Bacterial dysentery (BD) brings a major disease burden to developing countries. Exploring the influence of temperature and its interaction with other meteorological factors on BD is significant for the prevention and early warning of BD in the context of climate change. Daily BD cases and meteorological data from 2008 to 2018 were collected in all nine prefecture-level cities in Jilin Province. A one-stage province-level model and a two-stage city-specific multivariate meta-pooled level distributed lag non-linear model were established to explore the correlation between temperature and BD, then the weather-stratified generalised additive model was used to test the interaction. During the study period, a total of 26 971 cases of BD were developed. The one-stage and two-stage cumulative dose-response ‘J’ curves overlapped, and results showed a positive correlation between temperature and BD with a 1–6 days lag effect. Age group ⩾5 years was found to be more sensitive to the effects. Moreover, there was a significant interaction between temperature, humidity and precipitation (P = 0.004, 0.002, respectively) on BD under high temperature (>0 °C), reminding residents and policymakers to pay attention to the prevention of BD in situations with both high temperature and humidity, high temperature and precipitation during the temperate monsoon climate.

In extensive cohort studies, the ascertainment of covariate information on all individuals can be challenging. In hospital epidemiology, an additional issue is often the time-dependency of the exposure of interest. We revisit and compare two sampling designs constructed for rare time-dependent exposures and possibly common outcomes – the nested exposure case-control design and exposure density sampling. Both designs enable efficient hazard ratio estimation by sampling all exposed individuals but only a small fraction of the unexposed ones. Moreover, they account for time-dependent exposure to avoid immortal time bias. We evaluate and compare their performance using data of patients hospitalised in the neuro-intensive care unit at the Burdenko Neurosurgery Institute in Moscow, Russia. Three different types of hospital-acquired infections with different prevalence are considered. Additionally, inflation factors, a primary performance measure, are discussed. We enhance both designs to allow for a competitive analysis of combined and competing endpoints compared to the full cohort approach while substantially reducing the amount of necessary information. Nonetheless, exposure density sampling outperforms the nested exposure case-control design concerning efficiency and accuracy in most considered settings.

We investigated likelihood to vaccinate and reasons for and against accepting a coronavirus disease 2019 (COVID-19) vaccine among adult residents of Finland. Vaccine acceptance declined from 70% in April to 64% in December 2020. Complacency and worry about side effects were main reasons against vaccination while concern about severe disease was a strong motive for vaccination. Convenience of vaccination and recommendations by healthcare workers were identified as enablers for vaccination among those aged under 50 years. Understanding barriers and enablers behind vaccine acceptance is decisive in ensuring a successful implementation of COVID-19 vaccination programmes, which will be key to ending the pandemic.

In August 2017, a cluster of four persons infected with genetically related strains of Shiga toxin-producing Escherichia coli (STEC) O157:H7 was identified. These strains possessed the Shiga toxin (stx) subtype stx2a, a toxin type known to be associated with severe clinical outcome. One person died after developing haemolytic uraemic syndrome. Interviews with cases revealed that three of the cases had been exposed to dogs fed on a raw meat-based diet (RMBD), specifically tripe. In two cases, the tripe had been purchased from the same supplier. Sampling and microbiological screening of raw pet food was undertaken and indicated the presence of STEC in the products. STEC was isolated from one sample of raw tripe but was different from the strain causing illness in humans. Nevertheless, the detection of STEC in the tripe provided evidence that raw pet food was a potential source of human STEC infection during this outbreak. This adds to the evidence of raw pet food as a risk factor for zoonotic transmission of gastrointestinal pathogens, which is widely accepted for Salmonella, Listeria and Campylobacter spp. Feeding RMBD to companion animals has recently increased in popularity due to the belief that they provide health benefits to animals. Although still rare, an increase in STEC cases reporting exposure to RMBDs was detected in 2017. There has also been an increased frequency of raw pet food incidents in 2017, suggesting an increasing trend in potential risk to humans from raw pet food. Recommendations to reduce the risk of infection included improved awareness of risk and promotion of good hygiene practices among the public when handling raw pet food.

