Phenomenological and mechanistic models are widely used to assist resource planning for pandemics and emerging infections. We conducted a systematic review, to compare methods and outputs of published phenomenological and mechanistic modelling studies pertaining to the 2013–2016 Ebola virus disease (EVD) epidemics in four West African countries – Sierra Leone, Liberia, Guinea and Nigeria. We searched Pubmed, Embase and Scopus databases for relevant English language publications up to December 2015. Of the 874 articles identified, 41 met our inclusion criteria. We evaluated these selected studies based on: the sources of the case data used, and modelling approaches, compartments used, population mixing assumptions, model fitting and calibration approaches, sensitivity analysis used and data bias considerations. We synthesised results of the estimated epidemiological parameters: basic reproductive number (R0), serial interval, latent period, infectious period and case fatality rate, and examined their relationships. The median of the estimated mean R0 values were between 1·30 and 1·84 in Sierra Leone, Liberia and Guinea. Much higher R0 value of 9·01 was described for Nigeria. We investigated several issues with uncertainty around EVD modes of transmission, and unknown observation biases from early reported case data. We found that epidemic models offered R0 mean estimates which are country-specific, but these estimates are not associating with the use of several key disease parameters within the plausible ranges. We find simple models generally yielded similar estimates of R0 compared with more complex models. Models that accounted for data uncertainty issues have offered a higher case forecast compared with actual case observation. Simple model which offers transparency to public health policy makers could play a critical role for advising rapid policy decisions under an epidemic emergency.

A latent tuberculosis infection (LTBI) prevalence survey was conducted using tuberculin skin test (TST) and Quantiferon test (QFT) in 1218 healthcare workers (HCWs) in Medellín, Colombia. In order to improve the prevalence estimates, a latent class model was built using a Bayesian approach with informative priors on the sensitivity and specificity of the TST. The proportion of concordant results (TST+,QFT+) was 41% and the discordant results contributed 27%. The marginal estimate of the prevalence P(LTBI+) was 62·1% [95% credible interval (CrI) 53·0–68·2]. The probability of LTBI+ given positive results for both tests was 99·6% (95% CrI 98·1–99·9). Sensitivity was 88·5 for TST and 74·3 for QFT, and specificity was 87·8 for TST and 97·6 for QFT. A high LTBI prevalence was found in HCWs with time-accumulated exposure in hospitals that lack control plans. In a context of intermediate tuberculosis (TB) incidence it is recommended to use only one test (either QFT or TST) in prevalence surveys or as pre-employment tests. Results will be useful to help implement TB infection control plans in hospitals where HCWs may be repeatedly exposed to unnoticed TB patients, and to inform the design of TB control policies.

We compared the cost-effectiveness (CE) of an active case-finding (ACF) programme for household contacts of tuberculosis (TB) cases enrolled in first-line treatment to routine passive case-finding (PCF) within an established national TB programme in Peru. Decision analysis was used to model detection of TB in household contacts through: (1) self-report of symptomatic cases for evaluation (PCF), (2) a provider-initiated ACF programme, (3) addition of an Xpert MTB/RIF diagnostic test for a single sputum sample from household contacts, and (4) all strategies combined. CE was calculated as the incremental cost-effectiveness ratio (ICER) in terms of US dollars per disability-adjusted life years (DALYs) averted. Compared to PCF alone, ACF for household contacts resulted in an ICER of $2155 per DALY averted. The addition of the Xpert MTB/RIF diagnostic test resulted in an ICER of $3275 per DALY averted within a PCF programme and $3399 per DALY averted when an ACF programme was included. Provider-initiated ACF of household contacts in an urban setting of Lima, Peru can be highly cost-effective, even including costs to seek out contacts and perform an Xpert/MTB RIF test. ACF including Xpert MTB/RIF was not cost-effective if TB cases detected had high rates of default from treatment or poor outcomes.

