A retrospective cohort study was conducted to identify risk factors for bovine tuberculosis (bTB) recurrence in New Zealand cattle and deer herds identified as bTB-infected from 1 June 2006 to 1 November 2010. A Cox proportional hazards model identified a positive relationship between the daily hazard of bTB recurrence and: (1) the number of prior bTB episodes for two episodes [hazard ratio (HR) 3·22, 95% confidence interval (CI) 1·21–8·60], and for five episodes (HR 89·5, 95% CI 13·8–580), (2) more than one positive bTB case animal at the index episode (HR 2·25, 95% CI 1·19–4·25) and (3) the presence of cleared test-positives at the final test of the index episode. The proportional hazards assumption was violated for the latter variable so a time-dependent covariate was introduced. Up to 2 years post-clearance, the daily hazard of bTB recurrence was greater in herds with test-positives at the final test (HR 2·59, 95% CI 1·30–5·13), but this effect was not observed more than 2 years' post-clearance (HR 1·05, 95% CI 0·28–3·91). We conclude that unresolved infection contributes to further bTB episodes in the first 2 years after herd clearance.

The objective of this study was to evaluate the impact of restricting high-risk antibiotics on methicillin-resistant Staphylococcus aureus (MRSA) incidence rates in a hospital setting. A secondary objective was to assess the impact of reducing fluoroquinolone use in the primary-care setting on MRSA incidence in the community. This was an interventional, retrospective, ecological investigation in both hospital and community (January 2006 to June 2010). Segmented regression analysis of interrupted time-series was employed to evaluate the intervention. The restriction of high-risk antibiotics was associated with a significant change in hospital MRSA incidence trend (coefficient = −0·00561, P = 0·0057). Analysis showed that the intervention relating to reducing fluoroquinolone use in the community was associated with a significant trend change in MRSA incidence in community (coefficient = −0·00004, P = 0·0299). The reduction in high-risk antibiotic use and fluoroquinolone use contributed to both a reduction in incidence rates of MRSA in hospital and community (primary-care) settings.

This study reports clinico-epidemiological features and viral agents causing acute encephalitis syndrome (AES) in the eastern Indian region through hospital-based case enrolment during April 2011 to July 2012. Blood and CSF samples of 526 AES cases were investigated by serology and/or PCR. Viral aetiology was identified in 91 (17·2%) cases. Herpes simplex virus (HSV; types I or II) was most common (16·1%), followed by measles (2·6%), Japanese encephalitis virus (1·5%), dengue virus (0·57%), varicella zoster virus (0·38%) and enteroviruses (0·19%). Rash, paresis and cranial nerve palsies were significantly higher (P < 0·05) with viral AES. Case-fatality rates were 10·9% and 6·2% in AES cases with and without viral aetiology, respectively. Simultaneous infection of HSV I and measles was observed in seven cases. This report provides the first evidence on viral aetiology of AES viruses from eastern India showing dominance of HSV that will be useful in informing the public health system.

Two outbreaks of Leptospira borgpetersenii serovar Hardjo infection in dairy cattle herds were managed through the application of enhanced biosecurity measures, whole-herd antibiotic treatment and vaccination. Micro-agglutination test antibody titres were determined in paired serum samples at 3 weeks (T1: n = 125, 97% seropositivity, median 800, range 100–12 800) and 24 weeks (T2: n = 110, 88% seropositivity, median 200, range 100–6400) after vaccination and studied in relation to cows' age, herd of origin and sampling time. From T1 to T2, vaccine-elicited antibody titres decreased by 84·7% (95% CI 76·2–90·1). Consistent with increasing immunocompetence in calves (aged <12 months) and immunosenescence in adult cows (aged >36 months) associated with ageing, antibody titres correlated positively with calves' age and negatively with adult cows' age. No cow had cultivable, (histo)pathologically detectable and/or PCR-detectable leptospires in urine or kidney samples after treatment and vaccination. Vaccination together with proper biosecurity measures and chemoprophylaxis are an affordable insurance to control bovine leptospirosis.

