This study estimated the effect of discontinued use of antimicrobial growth promoters (duAGPs) on the risk of antibiotic treatment for diarrhoea, arthritis, pneumonia, unthriving and miscellaneous disorders in Danish pig farms. The estimation was done in a case-crossover study comparing: (1) the proportion of days per farm where treatment was performed (PDT) and (2) the proportion of pigs treated per day per farm at days where treatment was performed (PPT) before and after duAGPs at 68 farrow-to-finish farms. The farms were selected using a two-stage (veterinarian/farm) convenience sampling. On average, during the first year after duAGPs there was a significant increase in the risk of antibiotic treatment for diarrhoea (PDT: OR 2·5, 95% CI 1·7–3·8; PPT: OR 1·6, 95% CI 1·1–2·2). However, the effect varied among farms – some farms experienced substantial problems, while others experienced few problems after duAGPs. No effect was identified for the risk of treatment for other diseases.

We studied the role of host genetics in the susceptibility to severe Salmonella and Campylobacter infections and chronic sequelae of these infections. Participants of a previous case-control study were sent a buccal swab kit and a questionnaire about occurrence of chronic sequelae. Single nucleotide polymorphisms (SNPs) in the TLR4 (rs4986790), IFNG (rs2430561 and rs1861493), STAT1 (rs1914408), IL1B (rs16944), NRAMP (SLC11A1 rs2276631), JUN (rs11688) and VDR (rs10735810) genes were determined. In total, 687 controls, 457 Campylobacter cases and 193 Salmonella cases participated. None of the SNPs were associated with Campylobacter or Salmonella infections. None of the participants developed Guillain–Barré, Miller–Fisher or Reiter's syndrome. Reactive arthritis occurred in 5% and 2% of cases and controls, respectively. Campylobacter cases more frequently experienced gastroenteritis episodes than controls. Campylobacter or Salmonella infection in women, use of proton pump inhibitors and an SNP in the IFNG gene were independent risk factors for reactive arthritis. Another SNP in the IFNG gene and use of proton pump inhibitors were risk factors for recurrent episodes of gastroenteritis. In conclusion, reactive arthritis and recurrent gastroenteritis episodes are common after infection and host genetic factors play a role in susceptibility to these long-term health effects.

A follow-on study was carried out on 23 holdings identified as Salmonella positive in the 2004/2005 European Union (EU) baseline survey of Salmonella in laying hens. Eleven of 13 cage and 4/7 floor houses remained positive for Salmonella when the new flock was tested, and from 10/13 cage and 3/7 floor houses a Salmonella of the same serovar/phage type as found in the EU survey was isolated. There was a high correlation between the level of contamination in the houses at the time of the EU survey and in the follow-on flock. On seven occasions the house identified as positive in the EU survey was sampled after cleaning and disinfection but before a new flock was placed, and in all of them Salmonella could be isolated from the houses. The observed number of infected houses in infected holdings suggests that the holding-level prevalence in the United Kingdom would be about 21% higher than the results obtained in the EU survey.

In New Zealand human cryptosporidiosis demonstrates spring and autumn peaks of incidence with the spring peak being three times greater in magnitude than the autumn peak. The imbalance between the two peaks is notable, and may be associated with the high livestock density in New Zealand. In the summer and autumn the cryptosporidiosis rate was positively associated with temperatures in the current and previous month, highlighting the importance of outdoor recreation to transmission. No associations between spring incidence and weather were found providing little support for the importance of drinking-water pathways. Imported travel cases do not appear to be an important factor in the aetiology of cryptosporidiosis in New Zealand.