Tuberculosis (TB) affects people globally and is being reconsidered as a serious public health problem in China. Reliable forecasting is useful for the prevention and control of TB. This study proposes a hybrid model combining autoregressive integrated moving average (ARIMA) with a nonlinear autoregressive (NAR) neural network for forecasting the incidence of TB from January 2007 to March 2016. Prediction performance was compared between the hybrid model and the ARIMA model. The best-fit hybrid model was combined with an ARIMA (3,1,0) × (0,1,1)12 and NAR neural network with four delays and 12 neurons in the hidden layer. The ARIMA-NAR hybrid model, which exhibited lower mean square error, mean absolute error, and mean absolute percentage error of 0·2209, 0·1373, and 0·0406, respectively, in the modelling performance, could produce more accurate forecasting of TB incidence compared to the ARIMA model. This study shows that developing and applying the ARIMA-NAR hybrid model is an effective method to fit the linear and nonlinear patterns of time-series data, and this model could be helpful in the prevention and control of TB.

The goals of this article are: (i) to understand how individual characteristics affect the likelihood of patients defaulting their pulmonary tuberculosis (PTB) treatment regimens; (ii) to quantify the predictive capacity of these risk factors; and (iii) to quantify and map spatial variation in the risk of defaulting. We used logistic regression models and generalized additive models with a spatial component to determine the odds of default across continental Portugal. We focused on new PTB cases, diagnosed between 2000 and 2013, and included some individual information (sex, age, residence area, alcohol abuse, intravenous drug use, homelessness, HIV, imprisonment status). We found that the global default rate was 4·88%, higher in individuals with well-known risk profiles (males, immigrants, HIV positive, homeless, prisoners, alcohol and drug users). Of specific epidemiological interest was that our geographical analysis found that Portugal's main urban areas (the two biggest cities) and one tourist region have higher default rates compared to the rest of the country, after adjusting for the previously mentioneded risk factors. The challenge of treatment defaulting, either due to other individual non-measured characteristics, healthcare system failure or patient recalcitrance requires further analysis in the spatio-temporal domain. Our findings suggest the presence of significant within-country variation in the risk of defaulting that cannot be explained by these classical individual risk factors alone. The methods we advocate are simple to implement and could easily be applied to other diseases.

It has been suggested that zoonotic transmission of Staphylococcus aureus (SA) and methicillin-resistant S. aureus (MRSA) can occur between owners and their pets within the same household. However, the influence that pet-ownership could have in the biodiversity of SA/MRSA strains circulating among owners is not fully understood. The objective of this study was to perform a molecular epidemiological analysis to evaluate and compare the biodiversity of SA/MRSA strains in dog-owning and non-dog-owning healthy households within the same community. Antimicrobial resistance, SCCmec type, USA type and clonality were assessed. Overall, 33·1% (165/499) of human subjects carried SA and 2·8% (14/499) carried MRSA. Among dogs, 7·1% (8/113) carried SA but none were MRSA positive. No difference was detected in the diversity index of SA/MRSA pulsotypes between dog-owning and non-dog-owning households; but, a marked variation was still observed in the pulsotypes circulating in each type of household. Additionally, simultaneous carriage of the same SA pulsotype in owner(s) and dog was observed in 57% of households with positive humans and pets. These results demonstrate that dogs can indeed participate in the circulation of SA/MRSA pulsotypes within a home and that the presence of a pet does not seem to favour certain strains within their household.

Cross-sectorial surveillance and general collaboration between the animal and the public health sectors are increasingly recognized as needed to better manage the impacts of zoonoses. From 2009, the Swiss established a Campylobacter mitigation system that includes human and poultry surveillance data-sharing within a multi-sectorial platform, in a ‘One Health’ approach. The objective of this study was to explore the economics of this cross-sectorial approach, including surveillance and triggered interventions. Costs and benefits of the One Health and of the uni-sectorial approach to Campylobacter surveillance were identified using an economic assessment framework developed earlier. Cost information of surveillance activities and interventions was gathered and disability-adjusted life years (DALYs) associated with the disease estimated for 2008 and 2013. In the first 5 years of this One Health approach to Campylobacter mitigation, surveillance contributed with information mainly used to perform risk assessments, monitor trends and shape research efforts on Campylobacter. There was an increase in costs associated with the mitigation activities following integration, due mainly to the allocation of additional resources to research and implementation of poultry surveillance. The overall burden of campylobacteriosis increased by 3·4–8·8% to 1751–2852 DALYs in 2013. In the timing of the analysis, added value associated with this cross-sectorial approach to surveillance of Campylobacter in the country was likely generated through non-measurable benefits such as intellectual capital and social capital.