This study evaluates the usefulness of spatio-temporal statistical tools to detect outbreaks using routine surveillance data where limited epidemiological information is available. A dataset from 2002 to 2007 containing information regarding date, origin, source and serotype of 29 586 Salmonella isolates from Thailand was analysed. Data was grouped into human and non-human categories and the analysis was performed for the top five occurring serovars for each year of the study period. A total 91 human and 39 non-human significant spatio-temporal clusters were observed, accounting for 11% and 16% of the isolates, respectively. Serovar-specific associations between human and non-human clusters were also evaluated. Results show that these statistical tools can provide information for use in outbreak prevention and detection, in countries where only limited data is available. Moreover, it is suggested that monitoring non-human reservoirs can be relevant in predicting future Salmonella human cases.

In September 2010, an outbreak of cryptosporidiosis affected members of a swimming club. A cohort study was undertaken to identify the number affected and risk factors for infection. Of 101 respondents, 48 met the case definition for probable cryptosporidiosis. Multivariate analysis demonstrated a strong and highly significant association between illness and attendance at a training session on 13 September 2010 (adjusted odds ratio 28, P < 0·0001). No faecal incidents were reported and pool monitoring parameters were satisfactory. The competitive nature of club swimming requires frequent training and participation in galas, potentially facilitating contamination into other pools and amplification of outbreaks among wider groups of swimmers. There was a lack of awareness of the 2-week exclusion rule among swimmers and coaches, and a high level of underreporting of illness. The study demonstrates the benefits of rapid field epidemiology in identifying the true burden of illness, the source of infection and limiting spread.

We estimated the incidence of pertussis in patients consulting general practitioners (GPs). Between July 2009 and April 2011, we conducted a prospective cohort study of patients attending 78 general practices (158 863 persons overall). We included patients aged ⩾3 years, with cough lasting 2–15 weeks, who gave informed consent. GPs interviewed eligible patients, collected a blood specimen, and a nasopharyngeal swab. At follow-up 30–60 days after the initial visit, physicians collected a second blood specimen and conducted patient interview. Cases were confirmed by specific IgA and/or IgG antibody titre exceeding significantly the general population background level or detection of bacterial DNA by real-time PCR. During the study period, 3864 patients with prolonged cough consulted the participating GPs, of those 1852 met the inclusion criteria, 1232 were recruited, and 288 were confirmed as pertussis cases (4% by PCR, 96% by serology). The adjusted incidence rate was 201·1/100 000 person-years [95% confidence interval (CI) 133·9–302·0], ranging from 456·5 (95% CI 239·3–870·8) in the 15–19 years group to 94·0 (95% CI 33·4–264·5) in the 25–29 years group. The reporting ratio was 61, ranging from 4 in those aged 3–5 years, to 167 in those aged 65–69 years. The study confirmed high incidence of pertussis in all age groups in the general population, in particular in adults, not appropriately documented by the existing surveillance system.

The exposure of indigenous humans and native fauna in Australia and the Wallacea zoogeographical region of Indonesia to exotic Salmonella serovars commenced during the colonial period and has accelerated with urbanization and international travel. In this study, the distribution and prevalence of exotic Salmonella serovars are mapped to assess the extent to which introduced infections are invading native wildlife in areas of high natural biodiversity under threat from expanding human activity. The major exotic Salmonella serovars, Bovismorbificans, Derby, Javiana, Newport, Panama, Saintpaul and Typhimurium, isolated from wildlife on populated coastal islands in southern temperate areas of Western Australia, were mostly absent from reptiles and native mammals in less populated tropical areas of the state. They were also not recorded on the uninhabited Mitchell Plateau or islands of the Bonaparte Archipelago, adjacent to south-eastern Indonesia. Exotic serovars were, however, isolated in wildlife on 14/17 islands sampled in the Wallacea region of Indonesia and several islands off the west coast of Perth. Increases in international tourism, involving islands such as Bali, have resulted in the isolation of a high proportion of exotic serovar infections suggesting that densely populated island resorts in the Asian region are acting as staging posts for the interchange of Salmonella infections between tropical and temperate regions.

