General Practitioner consultation rates for influenza-like illness (ILI) are monitored through several geographically distinct schemes in the UK, providing early warning to government and health services of community circulation and intensity of activity each winter. Following on from the 2009 pandemic, there has been a harmonization initiative to allow comparison across the distinct existing surveillance schemes each season. The moving epidemic method (MEM), proposed by the European Centre for Disease Prevention and Control for standardizing reporting of ILI rates, was piloted in 2011/12 and 2012/13 along with the previously proposed UK method of empirical percentiles. The MEM resulted in thresholds that were lower than traditional thresholds but more appropriate as indicators of the start of influenza virus circulation. The intensity of the influenza season assessed with the MEM was similar to that reported through the percentile approach. The MEM pre-epidemic threshold has now been adopted for reporting by each country of the UK. Further work will continue to assess intensity of activity and apply standardized methods to other influenza-related data sources.

Multicomponent cyclicity in influenza (flu) incidence had been observed in various countries (e.g. periods T = 1, 2–3, 5–6, 8·0, 10·6–11·3, 13, 18–19 years) and its close similarity with cycles in natural environmental phenomena as meteorological factors and heliogeophysical activity (HGA) suggested. This report aimed at verifying previous results on cyclic patterns of flu incidence by exploring whether flu annual cyclicity (seasonality) and trans-year (13 to <24 months) and/or multiannual (long-term, ⩾24 months) cycles might be present. For this purpose, a relatively long monthly flu incidence dataset consisting of absolute numbers of new cases from the Grand Baku area, Azerbaijan, for the years 1976–2000 (300 months) was analysed. The exploration of underlying chronomes or, time structures, was done by linear and nonlinear parametric regression models, autocorrelation, spectral analysis and periodogram regression analysis. We analysed temporal dynamics and described multicomponent cyclicity, determining its statistical significance. The analysis, considering the flu data specifically stratified in three distinct intervals (1976–1990, 1991–1995, 1996–2000), and also combinations thereof, indicated that the main cyclic pattern was a seasonal one, with a period of T = 12 months. Further, a number of multiannual cycles with periods T in the ranges of 26–36, 62–85 or 113–162 months were observed, i.e. average periods of 2·5, 6·1 and 11·5 years, respectively. Indeed, most of these cycles correspond to similar cyclic parameters of HGA and further analyses are warranted to investigate such relationships. In conclusion, our study revealed the presence of multicomponent cyclic dynamics in influenza incidence by using relatively long time-series of monthly data. The specific cyclic patterns of flu incidence in Azerbaijan allows further, more specific modelling and correlations with environmental factors of similar cyclicity, e.g. HGA, to be explored. These results might contribute more widely to a better understanding of influenza dynamics and its aetiology as well as to the derivation of more precise forecasted estimates for planning and prevention purposes.

Influenza poses a significant public health burden worldwide. Understanding how and to what extent people would change their behaviour in response to influenza outbreaks is critical for formulating public health policies. We incorporated the information-theoretic framework into a behaviour-influenza (BI) transmission dynamics system in order to understand the effects of individual behavioural change on influenza epidemics. We showed that information transmission of risk perception played a crucial role in the spread of health-seeking behaviour throughout influenza epidemics. Here a network BI model provides a new approach for understanding the risk perception spread and human behavioural change during disease outbreaks. Our study allows simultaneous consideration of epidemiological, psychological, and social factors as predictors of individual perception rates in behaviour-disease transmission systems. We suggest that a monitoring system with precise information on risk perception should be constructed to effectively promote health behaviours in preparation for emerging disease outbreaks.

Respiratory virus infections cause a significant number of hospitalization and deaths globally. This study investigated the association between single and multiple respiratory virus infections and risk of admission to a general ward, intensive care unit or death in patients aged 0–105 years (mean ± s.d. = 24·4 ± 24·1 years), from North West England, that were tested for respiratory virus infections between January 2007 and June 2012. The majority of infections were in children aged ⩽5 years. Dual or multiple infections occurred in 10·4% (1214/11 715) of patients, whereas single infection occurred in 89·6% (10 501/11 715). Rhinovirus was the most common co-infecting virus (occurring in 69·5%; 844/1214 of co-infections). In a multivariate logistic regression model, multiple infections were associated with an increased risk of admission to a general ward [odds ratio (OR) 1·43, 95% confidence interval (CI) 1·2–1·7, P < 0·0001]. On the other hand, patients with respiratory syncytial virus (RSV) and human parainfluenza virus types 1–3 (hPIV1–3), as a single infection, had a higher risk of being admitted to a general ward (OR 1·49, 95% CI 1·28–1·73, P < 0·0001 and OR 1·34, 95% CI 1·003–1·8, P = 0·05, respectively); admitted to an intensive-care unit or dying (OR 1·5, 95% CI 1·20–2·0, P = 0·001 and OR 1·60, 95% CI 1·02–2·40, P = 0·04, respectively). This result emphasizes the importance of RSV, hPIV and mixed infections and calls for research on vaccines, drugs and diagnostic tests targeting these respiratory viruses.