Changes in seroprevalence of cysticercosis diagnosed in Chandigarh, India between 1998 and 2014 were investigated by extraction and analysis of data from records held at the Postgraduate Institute of Medical Education and Research in Chandigarh. Among the total number of samples for which cysticercosis had been suspected during this period (N = 9650), 1716 (17·8%) were seropositive. Adults were more likely to be seropositive than children, and women were more likely to be seropositive than men. In addition to there being fewer patients with suspicion of cysticercosis over the data analysis period, the proportion of patients seropositive also reduced significantly. Despite these reductions, which are probably associated with improved infrastructure and sanitation within Chandigarh, and despite meat consumption being relatively rare in this area, the extent of cysticercosis in this population remains problematic. Further efforts should be made to reduce transmission of this infection, with particular emphasis on women. Such efforts should follow the One Health concept, and involve medical efforts (including diagnosis and treatment of T. solium tapeworm carriers), veterinary efforts directed towards meat inspection and prevention of infection of pigs, and environmental health and sanitation engineers (to minimize environmental contamination with human waste).

Japan has been free from rabies since 1958. A strict import regimen has been adopted since 2004 consisting of identification of an animal with microchip, two-time rabies vaccination, neutralizing antibody titration test and a waiting period of 180 days. The present study aims to quantitatively assess the risk of rabies introduction into Japan through the international importation of dogs and cats and hence provide evidence-based recommendations to strengthen the current rabies prevention system. A stochastic scenario tree model was developed and simulations were run using @RISK. The probability of infection in a single dog or cat imported into Japan is estimated to be 2·16 × 10−9 [90% prediction interval (PI) 6·65 × 10−11–6·48 × 10−9]. The number of years until the introduction of a rabies case is estimated to be 49 444 (90% PI 19 170–94 641) years. The current import regimen is effective in maintaining the very low risk of rabies introduction into Japan and responding to future changes including increases in import level and rabies prevalence in the world. However, non-compliance or smuggling activities could substantially increase the risk of rabies introduction. Therefore, policy amendment which could promote compliance is highly recommended. Scenario analysis demonstrated that the waiting period could be reduced to 90 days and the requirement for vaccination could be reduced to a single vaccination, but serological testing should not be stopped.

We investigated the relationship between epidemics and soil radiation through an exploratory study using sentinel surveillance data (individuals aged <20 years) during the last three epidemic seasons of influenza and norovirus in Japan. We used a spatial analysis method of a geographical information system (GIS). We mapped the epidemic spreading patterns from sentinel incidence rates. We calculated the average soil radiation [dm (μGy/h)] for each sentinel site using data on uranium, thorium, and potassium oxide in the soil and examined the incidence rate in units of 0·01 μGy/h. The correlations between the incidence rate and the average soil radiation were assessed. Epidemic clusters of influenza and norovirus infections were observed in areas with relatively high radiation exposure. A positive correlation was detected between the average incidence rate and radiation dose, at r = 0·61–0·84 (P < 0·01) for influenza infections and r = 0·61–0·72 (P < 0·01) for norovirus infections. An increase in the incidence rate was found between areas with radiation exposure of 0 < dm < 0·01 and 0·15 ⩽ dm < 0·16, at 1·80 [95% confidence interval (CI) 1·47–2·12] times higher for influenza infection and 2·07 (95% CI 1·53–2·61) times higher for norovirus infection. Our results suggest a potential association between decreased immunity and irradiation because of soil radiation. Further studies on immunity in these epidemic-prone areas are desirable.

