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This study aims at providing estimates on the transmission risk of SARS-CoV-2 in schools and day-care centres. We calculated secondary attack rates (SARs) using individual-level data from state-wide mandatory notification of index cases in educational institutions, followed by contact tracing and PCR-testing of high-risk contacts. From August to December 2020, every sixth of overall 784 independent index cases was associated with secondary cases in educational institutions. Monitoring of 14 594 institutional high-risk contacts (89% PCR-tested) of 441 index cases during quarantine revealed 196 secondary cases (SAR 1.34%, 0.99–1.78). SARS-CoV-2 infection among high-risk contacts was more likely around teacher-indexes compared to student-/child-indexes (incidence rate ratio (IRR) 3.17, 1.79–5.59), and in day-care centres compared to secondary schools (IRR 3.23, 1.76–5.91), mainly due to clusters around teacher-indexes in day-care containing a higher mean number of secondary cases per index case (142/113 = 1.26) than clusters around student-indexes in schools (82/474 = 0.17). In 2020, SARS-CoV-2 transmission risk in educational settings was low overall, but varied strongly between setting and role of the index case, indicating the chance for targeted intervention. Surveillance of SARS-CoV-2 transmission in educational institutions can powerfully inform public health policy and improve educational justice during the pandemic.

To assess the current dynamic of an epidemic it is central to collect information on the daily number of newly diseased cases. This is especially important in real-time surveillance, where the aim is to gain situational awareness, e.g., if cases are currently increasing or decreasing. Reporting delays between disease onset and case reporting hamper our ability to understand the dynamic of an epidemic close to now when looking at the number of daily reported cases only. Nowcasting can be used to adjust daily case counts for occurred-but-not-yet-reported events. Here, we present a novel application of nowcasting to data on the current COVID–19 pandemic in Bavaria. It is based on a hierarchical Bayesian model that considers changes in the reporting delay distribution over time and associated with the weekday of reporting. Furthermore, we present a way to estimate the effective time-dependent case reproduction number Re(t) based on predictions of the nowcast. The approaches are based on previously published work, that we considerably extended and adapted to the current task of nowcasting COVID–19 cases. We provide methodological details of the developed approach, illustrate results based on data of the current epidemic, and evaluate the model based on synthetic and retrospective data on COVID–19 in Bavaria. Results of our nowcasting are reported to the Bavarian health authority and published on a webpage on a daily basis (https://corona.stat.uni-muenchen.de/). Code and synthetic data for the analysis is available from https://github.com/FelixGuenther/nc_covid19_bavaria and can be used for adaptions of our approach to different data.

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.

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) led to a significant disease burden and disruptions in health systems. We describe the epidemiology and transmission characteristics of early coronavirus disease 2019 (COVID-19) cases in Bavaria, Germany. Cases were reverse transcription polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections, reported from 20 January−19 March 2020. The incubation period was estimated using travel history and date of symptom onset. To estimate the serial interval, we identified pairs of index and secondary cases. By 19 March, 3546 cases were reported. A large proportion was exposed abroad (38%), causing further local transmission. Median incubation period of 256 cases with exposure abroad was 3.8 days (95%CI: 3.5–4.2). For 95% of infected individuals, symptom onset occurred within 10.3 days (95%CI: 9.1–11.8) after exposure. The median serial interval, using 53 pairs, was 3.5 days (95%CI: 3.0–4.2; mean: 3.9, s.d.: 2.2). Travellers returning to Germany had an important influence on the spread of SARS-CoV-2 infections in Bavaria in early 2020. Especially in times of low incidence, public health agencies should identify holiday destinations, and areas with ongoing local transmission, to monitor potential importation of SARS-CoV-2 infections. Travellers returning from areas with ongoing community transmission should be advised to quarantine to prevent re-introductions of COVID-19.

Estimating the case fatality ratio (CFR) for COVID-19 is an important aspect of public health. However, calculating CFR accurately is problematic early in a novel disease outbreak, due to uncertainties regarding the time course of disease and difficulties in diagnosis and reporting of cases. In this work, we present a simple method for calculating the case fatality ratio using only public case and death data over time by exploiting the correspondence between the time distributions of cases and deaths. The time-shifted distribution (TSD) analysis generates two parameters of interest: the delay time between reporting of cases and deaths and the case fatality ratio. These parameters converge reliably over time once the exponential growth phase has finished. Analysis is performed for early COVID-19 outbreaks in many countries, and we discuss corrections to CFR values using excess-death and seroprevalence data to estimate the infection fatality ratio (IFR). While CFR values range from 0.2-20% in different countries, estimates for IFR are mostly around 0.5-0.8% for countries that experienced moderate outbreaks and 1-3% for severe outbreaks. The simplicity and transparency of TSD analysis enhance its usefulness in characterizing a new disease as well as the state of the health and reporting systems.