Introduction of pneumococcal conjugate and polysaccharide vaccines into the United Kingdom's routine immunization programmes is expected to change the epidemiology of invasive pneumococcal disease (IPD). We have documented the epidemiology of IPD in an English region (South West) with high-quality surveillance data before these programmes were established. We analysed data on isolates of Streptococcus pneumoniae from blood and CSF between 1996 and 2005 from microbiology laboratories in the South West that were reported and/or referred for serotyping to the Health Protection Agency Centre for Infections. The mean annual incidence of IPD increased from 11·2/100 000 in 1996 to 13·6/100 000 in 2005 (P<0·04). After adjusting for annual blood-culture sampling rates in hospitals serving the same catchment populations, an increase in annual incidence of IPD was no longer observed (P=1·0). Variation in overall incidence between laboratories could also be explained by variation in blood culture rates. The proportion of disease caused by serotypes 6B, 9V and 14 decreased significantly (P=0·001, P=0·007, and P=0·027 respectively) whereas that caused by serotype 4, 7F and 1 increased (P=0·001, P=0·003, and P<0·001 respectively) between 2000 and 2005. The level of penicillin non-susceptibility and resistance to erythromycin remained stable (2% and 12% respectively). This study provides an important baseline to assess the impact of changing vaccination programmes on the epidemiology of IPD, thus informing future use of pneumococcal vaccines.

Deterministic SIR models were applied to simulate Susceptible–Infected–Removed and to estimate the threshold condition for varicella outbreaks in children, reported in Medellín, Colombia. The expected numbers of susceptible, infected and removed individuals were compared with observed cases from notification of varicella outbreaks to the local Board of Health and from survey data. The threshold condition was estimated by the basic reproductive ratio and by the relative removal rate, through which measures for preventing and curtailing the outbreaks were identified. The model demonstrated a reasonable fit to the observations, except in two of the six outbreaks which probably reflected under-registration of cases. In order to have prevented these outbreaks, between 4·4% and 52·9% of the susceptible population should have been vaccinated assuming an 85% vaccine effectiveness. Similarly, isolation of affected children should have been increased to between 4·3% and 44·8% per week.

A flexible hierarchical Bayesian spatiotemporal regression model for foot-and-mouth disease (FMD) was applied to data on the annual number of reported FMD cases in Turkey from 1996 to 2003. The longitudinal component of the model was specified as a latent province-specific stochastic process. This stochastic process can accommodate various types of FMD temporal profiles. The model accounted for differences in FMD occurrence across provinces and for spatial correlation. Province-level covariate information was incorporated into the analysis. Results pointed to a decreasing trend in the number of FMD cases in western Turkey and an increasing trend in eastern Turkey from 1996 to 2003. The model also identified provinces with high and with low propensities for FMD occurrence. The model's use of flexible structures for temporal trend and of generally applicable methods for spatial correlation has broad application to predicting future spatiotemporal distributions of disease in other regions of the world.

This study examines the validity of using ICD-10 codes to identify hospitalized pneumonia cases. Using a case-cohort design, subjects were randomly selected from monthly cohorts of patients aged ⩾65 years discharged from April 2000 to March 2002 from two large tertiary Australian hospitals. Cases had ICD-10-AM codes J10–J18 (pneumonia); the cohort sample was randomly selected from all discharges, frequency matched to cases by month. Codes were validated against three comparators: medical record notation of pneumonia, chest radiograph (CXR) report and both. Notation of pneumonia was determined for 5098/5101 eligible patients, and CXR reports reviewed for 3349/3464 (97%) patients with a CXR. Coding performed best against notation of pneumonia: kappa 0·95, sensitivity 97·8% (95% CI 97·1–98·3), specificity 96·9% (95% CI 96·2–97·5), positive predictive value (PPV) 96·2% (95% CI 95·4–97·0) and negative predictive value (NPV) 98·2% (95% CI 97·6–98·6). When medical record notation of pneumonia is used as the standard, ICD-10 codes are a valid method for retrospective ascertainment of hospitalized pneumonia cases and appear superior to use of complexes of symptoms and signs, or radiology reports.

Cercarial dermatitis is caused by exposure to the cercariae of schistosome species which have birds or mammals as their definitive hosts. A public alarm was raised in the summer of 2004 when this parasitic disease was observed for the first time in south-central Chile at Laguna Chica de San Pedro (36° 51″ S, 73° 05″ W). Swimmers at this eutrophic lake were surveyed in order to estimate the amount of cercarial dermatitis in the area; participants were observed during the summers of 2004 and 2005 for clinical signs of cercarial dermatitis and 25 Chilina dombeyana snails were collected monthly from Laguna Chica de San Pedro during one year and then examined for animal schistosome cercariae. We found that 3% of the swimmers had pruritic maculopapular rashes on their legs, arms, necks, or other body parts and that between 9·1% (May 2006) and 52·4% (November 2004) of the snails examined were infected with the bird schistosome cercariae Trichobilharzia sp.