The role of the Eurasian badger (Meles meles) as a wildlife host has complicated the management of bovine tuberculosis (bTB) in cattle. Badger ranging behaviour has previously been found to be altered by culling of badgers and has been suggested to increase the transmission of bTB either among badgers or between badgers and cattle. In 2014, a five-year bTB intervention research project in a 100 km2 area in Northern Ireland was initiated involving selective removal of dual path platform (DPP) VetTB (immunoassay) test positive badgers and vaccination followed by release of DPP test negative badgers (‘Test and Vaccinate or Remove’). Home range sizes, based on position data obtained from global positioning system collared badgers, were compared between the first year of the project, where no DPP test positive badgers were removed, and follow-up years 2–4 when DPP test positive badgers were removed. A total of 105 individual badgers were followed over 21 200 collar tracking nights. Using multivariable analyses, neither annual nor monthly home ranges differed significantly in size between years, suggesting they were not significantly altered by the bTB intervention that was applied in the study area.

Since 2015, the incidence of invasive meningococcal disease (IMD) caused by serogroup W (MenW) has increased in Sweden, due to the introduction of the 2013 strain belonging to clonal complex 11. The aim of this study was to describe the clinical presentation of MenW infections, in particular the 2013 strain, including genetic associations. Medical records of confirmed MenW IMD cases in Sweden during the years 1995–2019 (n = 113) were retrospectively reviewed and the clinical data analysed according to strain. Of all MenW patients, bacteraemia without the focus of infection was seen in 44%, bacteraemic pneumonia in 26%, meningitis in 13% and epiglottitis in 8%, gastrointestinal symptoms in 48% and 4% presented with petechiae. Phylogenetic analysis was used for possible links between genetic relationship and clinical picture. The 2013 strain infections, particularly in one cluster, were associated with more severe disease compared with other MenW infections. The patients with 2013 strain infections (n = 68) were older (52 years vs. 25 years for other strains), presented more often with diarrhoea as an atypical presentation (P = 0.045) and were more frequently admitted for intensive care (P = 0.032). There is a risk that the atypical clinical presentation of MenW infections, with predominantly gastrointestinal or respiratory symptoms rather than neck stiffness or petechiae, may lead to delay in life-saving treatment.

Coccidioidomycosis is endemic in the Southwestern United States. Disseminated infection can be life-threatening and is responsible for hospitalisation and significant healthcare resource utilisation. There are limited data evaluating factors associated with hospitalisation for coccidioidomycosis. We conducted a cross-sectional study to assess incidence and factors associated with coccidioidomycosis-associated hospitalisation in California and Arizona. We analysed hospital discharge data obtained from the State Inpatient Dataset for California and Arizona between 2005 and 2011 and performed multivariable logistic regression examining factors associated with coccidioidomycosis-associated hospitalisation. During our time frame, we found 23 758 coccidioidomycosis-associated hospitalisations. Coccidioidomycosis incidence was over sixfold higher in Arizona compared to California (198.9 vs. 29.6/100 000 person-years). In our multivariable model, coccidioidomycosis-associated hospitalisation was associated with age group 40–49 years (referent group: age 18–29 years, adjusted odds ratio (aOR) = 1.50 (95% confidence interval (CI) 1.43–1.59)), African American race (referent group: Caucasian, aOR = 1.98 (95% CI 1.89–2.06)), residing in a large rural town (referent group: urban area, aOR = 2.28 (95% CI 2.19–2.39)), uncomplicated diabetes (aOR = 1.47 (95% CI 1.41–1.52)) chronic obstructive pulmonary disease (aOR = 1.59 (95% CI 1.54–1.65)) and higher number of comorbidities (aOR = 1.02 (95% CI 1.02–1.03) for each point in the Elixhauser score). Identifying persons at highest risk for hospitalisation with coccidioidomycosis may be helpful for future prevention efforts.