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.

The outbreak of the novel coronavirus severe acute respiratory syndrome-coronavirus-2 has raised major health policy questions and dilemmas. Whilst respiratory droplets are believed to be the dominant transmission mechanisms, indirect transmission may also occur through shared contact of contaminated common objects that is not directly curtailed by a lockdown. The conditions under which contaminated common objects may lead to significant spread of coronavirus disease 2019 during lockdown and its easing is examined using the susceptible-exposed-infectious-removed model with a fomite term added. Modelling the weekly death rate in the UK, a maximum-likelihood analysis finds a statistically significant fomite contribution, with 0.009 ± 0.001 (95% CI) infection-inducing fomites introduced into the environment per day per infectious person. Post-lockdown, comparison with the prediction of a corresponding counterfactual model with no fomite transmission suggests fomites, through enhancing the overall transmission rate, may have contributed to as much as 25% of the deaths following lockdown. It is suggested that adding a fomite term to more complex simulations may assist in the understanding of the spread of the illness and in making policy decisions to control it.

We analysed associations between exposure to nightlife businesses and severe acute respiratory syndrome coronavirus 2 PCR test results at a tertiary hospital in Tokyo between March and April 2020. A nightlife group was defined as those who had worked at or visited the businesses. We included 1517 individuals; 196 (12.9%) were categorised as the nightlife group. After propensity score matching, the proportion of positive PCR tests in the nightlife group was significantly higher than that in the non-nightlife group (nightlife, 63.8%; non-nightlife, 23.0%; P < 0.001). An inclusive approach to mitigate risks related to the businesses needs to be identified.

Meningococcal carriage dynamics drive patterns of invasive disease. The distribution of carriage by age has been well described in Europe, but not in the African meningitis belt, a region characterised by frequent epidemics of meningitis. We aimed to estimate the age-specific prevalence of meningococcal carriage by season in the African meningitis belt. We searched PubMed, Web of Science, the Cochrane Library and grey literature for papers reporting carriage of Neisseria meningitidis in defined age groups in the African meningitis belt. We used a mixed-effects logistic regression to model meningococcal carriage prevalence as a function of age, adjusting for season, location and year. Carriage prevalence increased from low prevalence in infants (0.595% in the rainy season, 95% CI 0.482–0.852%) to a broad peak at age 10 (1.94%, 95% CI 1.87–2.47%), then decreased in adolescence. The odds of carriage were significantly increased during the dry season (OR 1.5 95% CI 1.4–1.7) and during outbreaks (OR 6.7 95% CI 1.6–29). Meningococcal carriage in the African meningitis belt peaks at a younger age compared to Europe. This is consistent with contact studies in Africa, which show that children 10–14 years have the highest frequency of contacts. Targeting older children in Africa for conjugate vaccination may be effective in reducing meningococcal transmission.

Another large outbreak of mumps occurred in Lothian from October 2017, which coincided with the commencement of the higher education term. During this period 324 cases were notified, most of whom were aged 18–22 years old. Although previous outbreaks had a focus in student populations, 43% of current cases reported that they were not a student. There has been increases in private student housing where students from all universities live, which may have contributed to the wide spread of the outbreak and complicated outbreak control. Information on vaccination status was available for 244 cases (75%), of whom the majority (75.8%) reported having two MMR doses. To investigate potential waning vaccine immunity the mean length of time since last mumps containing vaccine was calculated as 14.3 years. The outbreak was declared over in May 2018 after case numbers returned to background levels. This outbreak highlighted that mumps outbreaks occur cyclically coinciding with new cohorts of susceptible students entering the Lothian population. The lessons from this outbreak are to encourage students to have two MMR doses and also be prepared for mumps outbreaks in the near future. In future outbreaks the utility of a third MMR for outbreak control could be examined.