In 2013–2014, the Public Health Agency of Sweden developed a web-based participatory surveillance system, Hӓlsorapport, based on a random sample of individuals reporting symptoms weekly online, to estimate the community incidence of self-reported acute gastrointestinal (AGI), acute respiratory (ARI) and influenza-like (ILI) illnesses and their severity. We evaluated Hӓlsorapport's acceptability, completeness, representativeness and its data correlation with other surveillance data. We calculated response proportions and Spearman correlation coefficients (r) between (i) incidence of illnesses in Hӓlsorapport and (ii) proportions of specific search terms to medical-advice website and reasons for calling a medical advice hotline. Of 34 748 invitees, 3245 (9·3%) joined the cohort. Participants answered 81% (139 013) of the weekly questionnaires and 90% (16 351) of follow-up questionnaires. AGI incidence correlated with searches on winter-vomiting disease [r = 0·81, 95% confidence interval (CI) 0·69–0·89], and ARI incidence correlated with searches on cough (r = 0·77, 95% CI 0·62–0·86). ILI incidence correlated with the web query-based estimated incidence of ILI patients consulting physicians (r = 0·63, 95% CI 0·42–0·77). The high response to different questionnaires and the correlation with other syndromic surveillance systems suggest that Hӓlsorapport offers a reasonable representation of AGI, ARI and ILI patterns in the community and can complement traditional and syndromic surveillance systems to estimate their burden in the community.

Severe infections are recognized complications of coeliac disease (CD). In the present study we aimed to examine whether individuals with CD are at increased risk of invasive pneumococcal disease (IPD). To do so, we performed a population-based cohort study including 29 012 individuals with biopsy-proven CD identified through biopsy reports from all pathology departments in Sweden. Each individual with CD was matched with up to five controls (n = 144 257). IPD events were identified through regional and national microbiological databases, including the National Surveillance System for Infectious Diseases. We used Cox regression analyses to estimate hazard ratios (HRs) for diagnosed IPD. A total of 207 individuals had a record of IPD whereas 45/29 012 had CD (0·15%) and 162/144 257 were controls (0·11%). This corresponded to a 46% increased risk for IPD [HR 1·46, 95% confidence interval (CI) 1·05–2·03]. The risk estimate was similar after adjustment for socioeconomic status, educational level and comorbidities, but then failed to attain statistical significance (adjusted HR 1·40, 95% CI 0·99–1·97). Nonetheless, our study shows a trend towards an increased risk for IPD in CD patients. The findings support results seen in earlier research and taking that into consideration individuals with CD may be considered for pneumococcal vaccination.

Human parainfluenza virus (HPIV) infections are one of the commonest causes of upper and lower respiratory tract infections. In order to determine if there have been any recent changes in HPIV epidemiology in England and Wales, laboratory surveillance data between 1998 and 2013 were analysed. The UK national laboratory surveillance database, LabBase, and the newly established laboratory-based virological surveillance system, the Respiratory DataMart System (RDMS), were used. Descriptive analysis was performed to examine the distribution of cases by year, age, sex and serotype, and to examine the overall temporal trend using the χ2 test. A random-effects model was also employed to model the number of cases. Sixty-eight per cent of all HPIV detections were due to HPIV type 3 (HPIV-3). HPIV-3 infections were detected all year round but peaked annually between March and June. HPIV-1 and HPIV-2 circulated at lower levels accounting for 20% and 8%, respectively, peaking during the last quarter of the year with a biennial cycle. HPIV-4 was detected in smaller numbers, accounting for only 4% and also mainly observed in the last quarter of the year. However, in recent years, HPIV-4 detection has been reported much more commonly with an increase from 0% in 1998 to 3·7% in 2013. Although an overall higher proportion of HPIV infection was reported in infants (43·0%), a long-term decreasing trend in proportion in infants was observed. An increase was also observed in older age groups. Continuous surveillance will be important in tracking any future changes.

