Few countries routinely collect comprehensive encephalitis data, yet understanding the epidemiology of this condition has value for clinical management, detecting novel and emerging pathogens, and guiding timely public health interventions. When this study was conducted there was no standardized diagnostic algorithm to aid identification of encephalitis or systematic surveillance for adult encephalitis. In July 2012 we tested three pragmatic surveillance options aimed at identifying possible adult encephalitis cases admitted to a major Australian hospital: hospital admissions searches, clinician notifications and laboratory test alerts (CSF herpes simplex virus requests). Eligible cases underwent structured laboratory investigation and a specialist panel arbitrated on the final diagnosis. One hundred and thirteen patients were initially recruited into the 10-month study; 20/113 (18%) met the study case definition, seven were diagnosed with infectious or immune-mediated encephalitis and the remainder were assigned alternative diagnoses. The laboratory alert identified 90% (102/113) of recruited cases including six of the seven cases of confirmed encephalitis suggesting that this may be a practical data source for case ascertainment. The application of a standardized diagnostic algorithm and specialist review by an expert clinical panel aided diagnosis of patients with encephalitis.

Several epidemiological studies suggest a possible involvement of viral infection in the development of epilepsy. While recent research from in vitro studies increasingly supports the role of herpes simplex virus type 1 (HSV-1) in the pathogenesis of epilepsy, little is known about the role of other viral infections such as influenza. Using data from the Clinical Practice Research Datalink (CPRD), we conducted a matched case-control analysis to assess the association between GP-diagnosed influenza infections and the risk of developing an incident diagnosis of epilepsy. During the study period 11 244 incident epilepsy cases and 44 976 matched control patients were identified. Prior exposure to influenza was reported in 7·5% of epilepsy cases and 6·7% of controls [adjusted odds ratio (aOR) 1·12, 95% confidence interval (CI) 1·03–1·22]. Prior history of ‘complicated influenza’, i.e. influenza associated with a possible super-infection, was associated with a slightly increased epilepsy risk (aOR 1·64, 95% CI 1·10–2·46), particularly if recorded within the 2 months preceding the epilepsy diagnosis (aOR 6·03, 95% CI 1·10–33·2). Our findings suggest that prior influenza exposure does not appear to materially alter the risk of developing epilepsy. By contrast, influenza episodes accompanied by complications were associated with a slightly increased epilepsy risk.

There exists an urgent need to develop iterative risk assessment strategies of zoonotic diseases. The aim of this study is to develop a method of prioritizing 98 zoonoses derived from animal pathogens in Japan and to involve four major groups of stakeholders: researchers, physicians, public health officials, and citizens. We used a combination of risk profiling and analytic hierarchy process (AHP). Profiling risk was accomplished with semi-quantitative analysis of existing public health data. AHP data collection was performed by administering questionnaires to the four stakeholder groups. Results showed that researchers and public health officials focused on case fatality as the chief important factor, while physicians and citizens placed more weight on diagnosis and prevention, respectively. Most of the six top-ranked diseases were similar among all stakeholders. Transmissible spongiform encephalopathy, severe acute respiratory syndrome, and Ebola fever were ranked first, second, and third, respectively.

Two hundred and fourteen patients who had a cough illness lasting at least 2 weeks were studied to investigate Bordetella pertussis as a cause of prolonged cough in adolescents and adults. Medical history and nasopharyngeal swab specimens for culture and polymerase chain reaction (PCR) were obtained at presentation. Three (1·4%) patients were B. pertussis culture-positive; 15 (7%) were B. pertussis PCR-positive (including the culture-positive patients) and 11 (5·1%) were Bordetella spp. PCR-positive. Symptom combinations were significantly high both in patients with pertussis and patients with indeterminate results (P < 0·05). We conclude that B. pertussis should be considered among differential diagnoses of prolonged cough in adolescents and adults and PCR and culture should be used to detect these cases and facilitate public health response.