Encephalitis causes high morbidity and mortality. An incidence of 4.3 cases of encephalitis/100 000 population has been reported in the UK. We performed a retrospective evaluation of the diagnosis and management of adults admitted to hospital with a clinical diagnosis of encephalitis/meningoencephalitis. Clinical, laboratory and radiological data were collated from electronic records. Thirty-six patients, median age 55 years and 24 (67%) male were included. The aetiology was confirmed over nine months in 25 (69%) of whom 16 were infections (six viral, seven bacterial, two parasitic and one viral and parasitic co-infection); 7 autoimmune; 1 metabolic and 1 neoplastic. Of 24 patients with fever, 15 (63%) had an infection. The median time to computed topography, magnetic resonance imaging and electroencephalography (EEG) was 1, 8 and 3 days respectively. Neuroimaging was abnormal in 25 (69%) and 17 (89%) had abnormal EEGs. Only 19 (53%) received aciclovir treatment. Six (17%) made good recoveries, 16 (44%) had moderate disability, 8 (22%) severe disability and 6 (17%) died. Outcomes were worse for those with an infectious cause. In summary, a diagnosis was made in 69.4% of patients admitted with encephalitis/meningoencephalitis. Autoimmune causes are important to consider at an early stage due to a successful response to treatment. Only 53% of patients received aciclovir on admission. Neuroimaging and EEG studies were delayed. The results of this work resulted in further developing the clinical algorithm for managing these patients.

SummaryWe used social network analysis (SNA) to study the novel coronavirus (COVID-19) outbreak in Karnataka, India, and assess the potential of SNA as a tool for outbreak monitoring and control. We analyzed contact tracing data of 1147 Covid-19 positive cases (mean age 34.91 years, 61.99% aged 11–40, 742 males), anonymized and made public by the government. We used software tools Cytoscape and Gephi to create SNA graphics and determine network attributes of nodes (cases) and edges (directed links, determined by contact tracing, from source to target patients). Outdegree was 1–47 for 199 (17.35%) nodes, and betweenness 0.5–87 for 89 (7.76%) nodes. Men had higher mean outdegree and women, higher betweenness. Delhi was the exogenous source of 17.44% cases. Bangalore city had the highest caseload in the state (229, 20%), but comparatively low cluster formation. Thirty-four (2.96%) “super-spreaders” (outdegree≥5) caused 60% of the transmissions. Real-time social network visualization can allow healthcare administrators to flag evolving hotspots and pinpoint key actors in transmission. Prioritizing these areas and individuals for rigorous containment could help minimize resource outlay and potentially achieve a significant reduction in COVID-19 transmission.

We conducted a matched case-control (MCC), test-negative case-control (TNCC) and case-cohort study in 2016 in Lusaka, Zambia, following a mass vaccination campaign. Confirmed cholera cases served as cases in all three study designs. In the TNCC, control-subjects were cases with negative cholera culture and polymerase chain reaction results. Matched controls by age and sex were selected among neighbours of the confirmed cases in the MCC study. For the case-cohort study, we recruited a cohort of randomly selected individuals living in areas considered at-risk of cholera. We recruited 211 suspected cases (66 confirmed cholera cases and 145 non-cholera diarrhoea cases), 1055 matched controls and a cohort of 921. Adjusted vaccine effectiveness of one dose of oral cholera vaccine (OCV) was 88.9% (95% confidence interval (CI) 42.7–97.8) in the MCC study, 80.2% (95% CI: 16.9–95.3) in the TNCC design and 89.4% (95% CI: 64.6–96.9) in the case-cohort study. Three study designs confirmed the short-term effectiveness of single dose OCV. Major healthcare-seeking behaviour bias did not appear to affect our estimates. Most of the protection among vaccinated individuals could be attributed to the direct effect of the vaccine.

Identifying the transmission sources and reservoirs of Streptococcus pneumoniae (SP) is a long-standing question for pneumococcal epidemiology, transmission dynamics, and vaccine policy. Here we use serotype to identify SP transmission and examine acquisitions (in the same household, local community, and county, or of unidentified origin) in a longitudinal cohort of children and adults from the Navajo Nation and the White Mountain Apache American Indian Tribes. We found that adults acquire SP relatively more in the household than other age groups, and children 2–8 years old typically acquire in their own or surrounding communities. Age-specific transmission probability matrices show that transmissions within household were mostly seen from older to younger siblings. Outside the household, children most often transmit to other children in the same age group, showing age-assortative mixing behavior. We find toddlers and older children to be most involved in SP transmission and acquisition, indicating their role as key drivers of SP epidemiology. Although infants have high carriage prevalence, they do not play a central role in transmission of SP compared with toddlers and older children. Our results are relevant to inform alternative pneumococcal conjugate vaccine dosing strategies and analytic efforts to inform optimization of vaccine programs, as well as assessing the transmission dynamics of pathogens transmitted by close contact in general.

