COVID-19 vaccine effectiveness (VE) studies are limited in low- and middle-income countries. A case-control study was conducted among COVID-19 and other pneumonia patients admitted to a hospital in the Philippines during the pre-Omicron and Omicron periods. To elucidate factors associated with in-hospital death, 1782 COVID-19 patients were assessed. To estimate absolute VE for various severe outcomes, 1059 patients were assessed (869 [82.1%] COVID-19 cases; 190 [17.9%] controls). Factors associated with in-hospital death included older age, tuberculosis (adjusted odds ratio [aOR] 2.45 [95% confidence interval {95% CI} 1.69–3.57]), HIV (aOR 3.30 [95% CI 2.03–5.37]), and current smokers (aOR 2.65 [95% CI 1.72–4.10]). Pre-Omicron, the primary series provided high protection within a median of 2 months (hospitalization: 85.4% [95% CI 35.9–96.7%]; oxygen requirement: 91.0% [95% CI 49.4–98.4%]; invasive mechanical ventilation (IMV): 97.0% [95% CI 65.7–99.7%]; death: 96.5% [95% CI 67.1–99.6%]). During Omicron, the primary series provided moderate-high protection within a median of 6–9 months (hospitalization: 70.2% [95% CI 27.0–87.8%]; oxygen requirement: 71.4% [95% CI 29.3–88.4%]; IMV: 72.7% [95% CI −11.6–93.3%]; death: 58.9% [95% CI −82.8–90.8%]). Primary series VE against severe COVID-19 outcomes was consistently high for both pre-Omicron and Omicron in a setting where approximately half of the vaccinees received inactivated vaccines.

Highly pathogenic avian influenza (HPAI) outbreaks have repeatedly occurred in two districts of Kerala state, India, over the last few years. The outbreaks in the wetland areas coincided with the arrival of migratory birds. At the time, the factors responsible for local transmission in ducks were not known. This study aimed to identify the socio-economic factors responsible for spatial variation in the occurrence of HPAI outbreaks in the two districts using Bayesian network modelling (BNM) and Stochastic Partial Differential Equation (SPDE) model. Further, information was collected on the duck rearing practices in rice paddy fields to identify the risk factors for local – spread of the outbreaks. We found that the SPDE model without covariates explained variation in occurrence of outbreaks. The number of rice paddy fields used by the duck farmers was identified as risk factor. We concluded based on BNM and SPDE that the infected migratory birds were the source of infection for the first few duck farms in the wetland areas and subsequent transmission was driven by shifting of ducks from one rice paddy field to other fields. There is a probability of persistent and recurrent infections in the ducks and possible spill over to humans. Hence, it is important to have surveillance in ducks to prevent recurrent outbreaks in the region.

With the ongoing emergence of SARS-CoV-2 variants, there is a need for standard approaches to characterize the risk of vaccine breakthrough. We aimed to estimate the association between variant and vaccination status in case-only surveillance data. Included cases were symptomatic adult laboratory-confirmed COVID-19 cases, with onset between January 2021 and April 2022, reported by five European countries (Estonia, Ireland, Luxembourg, Poland, and Slovakia) to The European Surveillance System. Associations between variant and vaccination status were estimated using conditional logistic regression, within strata of country and calendar date, and adjusting for age and sex. We included 80,143 cases including 20,244 Alpha (B.1.1.7), 152 Beta (B.1.351), 39,900 Delta (B.1.617.2), 361 Gamma (P.1), 10,014 Omicron BA.1, and 9,472 Omicron BA.2. Partially vaccinated cases were more likely than unvaccinated cases to be Beta than Alpha (adjusted odds ratio [aOR] 2.48, 95% CI 1.29–4.74), and Delta than Alpha (aOR 1.75, 1.31–2.34). Fully vaccinated cases were relative to unvaccinated cases more frequently Beta than Alpha (aOR 4.61, 1.89–11.21), Delta than Alpha (aOR 2.30, 1.55–3.39), and Omicron BA.1 than Delta (aOR 1.91, 1.60–2.28). We found signals of increased breakthrough infections for Delta and Beta relative to Alpha, and Omicron BA.1 relative to Delta.