Human salmonellosis linked to contact with live poultry is an increasing public health concern. In 2012, eight unrelated outbreaks of human salmonellosis linked to live poultry contact resulted in 517 illnesses. In July 2012, PulseNet, a national molecular surveillance network, reported a multistate cluster of a rare strain of Salmonella Braenderup infections which we investigated. We defined a case as infection with the outbreak strain, determined by pulsed-field gel electrophoresis, with illness onset from 25 July 2012–27 February 2013. Ill persons and mail-order hatchery (MOH) owners were interviewed using standardized questionnaires. Traceback and environmental investigations were conducted. We identified 48 cases in 24 states. Twenty-six (81%) of 32 ill persons reported live poultry contact in the week before illness; case-patients named 12 different MOHs from eight states. The investigation identified hatchery D as the ultimate poultry source. Sampling at hatchery D yielded the outbreak strain. Hatchery D improved sanitation procedures and pest control; subsequent sampling failed to yield Salmonella. This outbreak highlights the interconnectedness of humans, animals, and the environment and the importance of industry knowledge and involvement in solving complex outbreaks. Preventing these infections requires a ‘One Health’ approach that leverages expertise in human, animal, and environmental health.

HBV genotypes have specific geographical distributions and can serve as epidemiological markers. Accumulated data have shown that the major HBV genotypes in China are B and C. Here, the HBV genotypes were examined from 6817 blood samples, which were collected from patients with chronic HBV infection in Fujian Province during 2006–2013; genotype B was identified in 3384 patients (49·6%), while genotype C was identified in 3430 patients (50·3%). The percentage of patients infected with genotype C gradually increased with age from 39·5% (patients aged <20 years) to 63·9% (patients aged >50 years), reaching a peak of 67·3% in the 45–50 years age group. These results clearly demonstrate that the genotype distribution of HBV in Fujian Province has significantly changed in recent years with almost equal numbers of genotype B and genotype C infections existing in the entire patient population, while higher incidence of genotype C infection exists in older patients, but genotype B is no longer dominant in the Fujian area as previously reported.

Noroviruses are a major cause of gastroenteritis. Vaccine strategies against norovirus are currently under consideration but depend on a detailed knowledge of the capsid genotypes. This study examined the incidence of norovirus outbreaks in residential aged-care facilities in Victoria, Australia over one year (2013) and documented the (capsid) norovirus genotypes associated with these outbreaks. It was found that 65·0% of 206 outbreaks tested were associated with norovirus infection, thereby showing norovirus to be the major cause of viral gastroenteritis in residential aged-care facilities. Fifteen capsid (open reading frame 2) genotypes were identified as follows: GI.2 (0·9%), GI.3 (1·8%), GI.4 (3·7%), GI.6 (0·9%), GI.7 (0·9%), GI.8 (0·9%), GII.1 (0·9%), GII.2 (0·9%), GII.3 (1·8%), GII.4 (2009-like) (0·9%), GII.4 (2012) (48·6%), GII.4 (2012-like) (16·5%), GII.4 (unknown) (9·2%), GII.5 (2·8%), GII.6 (0·9%), GII.7 (0·9%), GII.13 (6·4%) and an as yet unclassified GII genotype (0·9%). Although GII.4 was the most common norovirus capsid genotype detected, the great diversity of norovirus genotypes in the elderly indicates vaccination strategies for this demographic are not straightforward.

The deer ked (Lipoptena cervi) is a haematophagous ectoparasite of cervids that harbours haemotrophic Bartonella. A prerequisite for the vector competence of the deer ked is the vertical transmission of the pathogen from the mother to its progeny and transstadial transmission from pupa to winged adult. We screened 1154 pupae and 59 pools of winged adult deer keds from different areas in Finland for Bartonella DNA using PCR. Altogether 13 pupa samples and one winged adult deer ked were positive for the presence of Bartonella DNA. The amplified sequences were closely related to either B. schoenbuchensis or B. bovis. The same lineages were identified in eight blood samples collected from free-ranging moose. This is the first demonstration of Bartonella spp. DNA in a winged adult deer ked and, thus, evidence for potential transstadial transmission of Bartonella spp. in the species.

