The recent outbreak of H1N1 has provided the scientific community with a sad but timely opportunity to understand the influence of socioeconomic determinants on H1N1 pandemic mortality. To this end, we have used data collected from 341 US counties to model H1N1 deaths/1000 using 12 socioeconomic predictors to discover why certain counties reported fewer H1N1 deaths compared to other counties. These predictors were then used to build a decision tree. The decision tree developed was then used to predict H1N1 mortality for the whole of the USA. Our estimate of 7667 H1N1 deaths are in accord with the lower bound of the CDC estimate of 8870 deaths. In addition to the H1N1 death estimates, we have listed possible counties to be targeted for health-related interventions. The respective state/county authorities can use these results as the basis to target and optimize the distribution of public health resources.

The aim of this work was to use experimental infection data of human influenza to assess a simple viral dynamics model in epithelial cells and better understand the underlying complex factors governing the infection process. The developed study model expands on previous reports of a target cell-limited model with delayed virus production. Data from 10 published experimental infection studies of human influenza was used to validate the model. Our results elucidate, mechanistically, the associations between epithelial cells, human immune responses, and viral titres and were supported by the experimental infection data. We report that the maximum total number of free virions following infection is 103-fold higher than the initial introduced titre. Our results indicated that the infection rates of unprotected epithelial cells probably play an important role in affecting viral dynamics. By simulating an advanced model of viral dynamics and applying it to experimental infection data of human influenza, we obtained important estimates of the infection rate. This work provides epidemiologically meaningful results, meriting further efforts to understand the causes and consequences of influenza A infection.

Japanese weather data for areas that produced Campylobacter spp.-positive chicken products were compared with those for areas producing negative samples. Regarding samples produced during the period of rising temperature (spring and summer), the mean weekly air temperatures for Campylobacter-positive samples were higher than those for negative samples for the period of the week in which the samples were purchased (18·7°C vs. 13·1°C, P=0·006) to a 12-week lag (12 weeks before purchasing samples; 7·9°C vs. 3·4°C, P=0·009). Significant differences in weekly mean minimum humidity and sunshine duration per day were also observed for 1- and 2-week lag periods. We postulated that the high air temperature, high humidity and short duration of sunshine for the chicken-rearing period increased Campylobacter colonization in chickens during the period of rising temperature. Consequently, the number of Campylobacter-contaminated chicken products on the market in Japan may fluctuate because of the climatic conditions to which reared chickens are exposed.

In Spain hepatitis A is a compulsory notifiable disease and individual cases are reported to the national epidemiological surveillance network. Incidence rates show variations in different regions. The aim of this study was to analyse the space–time pattern of hepatitis A risk at municipal level in Spain and at global and local levels during the period 1997–2007. At global level we used two estimates of risk: the standardized incidence ratio (SIR) and the posterior probability that the smoothed relative risk is >1 (PP). At local level we used the scan statistic method to analyse the space–time clusters. The SIR and significant PP (>0·8) showed the highest risk concentrated in areas of the Mediterranean coast. The most likely cluster gave a relative risk of 53·530. These spatial statistics methodologies can be complementary tools in the epidemiological surveillance of infectious diseases.

In 2009, a 1-year retrospective survey was performed in The Netherlands to estimate the incidence and the disease burden of infectious intestinal disease (IID) in the community, to study the selection of patients consulting a general practitioner and to identify potential risk factors for IID in the community. A questionnaire was sent to 6000 persons selected at random from the population registries of 28 municipalities, with 500 persons being approached per month. A total of 1975 (33%) persons participated. The incidence rate of IID was 964/1000 person-years. Potential risk factors associated with IID in the community were young age (0–4 years) [odds ratio (OR) 3·9, 95% confidence interval (CI) 1·5–10·5], having asthma as a child (OR 3·4, 95% CI 1·1–10·3) and use of gastric acid suppressive medication by persons aged ⩾45 years (OR 2·8, 95% CI 1·4–5·6). Of the 146 cases with IID, 11 (8%) consulted a physician. Cases with a long duration of symptoms, blood in the stool, children with IID and cases with a low level of education were more likely to consult a physician. Two cases had a stool sample taken and one was admitted to hospital. In conclusion, IID is common and has a significant burden of illness in The Netherlands. Our data indicate that about 15·9 million episodes of IID occur in The Netherlands per year. The incidence rate is substantially higher than the rate of 283/1000 person-years as estimated in 1999 in The Netherlands. This is probably largely due to the retrospective nature of the present study and, to a lesser extent, to differences in case definitions.

The diagnosis and epidemiological studies of Q fever depend on serology. Among the main methods employed are the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescent assay test (IFAT). We show that two commercial assays representing the two methods with two different cut-off titres can lead to significant differences in diagnostic and seroprevalence estimates. This in turn emphasizes the need for a standardized gold method to compare the various assays; whether this standard is ‘in-house’ or commercially obtained.