Klebsiella pneumoniae are opportunistic pathogens which can cause mastitis in dairy cattle. K. pneumoniae mastitis often has a poor cure rate and can lead to the development of chronic infection, which has an impact on both health and production. However, there are few studies which aim to fully characterize K. pneumoniae by whole-genome sequencing from bovine mastitis cases. Here, K. pneumoniae isolates associated with mastitis in dairy cattle were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and whole-genome sequencing. Furthermore, whole-genome sequence data were used for phylogenetic analyses and both virulence and antimicrobial resistance (AMR) prediction, in parallel with phenotypic AMR testing. Forty-two isolates identified as K. pneumoniae were subject to whole-genome sequencing, with 31 multi-locus sequence types being observed, suggesting the source of these isolates was likely environmental. Isolates were examined for key virulence determinants encoding acquired siderophores, colibactin, and hypermucoidy. The majority of these were absent, except for ybST (encoding yersiniabactin) which was present in six isolates. Across the dataset, there were notable levels of phenotypic AMR against streptomycin (26.2%) and tetracycline (19%), and intermediate susceptibility to cephalexin (26.2%) and neomycin (21.4%). Of importance was the detection of two ESBL-producing isolates, which demonstrated multi-drug resistance to amoxicillin-clavulanic acid, streptomycin, tetracycline, cefotaxime, cephalexin, and cefquinome.

The course of COVID-19 is highly variable, with genetics playing a significant role. Through large-scale genetic association studies, a link between single nucleotide polymorphisms and disease susceptibility and severity was established. However, individual single nucleotide polymorphisms identified thus far have shown modest effects, indicating a polygenic nature of this trait, and individually have limited predictive performance. To address this limitation, we investigated the performance of a polygenic risk score model in the context of COVID-19 severity in a Russian population. A genome-wide polygenic risk score model including information from over a million common single nucleotide polymorphisms was developed using summary statistics from the COVID-19 Host Genetics Initiative consortium. Low-coverage sequencing (5x) was performed for ~1000 participants, and polygenic risk score values were calculated for each individual. A multivariate logistic regression model was used to analyse the association between polygenic risk score and COVID-19 outcomes. We found that individuals in the top 10% of the polygenic risk score distribution had a markedly elevated risk of severe COVID-19, with adjusted odds ratio of 2.9 (95% confidence interval: 1.8–4.6, p-value = 4e-06), and more than four times higher risk of mortality from COVID-19 (adjusted odds ratio = 4.3, p-value = 2e-05). This study highlights the potential of polygenic risk score as a valuable tool for identifying individuals at increased risk of severe COVID-19 based on their genetic profile.

With climate change, the geographic distribution of some VBDs has expanded, highlighting the need for adaptation, and managing the risks associated with emergence in new areas. We conducted a questionnaire survey on the knowledge, attitudes, and practices (KAP) about vector-borne diseases (VBDs) among sample of Finnish residents. The questions were scored and the level of KAP was determined based on scoring as poor, fair, good, or excellent. Binary logistic regression analysis was used to evaluate the associations of different KAP levels with sex, age, education, and possible previous VPD infection. We received 491/1995 (25%) responses across the country and detected generally good knowledge, but only fair practices towards VBDs. Sex and age of the respondents were most often significantly associated with the level of KAP (P > 0.05). Despite the generally good knowledge, we detected major gaps, especially regarding the distinction of tick-borne encephalitis and Lyme borreliosis (LB), risk of disease, and protective measures. Additionally, many respondents thought the vaccination protects against LB or tick bites. This calls for awareness raising on disease risk and prevention measures. With increasing cases and the effects of climate change, surveillance of VBDs communication to the general public should be strengthened.

Surveillance of antimicrobial consumption (AMC) is essential to anticipate and inform policies and public health decisions to prevent and/or contain antimicrobial resistance (AMR). This manuscript shares the experience on AMC data collection in Latin American & Caribbean (LAC). The WHO GLASS-AMC methodology for AMC surveillance was used for data registration during the period 2019–2022. Focal points belonging to each country were contacted and trained for AMC source of information detection, managing registration tools, and data analysis. Thirteen countries were enrolled with significant heterogeneity in the AMC results (range 2.55–36.26 DID-AMC). This experience reflects the heterogeneity of realities in LAC countries; how each one of the nations selected the best sources to collect AMC data, which were the main problems in applying the WHO-AMC collection tool, and the approach that each country gave to the analysis of its data. Finally, some examples are provided on the use of AMC information in making the best decision-making related to AMR control policies at the national level.