Studies evaluating the occurrence of enteropathogenic bacteria in urban rats (Rattus spp.) are scarce worldwide, specifically in the urban environments of tropical countries. This study aims to estimate the prevalence of diarrhoeagenic Escherichia coli (DEC) and Salmonella spp. with zoonotic potential in urban slum environments. We trapped rats between April and June 2018 in Salvador, Brazil. We collected rectal swabs from Rattus spp., and cultured for E. coli and Salmonella spp., and screened E. coli isolates by polymerase chain reaction to identify pathotypes. E. coli were found in 70% of Rattus norvegicus and were found in four Rattus rattus. DEC were isolated in 31.3% of the 67 brown rats (R. norvegicus). The pathotypes detected more frequently were shiga toxin E. coli in 11.9%, followed by atypical enteropathogenic E. coli in 10.4% and enteroinvasive E. coli in 4.5%. From the five black rats (R. rattus), two presented DEC. Salmonella enterica was found in only one (1.4%) of 67 R. norvegicus. Our findings indicate that both R. norvegicus and R. rattus are host of DEC and, at lower prevalence, S. enterica, highlighting the importance of rodents as potential sources of pathogenic agents for humans.

During the first wave of the severe acute respiratory syndrome-coronavirus-2 epidemic in the Netherlands, notifications consisted mostly of patients with relatively severe disease. To enable real-time monitoring of the incidence of mild coronavirus disease 2019 (COVID-19) – for which medical consultation might not be required – the Infectieradar web-based syndromic surveillance system was launched in mid-March 2020. Our aim was to quantify associations between Infectieradar participant characteristics and the incidence of self-reported COVID-19-like illness. Recruitment for this cohort study was via a web announcement. After registering, participants completed weekly questionnaires, reporting the occurrence of a set of symptoms. The incidence rate of COVID-19-like illness was estimated and multivariable Poisson regression used to estimate the relative risks associated with sociodemographic variables, lifestyle factors and pre-existing medical conditions. Between 17 March and 24 May 2020, 25 663 active participants were identified, who reported 7060 episodes of COVID-19-like illness over 131 404 person-weeks of follow-up. The incidence rate declined over the analysis period, consistent with the decline in notified cases. Male sex, age 65+ years and higher education were associated with a significantly lower COVID-19-like illness incidence rate (adjusted rate ratios (RRs) of 0.80 (95% CI 0.76–0.84), 0.77 (0.70–0.85), 0.84 (0.80–0.88), respectively) and the baseline characteristics ever-smoker, asthma, allergies, diabetes, chronic lung disease, cardiovascular disease and children in the household were associated with a higher incidence (RRs of 1.11 (1.04–1.19) to 1.69 (1.50–1.90)). Web-based syndromic surveillance has proven useful for monitoring the temporal trends in, and risk factors associated with, the incidence of mild disease. Increased relative risks observed for several patient factors could reflect a combination of exposure risk, susceptibility to infection and propensity to report symptoms.

Population-based seroprevalence studies on coronavirus disease 2019 (COVID-19) in low- and middle-income countries are lacking. We investigated the seroprevalence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antibodies in Sergipe state, Northeast Brazil, using rapid IgM−IgG antibody test and fluorescence immunoassay. The seroprevalence was 9.3% (95% CI 8.5–10.1), 10.2% (95% CI 9.2–11.3) for women and 7.9% (IC 95% 6.8–9.1) for men (P = 0.004). We found a decline in the prevalence of SARS-CoV-2 antibodies according to age, but the differences were not statistically significant: 0–19 years (9.9%; 95% CI 7.8–12.5), 20–59 years (9.3%; 95% CI 8.4–10.3) and ≥60 years (9.0%; 95% CI 7.5–10.8) (P = 0.517). The metropolitan area had a higher seroprevalence (11.7%, 95% CI 10.3–13.2) than outside municipalities (8.0%, 95% CI 7.2–8.9) (P < 0.001). These findings highlight the importance of serosurveillance to estimate the real impact of the COVID-19 outbreak and thereby provide data to better understand the spread of the virus, as well as providing information to guide stay-at-home measures and other policies. In addition, these results may be useful as basic data to follow the progress of COVID-19 outbreak as social restriction initiatives start to be relaxed in Brazil.