Salmonella Enteritidis has emerged as the most prevalent cause of human salmonellosis in Canada. Recent trends of S. Enteritidis subtypes and their potential sources were described by integrating Salmonella data from several Canadian surveillance and monitoring programmes. A threefold increase in S. Enteritidis cases from 2003 to 2009 was identified to be primarily associated with phage types 13, 8 and 13a. Other common phage types (4, 1, 6a) showed winter seasonality and were more likely to be associated with cases linked to international travel. Conversely, phage types 13, 8 and 13a had summer seasonal peaks and were associated with cases of domestically acquired infections. During agri-food surveillance, S. Enteritidis was detected in various commodities, most frequently in chicken (with PT13, PT8 and PT13a predominating). Antimicrobial resistance was low in human and non-human isolates. Continued integrated surveillance and collaborative prevention and control efforts are required to mitigate future illness.

Syndromic surveillance is vital for monitoring public health during mass gatherings. The London 2012 Olympic and Paralympic Games represents a major challenge to health protection services and community surveillance. In response to this challenge the Health Protection Agency has developed a new syndromic surveillance system that monitors daily general practitioner out-of-hours and unscheduled care attendances. This new national system will fill a gap identified in the existing general practice-based syndromic surveillance systems by providing surveillance capability of general practice activity during evenings/nights, over weekends and public holidays. The system will complement and supplement the existing tele-health phone line, general practitioner and emergency department syndromic surveillance systems. This new national system will contribute to improving public health reassurance, especially to meet the challenges of the London 2012 Olympic and Paralympic Games.

Histoplasma capsulatum was sampled in lungs from 87 migratory Tadarida brasiliensis bats captured in Mexico (n=66) and Argentina (n=21). The fungus was screened by nested-PCR using a sensitive and specific Hcp100 gene fragment. This molecular marker was detected in 81·6% [95% confidence interval (CI) 73·4–89·7] of all bats, representing 71 amplified bat lung DNA samples. Data showed a T. brasiliensis infection rate of 78·8% (95% CI 68·9–88·7) in bats captured in Mexico and of 90·4% (95% CI 75·2–100) in those captured in Argentina. Similarity with the H. capsulatum sequence of a reference strain (G-217B) was observed in 71 Hcp100 sequences, which supports the fungal findings. Based on the neighbour-joining and maximum parsimony Hcp100 sequence analyses, a high level of similarity was found in most Mexican and all Argentinean bat lung samples. Despite the fact that 81·6% of the infections were molecularly evidenced, only three H. capsulatum isolates were cultured from all samples tested, suggesting a low fungal burden in lung tissues that did not favour fungal isolation. This study also highlighted the importance of using different tools for the understanding of histoplasmosis epidemiology, since it supports the presence of H. capsulatum in T. brasiliensis migratory bats from Mexico and Argentina, thus contributing new evidence to the knowledge of the environmental distribution of this fungus in the Americas.

We determined the prevalence of microsporidia Enterocytozoon (Ent.) bieneusi and Encephalitozoon (E.) intestinalis infection in patients with chronic diarrhoea and hepatocellular carcinoma (HCC). A total of 330 stool samples were examined from 171 (52%) patients with chronic diarrhoea, 18 (5%) with HCC while 141 (43%) were controls. Stool microscopy, polymerase chain reaction (PCR) with species-specific primers for Ent. bieneusi and E. intestinalis and sequencing were carried out. Microsporidia were found by trichrome staining in 11/330 (3%) and E. intestinalis by PCR in 13/330 (4%) while Ent. bieneusi was not detected. PCR for E. intestinalis was positive in 8/171 (5%) stool samples from patients with chronic diarrhoea, 2/141 (1·4%) samples from healthy controls and in 3/18 (17%) samples from patients with HCC. In the chronic diarrhoea group, E. intestinalis was positive in 4/171 (2·3%) (P=0·69) stool samples compared to 2/18 (11%) (P=0·06) in the HCC group and 2/141 (1·4%) from healthy controls. E. intestinalis infection was significantly associated with chronic diarrhoea and HCC in these patients who were negative for HIV. Stool examination with trichrome or species-specific PCR for microsporidia may help establish the cause of chronic diarrhoea.

