We explored age-dependent patterns in haemagglutination inhibition (HI) titre to seasonal [1956 A(H1N1), 1977 A(H1N1), 2007 A(H1N1)] and pandemic [A(H1N1)pdm09] influenza strains using serological data collected from an adult French influenza cohort. Subjects were recruited by their general practitioners from 2008 to 2009 and followed until 2010. We explored age-related differences between strain-specific HI titres using 1053 serological samples collected over the study period from 398 unvaccinated subjects. HI titres against the tested seasonal and pandemic strains were determined using the HI technique. Geometric mean titres (GMTs) were estimated using regression models for interval-censored data. Generalized additive mixed models were fit to log-transformed HI estimates to study the relationship between HI titre and age (age at inclusion and/or age at initial strain circulation). GMT against one strain was consistently highest in the birth cohort exposed to that strain during childhood, with peak titres observed in subjects aged 7–8 years at the time of initial strain circulation. Our results complete previous findings on influenza A(H3N2) strains and identify a strain-dependent relationship between HI titre and age at initial strain circulation.

The objective of this study was to determine how clinicians make use of the modern multiplex PCR assays (MPAs) to manage patients hospitalized for community-acquired pneumonia (CAP). We studied the use of MPAs in 1648 patients hospitalized for CAP over a 3-year period at the moment of the setup of the new PCR assay. We observed that the use of MPAs for the identification of multiple respiratory pathogens marks a radical change in the investigation of CAP etiology. Surprisingly, the contribution of MPAs to the medical decision-making process varies drastically according to the units of care.

Post-mortem examination continues to play an important surveillance role in the bovine tuberculosis (bTB) eradication programme in Northern Ireland. It is estimated that 18–28% of new bTB herd breakdowns are disclosed by the detection of bTB lesions in animals routinely slaughtered. The purpose of this study was to compare the performance of different slaughterhouses in Northern Ireland in detecting bTB-lesioned animals at routine slaughter (LRS) and to apply the findings to maximize the sensitivity of bTB slaughterhouse surveillance. Univariate statistical analysis on cattle slaughtered in Northern Ireland during 2011–2013 revealed that the risk of LRS disclosure varied between slaughterhouses, ranging from 0·08% to 0·54%. Furthermore, the risk of confirmation of these LRS as bTB varied between slaughterhouses, ranging from 57·9% to 72·4%. Logistic regression modelling of selected risk factors found that the risk of LRS disclosure increased with age, and was higher in purchased animals, during winter months, in animals coming from high bTB incidence areas and in animals slaughtered from herds with a bTB restriction in the last 2–3 years. Adjusting for these selected factors, the risk of LRS disclosure and bTB confirmation changed very little from the univariable analysis, suggesting that differences in disclosure risks between slaughterhouses were likely to be due to factors related to the slaughterhouses, rather than to the risk status of the animals presented. Examination of procedures within these slaughterhouses is recommended to identify ways that could increase the sensitivity of their bTB surveillance.

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

The burden of dengue virus infections increased globally during recent years. Though India is considered as dengue hyper-endemic country, limited data are available on disease epidemiology. The present study includes molecular characterization of dengue virus strains occurred in Hyderabad, India, during the year 2014. A total of 120 febrile cases were recruited for this study, which includes only children and 41 were serologically confirmed for dengue positive infections using non-structural (NS1) and/or IgG/IgM ELISA tests. RT-PCR, nucleotide sequencing and evolutionary analyses were carried out to identify the circulating serotypes/genotypes. The data indicated a high percent of severe dengue (63%) in primary infections. Simultaneous circulation of all four serotypes and co-infections were observed for the first time in Hyderabad, India. In total, 15 patients were co-infected with more than one dengue serotype and 12 (80%) of them had severe dengue. One of the striking findings of the present study is the identification of serotype Den-1 as the first report from this region and this strain showed close relatedness to the Thailand 1980 strains but not to any of the strains reported from India until now. Phylogenetically, all four strains of the present study showed close relatedness to the strains, which are reported to be high virulent.