SUMMARYAlthough contamination of food can occur at any point from farm to table, restaurant food workers are a common source of foodborne illness. We describe the characteristics of restaurant-associated foodborne disease outbreaks and explore the role of food workers by analysing outbreaks associated with restaurants from 1998 to 2013 reported to the Centers for Disease Control and Prevention's Foodborne Disease Outbreak Surveillance System. We identified 9788 restaurant-associated outbreaks. The median annual number of outbreaks was 620 (interquartile range 618–629). In 3072 outbreaks with a single confirmed aetiology reported, norovirus caused the largest number of outbreaks (1425, 46%). Of outbreaks with a single food reported and a confirmed aetiology, fish (254 outbreaks, 34%) was most commonly implicated, and these outbreaks were commonly caused by scombroid toxin (219 outbreaks, 86% of fish outbreaks). Most outbreaks (79%) occurred at sit-down establishments. The most commonly reported contributing factors were those related to food handling and preparation practices in the restaurant (2955 outbreaks, 61%). Food workers contributed to 2415 (25%) outbreaks. Knowledge of the foods, aetiologies, and contributing factors that result in foodborne disease restaurant outbreaks can help guide efforts to prevent foodborne illness.

Some European countries recently reported an increase in hepatitis E virus genotype 3 (HEV-3) of the subtype 3c. No link between HEV-3 subtypes and severity is established to date. Here, we report that patients infected with HEV-3c were at lower risk of hospitalisation, compared to those infected with HEV-3f, the other main subtype circulating in Belgium.

We compared antibiotic prescribing to older people in different settings to inform antibiotic stewardship interventions. We used data linkage to stratify individuals aged 65 years and over in Northern Ireland, 1st January 2012–31st December 2013, by residence: community dwelling, care home dwelling or ‘transitioned’ if admitted to a care home. The odds of being prescribed an antibiotic by residence were analysed using logistic regression, adjusting for patient demographics and selected medication use (proxy for co-morbidities). Trends in monthly antibiotic prescribing were examined in the 6 months pre- and post-admission to the care home. The odds of being prescribed at least one antibiotic were twofold higher in care homes compared with community dwellers (adjusted odds ratio 2.05, 95% CI 1.93–2.17). There was a proportionate increase of 51.5% in the percentage prescribed an antibiotic on admission, with a monthly average of 23% receiving an antibiotic in the 6 months post admission. While clinical need likely accounts for some of the observed antibiotic prescribing in care homes we cannot rule out more liberal prescribing, given the twofold difference between care home residents and their community dwelling peers having accounted for co-morbidities. The appropriateness of antibiotic prescribing in the care home setting should be examined.

Antimicrobial resistance is a major health threat worldwide as it brings about poorer treatment outcome and places economic burden to the society. This study aims to estimate the annual relative increased in inpatient mortality from antimicrobial resistant (AMR) nosocomial infections (NI) in Thailand. A retrospective cohort study was conducted at Ramathibodi Hospital, Bangkok, Thailand, over 2008–2012. Survival model was used to estimate the hazard ratio of mortality of AMR relative to those patients without resistance (non-AMR) after controlling for nine potential confounders. The majority of NI (73.80%) were caused by AMR bacteria over the study period. Patients in the AMR and non-AMR groups had similar baseline clinical characteristics. Relative to patients in the non-AMR group, the expected hazard ratios of mortality for patients in the AMR group with Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were 1.92 (95% CI 0.10–35.52), 1.25 (95% CI 0.08–20.29), 1.60 (95% CI 0.13–19.10) and 1.84 (95% CI 0.04–95.58), respectively. In the complete absence of AMR bacteria, this study estimated that annually, in Thailand, there would be 111 295 fewer AMR cases and 48 258 fewer deaths.