Varicella poses an occupational risk and a nosocomial risk for susceptible healthcare personnel and patients, respectively. Patients with varicella are thought to be infectious from 1 to 2 days before rash onset until all lesions are crusted, typically 4–7 days after onset of rash. We searched Medline, Embase, Cochrane Library and CINAHL databases to assess evidence of varicella-zoster virus (VZV) transmission before varicella rash onset. Few articles (7) contributed epidemiologic evidence; no formal studies were found. Published articles reported infectiousness at variable intervals before rash onset, between <1 day to 4 days prior to rash, with 1–2 patients for each interval. Laboratory assessment of transmission before rash was also limited (10 articles). No culture-positive results were reported. VZV DNA was identified by PCR before rash onset in only one study however, PCR does not indicate infectivity of the virus. Based on available medical literature, VZV transmission before rash onset seems unlikely, although the possibility of pre-rash, respiratory transmission cannot be entirely ruled out.

The coronavirus disease 2019 (COVID-19) vaccine was launched in India on 16 January 2021, prioritising health care workers which included medical students. We aimed to assess vaccine hesitancy and factors related to it among medical students in India. An online questionnaire was filled by 1068 medical students across 22 states and union territories of India from 2 February to 7 March 2021. Vaccine hesitancy was found among 10.6%. Concern regarding vaccine safety and efficacy, lack of awareness regarding their eligibility for vaccination and lack of trust in government agencies predicted COVID-19 vaccine hesitancy among medical students. On the other hand, the presence of risk perception regarding themselves being affected with COVID-19 reduced vaccine hesitancy as well as hesitancy in participating in COVID-19 vaccine trials. Vaccine-hesitant students were more likely to derive information from social media and less likely from teachers at their medical colleges. Choosing between the two available vaccines (Covishield and Covaxin) was considered important by medical students both for themselves and for their future patients. Covishield was preferred to Covaxin by students. Majority of those willing to take the COVID-19 vaccine felt that it was important for them to resume their clinical posting, face-to-face classes and get their personal life back on track. Around three-fourths medical students viewed that COVID-19 vaccine should be made mandatory for both health care workers and international travellers. Prior adult vaccination did not have an effect on COVID-19 vaccine hesitancy. Targeted awareness campaigns, regulatory oversight of vaccine trials and public release of safety and efficacy data and trust building activities could further reduce COVID-19 vaccine hesitancy among medical students.

Hong Kong is an intermediate tuberculosis (TB) burden city in Asia Pacific with slow decline of case notification in the last decade. By 24-loci mycobacterial interspersed repetitive units – variable number of tandem repeats genotyping, we examined 534 Mycobacterium tuberculosis isolates collected from culture-positive hospitalised TB patients in a 1.7 million population geographic region in the city. Overall, 286 (75%) were classified as Beijing genotype, of which 216 (76%) and 59 (21%) belonged to modern and ancient sub-lineage, respectively. Only two cases were genetically clustered while spatial clustering was absent. Male gender, permanent residency in Hong Kong and born in Hong Kong or Mainland China were associated with Beijing genotype. The high prevalence of Beijing modern lineage was similar to that in East Asia, which reflected the pattern resulting from population migration. The paucity of clustering suggested that reactivation accounted for most of the TB disease cases, which was and echoed by observation that half were 60 years old or above, and the presence of co-morbid medical conditions. The predominance of reactivation TB cases in intermediate burden localities implies that the detection and control of latent TB infection would be the major challenge in achieving TB elimination.