We studied the evolution, genotypes, and the molecular clock of dengue virus serotype 1 (DENV-1), between 2001 and 2014 in Guangzhou, China. The analysis of the envelope (E) gene sequences of 67 DENV-1 strains isolated in Guangzhou, together with 58 representative sequences downloaded from NCBI, have shown shifts in viral genotypes. The genotype changed several times, from genotype I to IV in 2002, from IV to I in 2005, and from I to V in 2014. These genotype shifts may be the cause of DENV outbreaks. The diversity of genotypes and clades demonstrates a high risk of future outbreaks in Guangzhou. The mean rate of virus nucleotide substitution in Guangzhou was determined to be 7·77 × 10−4 per site per year, which represents a medium substitution rate compared to two other countries. Our research can point to different ancestors of the isolated strains, which may further reveal the different origins and transmission of DENV-1 strains in Guangzhou.

In recent years, hand, foot, and mouth disease (HFMD) has been increasingly recognized as a critical challenge to disease control and prevention in China. Previous studies have found that meteorological factors such as mean temperature and relative humidity were associated with HFMD. However, little is known about whether the diurnal temperature range (DTR) has any impact on HFMD. This study aimed to quantify the impact of DTR on childhood HFMD in 18 cities in Sichuan Province. A distributed lag non-linear model was adopted to explore the temporal lagged association of daily temperature with age-, gender- and pathogen-specific HFMD. A total of 290 123 HFMD cases aged 0–14 years were reported in the 18 cities in Sichuan Province. The DTR–HFMD relationships were non-linear in all subgroups. Children aged 6–14 years and male children were more vulnerable to the temperature changes. Large DTR had the higher risk estimates of HFMD incidence in cases of EV71 infection, while small DTR had the higher risk estimates of HFMD incidence in cases of CV-A16 infection. Our study suggested that DTR played an important role in the transmission of HFMD with non-linear and delayed effects.

In South Korea, the resurgence of mumps was noted primarily among school-aged children and adolescents since 2000. We analyzed spatial patterns in mumps incidence to give an indication to the geographical risk. We used National Notifiable Disease Surveillance System data from 2001 to 2015, classifying into three periods according to the level of endemicity. A geographic-weighted regression analysis was performed to find demographic predictors of mumps incidence according to district level. We assessed the association between the total population size, population density, percentage of children (age 0–19 years), timely vaccination rate of measles–mumps–rubella vaccines and the higher incidence rate of mumps. During low endemic periods, there were sporadic regional distributions of outbreak in the central and northern part of the country. During intermediate endemic periods, the increase of incidence was noted across the country. During high endemic period, a nationwide high incidence of mumps was noted especially concentrated in southwestern regions. A clear pattern for the mumps cluster shown through global spatial autocorrelation analysis from 2004 to 2015. The ‘non-timely vaccination coverage’ (P = 0·002), and ‘proportion of children population’ (P < 0·001) were the predictors for high mumps incidence in district levels. Our study indicates that the rate of mumps incidence according to geographic regions vary by population proportion and neighboring regions, and timeliness of vaccination, suggesting the importance of community-level surveillance and improving of timely vaccination.

An upsurge of fever cases of unknown origin, but resembling dengue and leptospirosis was reported in Havelock, Andaman & Nicobar Islands, an important tourism spot, during May 2014. Investigations were carried out to determine the aetiology, and to describe the epidemiology of the outbreak. The data on fever cases attending Primary Health Centre (PHC), Havelock showed that the average number of cases reporting per week over the last 2 years was 46·1 (95% confidence interval 19·4–72·9). A total of 27 (43·5%) patients out of the 62 suspected cases were diagnosed as having DENV infection based on a positive enzyme immunoassay or reverse transcriptase–polymerase chain reaction. The overall attack rate was 9·4 cases/1000 population and it ranged between 2·8 and 18·8/1000 in different villages. The nucleotide sequencing showed that the virus responsible was DENV-3. DENV-3 was first detected in the Andaman & Nicobar Islands in 2013 among wharf workers in Port Blair and within a year it has spread to Havelock Island which is separated from South Andaman by 36 nautical miles.