Varicella accounts for substantial morbidities and remains a public health issue worldwide, especially in children. Little is known about the effect of meteorological variables on varicella infection risk for children. This study described the epidemiology of paediatric varicella notifications in Hong Kong from 2004 to 2010, and explored the association between paediatric varicella notifications in children aged <18 years and various meteorological factors using a time-stratified case-crossover model, with adjustment of potential confounding factors. The analysis found that daily mean temperature, atmospheric pressure and Southern Oscillation Index (SOI) were positively associated with paediatric varicella notifications. We found that an interquartile range (IQR) increase in temperature (8·38°C) at lag 1 day, a 9·50 hPa increase in atmospheric pressure for the current day, and a 21·91 unit increase in SOI for the current day may lead to an increase in daily cases of 5·19% [95% confidence interval (CI) 1·90–8·58], 5·77% (95% CI 3·01–8·61), and 4·32% (95% CI 2·98–5·68), respectively. An IQR increase in daily relative humidity (by 11·96%) was associated with a decrease in daily paediatric varicella (−2·79%, 95% CI −3·84 to −1·73). These findings suggest that meteorological factors might be important predictors of paediatric varicella infection in Hong Kong.

Aquatic wild birds are often carriers of low-pathogenic avian influenza viruses (LPAIVs). If H5 and H7 LPAIVs are transmitted to poultry and have the opportunity to circulate, a highly pathogenic AIV may arise. Contact with aquatic wild birds is one of the most important ways in which these LPAIVs can be introduced into poultry flocks. In this study, the transmissibility of a duck-originated H5 LPAIV between ducks and chickens was analysed in a series of animal experiments, using different transmission routes. Results indicate that the outcome of virus intake by chickens exposed to infectious ducks depends on the way the virus is presented. Faecally contaminated drinking water proved to be the most efficient route by which the virus can be transmitted to chickens. The results from this study also suggest that some duck-originated H5 LPAIVs may be introduced to poultry but do not have the potential to become established in poultry populations.

This research is focused on the epidemiological analysis of the transmission of the highly pathogenic avian influenza (HPAI) H5N1 virus outbreak in Nigeria. The data included 145 outbreaks together with the locations of the infected farms and the date of confirmation of infection. In order to investigate the environmental conditions that favoured the transmission and spread of the virus, weather stations were realigned with the locations of the infected farms. The spatial Kolmogorov–Smirnov test for complete spatial randomness rejects the null hypothesis of constant intensity (P < 0·0001). Preliminary exploratory analysis showed an increase in the incidence of H5N1 virus at farms located at high altitude. Results from the Poisson log-linear conditional intensity function identified temperature (−0·9601) and wind speed (0·6239) as the ecological factors that influence the intensity of transmission of the H5N1 virus. The model also includes distance from the first outbreak (−0·9175) with an Akaike's Information Criterion of −103·87. Our analysis using a point process model showed that geographical heterogeneity, seasonal effects, temperature, wind as well as proximity to the first outbreak are very important components of spread and transmission of HPAI H5N1.

Hepatitis C virus is the most common chronic blood-borne infection in the USA. Based on results of a serosurvey, national prevalence is estimated to be 1·3% or 3·2 million people. Sub-national estimates are not available for most jurisdictions. Hepatitis C surveillance data was adjusted for death, out-migration, under-diagnosis, and undetectable blood RNA, to estimate prevalence in New York City (NYC). The prevalence of hepatitis C infection in adults aged ⩾20 years in NYC is 2·37% (range 1·53–4·90%) or 146 500 cases of hepatitis C. This analysis presents a mechanism for generating prevalence estimates using local surveillance data accounting for biases and difficulty in accessing hard to reach populations. As the cohort of patients with hepatitis C age and require additional medical care, local public health officials will need a method to generate prevalence estimates to allocate resources. This approach can serve as a guideline for generating local estimates using surveillance data that is less resource prohibitive.