Human papillomavirus (HPV) has been confirmed as the causative agent for cervical cancer. In this study, a total of 301 880 women were recruited from four different regions of Western China, with 301 880 exfoliated cervical cell samples collected from women for DNA isolation and purification. The HPV genotype was tested by polymerase chain reaction. The overall HPV prevalence rate, high-risk (HR) HPV infection rate, low-risk (LR) HPV infection rate and mixed HPV infection rate was 18.24%, 79.14%, 12.56% and 8.30%, respectively. The four most common HR HPV subtypes were HPV-52, 16, 58 and 53, which accounted for 20.49%, 19.93%, 14.54% and 10.01%, respectively. In LR HPV genotype, HPV-6 ranked the highest (28.17%), followed by HPV-81 (9.09%) and HPV-11 (3.78%). HPV genotype subgroup analysis also showed that single-type infection was the most common (77.26%) among HPV-positive individuals. Among multi-infection genotypes, double infection was the most common with frequencies of 76.04%. The overall prevalence of HPV is high in Western China, whose distribution demonstrates different patterns across different ages and regions. Viral genotypes HPV 53, 6 were frequently detected in this population, which is worth of significant clinical attention.

Brucellosis is one of the most serious and widespread zoonotic diseases, which seriously threatens human health and the national economy. This study was based on the T/B dominant epitopes of Brucella outer membrane protein 22 (Omp22), outer membrane protein 19 (Omp19) and outer membrane protein 28 (Omp28), with bioinformatics methods to design a safe and effective multi-epitope vaccine. The amino acid sequences of the proteins were found in the National Center for Biotechnology Information (NCBI) database, and the signal peptides were predicted by the SignaIP-5.0 server. The surface accessibility and hydrophilic regions of proteins were analysed with the ProtScale software and the tertiary structure model of the proteins predicted by I-TASSER software and labelled with the UCSF Chimera software. The software COBEpro, SVMTriP and BepiPred were used to predict B cell epitopes of the proteins. SYFPEITHI, RANKpep and IEDB were employed to predict T cell epitopes of the proteins. The T/B dominant epitopes of three proteins were combined with HEYGAALEREAG and GGGS linkers, and carriers sequences linked to the N- and C-terminus of the vaccine construct with the help of EAAAK linkers. Finally, the tertiary structure and physical and chemical properties of the multi-epitope vaccine construct were analysed. The allergenicity, antigenicity and solubility of the multi-epitope vaccine construct were 7.37–11.30, 0.788 and 0.866, respectively. The Ramachandran diagram of the mock vaccine construct showed 96.0% residues within the favoured and allowed range. Collectively, our results showed that this multi-epitope vaccine construct has a high-quality structure and suitable characteristics, which may provide a theoretical basis for future laboratory experiments.

The novel coronavirus identified as severe acute respiratory syndrome-coronavirus-2 causes acute respiratory distress syndrome (ARDS). Our aim in this study is to assess the incidence of life-threatening complications like pneumothorax, haemothorax, pneumomediastinum and subcutaneous emphysema, probable risk factors and effect on mortality in coronavirus disease-2019 (COVID-19) ARDS patients treated with mechanical ventilation (MV). Data from 96 adult patients admitted to the intensive care unit with COVID-19 ARDS diagnosis from 11 March to 31 July 2020 were retrospectively assessed. A total of 75 patients abiding by the study criteria were divided into two groups as the group developing ventilator-related barotrauma (BG) (N = 10) and the group not developing ventilator-related barotrauma (NBG) (N = 65). In 10 patients (13%), barotrauma findings occurred 22 ± 3.6 days after the onset of symptoms. The mortality rate was 40% in the BG-group, while it was 29% in the NBG-group with no statistical difference identified. The BG-group had longer intensive care admission duration, duration of time in prone position and total MV duration, with higher max positive end-expiratory pressure (PEEP) levels and lower min pO2/FiO2 levels. The peak lactate dehydrogenase levels in blood were higher by statistically significant level in the BG-group (P < 0.05). The contribution of MV to alveolar injury caused by infection in COVID-19 ARDS patients may cause more frequent barotrauma compared to classic ARDS and this situation significantly increases the MV and intensive care admission durations of patients. In terms of reducing mortality and morbidity in these patients, MV treatment should be carefully maintained within the framework of lung-protective strategies and the studies researching barotrauma pathophysiology should be increased.

