To estimate illness incidence or prevalence from wastewater data, modelling approaches may benefit from incorporating faecal shedding parameters. We systematically searched PubMed and a public repository on shedding data and included 33 studies that met at least one of our objectives. Among 32 studies, the proportion of SARS-CoV-2-infected individuals with detectable virus in stool ranged from 18 to 100%, with a pooled estimate of 54% (95% CI: 52–56%). Stratification by four clinical severity categories, ranging from asymptomatic to critically ill, showed no significant differences among categories (p-value = 0.49). The proportion of individuals with detectable SARS-CoV-2 RNA in stool was higher in children (61%) than in adults (53%; p-value = 0.02). In half of the individuals who initially shed the virus in stool, it remained detectable for an estimated 22 days post-symptom onset. Three studies documented viral load kinetics, indicating a peak between days 3 and 9. Twenty-five studies reported maximum shedding durations ranging from 2 to 12 weeks. Our review summarizes the frequency, dynamics, and duration of SARS-CoV-2 shedding in stool and may serve as a valuable foundation for modelling efforts involving faecal shedding indicators.

This retrospective, cross-sectional study assessed the burden of HIV in Israel’s Maccabi Healthcare Services in 2022. Among 2.6 million individuals assessed (lookback period: > 2 decades), 1973 PWH were identified and age-sex-matched (1:5) to 9,865 randomly selected controls without HIV. We compared sociodemographic, clinical characteristics, and healthcare resource utilization (HRU; Jan–Dec 2022) between people with and without HIV and characterized antiretroviral therapy (ART) treatment patterns among PWH (Jan–Dec 2022). Compared to controls, PWH had a higher lifetime prevalence (since 1988; P < 0.001) of several comorbid conditions, including liver disease, chronic kidney disease, any cancer, and hepatitis B and C infections. Additionally, PWH had a higher rate of anxiety and depression (26.2% vs. 13.5%; P < 0.001). PWH showed higher annual HRU than controls, including ~2-fold higher hospitalizations (≥1 new admissions; P < 0.001) and frequent use of emergency, urgent, primary, specialist, and nursing care (P < 0.05). Among 1907 PWH with ≥1 ART prescription, 78.1% had ≥90% coverage in 2022, although 69.1% experienced ART interruption and 7.2% discontinuation, the latter associated with mental health issues. This study recognizes critical gaps in care that could inform strategies to improve clinical outcomes and resource allocation in health systems for PWH.

Mpox (formerly called monkeypox) is a zoonotic viral disease caused by the monkeypox virus (MPXV) that has recently emerged as a notable global health issue by spreading beyond its typical geographical zones in Central and West Africa. In this study, we conducted a phylogenetic and evolutionary investigation of MPXV in West Africa. We focussed on 167 complete genome sequences collected from human infections in Nigeria and Cameroon between 2019 and 2024, all of which were retrieved from the GSAID database. To analyse these sequences, we employed multiple sequence alignment using fast Fourier transform (MAFFT) and maximum likelihood techniques to identify conserved genomic variants and trace evolutionary patterns within the virus. Our findings revealed that all the MPXV strains studied belong to clade II, which is further subdivided into two subclades. Notably, this study documents the presence of two distinct subclades IIa and IIb, reflecting the complex and ongoing evolution of the virus in the region. The phylogenetic analysis reveals rapid mutations and suggests that MPXV is being transmitted from multiple lineages between Nigeria and Cameroon. This demands the need to further strengthen the surveillance and containment efforts in West Africa. This study highlights the role of genomic surveillance in monitoring the evolution and spread of the MPXV, particularly in regions with limited available data.

This retrospective study analysed 14,625 isolates of the six major hospital-associated ‘ESKAPE’ pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) collected between 2002 and 2024 in a Hungarian tertiary-care centre. Antimicrobial resistance was assessed using the antibiotic resistance index (ARI), multidrug resistance (MDR) ratios, and resistance instability index (RII). A. baumannii and E. faecium showed the highest resistance burdens and instability. Age showed a significant monotonic association with resistance (Spearman r = 0.88), with peaks in infants, middle-aged women, and the elderly. Species-specific age trends varied, with a negative correlation seen in Enterobacter spp. Hierarchical clustering grouped pathogens by resistance trajectory rather than taxonomy. Pairwise resistance distances confirmed divergence between Gram-positive and Gram-negative species. Resistance to aminoglycosides and sulphonamides showed the highest year-to-year variability, as quantified by the RII, particularly in A. baumannii and E. faecium. Vector autoregressive (VAR) modelling predicted continued MDR increases in these species. A strong correlation was found between ARI and RII (Pearson r = 0.85, p = 0.032). These findings underscore the importance of integrating resistance magnitude and volatility in surveillance.