Pertussis epidemics have displayed substantial spatial heterogeneity in countries with high socioeconomic conditions and high vaccine coverage. This study aims to investigate the relationship between pertussis risk and socio-environmental factors on the spatio-temporal variation underlying pertussis infection. We obtained daily case numbers of pertussis notifications from Queensland Health, Australia by postal area, for the period January 2006 to December 2012. A Bayesian spatio-temporal model was used to quantify the relationship between monthly pertussis incidence and socio-environmental factors. The socio-environmental factors included monthly mean minimum temperature (MIT), monthly mean vapour pressure (VAP), Queensland school calendar pattern (SCP), and socioeconomic index for area (SEIFA). An increase in pertussis incidence was observed from 2006 to 2010 and a slight decrease from 2011 to 2012. Spatial analyses showed pertussis incidence across Queensland postal area to be low and more spatially homogeneous during 2006–2008; incidence was higher and more spatially heterogeneous after 2009. The results also showed that the average decrease in monthly pertussis incidence was 3·1% [95% credible interval (CrI) 1·3–4·8] for each 1 °C increase in monthly MIT, while average increase in monthly pertussis incidences were 6·2% (95% CrI 0·4–12·4) and 2% (95% CrI 1–3) for SCP periods and for each 10-unit increase in SEIFA, respectively. This study demonstrated that pertussis transmission is significantly associated with MIT, SEIFA, and SCP. Mapping derived from this work highlights the potential for future investigation and areas for focusing future control strategies.

Foodborne disease outbreaks (FBDOs) occur frequently in Europe. Employing analytical epidemiological study designs increases the likelihood of identifying the suspected vehicle(s), but these studies are rarely applied in FBDO investigations. We used multivariable binary logistic regression analysis to identify characteristics of investigated FBDOs reported to the European Food Safety Authority (2007–2011) that were associated with analytical epidemiological evidence (compared to evidence from microbiological investigations/descriptive epidemiology only). The analysis was restricted to FBDO investigations, where the evidence for the suspected vehicle was considered ‘strong’, i.e. convincing. The presence of analytical epidemiological evidence was reported in 2012 (50%) of these 4038 outbreaks. In multivariable analysis, increasing outbreak size, number of hospitalizations, causative (i.e. aetiological) agent (whether identified and, if so, which one), and the setting in which these outbreaks occurred (e.g. geographically dispersed outbreaks) were independently associated with presence of analytical evidence. The number of investigations with reported analytical epidemiological evidence was unexpectedly high, likely indicating the need for quality assurance within the European Union foodborne outbreak reporting system, and warranting cautious interpretation of our findings. This first analysis of evidence implicating a food vehicle in FBDOs may help to inform public health authorities on when to use analytical epidemiological study designs.

In August 2015 a gastroenteritis outbreak occurred following a wedding. An outbreak investigation was undertaken and a cohort study was conducted using an online survey. Of 140 guests, 134 received the survey and 113 responded (84·3% response rate). Seventy respondents met the case definition of vomiting and/or diarrhoea within 72 h of the wedding (61·9% attack rate). Fifteen exposures were associated with illness; on stratification, all were confounded by the ham hock starter. Multivariable analysis showed a significant association with exposure to ham hock (risk ratio 6·62, 95% confidence interval 2·19–20·03). Eight guests and two catering staff submitted stool samples. All tested positive for norovirus GI-6 infection, including a food handler who had vomiting less than 48 h before the wedding. A single genotype was detected among all samples, suggesting a single source of contamination. The transmission pattern suggested point-source exposure. The most plausible cause of the outbreak was transmission from an infected food handler via contaminated food. This highlights the importance of appropriate exclusions for symptomatic food handlers. Additionally, the food handler's stool sample was submitted 7 days after symptom resolution. The potential for extended viral excretion, and the extremely low infective dose of norovirus, may mean that current exclusion guidelines are not of sufficient duration.