The disease caused by the influenza virus is a global public health problem due to its high rates of morbidity and mortality. Thus, analysis of the information generated by epidemiological surveillance systems has vital importance for health decision making. A retrospective analysis was performed using data generated by the four molecular diagnostic laboratories of the Mexican Social Security Institute between 2010 and 2016. Demographics, influenza positivity, seasonality, treatment choices and vaccination status analyses were performed for the vaccine according to its composition for each season. In all cases, both the different influenza subtypes and different age groups were considered separately. The circulation of A/H1N1pdm09 (48.7%), influenza A/H3N2 (21.1%), influenza B (12.6%), influenza A not subtyped (11%) and influenza A/H1N1 (6.6%) exhibited well-defined annual seasonality between November and March, and there were significant increases in the number of cases every 2 years. An inadequate use of oseltamivir was determined in 38% of cases, and the vaccination status in general varied between 12.1 and 18.5% depending on the season. Our results provide current information about influenza in Mexico and demonstrate the need to update both operational case definitions and medical practice guidelines to reduce the inappropriate use of antibiotics and antivirals.

Hendra virus (HeV) continues to cause fatal infection in horses and threaten infection in close-contact humans in eastern Australia. Species of Pteropus bats (flying-foxes) are the natural reservoir of the virus. We caught and sampled flying-foxes from a multispecies roost in southeast Queensland, Australia on eight occasions between June 2013 and June 2014. The effects of sample date, species, sex, age class, body condition score (BCS), pregnancy and lactation on HeV antibody prevalence, log-transformed median fluorescent intensity (lnMFI) values and HeV RNA status were assessed using unbalanced generalised linear models. A total of 1968 flying-foxes were sampled, comprising 1012 Pteropus alecto, 742 P. poliocephalus and 214 P. scapulatus. Sample date, species and age class were each statistically associated with HeV RNA status, antibody status and lnMFI values; BCS was statistically associated with HeV RNA status and antibody status. The findings support immunologically naïve sub-adult P. alecto playing an important role in maintaining HeV infection at a population level. The biological significance of the association between BCS and HeV RNA status, and BCS and HeV antibody status, is less clear and warrants further investigation. Contrary to previous studies, we found no direct association between HeV infection and pregnancy or lactation. The findings in P. poliocephalus suggest that HeV exposure in this species may not result in systemic infection and virus excretion, or alternatively, may reflect assay cross-reactivity with another (unidentified) henipavirus.

Gender inequality has severe consequences on public health in terms of delay in diagnosis of pulmonary tuberculosis (PTB). In order to explore gender-related differences in diagnosis delay, a cross-sectional study of 10 686 patients diagnosed with PTB in Yulin from 1 January 2009 to 31 December 2014 was conducted. Diagnosis delay was categorised into ‘short delay’ and ‘long delay’ by four commonly used cut-off points of 14, 30, 60 and 90 days. Logistic regression analysis was used to analyse gender differences in diagnostic delay. Stratified analyses by smear results, age, urban/rural were performed to examine whether the effect persisted across the strata. The median delay was 31 days (interquartile range 13–65). Diagnostic delay in females at cut-off points of 14, 30, 60 and 90 days had odds ratios (OR) of 0.99 (95% CI 0.91–1.09), 1.09 (95% CI 1.01–1.18), 1.15 (95% CI 1.05–1.26) and 1.18 (95% CI 1.06–1.31), respectively, compared with males. Stratified analysis showed that females were associated with increased risk of longer delay among those aged 30–60 years, smear positive and living in the rural areas (P < 0.05). The female-to-male OR increased along with increased delay time. Further inquiry into the underlying reasons for gender differences should be urgently addressed to improve the current situation.

We aimed to provide comprehensive estimates of laboratory-confirmed respiratory syncytial virus (RSV)-associated hospitalisations. Between 2012 and 2015, active surveillance of acute respiratory infection (ARI) hospitalisations during winter seasons was used to estimate the seasonal incidence of laboratory-confirmed RSV hospitalisations in children aged

We studied trends in the incidence of health care-associated infections (HAIs) in LTCFs between 2009 and 2015 and determined the effect of participation in our network. Elder-care physicians reported weekly the number of cases of influenza-like illness, gastroenteritis, (probable) pneumonia, urinary tract infections (UTIs) and all-cause mortality. Trends in the incidence of infection and mortality in relation to LTCF characteristics were calculated using multilevel univariate and multivariate logistic regression. Thirty LTCF participated for 3 years or more, 16 for 2 years and the remaining 12 LTCF for 1 year. During the study period, the median number of beds decreased from 158 to 139, whereas the percentage of residents with private bedrooms increased from 14% to 87%. UTIs were the most frequently reported infections, followed by (probable) pneumonia and gastroenteritis. Adjusted for calendar year and season, we observed a statistically significant decrease in the incidence of influenza-like illness (odds ratio (OR) = 0.8, P < 0.01) and (probable) pneumonia (OR = 0.8, P < 0.01) for each extra year an LTCF participated. Although there are other likely contributors, such as more private rooms and enhanced infection control measures, the decreasing trend of HAI in LTCFs participating in surveillance implies that surveillance is a valuable addition to current strategies to optimise infection control.