In sub-Saharan Africa, many nomadic pastoralists have begun to settle in permanent communities as a result of long-term water, food, and civil insecurity. Little is known about the epidemiology of cholera in these emerging semi-nomadic populations. We report the results of a case-control study conducted during a cholera outbreak among semi-nomadic pastoralists in the Karamoja sub-region of northeastern Uganda in 2010. Data from 99 cases and 99 controls were analysed. In multivariate analyses, risk factors identified were: residing in the same household as another cholera case [adjusted odds ratio (aOR) 6·67, 95% confidence interval (CI) 2·83–15·70], eating roadside food (aOR 2·91, 95% CI 1·24–6·81), not disposing of children's faeces in a latrine (aOR 15·76, 95% CI 1·54–161·25), not treating drinking water with chlorine (aOR 3·86, 95% CI 1·63–9·14), female gender (aOR 2·43, 95% CI 1·09–5·43), and childhood age (10–17 years) (aOR 7·14, 95% CI 1·97–25·83). This is the first epidemiological study of cholera reported from a setting of semi-nomadic pastoralism in sub-Saharan Africa. Public health interventions among semi-nomadic pastoralists should include a two-faceted approach to cholera prevention: intensive health education programmes to address behaviours inherited from insecure nomadic lifestyles, as well as improvements in water and sanitation infrastructure. The utilization of community-based village health teams provides an important method of implementing such activities.

In Chile, dog rabies has been controlled and insectivorous bats have been identified as the main rabies reservoir. This study aimed to determine the rabies virus (RABV) variants circulating in the country between 2002 and 2008. A total of 612 RABV isolates were tested using a panel with eight monoclonal antibodies against the viral nucleoprotein (N-mAbs) for antigenic typing, and a product of 320-bp of the nucleoprotein gene was sequenced from 99 isolates. Typing of the isolates revealed six different antigenic variants but phylogenetic analysis identified four clusters associated with four different bat species. Tadarida brasiliensis bats were confirmed as the main reservoir. This methodology identified several independent rabies enzootics maintained by different species of insectivorous bats in Chile.

We analysed the incidence of cattle herd breakdowns due to bovine tuberculosis (Mycobacterium bovis) in relation to experimental badger culling, badger populations and farm characteristics during the Randomized Badger Culling Trial (RBCT). Mixed modelling and event history analysis were used to examine the individual risk factors. The interdependencies of covariates were examined using structural equation modelling. There were consistent findings among the different analyses demonstrating that during a badger culling programme farms experiencing: reactive culling, larger herd sizes, larger holdings and holdings with multiple parcels of land were all at greater risk of a herd breakdown. Proactive culling reduced risks within the culling area, but we did not assess any potential effects in the periphery of the treatment area. Badger-related variables measured prior to the start of culling (number of social groups and length of badger territorial boundaries) did not consistently point to an increase in risk, when set against a background of ongoing badger culling. This could be because (1) the collected variables were not important to risk in cattle, or (2) there were insufficient data to demonstrate their importance. Our findings highlight the difficulty in identifying simple predictors of spatial variation in transmission risks from badger populations and the consequent challenge of tailoring management actions to any such field data.

The relationship between knowledge, risk perceptions, health belief towards seasonal influenza and vaccination and the vaccination behaviours of nurses was explored. Qualified nurses attending continuing professional education courses at a large London university between 18 April and 18 October 2010 were surveyed (522/672; response rate 77·7%). Of these, 82·6% worked in hospitals; 37·0% reported receiving seasonal influenza vaccination in the previous season and 44·9% reported never being vaccinated during the last 5 years. All respondents were categorized using two-step cluster analyses into never, occasionally, and continuously vaccinated groups. Nurses vaccinated the season before had higher scores of knowledge and risk perception compared to the unvaccinated (P<0·001). Nurses never vaccinated had the lowest scores of knowledge and risk perception compared to other groups (P<0·001). Nurses' seasonal influenza vaccination behaviours are complex. Knowledge and risk perception predict uptake of vaccination in nurses.

The aim of the study was to describe the epidemiology and determinants of anti-hepatitis A seroprevalence in 2- to 19-year-olds in the USA for 2007–2008. This study was conducted in a sample of 2621 individuals aged 2–19 years in the USA using data from National Health and Nutrition Examination Survey (NHANES) 2007–2008. The overall seroprevalence of anti- hepatitis A virus (HAV) in this population was 39% (95% confidence interval 32·6–45·3). HAV seroprevalence was higher in Mexican Americans than other ethnic groups, in younger persons, and in those who reported previous vaccination compared to those who did not. We concluded that anti-hepatitis A seroprevalence rates are increasing in younger individuals in the USA, indicating a shift of seroprevalence over time due to vaccination status. Findings are consistent with a persistent influx of infection through international travel and migration and highlight the need to discern hepatitis A infection from vaccination status when assessing the effectiveness of vaccination using seroprevalence data.