Open-water swimming is increasingly popular, often in water not considered safe for bathing. Limited evidence exists on the associated health risks. We investigated gastrointestinal illness in 1100 swimmers in a River Thames event in London, UK, to describe the outbreak and identify risk factors. We conducted a retrospective cohort study. Our case definition was swimmers with any: diarrhoea, vomiting, abdominal cramps lasting ⩾48 h, nausea lasting ⩾48 h, with onset within 9 days after the event. We used an online survey to collect information on symptoms, demographics, pre- and post-swim behaviours and open-water experience. We tested associations using robust Poisson regression. We followed up case microbiological results. Survey response was 61%, and attack rate 53% (338 cases). Median incubation period was 34 h and median symptom duration 4 days. Five cases had confirmed microbiological diagnoses (four Giardia, one Cryptosporidium). Wearing a wetsuit [adjusted relative risk (aRR) 6·96, 95% confidence interval (CI) 1·04–46·72] and swallowing water (aRR 1·42, 95% CI 1·03–1·97) were risk factors. Recent river-swimming (aRR 0·78, 95% CI 0·67–0·92) and age >40 years (aRR 0·83, 95% CI 0·70–0·98) were protective. Action to reduce risk of illness in future events is recommended, including clarification of oversight arrangements for future swims to ensure appropriate risk assessment and advice is provided.

Many infectious diseases in humans may manifest with no or mild symptoms. While numerous studies have estimated the proportion of infectious individuals in whom symptoms are absent during the entire course of infection, the contribution of asymptomatic cases to the overall cumulative incidence is difficult to untangle. Here, with a mathematical model, we provide a simple analytical formula to quantify this contribution and highlight the potential for large errors that can arise when naively estimating it.

People who use drugs (PWUD) are a key population for hepatitis B virus (HBV) vaccination and screening. We aimed to estimate the seroprevalence of HBs antigen (HBsAg) and self-reported HBV vaccination history in French PWUD attending harm reduction centres using data from the ANRS-Coquelicot multicentre survey conducted in 2011–2013 in 1718 PWUD. Self-fingerprick blood samples were collected on dried blood spots to detect the presence of HBsAg. HBsAg seroprevalence was estimated at 1·4% [95% confidence interval (CI) 0·8–2·5]. It varied between PWUD born in high (7·6%, 95% CI 2·7–19·1), moderate (2·2%, 95% CI 0·8–5·7) and low (0·7%, 95% CI 0·3–1·5) endemic zones. Factors independently associated with HBsAg carriage were being born in a moderate or high endemic zone or reporting precarious housing. Self-reported HBV vaccination history varied from 47·4% in high endemic zones, to 59·3% and 62·6% for moderate and low endemic zones, respectively. Our results suggest that drug use plays a small and substantial role, respectively, in HBsAg carriage in PWUD born in high/moderate and low endemic zones.

Few studies have examined the impact of cigarette smoking on the risk for herpes zoster. The Shozu Herpes Zoster (SHEZ) Study is a community-based prospective cohort study over 3 years in Japan aiming to clarify the incidence and predictive and immunological factors for herpes zoster. We investigated the associations of smoking status with past history and incidence of herpes zoster. A total of 12 351 participants provided valid information on smoking status and past history of herpes zoster at baseline survey. Smoking status was classified into three categories (current, former, never smoker), and if currently smoking, the number of cigarettes consumed per day was recorded. The participants were under the active surveillance for first-ever incident herpes zoster for 3 years. We used a logistic regression model for the cross-sectional study on the association between smoking status and past history of herpes zoster, and a Cox proportional hazards regression model for the cohort study on the association with risk of incidence. The multivariable adjusted odd ratios (95% CI) of past history of herpes zoster for current vs. never smokers were 0·67 (0·54–0·80) for total subjects, 0·72 (0·56–0·93) for men and 0·65 (0·44–0·96) for women. The multivariable adjusted hazard ratios (95% CI) of incident herpes zoster for current vs. never smokers were 0·52 (0·33–0·81) for total subjects, 0·49 (0·29–0·83) for men and 0·52 (0·19–1·39) for women. Smoking status was inversely associated with the prevalence and incidence of herpes zoster in the general population of men and women aged ⩾50 years.