The weekly number of dengue cases in Peru, South America, stratified by province for the period 1994–2006 were analysed in conjunction with associated demographic, geographic and climatological data. Estimates of the reproduction number, moderately correlated with population size (Spearman ρ=0·28, P=0·03), had a median of 1·76 (IQR 0·83–4·46). The distributions of dengue attack rates and epidemic durations follow power-law (Pareto) distributions (coefficient of determination >85%, P<0·004). Spatial heterogeneity of attack rates was highest in coastal areas followed by mountain and jungle areas. Our findings suggest a hierarchy of transmission events during the large 2000–2001 epidemic from large to small population areas when serotypes DEN-3 and DEN-4 were first identified (Spearman ρ=−0·43, P=0·03). The need for spatial and temporal dengue epidemic data with a high degree of resolution not only increases our understanding of the dynamics of dengue but will also generate new hypotheses and provide a platform for testing innovative control policies.

Over 50% of the global burden of tuberculosis occurs in South East Asia and the Western Pacific. Since 1950, notification rates in high-income countries in these settings have declined slowly and have remained over ten-fold greater than those in Western populations. The reasons for the slow decline are poorly understood. Using an age-structured model describing the incidence of Mycobacterium tuberculosis infection and disease applied to notification data from Hong Kong, we illustrate that in Hong Kong, a high prevalence of M. tuberculosis infection among older individuals and a high risk of disease through reactivation (e.g. up to 17-fold greater than that estimated for infected males in the United Kingdom) may explain this slow decline. If this feature of the epidemiology of tuberculosis is widespread, the WHO directly observed treatment short-course (DOTS) strategy may have a smaller impact in Asia in the short term than has been implied by recent predictions, all of which have been based on disease risk estimates derived from Western Europe. As a result, it may be difficult to meet the targets for tuberculosis control, which have been prescribed by the UN Millennium Development Goals.

The first dog-associated outbreak of rabies in swine in China (Hunan province) has been diagnosed and the related virus isolated. Sequence analysis showed that the pig isolate was a genotype 1 rabies virus with a very high nucleotide identity to local dog isolates.

Rapid notification of infectious diseases is essential for prompt public health action and for monitoring of these diseases in the Irish population at both a local and national level. Anecdotal evidence suggests, however, that the occurrence of notifiable infectious diseases is seriously underestimated. This study aims to assess the level of hospitalization for notifiable infectious diseases for a 6-year period in one health board region in Ireland and to assess whether or not there was any under-reporting during this period. All hospital in-patient admissions from 1997 to 2002 inclusive with a principal diagnosis relating to ‘infectious and parasitic diseases’ (ICD codes 001–139) of residents from a health board region in Ireland were extracted from the Hospital In-Patient Enquiry System (HIPE). All notifiable infectious diseases were identified based on the 1981 Irish Infectious Disease Regulations and the data were analysed in the statistical package, JMP. These data were compared with the corresponding notification data. Analysis of the hospital in-patient admission data revealed a substantial burden associated with notifiable infectious diseases in this health board region: there were 2758 hospitalizations by 2454 residents, 17 034 bed days and 33 deaths. The statutory notification data comprises both general practitioner and hospital clinician reports of infectious disease. Therefore, only in cases where there are more hospitalizations than notifications can under-reporting be demonstrated. This occurred in nine out of 22 notifiable diseases and amounted to an additional 18% of notifications (or 572 cases) which were ‘missed’ due to hospital clinician under-reporting. The majority of these under-reported cases were for viral meningitis (45%), infectious mononucleosis (27%), viral hepatitis C unspecified (15%) and acute encephalitis (5·8%). This study has highlighted the extent of under-reporting of hospitalized notifiable infectious diseases, in a health board region in Ireland, which is a cause for concern from a surveillance point of view. If this under-reporting is similar in other health boards, then it would appear that the epidemiology of some notifiable diseases is incomplete both regionally and nationally. This under-reporting negatively impacts on the effectiveness of the notification process as a ‘real-time’ surveillance tool and an early warning system for outbreaks.