Although researchers have described numerous risk factors for salmonellosis and for infection with specific common serotypes, the drivers ofSalmonellaserotype diversity among human populations remain poorly understood. In this retrospective observational study, we partition records of serotyped non-typhoidalSalmonellaisolates from human clinical specimens reported to CDC national surveillance by demographic, geographic and seasonal characteristics and adapt sample-based rarefaction methods from the field of community ecology to study howSalmonellaserotype diversity varied within and among these populations in the USA during 1996–2016. We observed substantially higher serotype richness in children

Here we wanted to assess whether sexual risk behaviour differs dependent by human immunodeficiency virus (HIV) status by following 100 HIV- and 137 HIV+ women recruited at two university teaching hospitals in Rwanda. Women were tested for sexually transmitted infections (STIs; trichomoniasis, syphilis, hepatitis B and C) and for reproductive tract infections (RTIs; candidiasis, bacterial vaginosis (BV)) and were interviewed at baseline and 9 months later. BV was the most prevalent infection, while syphilis was the most common STI with a 9-month incidence of 10.9% in HIV+ women. Only 24.5% of women positive for any RTI/STI contacted their health facility and got treatment. More HIV- women than HIV+ women had had more than one sexual partner and never used condoms during the follow-up period. The use of condoms was affected neither by marital status nor by concomitant STIs besides HIV. Our data highlight the importance of public education regarding condom use to protect against STIs in an era when HIV no longer is a death sentence.

Significant ethnic and socio-economic disparities exist in infectious diseases (IDs) rates in New Zealand, so accurate measures of these characteristics are required. This study compared methods of ascribing ethnicity and socio-economic status. Children in the Growing Up in New Zealand longitudinal cohort were ascribed to self-prioritised, total response and single-combined ethnic groups. Socio-economic status was measured using household income, and both census-derived and survey-derived deprivation indices. Rates of ID hospitalisation were compared using linked administrative data. Self-prioritised ethnicity was simplest to use. Total response accounted for mixed ethnicity and allowed overlap between groups. Single-combined ethnicity required aggregation of small groups to maintain power but offered greater detail. Regardless of the method used, Māori and Pacific children, and children in the most socio-economically deprived households had a greater risk of ID hospitalisation. Risk differences between self-prioritised and total response methods were not significant for Māori and Pacific children but single-combined ethnicity revealed a diversity of risk within these groups. Household income was affected by non-random missing data. The census-derived deprivation index offered a high level of completeness with some risk of multicollinearity and concerns regarding the ecological fallacy. The survey-derived index required extra questions but was acceptable to participants and provided individualised data. Based on these results, the use of single-combined ethnicity and an individualised survey-derived index of deprivation are recommended where sample size and data structure allow it.

SUMMARYCytomegalovirus (CMV) is the leading cause of congenital infection and non-genetic sensorineural hearing loss in children. There are no recent data on the incidence of CMV infection during pregnancy in Canada. This present study was undertaken to determine the seroprevalence of CMV IgG antibodies and the rate of seroconversion in a cohort of pregnant women in the province of Québec, Canada. We used serum samples and questionnaire data collected as part of the 3D Pregnancy and Birth Cohort Study (2010–2013) conducted in Québec, Canada. CMV IgG antibodies were determined in serum samples collected at the first and third trimesters. Associations between independent variables and seroprevalence were assessed using logistic regression, and associations with seroconversions, by Poisson regression. Of 1938 pregnant women tested, 40·4% were seropositive for CMV at baseline. Previous CMV infection was associated with: working as a daycare educator, lower education, lower income, having had children, first language other than French or English, and being born outside Canada or the United States. Of the 1122 initially seronegative women, 24 (2·1%) seroconverted between their first and third trimesters. The seroconversion rate was 1·4 [95% confidence interval (CI) 0·9–2·1]/10 000 person-days at risk or 3·9 (95% CI 2·5–5·9)/100 pregnancies (assuming a 280-day gestation). The high proportion of pregnant women susceptible to CMV infection (nearly 60%) and the subsequent rate of seroconversion are of concern.