After an outbreak of pandemic influenza A/H1N1 (pH1N1) virus, we had previously reported the emergence of a recombinant canine influenza virus (CIV) between the pH1N1 virus and the classic H3N2 CIV. Our ongoing routine surveillance isolated another reassortant H3N2 CIV carrying the matrix gene of the pH1N1 virus from 2012. The infection dynamics of this H3N2 CIV variant (CIV/H3N2mv) were investigated in dogs and ferrets via experimental infection and transmission. The CIV/H3N2mv-infected dogs and ferrets produced typical symptoms of respiratory disease, virus shedding, seroconversion, and direct-contact transmissions. Although indirect exposure was not presented for ferrets, CIV/H3N2mv presented higher viral replication in MDCK cells and more efficient transmission was observed in ferrets compared to classic CIV H3N2. This study demonstrates the effect of reassortment of the M gene of pH1N1 in CIV H3N2.

Diabetes mellitus (DM) is currently known to be one of the risk factors for pulmonary tuberculosis (PTB) and the proportion of DM in PTB is rising along with the increased prevalence of DM in countries with high PTB burden. This study was designed to explore the impact of DM on clinical presentation and treatment outcome of PTB in China. In an urban setting in Beijing, 1126 PTB patients, 30·6% with positive sputum smear, registered in two PTB dispensaries from January 2010 to December 2011 were screened for DM and were followed up prospectively during PTB treatment. DM was observed in 16·2% of patients with PTB. PTB with DM appeared to be associated with older age and a higher proportion of re-treatment. On presentation, DM was associated with more severe PTB signs with higher proportions of smear positivity [odds ratio (OR) 2·533, 95% confidence interval (CI) 1·779–3·606], cavity (OR 2·253, 95% CI 1·549–3·276) and more symptoms (OR 1·779, 95% CI 1·176–2·690). DM was also associated with non-TB deaths (OR 5·580, 95% CI 2·182–14·270, P < 0·001) and treatment failure (OR 6·696, 95% CI 2·019–22·200, P = 0·002). In Beijing, the findings of this study underlined the need to perform early bi-directional screening programmes and explore the underlying mechanism for different treatment outcomes for PTB with DM.

Simulation models can offer valuable insights into the effectiveness of different control strategies and act as important decision support tools when comparing and evaluating outbreak scenarios and control strategies. An international modelling study was performed to compare a range of vaccination strategies in the control of foot-and-mouth disease (FMD). Modelling groups from five countries (Australia, New Zealand, USA, UK, The Netherlands) participated in the study. Vaccination is increasingly being recognized as a potentially important tool in the control of FMD, although there is considerable uncertainty as to how and when it should be used. We sought to compare model outputs and assess the effectiveness of different vaccination strategies in the control of FMD. Using a standardized outbreak scenario based on data from an FMD exercise in the UK in 2010, the study showed general agreement between respective models in terms of the effectiveness of vaccination. Under the scenario assumptions, all models demonstrated that vaccination with ‘stamping-out’ of infected premises led to a significant reduction in predicted epidemic size and duration compared to the ‘stamping-out’ strategy alone. For all models there were advantages in vaccinating cattle-only rather than all species, using 3-km vaccination rings immediately around infected premises, and starting vaccination earlier in the control programme. This study has shown that certain vaccination strategies are robust even to substantial differences in model configurations. This result should increase end-user confidence in conclusions drawn from model outputs. These results can be used to support and develop effective policies for FMD control.

To determine risk factors for sporadic Vibrio parahaemolyticus gastroenteritis, we conducted a population-based case-control study in sentinel hospital surveillance areas of Shanghai and Jiangsu province, China. Seventy-one patients with diarrhoea and confirmed V. parahaemolyticus infections were enrolled, and they were matched with 142 controls for gender, age and residential area. From the multivariable analysis, V. parahaemolyticus infections were associated with antibiotics taken during the 4 weeks prior to illness [odds ratio (OR) 8·1, 95% confidence interval (CI) 1·2–56·4)], frequent eating out (OR 3·3, 95% CI 1·1–10·1), and shellfish consumption (OR 3·2, 95% CI 1·0–9·9), with population-attributable fractions of 0·09, 0·25, and 0·14, respectively. Protective factors included keeping the aquatic products refrigerated (OR 0·4, 95% CI 0·1–0·9) and pork consumption (OR 0·2, 95% CI 0·1–0·8). Further study of the association of V. parahaemolyticus gastroenteritis with prior antibiotic use and shellfish consumption is needed.