Patients with a lower respiratory tract infection (LRTI) might be at risk for long-term impaired health status. We assessed whether LRTI patients without Q fever are equally at risk for developing long-term symptoms compared to LRTI patients with Q fever. The study was a cross-sectional cohort design. Long-term health status information of 50 Q fever-positive and 32 Q fever-negative LRTI patients was obtained. Health status was measured by the Nijmegen Clinical Screening Instrument. The most severely affected subdomains of the Q fever-positive group were ‘general quality of life’ (40%) and ‘fatigue’ (40%). The most severely affected subdomains of the Q fever-negative group were ‘fatigue’ (64%) and ‘subjective pulmonary symptoms’ (35%). Health status did not differ significantly between Q fever-positive LRTI patients and Q fever-negative LRTI patients for all subdomains, except for ‘subjective pulmonary symptoms’ (P = 0·048).

Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06–40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

To investigate the frequencies of dendritic cells (DCs) and Toll-like receptor 3 (TLR3) in neonates of HBsAg-positive mothers with different HBV serological profiles, we conducted a study in Taiyuan, China. The study included 144 HBsAg-positive mothers and their neonates. The frequencies of DCs and TLR3 were determined using four-colour flow-cytometric analysis. DC and TLR3 frequencies were not related to HBV intrauterine transmission, maternal HBeAg positivity, maternal HBV DNA positivity and HBeAg/HBV DNA double-positivity. The plasmacytoid dendritic cell (pDC) frequencies in neonates whose maternal HBV DNA was >5 × 107 copies/ml decreased significantly compared to that in neonates whose maternal HBV DNA was ⩽5 × 107 copies/ml (Z = − 2·170, P = 0·03) or whose maternal HBV DNA was negative (Z = − 1·981 P = 0·048). This study suggests that neonatal pDC frequencies decrease when maternal HBV DNA loads are >5 × 107 copies/ml.

We conducted a case-control study involving 150 genotype 3 chronic hepatitis C virus (HCV) patients and 150 healthy controls to investigate the association of polymorphisms in the interleukin-10 (IL-10) gene with chronic HCV infection and the association of these polymorphic variants with the combination of pegylated interferon (Peg-IFN) and ribavirin therapy response. Our data revealed that the GG genotype of IL-10 –1082A/G exhibited significant association with genotype 3 chronic HCV infection compared to controls. Treatment response data also showed a significant increase in risk for the GG genotype of IL-10 –1082A/G in response-relapse patients or non-responder patients compared to sustained virological response patients. Further, a significant increase in risk was also revealed for the CC genotype of IL-10 –592A/C in response-relapse patients or non-responder patients compared to sustained virological response patients, suggesting a role of the GG genotype of IL-10 –1082A/G and CC genotype of IL-10 –592A/C in the treatment outcome of combined Peg-IFN/ribavirin therapy.

Our goal was to identify climate variables and management practices associated with the presence of E. coli O157 in rangeland cow-calf operations located in a major leafy green production region in the California Central Coast. E. coli O157 was present in 2·6% (68/2654) of faecal, 1·5% (3/204) of water and 1·1% (1/93) of sediment samples collected on eight ranches over 2.5 years. Five (62·5%) ranches were positive at least once during the study. The odds of detecting E. coli O157 in faecal samples was higher during periods of higher maximum soil temperature, higher maximum relative humidity, and larger herd sizes, but decreased as wind speed increased. Molecular subtyping of isolates from cattle faeces and streams/sediments suggested minimal movement of strains between ranches. The findings suggest that E. coli O157 prevalence is relatively low on cow-calf ranches in this region, spatially constrained, but may vary by weather conditions and herd size.

We investigated faecal samples collected from the rectum of 518 cattle on 371 randomly selected smallholdings in Bangladesh for the presence of sorbitol non-fermenting (SN-F) shiga toxin-producing Escherichia coli (STEC). The SN-F isolates were tested for the presence of rfb O157, stx1, stx2, eae and hlyA genes by polymerase chain reaction (PCR). Seven SN-F isolates lacking these genes were profiled by pulsed-field gel electrophoresis (PFGE) to verify their clonality. SN-F E. coli was identified in 44 [8·5%, 95% confidence interval (CI) 6·4–11·2] samples; of these, 28 (5·4%, 95% CI 3·8–7·7) had shiga toxin-producing strains, although only two carried the rfb O157 gene. Thirteen isolates carried the hlyA gene while 18 harboured the eae gene. Based on PFGE, six pulsotypes were observed among the seven isolates that had no virulence genes. To the best of our knowledge this is the first report on shiga toxin-producing E. coli from direct rectal faecal samples of cattle on smallholdings.