We assessed the association between voluntary polymerase chain reaction testing of travellers and reported infection rates in the Ogasawara Islands compared with those in several other Tokyo islands. The implementation of polymerase chain reaction testing over a 2-year period was evaluated. Between September 2020 and September 2022, 38,943 of 45,900 travellers to the Ogasawara Islands underwent pre-travel polymerase chain reaction testing, with a notable increase in uptake during states of emergency. Ogasawara reported 385 positive coronavirus disease 2019 cases, with no hospitalizations or severe cases among residents, in contrast to the higher infection and hospitalization rates in Tokyo. Pre-boarding polymerase chain reaction tests were associated with lower reported infection rates in this island setting. These findings suggest that combining pre-travel testing with local mitigation measures, including case isolation systems, may help safeguard the communities of small, geographically isolated islands. These results may inform public health preparedness and response strategies for future infectious disease outbreaks.

This study assessed changes in complete pneumococcal vaccination coverage (CPVC) among Peruvian children <5 years before and after the COVID 19 pandemic and evaluated regional differences, associated sociodemographic factors and wealth-related inequality. 2018–2023 Demographic and Health Surveys (DHS) was analyzed. CPVC was defined as receiving the full 2 + 1 schedule of the 13 valent pneumococcal vaccine. Children aged 13–60 months were included. Multivariable analysis used modified Poisson regression and wealth related inequality was assessed using the Concentration index and Erreygers’s corrected Concentration index at national and regional levels. Among 95,586 children, CPVC decreased from 71.9% in 2019 to 69.4% in 2020 (p = 0.003), then returned to pre Covid levels from 2021 onward (72.2% in 2023; p = 0.001), particularly in Lima Metropolitana. Puno (53.3–58.6%) and Madre de Dios (50.9–62.1%) consistently showed the lowest coverage. Nationally, wealth- or sociodemographic related inequalities were minimal; however, regional interactions indicated that the effect of wealth on CPVC varied by area. Depending on the region, factors such as age group, household members and mather’s education were associated with lower CPVC, whereas age at first pregnancy, institutional birth, antenatal care and access to information increased CPVC. Ucayali showed persistently higher CPVC among wealthier populations. Despite a temporary decline during the pandemic, CPVC in Peru rapidly recovered, although regional gaps persist.

In low-prevalence settings, the epidemiological yield of screening strategies for controlling vancomycin-resistant enterococci (VRE) outbreaks has not been fully established. We retrospectively analysed a prolonged VRE outbreak at a 536-bed tertiary-care hospital in Japan from 2010 to 2021 to evaluate sequential screening strategies across epidemic phases and to identify risk factors for VRE acquisition. Hospital-wide, admission-based, antimicrobial exposure-based, passive, and haemodialysis-targeted screening strategies were implemented over time. Screening yields were compared longitudinally, and a retrospective case–control study was performed using data from the initial hospital-wide screening phase. Molecular epidemiology was assessed by pulsed-field gel electrophoresis (PFGE). In total, 169 VRE-positive patients were identified, including seven infections and 162 asymptomatic carriers. Hospital-wide screening in the early epidemic phase showed the highest positivity rate (0.91%), whereas targeted strategies consistently yielded lower rates (0.09–0.34%). Haemodialysis, specific oral care practices, and prior exposure to carbapenems, glycopeptides, and piperacillin/tazobactam were independently associated with VRE acquisition. PFGE revealed substantial genetic diversity, suggesting sustained nosocomial transmission with repeated introductions. Early broad-based screening may be epidemiologically efficient in the initial phase of VRE outbreaks in low-prevalence settings, followed by adaptive refinement for long-term control.

This study assessed whether systematically using finetype data in national surveillance of invasive meningococcal disease serogroup B (IMD-B) in the Netherlands could improve cluster detection in order to prevent further cases through public health actions. We analysed 2005–2023 data, including 1,642 IMD-B cases with complete finetype and municipality information (95%; N = 1729). Using a generalized linear model, we calculated expected baselines for each finetype, including temporal trends. Using SaTScan™, we applied Poisson scan-statistics with a 365-day window to identify spatiotemporal clusters, comparing results to epidemiological and core-genome multi-locus sequence typing (cgMLST) data. Of 453 finetypes, 308 (68%) occurred once; diversity was high (Gini-Simpson index 0.96). We identified 42 spatiotemporal clusters across 37 finetypes, comprising 132 cases (8%), with a median cluster size of two (range 2–21) and duration of 45 days (range 6–356). Between zero and five clusters were detected yearly. Among 18 cases with known epidemiological links, 14 (78%) were within detected spatiotemporal clusters. CgMLST data from eight clusters supported some clusters but rejected others. Systematic cluster detection using finetype could reveal missed epidemiological links, potentially enabling public health action. However, its impact in preventing additional IMD-B cases is likely limited due to small cluster sizes, though meaningful given the severity of IMD-B. Simple finetype mapping may provide a resource-efficient alternative to SaTScan™.