SUMMARYSurveillance data on the burden of pertussis in Asian adults are limited. This cross-sectional study evaluated the prevalence of serologically confirmed pertussis in adults with prolonged cough in Malaysia, Taiwan and Thailand. Adults (⩾19 years) with cough lasting for ⩾14 days without other known underlying cause were enrolled from outpatient clinics of seven public and/or private hospitals. Single blood samples for anti-pertussis toxin antibodies (anti-PT IgG) were analysed and economic impact and health-related quality of life (EQ-5D) questionnaires assessed. Sixteen (5·13%) of the 312 chronically coughing adults had serological evidence of pertussis infection within the previous 12 months (anti-PT IgG titre ⩾62·5 IU/ml). Three of them were teachers. Longer duration of cough, paroxysms (75% seroconfirmed, 48% non-seroconfirmed) and breathlessness/chest pain (63% seroconfirmed, 36% non-seroconfirmed) were associated with pertussis (P< 0·04). Of the seroconfirmed patients, the median total direct medical cost per pertussis episode in public hospitals (including physician consultations and/or emergency room visits) was US$13 in Malaysia, US$83 in Taiwan (n= 1) and US$26 in Thailand. The overall median EQ-5D index score of cases was 0·72 (range 0·42–1·00). Pertussis should be considered in the aetiology of adults with a prolonged or paroxysmal cough, and vaccination programmes considered.

Background Austria has been among the main European countries hosting incoming asylum seekers since 2015. Consequently, there was an urgent need to predict any public health threats associated with the arriving asylum seekers. The Department of Surveillance and Infectious Disease Epidemiology at the Austrian Agency for Health and Food Safety (AGES) was mandated to implement a national syndrome-based surveillance system in the 7 reception centers by the Austrian Ministry of Interior and Ministry of Health. Objective We aimed to analyze the occurrence and spread of infectious diseases among asylum seekers using data reported by reception centers through the syndrome-based surveillance system from September 2015 through February 2018. Methods We deployed a daily data collection system for 13 syndromes: rash with fever; rash without fever; acute upper respiratory tract infection; acute lower respiratory tract infection; meningitis or encephalitis; fever and bleeding; nonbloody gastroenteritis or watery diarrhea; bloody diarrhea; acute jaundice; skin, soft tissue, or bone abnormalities; acute flaccid paralysis; high fever with no other signs; and unexplained death. General practitioners, the first professionals to consult for health problems at reception centers in Austria, sent the tally sheets on identified syndromes daily to the AGES. Results We identified a total of 2914 cases, presenting 8 of the 13 syndromes. A total of 405 signals were triggered, and 6.4% (26/405) of them generated alerts. Suspected acute upper respiratory tract infection (1470/2914, 50.45% of cases), rash without fever (1174/2914, 40.29% of cases), suspected acute lower respiratory tract infection (159/2914, 5.46% of cases), watery diarrhea (73/2914, 2.51% of cases), and skin, soft tissue, or bone abnormalities (32/2914, 1.10% of cases) were the top 5 syndromes. Conclusions The cooperation of the AGES with reception center health care staff, supported by the 2 involved ministries, was shown to be useful for syndromic surveillance of infectious diseases among asylum seekers. None of the identified alerts escalated to an outbreak.

Vaccination programmes are considered a main contributor to the decline of infectious diseases over the 20th century. In recent years, the national vaccination coverage in the Netherlands has been declining, highlighting the need for continuous monitoring and evaluation of vaccination programmes. Our aim was to quantify the impact of long-standing vaccination programmes on notified cases in the Netherlands. We collected and digitised previously unavailable monthly case notifications of diphtheria, poliomyelitis, mumps and rubella in the Netherlands over the period 1919–2015. Poisson regression models accounting for seasonality, multi-year cycles, secular trends and auto-correlation were fit to pre-vaccination periods. Cases averted were calculated as the difference between observed and expected cases based on model projections. In the first 13 years of mass vaccinations, case notifications declined rapidly with 82.4% (95% credible interval (CI): 74.9–87.6) of notified cases of diphtheria averted, 92.9% (95% CI 85.0–97.2) cases of poliomyelitis, and 79.1% (95% CI 67.1–87.4) cases of mumps. Vaccination of 11-year-old girls against rubella averted 49.9% (95% CI 9.3–73.5) of cases, while universal vaccination averted 68.1% (95% CI 19.4–87.3) of cases. These findings show that vaccination programmes have contributed substantially to the reduction of infectious diseases in the Netherlands.