Two community-based density case-control studies were performed to assess risk factors for cholera transmission during inter-peak periods of the ongoing epidemic in two Haitian urban settings, Gonaives and Carrefour. The strongest associations were: close contact with cholera patients (sharing latrines, visiting cholera patients, helping someone with diarrhoea), eating food from street vendors and washing dishes with untreated water. Protective factors were: drinking chlorinated water, receiving prevention messages via television, church or training sessions, and high household socioeconomic level. These findings suggest that, in addition to contaminated water, factors related to direct and indirect inter-human contact play an important role in cholera transmission during inter-peak periods. In order to reduce cholera transmission in Haiti intensive preventive measures such as hygiene promotion and awareness campaigns should be implemented during inter-peak lulls, when prevention activities are typically scaled back.

The last report on pertussis seroprevalence in Belgium concerned samples collected during 1993–1994. In the context of the Eupert-Labnet WP6 seroprevalence study (comparing sera from 16 European member states), 1500 anonymized leftover diagnostic samples were collected randomly during the second semester of 2012 by the clinical chemistry laboratories of six participating Belgian centres, distributed equally between Flanders, Wallonia and Brussels Capital Region. As suggested by the WP6 organizers, a total of 750 samples (125/centre) were selected from subjects in the 20–29 years age group and 750 samples (125/centre) from subjects in the 30–39 years age group. Anti-PT IgG levels were measured using Virion-Serion ELISA and analysed using predefined cut-off levels. Sixty-one (4%) sera were indicative of an infection in the past 2 years (between 50 and 100 IU/ml) and another 61 (4%) sera had anti-PT IgG antibodies reflecting acute infection (>100 IU/ml). These results highlight the presence of a Bordetella pertussis reservoir in the adult ‘healthy’ Belgian population.

We aimed to assess whether the characteristics of influenza-like illness (ILI) cases in the general population were similar during the seasonal and pandemic A(H1N1)pdm09 influenza periods. We conducted a study using a general population database, which included demographic (sex, age) and clinical (underlying medical conditions, influenza vaccination status) information on more than 80 000 subjects. We assessed the most important predictors of ILI during each season by using multiple logistic regression. We descriptively compared whether they were similar during different seasons. The model, including all demographic and clinical characteristics, showed that age ⩾60 years decreased the odds for ILI by 52% and 81% during the seasonal and A(H1N1)pdm09 pandemic periods, respectively. Being vaccinated decreased the odds of ILI for seasonal influenza by 32%, while suffering from the comorbidities other than lung or cardiovascular diseases doubled the odds of ILI during the A(H1N1)pdm09 pandemic.

We studied the association between drinking water, agriculture and sporadic human campylobacteriosis in one region of British Columbia (BC), Canada. We compared 2992 cases of campylobacteriosis to 4816 cases of other reportable enteric diseases in 2005–2009 using multivariate regression. Cases were geocoded and assigned drinking water source, rural/urban environment and socioeconomic status (SES) according to the location of their residence using geographical information systems analysis methods. The odds of campylobacteriosis compared to enteric disease controls were higher for individuals serviced by private wells than municipal surface water systems (odds ratio 1·4, 95% confidence interval 1·1–1·8). In rural settings, the odds of campylobacteriosis were higher in November (P = 0·014). The odds of campylobacteriosis were higher in individuals aged ⩾15 years, especially in those with higher SES. In this region of BC, campylobacteriosis risk, compared to other enteric diseases, seems to be mediated by vulnerable drinking water sources and rural factors. Consideration should be given to further support well-water users and to further study the microbiological impact of agriculture on water.