Previous studies examining the weather–bacillary dysentery association were of a large time scale (monthly or weekly) and examined the linear relationship without checking the linearity assumption. We examined this association in Beijing at a daily scale based on the exposure-response curves using generalized additive models. Our analyses suggested that there were thresholds for effects of temperature and relative humidity, with an approximately linear effect for temperature >12·5 °C [excess risk (ER) for 1 °C increase: 1·06%, 95% confidence interval (CI) 0·63–1·49 on lag day 3] and for relative humidity >40% (ER for 1% increase: 0·18%, 95% CI 0·12–0·24 at lag day 4); and there were linear effects of rainfall (ER for 1-mm increase: 0·22%, 95% CI 0·12–0·32), negative effects for wind speed (ER: −2·91%, 95% CI −4·28 to −1·52 at lag day 3) and sunshine duration (ER: −0·25% 95% CI −0·43 to −0·07 at lag day 4). This study suggests that there are thresholds for the effects of temperature and relative humidity on bacillary dysentery, and these findings should be considered in its prevention and control programmes.

Many cases of giardiasis in the UK are undiagnosed and among other things, diagnosis is dependent upon the readiness of GPs to request a specimen. The aim of this study is to assess the rate of specimens requested per GP practice in Central Lancashire, to examine the differences between GP practices and to estimate the pattern of unexplained spatial variation in the practice rate of specimens after adjustment for deprivation. To achieve this, we fitted a set of binomial and Poisson regression models, with random effects for GP practice. Our analysis suggests that there were differences in the rate of specimens by GP practices (P < 0·001) for a single year, but no difference in the proportion of positive tests per specimen submitted or in the rate of positive specimens per practice population. There was a difference in the cumulative rate of positive specimens per practice population over a 9-year period (P < 0·001). Neither the specimen rate per practice for a single year nor the cumulative rate of positive specimens over multiple years demonstrated significant spatial correlation. Hence, spatial variation in the incidence of giardiasis is unlikely to be confounded by variation in GP rate of specimens.

Genetic association studies of the cytokine interleukin-10 (IL-10) and sepsis have provided inconsistent results. This work attempts to further quantitatively assess the association of three widely evaluated polymorphisms of IL-10 (−592C/A, −819C/T, −1082A/G) with sepsis susceptibility through a meta-analysis. A search of Pubmed, Web of Science and EMBASE databases was performed. Overall, the three polymorphisms have no strong association with sepsis risk. Subgroup analysis by ethnicity showed there was association between sepsis susceptibility with −592C/A in Caucasians (A vs. C: OR 0·78, 95% CI 0·62–1·00, P = 0·05; AA + CA vs. CC: OR 0·75, 95% CI 0·56–1·00, P = 0·05), and with −1082A/G in Asians (G vs. A: OR 1·41, 95% CI 1·04–1·91, P = 0·03; GG + AG vs. AA: OR 2·11, 95% CI 1·07–4·16, P = 0·03). This meta-analysis suggests that −592C/A and −1082A/G polymorphisms are associated with sepsis susceptibility in Caucasian, and Asian populations, respectively.

This paper explores the utility of cluster- and case-based surveillance established in government hospitals in Bangladesh to detect Nipah virus, a stage III zoonotic pathogen. Physicians listed meningo-encephalitis cases in the 10 surveillance hospitals and identified a cluster when ⩾2 cases who lived within 30 min walking distance of one another developed symptoms within 3 weeks of each other. Physicians collected blood samples from the clustered cases. As part of case-based surveillance, blood was collected from all listed meningo-encephalitis cases in three hospitals during the Nipah season (January–March). An investigation team visited clustered cases’ communities to collect epidemiological information and blood from the living cases. We tested serum using Nipah-specific IgM ELISA. Up to September 2011, in 5887 listed cases, we identified 62 clusters comprising 176 encephalitis cases. We collected blood from 127 of these cases. In 10 clusters, we identified a total of 62 Nipah cases: 18 laboratory-confirmed and 34 probable. We identified person-to-person transmission of Nipah virus in four clusters. From case-based surveillance, we identified 23 (4%) Nipah cases. Faced with thousands of encephalitis cases, integrated cluster surveillance allows targeted deployment of investigative resources to detect outbreaks by stage III zoonotic pathogens in resource-limited settings.