SUMMARYType D bovine botulism outbreaks associated with poultry litter are increasingly reported in European countries, but the circumstances of exposure toClostridium botulinumtoxins remain unclear. In spring 2015, a large type D/C bovine botulism outbreak affected a farm with dairy and poultry operations. Epidemiological and laboratory investigations strongly suggest that the outbreak was caused by feeding cattle with insufficiently acidified grass silage that was contaminated by type D/CC. botulinumspores. The source of the spores remains unclear, but could have been a stack of poultry litter stored in the grass silage pasture before harvesting. The presence of putrefied poultry carcasses mixed in with the litter is relatively unlikely considering the careful daily removal of poultry carcasses. These findings reinforce the importance of proper ensiling of feed materials and highlight the need for safe disposal of poultry litter, even in the case of good management of poultry deadstock, in order to prevent bovine botulism.

SUMMARYIndigenous, foodborne transmission of hepatitis E has been increasing across industrialised countries. Public Health England has conducted enhanced surveillance in England and Wales since 2003.This report gives an account of acute infections from 2010 to 2016 and describes modification made to the methods of surveillance to account for changes in reporting behaviours and improve ascertainment.

SUMMARYHistorical survey data suggest that the seroprevalence of antibodies againstCoxiella burnetiiin the general population of The Netherlands decreased from more than 40% in 1983 to 2·4% in 2007, just before the start of the large 2007–2010 Q fever epidemic. To assess whether the sharp decline in seroprevalence was real, we performed a cross-sectional study using historical samples. We tested samples using a contemporary commercial indirect immunofluorescence assay. In plasma samples from the south of The Netherlands from 1987, we found an age- and sex-standardized seroprevalence of 14·4% (95% confidence interval 11·2–18·3). This was significantly lower than a 1983 estimate from the same area (62·5%), but significantly higher than 2008 (1·0%) and 2010 (2·3%) estimates from the same area. The study suggests that there was a steady and sharp decline in Q fever seroprevalence in the south of The Netherlands from 1987 to 2008. We assume that seroprevalence has decreased in other parts of The Netherlands as well and seroprevalence surveys in other European countries have shown a similar declining trend. Waning population immunity in The Netherlands may have contributed to the scale of the 2007–2010 Q fever epidemic. For a better understanding of the infection dynamics of Q fever, we advocate an international comparative study of the seroprevalence ofC. burnetii.

Background: Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy. Objective: The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems. Methods: We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States. Results: The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present. Conclusions: Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.

SUMMARYAlthough Kawasaki disease (KD), which was first reported in the 1960s, is assumed to be infectious, its aetiological agent(s) remains unknown. We compared the geographical distribution of the force of infection and the super-annual periodicity of KD and seven other paediatric infectious diseases in Japan. The geographical distribution of the force of infection, which was estimated as the inverse of the mean patient age, was similar in KD and other paediatric viral infections. This similarity was due to the fact that the force of infection was determined largely by the total fertility rate. This finding suggests that KD shares a transmission route, i.e. sibling-to-sibling infection, with other paediatric infections. The super-annual periodicity, which is positively associated with the sum of an infectious disease's incubation period and infectious period, was much longer for KD and exanthema subitum than other paediatric infectious diseases. The virus for exanthema subitum is known to persist across the host's lifespan, which suggests that the aetiological agent for KD may also be capable of persistent infection. Taken together, these findings suggest that the aetiological agent for KD is transmitted through close contact and persists asymptomatically in most hosts.

SUMMARYThere is limited knowledge about the effect of livestock-associated methicillin-resistantStaphylococcus aureus(LA-MRSA) carriage on health-related quality of life (QoL). With this study, we explored whether LA-MRSA causes infections or affects health-related QoL in pig farmers. This prospective cohort study surveyed persons working on 49 farrowing pig farms in The Netherlands for 1 year (2010–2011). On six sampling moments, nasal swabs, environmental samples and questionnaires on activities and infections were collected. At the end of the study year, persons were asked about their QoL using the validated SF-36 and EQ-5D questionnaires. Of 120 persons, 44 (37%) were persistent MRSA carriers. MRSA carriage was not associated with infections, use of antimicrobials, healthcare contact and health-related QoL items in univariate or multivariate analysis, most likely due to the ‘healthy worker effect’. Despite high carriage rates, the impact of LA-MRSA carriage in this population of relatively healthy pig farmers on health and health-related QoL appears limited; more research is needed for confirmation.