We describe a prolonged outbreak of Salmonella enterica serotype Poona (S. Poona) sequence type (ST) 308, which comprised 13 cases occurring intermittently in North West England between 2016 and 2021. Whole genome sequencing (WGS) results indicated potential exposure to a single source but a lack of good quality data from routine surveillance questionnaires initially made it challenging to identify the cause. Continuing identification of cases in young children in a small geographical area prompted further public health actions, including trawling interviews which identified that ten cases attended the same nursery. As part of enhanced case finding in this nursery, childcare staff were asked to submit faecal samples. One asymptomatic staff member was positive for S. Poona and had worked at another nursery, attended at the time by the first S. Poona child case in this outbreak. Further investigations revealed that the case had previously undergone a cholecystectomy. We report an outbreak caused by persistent carriage and shedding of S. Poona in an asymptomatic individual working with vulnerable groups, which necessitated introduction of risk management measures similar to that for Typhoidal Salmonella. We also demonstrate the utility of combining epidemiological and WGS data in the public health response to Salmonella outbreaks.

Influenza increases the risk of secondary diseases, but other than pneumonia, many of these diseases (e.g., sinusitis, otitis media, acute myocardial infarctions) are not consistently considered in estimates of influenza burden. We used the Merative Marketscan database (2001–2019) and time-series methods to identify age-specific categories of diseases that were temporally associated with patterns of influenza activity. Next, we estimated hypothetical reductions in the incidence and costs of these diseases if influenza incidence were reduced. Of 282 different disease categories evaluated, 23 (8.2%) were strongly associated with influenza (e.g., acute bronchitis, otitis media, myocardial infarctions, sinusitis, COPD) in at least one age group. For example, we estimated a 20% decrease in peak influenza incidence could decrease acute bronchitis cases by 6.5% and pneumonia cases by 5.3%, corresponding to a $1.6 billion reduction in healthcare costs. Excluding secondary diseases associated with influenza may lead to substantial underestimates of influenza’s burden and costs.

In September 2020, an unexpected increase in Salmonella Muenchen patient isolates and notifications was observed. We investigated the outbreak to identify the vehicle of infection. RKI defined cases as patients with laboratory-confirmed S. Muenchen infections reported between September 2020 and July 2021. Genomes of clinical, food, and animal S. Muenchen isolates were analysed using cgMLST. We conducted interviews and performed a frequency-matched case–control study. We calculated frequencies and adjusted odds ratios (aOR) using logistic regression. We identified 301 cases in eight federal states in Germany. Hypothesis-generating interviews did not provide a conclusive hint of a possible vehicle. S. Muenchen strains were detected in dried coconut pieces, milk powder used for chocolate production, and a wild swan, all with a cgMLST profile indistinguishable from the prominent node comprising 116 patient isolates. Cases included in the case–control study more often consumed dried coconut pieces (22/30) than controls (2/116) (aOR: 176 (95% confidence interval: 32–954)). In this investigation, cgMLST analysis presented identical strains in three different isolate sources. The case–control study supported dried coconut pieces as vehicle of infection demonstrating the importance of interdisciplinary investigations and underscoring the potential impact of unusual vehicles.

Genomic epidemiology was essential for characterizing SARS-CoV-2 transmission during the early COVID-19 pandemic. This systematic review examined how whole-genome sequencing was used in local outbreak investigations published between March 2020 and March 2021. Searches of PubMed, Scopus, and Web of Science identified 32 studies from 18 countries that integrated genomic and epidemiological data for local outbreak investigations. Most studies were conducted in healthcare settings or in high-income countries. A limited number of studies were conducted in low- and middle-income countries, except for China and Vietnam. Illumina or Oxford Nanopore platforms and tiled-amplicon protocols were the most common sequencing methods. Phylogenetic trees were the most common genomic epidemiology analytical approach. Genomic data enabled confirmation of suspected transmission links, detection of multiple introductions, and identification of asymptomatic or presymptomatic transmission. Important enablers of early implementation included open-access genomics databases, standardized protocols (e.g. ARTIC), open-source tools (e.g. Nextstrain), and cross-sector partnerships and funding. Study quality and adherence to common observational study reporting guidelines varied widely. Familiarity with the STROME-ID guidelines for molecular epidemiology studies would have improved overall quality. These findings highlight the utility of genomic epidemiology in outbreak response and support its continued integration into public health surveillance systems.

