, implementation, and maintenance of the VRA’s quality improvement intervention for their mass drug administration (MDA) for schistosomiasis. Baseline and endline surveys were analysed using STATA and qualitative data from in-depth interviews (IDIs) and focus group discussions (FGDs) were coded and analysed thematically using Taguette. Urogenital schistosomiasis prevalence decreased by 87.83% in Shai Osudoku, 88.98% in South Tongu, and 90.96% in Asuogyaman after the intervention. The findings revealed high training levels among district health management staff and community drug distributors, high health worker satisfaction with the training, and positive community reception of the intervention. However, praziquantel side effects and related opportunity costs may have posed a barrier to drug uptake. Moreover, re-infection remains a challenge, which could be attributed to high domestic and economic reliance on the Volta River.

The activity of respiratory viruses (RVs) displays large variability in tropical regions, posing challenges for public health response strategies. Data from most RVs in south-eastern Mexico remain limited, particularly in the Yucatan Peninsula, the largest tourism hub in the country. This retrospective study analyses the regional epidemiology of RVs in Merida, the largest city in the region, using laboratory test data from a local hospital (January 2018–April 2024). Test results of 143292 RVs were collected, including 121976 for SARS-CoV-2, 19355 for influenza A and B viruses, and 1961 for 17 distinct RVs. We found that non-SARS-CoV-2 RVs circulated year-round, with higher activity in autumn and spring, while SARS-CoV-2 peaked in summer and winter. Influenza A virus, respiratory syncytial virus, and influenza B virus reached their highest activity in autumn, earlier than in other regions of Mexico. Human metapneumovirus peaked during autumn-winter. Rhinovirus/enterovirus and parainfluenza showed year-round activity, with peaks in autumn and spring. Other coronaviruses were more frequent during winter-spring. In post-pandemic years (2022–2023), adenovirus outbreaks emerged, as well as an increased prevalence of non-SARS-CoV-2 RV co-infections. This study highlights the need for region-specific public health strategies, including optimized vaccination schedules, such as for influenza A virus, and enhanced diagnostic surveillance.

Effectiveness of nirsevimab against respiratory syncytial virus (RSV) hospitalization during the 2024/2025 season in Spain was estimated using a test-negative design (TND) and hospital-based respiratory infections surveillance data. Children born between 1 April 2024 and 31 March 2025 and hospitalized with severe respiratory infection between the start of the 2024 immunization campaign (regionally variable, between 16 September and 1 October 2024) and 31 March 2025 were systematically RT-PCR RSV-tested within 10 days of symptom onset and classified as cases if positive or controls if negative. Nirsevimab effectiveness ((1 − odds ratio) × 100) was estimated using logistic regression, adjusted for admission week, age, sex, high-risk factors, and regional RSV hospitalization rate. We included 199 cases (68.8% immunized) and 360 controls (86.4% immunized). Overall effectiveness was 65.5% (95% confidence interval: 45.2 to 78.3). Effectiveness was similar among infants born before and after the campaign start (63.6% vs. 70.4%, respectively). We found an unexpected early decrease in effectiveness with increasing time since immunization and age, albeit with wide confidence intervals for some groups. Strong age–period–cohort effects and potential sources of bias were identified, highlighting the need to further explore methodological challenges of implementing the TND in the dynamic population of newborns.