Hepatitis E virus (HEV) is one of the most common causes of viral hepatitis. We examined HEV seroprevalence and associations of sociodemographic and lifestyle characteristics with HEV immunoglobulin G (IgG) seropositivity in the Arab population. A cross-sectional single-centre study was conducted among adults in the Nazareth area during 2022. Blood samples were tested using the Altona Real-Star HEV-RNA and the Wantai IgG assays. Data on sociodemographics, health status, and lifestyle were collected using structured questionnaires.

Overall, 490 individuals (55.9% males) aged 18 − 96 (mean = 53.2, SD = 28.0) were enrolled. HEV IgG seropositivity was estimated at 21.4% (95% CI 17.9–25.3). No samples were HEV-RNA positive. The correlates of HEV IgG seropositivity were older age (prevalence ratio (PR) 1.07, 95% CI 1.04–1.09, P < 0.001) and consuming beef frequently (PR 2.81, 95% CI 1.40–5.63, P = 0.003). No associations were found between Arab religious groups (Muslim, Christian or Druze, representing different socioeconomic status and dietary habits) or pork consumption and HEV IgG seropositivity. In conclusion, HEV seropositivity was high in the Arab population, and assessing HEV in Ruminants, particularly cows, is warranted.

The financial burden of hospitalization from life-threatening infectious diseases on the U.S. healthcare system is substantial and continues to increase. The purpose of this study was to identify key predictors of high hospital charges for infective endocarditis at a major university-affiliated cardiac care centre in West Virginia.

A retrospective electronic medical records’ review was undertaken of all adult patients admitted for endocarditis between 2014–2018. Multiple linear regression analysis assessed the total charges billed to the patient account for their endocarditis hospitalization in the medical record.

Hospital charges have increased 12-fold during 2014–2018. Among the 486 patients, the median hospital charge was $198 678. About 47% of the patients underwent surgery incurring 70% of the total charges. Patients with hospital stays of ≥50 days accounted for a third of all charges. The multiple linear regression model accounted for 85% of the linear variance in the hospital charges. Median charges increased by 30.87% for patients with ≥9 consultations, 60.32% for those who died in the hospital, and 81.85% for those who underwent surgical intervention.

The study findings showed that complex care requiring multiple consultations, surgical interventions, and longer hospital stays were significantly associated with higher hospital charges for endocarditis treatment.

In September 2023, the UK Health Security Agency’s (UKHSA) South West Health Protection Team received notification of patients with Pseudomonas aeruginosa perichondritis. All five cases had attended the same cosmetic piercing studio and a multi-disciplinary outbreak control investigation was subsequently initiated. An additional five cases attending the same studio were found. Seven of the ten cases had isolates available for Variable Number Tandem Repeat (VNTR) typing at the UKHSA national reference laboratory. Clinical and environmental P. aeruginosa isolates from the patients, handwash sink, tap water and throughout the wall-mounted point-of-use water heater (including outlet water) were indistinguishable by VNTR typing (11,6,2,2,1,3,6,3,11). No additional cases were identified after control measures were implemented, which included replacing the sink and point-of-use heater.

The lack of specific recommendations to control for P. aeruginosa within Council-adopted ear-piercing byelaws or national guidance means that a cosmetic piercing artist could inadvertently overlook the risks from this bacterial pathogen despite every intention to comply with the law and follow industry best practice advice. Clinicians, Environmental Health Officers and public health professionals should remain alert for single cases of Pseudomonas perichondritis infections associated with piercings and have a low threshold for notification to local health protection teams.

This study investigated cases of pregnancy-related listeriosis in British Columbia (BC), Canada, from 2005 to 2014. We described all diagnosed cases in pregnant women (n = 15) and neonates (n = 7), estimated the excess healthcare costs associated with listeriosis, and calculated the fraction of stillbirths attributable to listeriosis, and mask cell sizes 1–5 due to data requirements. Pregnant women had a median gestational age of 31 weeks at listeriosis onset (range: 20–39) and on average delivered at a median of 37 weeks gestation (range: 20–40). Neonates experienced complications but no fatalities. Stillbirths occurred in 1–5 of 15 pregnant women with listeriosis, and very few (0.05–0.24%) of the 2,088 stillbirths in BC in the 10 years were attributed to listeriosis (exact numbers masked). Pregnant women and neonates with listeriosis had significantly more hospital visits, days in the hospital and physician visits than those without listeriosis. Pregnant women with listeriosis had 2.59 times higher mean total healthcare costs during their pregnancy, and neonates with listeriosis had 9.85 times higher mean total healthcare costs during their neonatal period, adjusting for various factors. Despite small case numbers and no reported deaths, these results highlight the substantial additional health service use and costs associated with individual cases of pregnancy-related listeriosis in BC.