Zika virus infection was declared a public health emergency of international concern in February 2016 in response to the outbreak in Brazil and its suspected link with congenital anomalies. In this study, we use notification data and disease natural history parameters to estimate the basic reproduction number (R0) of Zika in Rio de Janeiro, Brazil. We also obtain estimates of R0 of dengue from time series of dengue cases in the outbreaks registered in 2002 and 2012 in the city, when DENV-3 and DENV-4 serotypes, respectively, had just emerged. Our estimates of the basic reproduction number for Zika in Rio de Janeiro based on surveillance notifications (R0 = 2·33, 95% CI: 1·97–2·97) were higher than those obtained for dengue in the city (year 2002: R0 = 1·70 [1·50–2·02]; year 2012: R0 = 1·25 [1·18–1·36]). Given the role of Aedes aegypti as vector of both the Zika and dengue viruses, we also derive R0 of Zika as a function of both dengue reproduction number and entomological and epidemiological parameters for dengue and Zika. Using the dengue outbreaks from previous years allowed us to estimate the potential R0 of Zika. Our estimates were closely in agreement with our first Zika's R0 estimation from notification data. Hence, these results validate deriving the potential risk of Zika transmission in areas with recurring dengue outbreaks. Whether transmission routes other than vector-based can sustain a Zika epidemic still deserves attention, but our results suggest that the Zika outbreak in Rio de Janeiro emerged due to population susceptibility and ubiquitous presence of Ae. aegypti.

An outbreak of gastroenteritis affected 453 attendees (attack rate 28·5%) of six separate events held at a hotel in Singapore. Active case detection, case-control studies, hygiene inspections and microbial analysis of food, environmental and stool samples were conducted to determine the aetiology of the outbreak and the modes of transmission. The only commonality was the food, crockery and cutlery provided and/or handled by the hotel's Chinese banquet kitchen. Stool specimens from 34 cases and 15 food handlers were positive for norovirus genogroup II. The putative index case was one of eight norovirus-positive food handlers who had worked while they were symptomatic. Several food samples and remnants tested positive for Escherichia coli or high faecal coliforms, aerobic plate counts and/or total coliforms, indicating poor food hygiene. This large common-source outbreak of norovirus gastroenteritis was caused by the consumption of contaminated food and/or contact with contaminated crockery or cutlery provided or handled by the hotel's Chinese banquet kitchen.

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.

The presence of parasites on the farm can be a cause of losses in animal production, and often a threat to public health. A cross-sectional study was carried out in rural areas of the western highlands of Cameroon to determine the prevalence and husbandry-related risk factors associated with Cordylobia anthropophaga infestations in domestic cavies. The overall prevalence of myiasis in animals was 2·80% [95% confidence interval (CI) 1·50–5·10]; myiasis was found in 2% and 4·30% animals in Menoua and Bamboutos divisions, respectively. Eleven farms (8·95%) in total were infested with C. anthropophaga, with 6·41% and 13·34% of farms in the Menoua and Bamboutos divisions, respectively. The relative risk of infestation within each factor showed that the risk of myiasis in animals kept in kitchen compartments without litter was 6·16 times higher (95% CI 1·71–22·29, P = 0·04) than in animals kept in kitchens and house floors. Despite the low prevalence, the burden of cordylobiasis needs to be assessed. It is assumed that the risk of humans acquiring the disease is higher in farmers keeping cavies in kitchen compartments without litter. Farmers need to be educated on control measures to reduce the risk of infestation, which include both sanitation and medical (larvae extraction) measures.