Multi-locus variable number tandem repeat analysis (MLVA) is used in clinical and reference laboratories for subtyping verocytotoxin-producing Escherichia coli O157 (VTEC O157). However, as yet there is no common allelic or profile nomenclature to enable laboratories to easily compare data. In this study, we carried out an inter-laboratory comparison of an eight-loci MLVA scheme using a set of 67 isolates of VTEC O157. We found all but two isolates were identical in profile in the two laboratories, and repeat units were homogeneous in size but some were incomplete. A subset of the isolates (n = 17) were sequenced to determine the actual copy number of representative alleles, thereby enabling alleles to be named according to international consensus guidelines. This work has enabled us to realize the potential of MLVA as a portable, highly discriminatory and convenient subtyping method.

This study developed a fast and high throughput dot-blot technique to evaluate the presence of Entamoeba in stool samples (n = 643) followed by a PCR-based method to validate and differentiate the two species E. histolytica and E. dispar. The prevalence rate of the parasite has been detected in a cross-sectional study carried out in the population of the Eastern and Northern parts of India. Of the various demographic features, prevalence was highest in the monsoon season (P = 0·017), in the <15 years age group (P = 0·015). In HIV-positive individuals, the prevalence rate was significantly high (P = 0·008) in patients with a CD4 cell count <200 as well as in patients without antiretroviral therapy (ART) (P = 0·011). Our analysis further confirmed that risk factors such as toilet facilities, living conditions, hygienic practices, drinking water source, occupation and level of education are important predictors as they were found to contribute significantly in the prevalence of the parasite.

People who inject drugs (PWID) are vulnerable to infections and injuries at injection sites. The factors associated with reporting symptoms of these, seeking related advice, and hospital admission are examined. PWID were recruited in Birmingham, Bristol and Leeds using respondent-driven sampling (N = 855). During the preceding year, 48% reported having redness, swelling and tenderness (RST), 19% an abscess, and 10% an open wound at an injection site. Overall, 54% reported ⩾1 symptoms, with 45% of these seeking medical advice (main sources emergency departments and General Practitioners). Advice was often sought ⩾5 days after the symptom first appeared (44% of those seeking advice about an abscess, 45% about an open wound, and 35% for RST); the majority received antibiotics. Overall, 9·5% reported hospital admission during the preceding year. Ever being diagnosed with septicaemia and endocarditis were reported by 8·8% and 2·9%, respectively. Interventions are needed to reduce morbidity, healthcare burden and delays in accessing treatment.

People who inject drugs are vulnerable to infections and injuries at injection sites, but these have rarely been studied in those injecting image- and performance-enhancing drugs (IPEDs). This study examined the factors associated with reported symptoms of injection site infections and injuries in IPED injectors. Of the 366 male IPED injectors surveyed, 42% reported ever having redness, swelling and tenderness (36% in the preceding year), and 6·8% had ever had an abscess or open wound at an injection site. Having these symptoms was associated with a range of factors related to drug use and healthcare utilization. One sixth (17%) of those reporting redness, tenderness and swelling had ever sought treatment, as had the majority (76%) of those reporting an abscess, sore or open wound. Most common sources of advice were emergency clinics and General Practitioners. Interventions are needed to support access to appropriate injecting equipment and provide targeted harm reduction advice.

The Beijing/W lineage strains are the major prevalent strains in China. The prevalence, mortality and drug-resistant rates of tuberculosis in Xinjiang, Northwestern China are higher than in other parts of the country. Our previous study results showed that the dominant strains of Mycobacterium tuberculosis (MTB) were ‘Beijing/W lineage’ MTB in Xinjiang; those strains had no significant correlation with drug resistance. We investigated whether the prevalence of ‘Beijing/W lineage’ sublineage strains was associated with drug resistance. We collected 478 sputum specimens from patients with pulmonary tuberculosis. Beijing/W strains and their sublineages were identified by distinguishing five specific large sequence polymorphisms, using polymerase chain reaction. All strains were subjected to a drug susceptibility test using the proportion method on Löwenstein–Jensen culture medium. In total, 379 clinical isolates of MTB were isolated and identified, 57·26% of these isolates were identified as Beijing/W strains, of which 11·06% isolates were in sublineage 105, 14·74% isolates in sublineage 207, 69·59% isolates in sublineage 181, and 4·61% isolates in sublineage 150. None of the isolates was in sublineage 142. Our data showed there were four sublineages of Beijing/W isolates in Xinjiang province, China. However, there were no correlations between drug resistance and the sublineages of Beijing/W strains.