We studied the seasonal fluctuation of norovirus and other enteric viruses in Cameroon. Two hundred participants aged between 1 and 69 years were prospectively followed up. Each participant provided monthly faecal samples over a 12-month period. A total of 2484 samples were tested using multiplex real-time PCR assay for the detection of norovirus, rotavirus and enterovirus. The effect of weather variables and risk factors were analysed by Pearson correlation and bivariate analysis. Overall, enterovirus was the most commonly detected virus (21·6% of specimens), followed by norovirus (3·9%) and rotavirus (0·4%). Norovirus and enterovirus were detected throughout the year with a peak of norovirus detection at the beginning of the rainy season and a significant alternation of circulation of norovirus genogroups from one month to the next. Age <5 years and consumption of tap water were risk factors for norovirus infection. Better understanding of factors influencing transmission and seasonality may provide insights into the relationship between physical environment and risk of infection for these viruses.

Community-acquired Staphylococcus aureus infections are a public health concern, yet little is known about infections that do not present to hospital. We identified community-onset S. aureus infections via specimens submitted to a community-based pathology service. Referring doctors confirmed eligibility and described infection site, severity and treatment. Isolates were characterized on antibiotic resistance, PFGE, MLST/SCCmec, and Panton–Valentine leukocidin (PVL), representing 106 community-onset infections; 34 non-multiresistant methicillin-resistant S. aureus (nmMRSA) (resistant to <3 non-β-lactam antibiotics), 15 multiply antibiotic-resistant MRSA (mMRSA) and 57 methicillin-sensitive S. aureus (MSSA). Most (93%) were skin and soft tissue infections. PVL genes were carried by 42% of nmMRSA isolates [95% confidence interval (CI) 26–61] and 15% of MSSA (95% CI 8–28). PVL was associated with infections of the trunk, head or neck (56·4% vs. 24·3%, P = 0·005) in younger patients (23 vs. 52 years, P < 0·001), and with boils or abscesses (OR 8·67, 95% CI 2·9–26·2), suggesting underlying differences in exposure and/or pathogenesis.

Socio-behavioural factors and pathogens associated with childhood diarrhoea are of global public health concern. Our survey in 696 children aged ⩽2 years in rural West Bengal detected rotavirus as sole pathogen in 8% (17/199) of diarrhoeic stool specimens. Other organisms were detected along with rotavirus in 11% of faecal specimens. A third of the children with rotavirus diarrhoea, according to Vesikari score, had severe illness. The top four rotavirus genotypes were G9P[4] (28%), G1P[8] (19%), G2P[4] (14%) and G8P[4] (8%). In the multivariate model, the practice of ‘drawing drinking water by dipping a pot in the storage vessel’ [adjusted odds ratio (aOR) 2·21, 95% confidence interval (CI) 1·03–4·74, P = 0·041], and ‘children aged ⩽6 months with non-exclusive breastfeeding’ (aOR 2·07, 95% CI 1·1–3·82, P = 0·024) had twice the odds of having diarrhoea. Incidence of rotavirus diarrhoea was 24/100 child-years in children aged >6–18 months, 19/100 child-years in children aged >18–24 months and 5/100 child-years in those aged ⩽6 months. Results have translational implications for future interventions including vaccine development.

Botulism has rarely been reported in Africa. In October 2008, botulism was reported in three Ugandan boarding-school students. All were hospitalized and one died. A cohort study was performed to assess food exposures among students, and clinical specimens and available food samples were tested for botulinum toxin. Three case-patients were identified; a homemade, oil-based condiment was eaten by all three. In the cohort study, no foods were significantly associated with illness. Botulinum toxin type A was confirmed in clinical samples. This is the first confirmed outbreak of foodborne botulism in Uganda. A homemade, oil-based condiment was the probable source. Consumption of homemade oil-based condiments is widespread in Ugandan schools, putting children at risk. Clinicians and public health authorities in Uganda should consider botulism when clusters of acute flaccid paralysis are seen. Additionally, schools should be warned of the hazard of homemade oil-based condiments, and take steps to prevent their use.