Little is known about Clostridium difficile infection (CDI) in Asia. The aims of our study were to explore (i) the prevalence, risk factors and molecular epidemiology of CDI and colonization in a tertiary academic hospital in North-Eastern Peninsular Malaysia; (ii) the rate of carriage of C. difficile among the elderly in the region; (iii) the awareness level of this infection among the hospital staffs and students. For stool samples collected from hospital inpatients with diarrhea (n = 76) and healthy community members (n = 138), C. difficile antigen and toxins were tested by enzyme immunoassay. Stool samples were subsequently analyzed by culture and molecular detection of toxin genes, and PCR ribotyping of isolates. To examine awareness among hospital staff and students, participants were asked to complete a self-administered questionnaire. For the hospital and community studies, the prevalence of non-toxigenic C. difficile colonization was 16% and 2%, respectively. The prevalence of CDI among hospital inpatients with diarrhea was 13%. Out of 22 C. difficile strains from hospital inpatients, the toxigenic ribotypes 043 and 017 were most common (both 14%). In univariate analysis, C. difficile colonization in hospital inpatients was significantly associated with greater duration of hospitalization and use of penicillin (both P < 0·05). Absence of these factors was a possible reason for low colonization in the community. Only 3% of 154 respondents answered all questions correctly in the awareness survey. C. difficile colonization is prevalent in a Malaysian hospital setting but not in the elderly community with little or no contact with hospitals. Awareness of CDI is alarmingly poor.

As endemic measles is eliminated through immunization, countries must determine the risk factors for the importation of measles into highly immunized populations to target control measures. Despite eliminating endemic measles, New Zealand suffers from outbreaks after introductions from abroad, enabling us to use it as a model for measles introduction risk. We used a generalized linear model to analyze risk factors for 1137 measles cases from 2007 to June 2014, provide estimates of national immunity levels, and model measles importation risk. People of European ethnicity made up the majority of measles cases. Age is a positive risk factor, particularly 0–2-year-olds and 5–17-year-old Europeans, along with increased wealth. Pacific islanders were also at greater risk, but due to 0–2-year-old cases. Despite recent high measles, mumps, and rubella vaccine immunization coverage, overall population immunity against measles remains ~90% and is lower in people born between 1982 and 2005. Greatest measles importation risk is during December, and countries predicted to be sources have historical connections and highest travel rates (Australia and UK), followed by Asian countries with high travel rates and higher measles incidences. Our results suggest measles importation due to travel is seeding measles outbreaks, and immunization levels are insufficient to continue to prevent outbreaks because of heterogeneous immunity in the population, leaving particular age groups at risk.

Early prediction of the final size of any epidemic and in particular for Zika disease outbreaks can be useful for health authorities in order to plan the response to the outbreak. The Richards model is often been used to estimate epidemiological parameters for arboviral diseases based on the reported cumulative cases in single- and multi-wave outbreaks. However, other non-linear models can also fit the data as well. Typically, one follows the so called post selection estimation procedure, i.e., selects the best fitting model out of the set of candidate models and ignores the model uncertainty in both estimation and inference since these procedures are based on a single model. In this paper we focus on the estimation of the final size and the turning point of the epidemic and conduct a real-time prediction for the final size of the outbreak using several non-linear models in which these parameters are estimated via model averaging. The proposed method is applied to Zika outbreak data in four cities from Colombia, during the outbreak ocurred in 2015–2016.

The purpose of this study was to develop a method for identifying newly diagnosed tuberculosis (TB) patients at risk for TB adverse events in Tamaulipas, Mexico. Surveillance data between 2006 and 2013 (8431 subjects) was used to develop risk scores based on predictive modelling. The final models revealed that TB patients failing their treatment regimen were more likely to have at most a primary school education, multi-drug resistance (MDR)-TB, and few to moderate bacilli on acid-fast bacilli smear. TB patients who died were more likely to be older males with MDR-TB, HIV, malnutrition, and reporting excessive alcohol use. Modified risk scores were developed with strong predictability for treatment failure and death (c-statistic 0·65 and 0·70, respectively), and moderate predictability for drug resistance (c-statistic 0·57). Among TB patients with diabetes, risk scores showed moderate predictability for death (c-statistic 0·68). Our findings suggest that in the clinical setting, the use of our risk scores for TB treatment failure or death will help identify these individuals for tailored management to prevent these adverse events. In contrast, the available variables in the TB surveillance dataset are not robust predictors of drug resistance, indicating the need for prompt testing at time of diagnosis.