Q fever has been associated with exposure to domesticated livestock and the agricultural industry. However large population-based studies examining the relationship are lacking. This report sought to describe the association between Coxiella burnetii infection and participation in agricultural work in the 2003–2004 National Health and Nutrition Examination Survey. Adjusted logistic regression analysis showed that agricultural workers were six times more likely to have antibody evidence of C. burnetii infection than those employed in other occupations (odds ratio 6·5, 95% confidence interval 1·7–25·3). These findings suggest that agricultural workers may experience greater C. burnetii infection and emphasize an important need for more detailed study of people engaged in this work.

During the early phase of the influenza pandemic in 2009, all cases of laboratory-confirmed pandemic (H1N1) 2009 (pH1N1) infection required compulsory isolation in hospital. These cases were offered oseltamivir treatment and only allowed to be discharged from the hospital when three consecutive respiratory specimens were negative for the virus by reverse transcription–polymerase chain reaction (RT–PCR). We reviewed the case records of these patients to assess the viral shedding kinetics of the pH1N1 virus. We defined viral shedding duration as the interval from illness onset date to the date of collection of the last positive specimen from the patients. Fifty-six patients were included in the study, of whom 96% received oseltamivir. The median viral shedding duration of pH1N1 virus by viral culture and RT–PCR were 3 days and 4 days, respectively. Patients who started oseltamivir treatment >48 h after onset had a significantly longer median viral shedding duration by viral culture than those who started treatment within 48 h of onset (4 days vs. 2 days, P=0·014).

A retrospective telephone survey (n=3490) was conducted in Italy between 2008 and 2009 to estimate the occurrence of self-reported acute gastrointestinal illness (AGI) and to describe subjects' recourse to healthcare, using a symptom-based case definition. Three hundred and ten AGI cases were identified. The annual incidence rate was 1·08 episodes/person-year (95% confidence interval 0·90–1·14). The proportion of subjects consulting physicians was 39·5% while only 0·3% submitted a specimen for laboratory investigation. Risk factors for AGI and medical care-seeking were identified using logistic regression analysis. Females, children and young adults had a significantly higher incidence rate of AGI. Factors associated with medical care-seeking were age <10 years, presence of fever, diarrhoea, and duration of illness >3 days. Our results provide a relevant contribution towards estimating the global burden of AGI using standard methods that ensure a good level of comparability with other studies.

The purpose of this study was to describe the characteristics of patients with bronchiolitis admitted to a paediatric intensive care unit (PICU), and to evaluate a national registry of hospitalizations (Programme de Médicalisation des Systèmes d'Information; PMSI) as a potential source of epidemiological data. Of the 49 French PICUs invited to take part in a retrospective survey of children aged <2 years who were hospitalized during the 2005–2006 epidemic season, 24 agreed to participate. Overall, 467 children were enrolled: 75% were aged <2 months, 76% had positive respiratory syncytial virus (RSV) tests, 34·9% required non-invasive ventilation, 36·6% were mechanically ventilated, and six infants died. The main neonatal characteristics were: prematurity (31·9%), respiratory disease (16·5%), congenital heart disease (6·4%), receiving mechanical ventilation (11·6%), and bronchopulmonary dysplasia at day 28 (3·8%). For bronchiolitis episode, the kappa coefficient between the survey and PMSI data was good only for mechanical ventilation (0·63) and the death rate (0·86).

The food service sector continues to be the most common setting for reported foodborne disease outbreaks in England and Wales. Using restaurant-associated foodborne outbreaks reported in England and Wales from 1992 to 2009, cuisine-specific risk factors were examined. Of 677 restaurant outbreaks, there were 11 795 people affected, 491 hospitalizations, and seven deaths; and Chinese, Indian, British and Italian cuisines were the most commonly implicated (26%, 16%, 13% and 10%, respectively). Salmonella spp. accounted for most outbreaks of all cuisine types, and particularly Chinese (76%, 133/175) and Italian (55%, 38/69). Poultry meat was the most frequently implicated food vehicle in outbreaks associated with Indian (30%), Chinese (21%), and British (18%) cuisines while for Italian cuisine, desserts and cakes were more frequently implicated (33%). Rice dishes were also a common outbreak food vehicle in those restaurants serving Chinese (22%) and Indian (16%) cuisine. Cross-contamination was the biggest contributory factor associated with Chinese (46%), British (33%) and Indian (30%) cuisines whereas inadequate cooking (38%) and use of raw shell eggs in lightly cooked or uncooked food (35%) were more often associated with Italian cuisine. Over the surveillance period, the proportion of Salmonella Enteritidis PT4 outbreaks in restaurants serving Chinese cuisine significantly decreased (P<0·0001) and this was mirrored by an increase in S. Enteritidis non-PT4 outbreaks (P<0·0001). Despite this change in proportion, contributory factors such as cross-contamination have continued to cause outbreaks throughout the 18 years. The results show that by stratifying the risks associated with restaurants by cuisine type, specific evidence of food control failures can be used to target foodborne illness reduction strategies.