Susceptible S-Infected I-Recovered R-Death D (SIRD) compartmental models are often used for modelling of infectious diseases. On the basis of the analogy between SIRD and compartmental models in hydrology, this study makes mathematical formulations developed in hydrology available for modelling in epidemiology. We adapt the Hayami model solution of the diffusive wave equation generally used in hydrological modelling to compartmental I–R–D models in epidemiology by simulating the relationships between the number of infectious I(t), the number of recoveries R(t) and the number of deaths D(t). The Hayami model is easy-to-use, robust and parsimonious. We compare the empirical one-parameter exponential model usually used in SIRD models to the two-parameter Hayami model. Applications were implemented on the recent Covid-19 pandemic. The application on data from 24 countries shows that both models give comparable performances for modelling the I–D relationship. However, for modelling the I–R relationship and the active cases, the exponential model gives fair performances whereas the Hayami model substantially improves the model performances. The Hayami model also presents the advantage that its parameters can be easily estimated from the analysis of the data distributions of I(t), R(t) and D(t). The Hayami model is parsimonious with only two parameters which are useful to compare the temporal evolution of recoveries and deaths in different countries based on different contamination rates and recoveries strategies. This study highlights the interest of knowledge transfer between different scientific disciplines in order to model different processes.

The study aims to estimate and compare the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence, the fraction of asymptomatic or subclinical infections in the population, determine the demographic risk factors and analyse the antibody development at different time points among adults in Bhubaneswar city, India. This was a serial three-round cross-sectional, community-based study where participants were selected from the residents of Bhubaneswar city using multi-stage random sampling. Blood samples were collected during household visits along with demographic and clinical data from every participant. Total anti-SARS-CoV-2 antibody present in serum was assessed using the electro-chemiluminescence immunoassay platform. Temporal comparisons of the community seroprevalence were performed against the detected number of cumulative cases, active cases, recoveries and deaths. A total of 3693 participants were enrolled in this study with a cumulative non-response rate of 18.33% in all the three rounds. The gender-weighted seroprevalence for the city in the first round was 1.55% (95% confidence interval (CI) 0.84–2.58), second round was 5.27% (95% CI 4.13–6.59) and in the third round was 49.04% (95% CI 46.39–51.68). In the first round, the seroprevalence was found to be highest in the elderly population, whereas the seroprevalence for the second and third phases was highest in the age group of 30–39 years. Seroprevalence showed an increasing trend over the three time periods, with the highest seropositivity rates among individuals sampled between 16 and 18 September 2020. By the third round, 93.93% of those who had previously been tested positive by real-time reverse transcription polymerase chain reaction had seroconversion and 46.57% of those who had been tested negative also showed seroconversion. Infection to case ratio during first round was 27.05, for second round and third round it was 5.62 and 17.91, respectively.

The novel coronavirus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), is the causative agent of the 2020 worldwide coronavirus pandemic. Antibody testing is useful for diagnosing historic infections of a disease in a population. These tests are also a helpful epidemiological tool for predicting how the virus spreads in a community, relating antibody levels to immunity and for assessing herd immunity. In the present study, SARS-CoV-2 viral proteins were recombinantly produced and used to analyse serum from individuals previously exposed, or not, to SARS-CoV-2. The nucleocapsid (Npro) and spike subunit 2 (S2Frag) proteins were identified as highly immunogenic, although responses to the former were generally greater. These two proteins were used to develop two quantitative enzyme-linked immunosorbent assays (ELISAs) that when used in combination resulted in a highly reliable diagnostic test. Npro and S2Frag-ELISAs could detect at least 10% more true positive coronavirus disease-2019 (COVID-19) cases than the commercially available ARCHITECT test (Abbott). Moreover, our quantitative ELISAs also show that specific antibodies to SARS-CoV-2 proteins tend to wane rapidly even in patients who had developed severe disease. As antibody tests complement COVID-19 diagnosis and determine population-level surveillance during this pandemic, the alternative diagnostic we present in this study could play a role in controlling the spread of the virus.