Limited information is available on the prevalence of hepatitis C virus (HCV) in the general population in China. A community-based epidemiological study was conducted in three counties in eastern China. A total of 149 175 individuals were investigated in 60 communities in three counties in Jiangsu province, eastern China, of whom 1175 subjects [0·79%, 95% confidence interval (CI) 0·74–0·83] were HCV antibody positive. The prevalence was low in children (0·09%, 95% CI 0·04–0·17), but increased progressively from adolescents (0·20%, 95% CI 0·15–0·28) to adults aged ⩾21 years (95% CI 0·15–1·64). Women had a higher prevalence of HCV infection than men in most age groups. In a multilevel regression analysis, age, sex, education, occupation, blood transfusion [odds ratio (OR) 2·91, 95% CI 1·09–5·37], invasive testing (OR 1·28, 95% CI 1·14–1·61), and dental therapy (OR 2·27, 95% CI 1·41–3·42) were associated with HCV infection. In conclusion, although the prevalence of HCV in this population was lower than reported from national levels, the total reservoir of infection is significant and warrants public health measures, such as health education to limit the magnitude of the problem.

Clostridium difficile infection has gained importance in recent years as a result of the rapid spread of epidemic strains, including hypervirulent strains. This study reports the molecular epidemiology of C. difficile obtained from hospitalized patients in Chile. Seven hundred and nineteen isolates of toxigenic C. difficile from 45 hospitals across the country were characterized through toxin profile, pulsed-field gel electrophoresis (PFGE), and sequencing of the tcdC gene. In addition, polymerase chain reaction (PCR) ribotyping and multilocus sequence typing (MLST) were performed on a subset of selected strains. PFGE typing of 719 isolates of C. difficile produced 60 PFGE patterns (subtypes). Subtype 1 was predominant (79% of isolates) and related to the hypervirulent strain (NAP1). Subtype 1 showed 73% relatedness with nine other subtypes, which had a similar tcdC deletion. Subtype 1 corresponded to ribotype 027 and ST1. This report shows the wide dissemination of the hypervirulent strain NAP1/027/ST1 in Chile.

In Chile, while dog rabies has decreased markedly over the last 30 years, bat rabies is still reported frequently. In order to shed new light on the spatiotemporal trends of these reports, we analysed active and passive data from years 1985 and 2012, which included 61 076 samples from 289 counties of Chile. We found that from 1994 to 2012, more than 15 000 bat samples were submitted for diagnostics through passive surveillance, 9·5% of which tested positive for rabies. By contrast, the prevalence of infection was only ~0·4% among the nearly 12 000 bat samples submitted through active surveillance. We found that the prevalence of dog rabies dropped steadily over the same period, with just a single confirmed case since 1998. None of the 928 samples from wild animals, other than bats, were positive for rabies. Although there has been only one confirmed case of human rabies in Chile since 1985, and a single confirmed case in a dog since 1998, bats remain a reservoir for rabies viruses. While active surveillance indicates that rabies prevalence is low in bat colonies, the high proportion of positive bats submitted through passive surveillance is a concern. To prevent human rabies, local public health agencies should increase research on the basic ecology of bats and the role of stray dogs and cats as potential rabies amplifiers.

Transmission experiments are useful for investigating the mechanisms of low pathogenic notifiable avian influenza virus (LPNAI) transmission. In this study, the hypothesis that inoculation-infected chickens are more infectious than contact-infected chickens was tested. To this end, extended transmission experiments with one H5N2 and one H7N1 LPAIV which had previously been characterized in a series of standard transmission experiments were conducted in specific pathogen-free (SPF) chickens. For the H5N2 LPAIV, the infectivity of contact-infected chickens was similar to the infectivity of inoculated chickens. Despite results from a previous study suggesting the H7N1 LPAIV strain to be similarly infectious to SPF chickens as the H5N2 LPAIV strain, the acquisition of contact-infected chickens proved more difficult for H7N1 LPAIV. It was assumed that this might have been a consequence of the length and timing of the exposure period. In conclusion, for LPNAIVs that first seemed equally infectious, short-term transmissibility may vary considerably.