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.

In some French départements, the eradication of bovine tuberculosis is incomplete and usual skin tests [single intradermal tuberculin test (SIT) and single intradermal comparative cervical test (SICCT)] have poor specificity due to cross-reactions with non-pathogenic mycobacteria, causing economic losses. In Côte d'Or (Burgundy, France), an experimental serial testing scheme based on the combination of SICCT and gamma-interferon (IFN-γ) tests has been initiated in order to shorten the interval between suspicion and its invalidation in herds with false-positive results to skin tests. Our aim was to assess the scheme's sensitivity and to compare it to the sensitivity of the screening scheme recommended by the European Commission. Our study included 1768 animals from Côte d'Or. The sensitivities of both schemes were estimated using a Bayesian approach. The individual sensitivity of the IFN-γ test [88·1%, 95% credibility interval (CrI) 72·8–97·5] was not significantly different from individual SICCT sensitivity (80·3%, 95% CrI 61·6–98·0) and individual SIT sensitivity (84·2%, 95% CrI 59·0–98·2). The individual specificity of the IFN-γ test was 62·3% (95% CrI 60·2–64·5). No significant difference could be demonstrated between the sensitivities of the serial testing scheme used in Côte d'Or (73·1%, 95% CrI 41·1–100) and the European Union serial testing scheme (70·1%, 95% CrI 31·5–100·0).

Rheumatic fever (RF) is an important public health problem in New Zealand (NZ). There are three sources of RF surveillance data, all with major limitations that prevent NZ generating accurate epidemiological information. We aimed to estimate the likely RF incidence using multiple surveillance data sources. National RF hospitalization and notification data were obtained, covering the periods 1988–2011 and 1997–2011, respectively. Data were also obtained from four regional registers: Wellington, Waikato, Hawke's Bay and Rotorua. Coded patient identifiers were used to calculate the proportion of individuals who could be matched between datasets. Capture–recapture analyses were used to calculate the likely number of true RF cases for the period 1997–2011. A range of scenarios were used to correct for likely dataset incompleteness. The estimated sensitivity of each data source was calculated. Patients who were male, Māori or Pacific, aged 5–15 years and met the Jones criteria, were most likely to be matched between national datasets. All registers appeared incomplete. An average of 113 new initial cases occurred annually. Sensitivity was estimated at 80% for the hospitalization dataset and 60% for the notification dataset. There is a clear need to develop a high-quality RF surveillance system, such as a national register. Such a system could link important data sources to provide effective, comprehensive national surveillance to support both strategy-focused and control-focused activities, helping reduce the incidence and impact of this disease. It is important to remind clinicians that RF cases do occur outside the well-characterized high-risk group.

A retrospective case-control study of patients who had undergone cataract extraction at a Spanish hospital over a 13-year period was conducted to identify the risk factors for developing post-operative endophthalmitis (POE). During the study period, the type of antibiotic prophylaxis was changed from subconjunctival gentamicin to the addition of both vancomycin and gentamicin to the irrigating solution. The overall incidence of POE was 0·19% (35 cases/18 287 operations). For the period prior to the change in antibiotic prophylaxis, the incidence rate of POE was 3·4 cases/1000 operations while in the latter period the incidence rate decreased to 0·34 cases/1000 operations. All patients who presented a virulent microorganism had a final visual acuity worse than 20/200. The only significant risk factor identified was the type of prophylaxis used (odds ratio 1·97, 95% confidence interval 0·94–4·14, P = 0·07). There were no significant differences between cases and controls although choice of surgeon approached significance.

This study describes the incidence rate of reported lymphogranuloma venereum (LGV) in men who have sex with men (MSM) in Barcelona from 2007 to 2012. Epidemiological, clinical and sexual behaviour characteristics of LGV cases are described. Seroadaptive behaviours as a transmission risk factor were assessed by a telephone questionnaire during 2012. Data were handled on a strictly confidential basis. LGV annual rate ratios in MSM were compared with cases from 2007. Differences were statistically analysed with a Poisson test. The incidence rate of LGV in MSM aged 15–69 years ranged from 32·1/105 MSM per year in 2007 to 182·7/105 MSM per year in 2012. In 2012, 31/51 LGV cases (61%) answered the telephone questionnaire, of which 84% (26/31) were HIV positive, 39% (12/31) reported having sex according to their partners’ serostatus and 7% (2/31) used strategic positioning. The incidence of LGV has increased since 2007 and mainly affects HIV-positive MSM. It is probable that seroadaptation has facilitated LGV transmission.