Enterovirus A71 was first isolated in California in 1969, with the earliest retrospective detection traced back to 1963 in the Netherlands, but its early spread remains unclear. Using age-specific seroprevalence data from children aged 1–10 years in Kawasaki City, Japan, collected annually from 1966–1973, we applied serocatalytic models to estimate annual force of infection during 1959–1973. Several models were tested, incorporating different assumptions about time-varying force of infection, age-dependent susceptibility, and seroreversion, to identify the best fit to the data. Model comparison identified the models with independent annual infection probability or two distinct outbreak periods, both including age-dependent force of infection and seroreversion, as optimal. All top models consistently identified two major transmission periods: 1961–1962 and 1968–1969. The two-outbreak model estimated mean attack rates of 21.8% and 37.8% for the earlier and later outbreaks under seroreversion, and 19.8% and 34.9% under age-dependent force of infection. Our findings provide evidence of enterovirus A71 circulation in Japan during two distinct periods in the 1960s, coinciding with early detections in Europe and the USA, suggesting global distribution by that decade. This study underscores the value of testing archived sera for reconstructing pathogen emergence and spread.

Occupational blood exposure accidents (OBEAs) pose significant risks to healthcare workers, potentially exposing them to hepatitis B (HBV), hepatitis C (HCV), and HIV. While most research focuses on hospital settings, this study assessed OBEA management in non-hospital contexts. Although our data predate the COVID pandemic, findings remain highly relevant, especially for healthcare professionals working outside hospital settings. A retrospective analysis of OBEA registry data (2006–2014) was conducted in a southern Dutch region. Data included demographics, profession, workplace, injury type, source status (HBV, HCV, HIV), risk assessment, post-exposure measures, and lab results. Chi-square and t-tests were applied. In total, 975 OBEA were reported. Among nurses, medical assistants, students, and housekeeping staff, subcutaneous needles (51–67%) and lancets (25%) were common exposure sources. Police officers mainly reported biting (26%), scratching, or spitting (70%). HBV vaccination coverage ranged from 18% (housekeeping) to over 90% (nurses, police). Post-exposure measures were taken in 52% of cases. High-risk exposures (43%) mainly affected ambulance staff, sterilization workers, police, and dentists. Sources were tested in 85% of high-risk cases: 1.4% were HBV positive, 2% HCV positive, and 1.1% HIV positive. No seroconversions occurred. Results stress the need for better HBV vaccination coverage, targeted prevention, and prompt OBEA reporting outside hospital settings.

This study aimed to identify determinants of influenza vaccination among older adults using nationally representative data from the Turkey Older Persons Profile Survey 2023. Data from 11 657 individuals aged 65 and over, collected by the Turkish Statistical Institute, were analysed. Least Absolute Shrinkage and Selection Operator regression was employed for variable selection, followed by binary logistic regression to identify significant predictors. Only 19.4% of older adults reported receiving an influenza vaccine during the 2022/2023 influenza season. Higher education, income sufficiency, social security coverage, regular medication use, physical activity, and use of mobile health (mHealth) applications were significantly associated with higher vaccination uptake. Former smoking, alcohol consumption, older age, higher body mass index, and greater independence in daily living were also positive predictors. Traditional barriers to healthcare access (e.g., transportation, waiting times) were not significantly associated. Regional disparities were evident, with lower vaccination rates in the eastern regions. Vaccine uptake among older adults in Turkey is low despite universal access. Promoting engagement with primary healthcare services and increasing the use of mHealth applications may contribute to increasing vaccination coverage. Special attention should be given to socially disadvantaged groups and underperforming regions to enhance preventive healthcare among the aging population.

Diagnostic test accuracy studies assess a diagnostic test’s performance against a reference standard. In this review, we explore and compare statistical methods used in meta-analyses of diagnostic test accuracy studies. Specifically, we evaluate two frequentist methods – split component synthesis (SCS) and bivariate model (BM) – alongside two Bayesian approaches: Bayesian hierarchical summary receiver operating characteristic (BHSROC) and Bayesian bivariate model (BBM). We also include their latent class variants (LC-BHSROC and LC-BBM). Using a meta-analysis of various multiplex nucleic acid amplification tests (NAATs/PCRs) against Campylobacter spp. as a case study we illustrate the practical applications of these methods. The reference standard was culture, and due to differences in cut-off values and primers among the NAAT/PCR brands, substantial heterogeneity was anticipated. Our findings reveal that the BM and BBM methods tend to estimate higher sensitivities than the other approaches, even when the number of studies is substantial, and heterogeneity is moderate – as observed in this case study. In such scenario, the SCS method or the BHSROC model may offer more robust and reliable outcomes. While our review is based on a real-life meta-analysis rather than simulations, it offers practical insights into the strengths and limitations of these statistical approaches for diagnostic test accuracy studies.