Hong Kong is an intermediate tuberculosis (TB) endemicity city dominated by reactivation diseases. A cross-sectional study on the clinical and epidemiologic data of newly diagnosed TB cases was conducted in such a setting, to examine the association between ambient PM2.5 and TB reactivation. After the exclusion of cases most likely resulting from recent infection, four distinct TB population phenotypes were delineated by latent class analysis based on their reactivation risk and clinical profiles (N = 2,153): ‘Elderly male’ (26%), ‘Otherwise healthy younger adult’ (34%), ‘Older female’ (19%) and ‘Male smoker’ (21%). Overall, exposure to high concentrations of ambient PM2.5 6 and 12 months before the notification was significantly associated with ‘Otherwise healthy younger adults’ membership (OR = 1.07 and 1.11, respectively) compared with ‘Elderly male’. Such association was less evident for other phenotypes. The differential pattern of association between ambient PM2.5 exposure and TB population phenotypes suggested the role of ambient PM2.5 in TB reactivation.

This study explored the effect of SARS-CoV-2 infection and COVID-19 vaccination during pregnancy on neonatal outcomes among women from the general Dutch population. VASCO is an ongoing prospective cohort study aimed at assessing vaccine effectiveness of COVID-19 vaccination. Pregnancy status was reported at baseline and through regular follow-up questionnaires. As an extension to the main study, all female participants who reported to have been pregnant between enrolment (May–December 2021) and January 2023 were requested to complete an additional questionnaire on neonatal outcomes. Multivariable linear and logistic regression analyses were used to determine the associations between self-reported SARS-CoV-2 infection or COVID-19 vaccination during pregnancy and neonatal outcomes, adjusted for age, educational level, and presence of a medical risk condition. Infection analyses were additionally adjusted for COVID-19 vaccination before and during pregnancy, and vaccination analyses for SARS-CoV-2 infection before and during pregnancy. Of 312 eligible participants, 232 (74%) completed the questionnaire. In total, 196 COVID-19 vaccinations and 115 SARS-CoV-2 infections during pregnancy were reported. Infections were mostly first infections (86; 75%), caused by the Omicron variant (95; 83%), in women who had received ≥1 vaccination prior to infection (101; 88%). SARS-CoV-2 infection during pregnancy was not significantly associated with gestational age (β = 1.7; 95%CI: −1.6–5.0), birth weight (β = 82; −59 to 223), Apgar score <9 (odds ratio (OR): 1.3; 0.6–2.9), postpartum hospital stay (OR: 1.0; 0.6–1.8), or neonatal intensive care unit admission (OR: 0.8; 0.2–3.2). COVID-19 vaccination during pregnancy was not significantly associated with gestational age (β = −0.4; −4.0 to 3.2), birth weight (β = 88; −64 to 240), Apgar score <9 (OR: 0.9; 0.4–2.3), postpartum hospital stay (OR: 0.9; 0.5–1.7), or neonatal intensive care unit admission (OR: 1.6; 0.4–8.6). In conclusion, this study did not find an effect of SARS-CoV-2 infection or COVID-19 vaccination during pregnancy on any of the studied neonatal outcomes among a general Dutch, largely vaccinated, population. Together with data from other studies, this supports the safety of COVID-19 vaccination during pregnancy.