Shoe soles have been shown to transfer infectious microorganisms to floor and ground surfaces. However, the possible modes of transmission of infectious agents from floors or ground surfaces to human contact for infection have not been systematically reviewed. A systematic review was performed on articles indexed in medical databases (Medline, EMBASE, PubMed) using a pre-defined search strategy and MeSH terms (date of last search: 15 March 2016). Only primary research studies in English that investigated the transmission dynamics of infectious microorganisms from floor or ground surfaces to human infection were included. Extraction of articles was performed two independent reviewers using pre-defined data fields in an Excel sheet. Disagreements were resolved by consensus. Thirty studies met the inclusion criteria. Almost all hospital-associated microorganisms including methicillin-resistant Staphylococcus aureus, Clostridium difficile, and multidrug-resistant Gram-negative species were identified on floor or ground surfaces. Several modes of transmission dynamics, most commonly direct contact or aerosolization, were identified. In conclusion, interventions such as efficient cleaning of floor surfaces and vectors that transfer infectious organisms to floors such as shoe soles could be an effective infection control strategy to prevent human disease.

The outbreaks of varicella occurring in kindergartens and schools are increasingly notified in Shanghai despite the implementation of one-dose varicella vaccination. We analyzed surveillance data on the notified outbreaks of varicella in Minhang District of Shanghai during 2008–2014. A total of 13 511 varicella cases and 154 outbreaks involving 1558 (11·5%) cases were reported. Annual attack rates of outbreak-associated varicella in outbreak classes were 5·5%–12%. The mean age of the outbreak-associated cases was 8·6 ± 3·1 years. Among 1558 outbreak cases, 660 (42·4%) received one-dose varicella vaccine previously. The proportions of breakthrough varicella infection during outbreaks ranged from 21·5% in 2008 to 86·1% in 2014. Annual breakthrough infection rates in outbreak classes ranged from 5·4% to 7·4%. Breakthrough cases as index cases results in 9·7% of outbreaks, and the average duration of outbreaks was significantly longer in vaccinated cases as index cases than in unvaccinated cases as index cases (11·3 ± 5·8 days vs. 8·6 ± 6·1 days, P < 0·05). The mean time of breakthrough infection since vaccination was 6·2 ± 2·3 years (range 0·6–13·4 years). One-dose varicella vaccination cannot prevent the varicella outbreaks in kindergartens and schools. A second dose of varicella vaccine should be recommended for children.

Although most non-typhoidal Salmonella illnesses are self-limiting, antimicrobial treatment is critical for invasive infections. To describe resistance in Salmonella that caused foodborne outbreaks in the United States, we linked outbreaks submitted to the Foodborne Disease Outbreak Surveillance System to isolate susceptibility data in the National Antimicrobial Resistance Monitoring System. Resistant outbreaks were defined as those linked to one or more isolates with resistance to at least one antimicrobial drug. Multidrug resistant (MDR) outbreaks had at least one isolate resistant to three or more antimicrobial classes. Twenty-one per cent (37/176) of linked outbreaks were resistant. In outbreaks attributed to a single food group, 73% (16/22) of resistant outbreaks and 46% (31/68) of non-resistant outbreaks were attributed to foods from land animals (P < 0·05). MDR Salmonella with clinically important resistance caused 29% (14/48) of outbreaks from land animals and 8% (3/40) of outbreaks from plant products (P < 0·01). In our study, resistant Salmonella infections were more common in outbreaks attributed to foods from land animals than outbreaks from foods from plants or aquatic animals. Antimicrobial susceptibility data on isolates from foodborne Salmonella outbreaks can help determine which foods are associated with resistant infections.