Extraintestinal pathogenic Escherichia coli (ExPEC) causes invasive E. coli disease (IED), including bacteraemia and (uro)sepsis, resulting in a high disease burden, especially among older adults. This study describes the epidemiology of IED in England (2013–2017) by combining laboratory surveillance and clinical data. A total of 191 612 IED cases were identified. IED incidence increased annually by 4.4–8.2% across all ages and 2.8–7.6% among adults ≥60 years of age. When laboratory-confirmed urosepsis cases without a positive blood culture were included, IED incidence in 2017 reached 149.4/100 000 person-years among all adults and 368.4/100 000 person-years among adults ≥60 years of age. Laboratory-confirmed IED cases were identified through E. coli-positive blood samples (55.3%), other sterile site samples (26.3%), and urine samples (16.6%), with similar proportions observed among adults ≥60 years of age. IED-associated case fatality rates ranged between 11.8–13.2% among all adults and 13.1–14.7% among adults ≥60 years of age. This study reflects the findings of other published studies and demonstrates IED constitutes a major and growing global health concern disproportionately affecting the older adult population. The high case fatality rates observed despite available antibiotic treatments emphasize the growing urgency for effective intervention strategies. The burden of urosepsis due to E. coli is likely underestimated and requires additional investigation.

In 2023, Bangladesh experienced its largest and deadliest outbreak of the Dengue virus (DENV), reporting the highest-ever recorded annual cases and deaths. Historically, most of the cases were recorded in the capital city, Dhaka. We aimed to characterize the geographical transmission of DENV in Bangladesh. From 1 January–31 December 2023, we extracted and analyzed daily data on dengue cases and deaths from the Management Information System of the Ministry of Health and Family Welfare. We performed a generalized linear mixed model to identify the associations between division-wise daily dengue counts and various geographical and meteorological covariates. The number of dengue cases reported in 2023 was 1.3 times higher than the total number recorded in the past 23 years (321,179 vs. 244,246), with twice as many deaths than the total fatalities recorded over the past 23 years (1705 vs. 849). Of the 1,705 deaths in 2023, 67.4% (n = 1,015) died within one day after hospital admission. The divisions southern to Dhaka had a higher dengue incidence/1000 population (2.30 vs. 0.50, p <0.01) than the northern divisions. Festival-related travel along with meteorological factors and urbanization are likely to have contributed to the shift of dengue from Dhaka to different districts in Bangladesh.

As astroviral infection rapidly increased in the summer of 2022 in Korea, this study aimed to determine the cause and genotype of astroviruses during this period. From January to December 2022, we tested 43,312 stool samples from patients with acute gastroenteritis utilizing multiplex PCR to detect HAstV. For the HAstV-positive samples, we determined the genotypes of the HAstVs by PCR and sequencing. The monthly positive rate from 2015 to 2022 showed a notable and abrupt increase of HAstV infection between June and August 2022, peaking at 9.8% in July 2022. The annual positivity rate of HAstV remained at 2–3% between 2015 and 2019, and then decreased to 0.5% in 2020, followed by an increase to 1.5% in 2021 and 3.6% in 2022.The genotyped astroviruses in 2022 were all identified as HAstV-1 type, and the nucleotide identity% among them was >99%. The GenBank accession number for the strain genetically closest to the strains identified in our study was ON571597.1, which was HAstV-1 isolated from Pingtan in 2019. Our results provide recent epidemiological data on HAstVs in Korea. The decline and surge in astrovirus positivity in recent years may be related to the COVID-19 pandemic.

Group B streptococcus (GBS) is a major global cause of neonatal, infant, and maternal infections. In Japan, national guidelines based on Centers for Disease Control and Prevention recommendations mandate culture-based screening and intrapartum antibiotic prophylaxis (IAP) for GBS-positive pregnant women. Despite initial reductions in GBS infections, the incidence has plateaued, and there are notable limitations in current prevention methods. Approximately 15% of pregnant women are not screened for GBS, and intermittent colonization undermines screening accuracy, contributing to early-onset disease. IAP does not prevent late-onset disease, the incidence of which is increasing in Japan. This study reviewed maternal and neonatal GBS colonization using polymerase chain reaction, evaluated capsular type distributions, and explored late-onset disease infection routes. Among 525 mother-neonate pairs, the study found a higher detection rate of GBS via polymerase chain reaction compared to culture methods and identified significant discrepancies between antepartum and intrapartum colonization. GBS was detected in 3.5% of neonates from initially negative mothers at 4 days of age. Capsular types varied between mothers and neonates, indicating potential horizontal transmission. This study underscores the need for improved rapid diagnostic tests and highlights the potential of maternal GBS vaccination as a future prevention strategy.