A national, population-based laboratory surveillance of bloodstream infections (BSI) in Finland was performed. Blood-culturing rates were determined from data from clinical microbiology laboratories and trends in rates were evaluated using Poisson regression. During 1995–2002, 51 510 cases of BSI were notified; the annual incidence increased from 104 to145 cases/100 000 (40%). Rates increased in all age groups but persons aged ⩾75 years accounted for 28% of cases and showed the largest rate increase. Escherichia coli, coagulase-negative staphylococci, Staphylococcus aureus and Streptococcus pneumoniae accounted for 58% of isolates and their relative proportions were unchanged over time. The annual blood-culturing rate increased by one-third during the study period but the number of BSI detected per blood cultures remained unchanged. Regional BSI incidence was significantly associated with blood-culturing rates. We conclude that the increase in BSI rates may have been due to more frequent blood culturing but was not associated with changes in the reporting system or aetiology of BSI.

The objectives of this study were to identify factors associated with Salmonella status at the farm, pen, and pig level; explore the nature of variation in the association between the pen-level Salmonella status and pen-level covariates, and pig-level Salmonella status and pig- and pen-level covariates; and to identify the relative importance of factors operating at geographical, farm, and pen level for Salmonella shedding of pigs. For these purposes, samples from 799 pigs and 374 pens on 80 farms in Ontario in 2004 were collected and bacteriologically tested in a cross-sectional study. Census division was the least variable level, and farm the most variable level for shedding. Increased frequency of disinfection and washing with cold water were positively associated with Salmonella positivity, whereas liquid and mash feed and completely closed barns were sparing factors. After farm, pen was the second most variable level for shedding. However, no measured pen-level variables were associated with Salmonella status of pigs or pens. The shedding of Salmonella at the pig level tended to be associated with pig weight, and there was no random variation around this association. Results of this study suggest that a herd test based on bacteriological culture would probably have higher sensitivity if growing animals of lower weight were sampled instead of market weight animals, and this might be beneficial for Salmonella monitoring.

A prospective survey on scabies in Ghent, Belgium was performed in 2004. Sixty-four individual cases were reported, corresponding to a crude incidence rate of 28/100 000 inhabitants. The incidence was higher in the elderly (51/100 000 in persons aged >75 years) and a higher incidence was also found in immigrants (88/100 000). More than 40% of the registered scabies patients had symptoms for more than 4 weeks at the time of presentation. In 54% of the consultations, the patient had already consulted a physician for his/her skin problem. Of this group, 44% had not yet received any scabicidal treatment, indicating that scabies was not yet diagnosed or that an inappropriate treatment was prescribed. The observations suggest that the diagnosis and/or treatment of scabies in this region can still be improved.

Interactive water fountains are established sources of gastrointestinal infections yet most health codes fail to regulate their design and operation. This report describes multi-agency, concurrent interactive fountain-associated cryptosporidiosis and salmonellosis outbreak investigations and highlights the need for the adoption of appropriate regulations for interactive fountains.

Forty-one newly sequenced isolates of Arctic and Arctic-like rabies viruses, were genetically compared to each other and to those available from GenBank. Four phylogenetic lineages of Arctic viruses were identified. Arctic-1 viruses circulate in Ontario, Arctic-2 viruses circulate in Siberia and Alaska, Arctic-3 viruses circulate circumpolarly, and a newly described lineage Arctic-4 circulates locally in Alaska. The oldest available isolates from Siberia (between 1950 and 1960) belong to the Arctic-2 and Arctic-3 lineages and share 98·6–99·2% N gene identity with contemporary viruses. Two lineages of Arctic-like viruses were identified in southern Asia and the Middle East (Arctic-like-1) and eastern Asia (Arctic-like-2). A time-scaled tree demonstrates that the time of the most recent common ancestor (TMRCA) of Arctic and Arctic-like viruses is dated between 1255 and 1786. Evolution of the Arctic viruses has occurred through a northerly spread. The Arctic-like-2 lineage diverged first, whereas Arctic viruses share a TMRCA with Arctic-like-1 viruses.

Case reports have indicated transmission of Staphylococcus aureus between humans and pets. We investigated associations between level of contact between dog and owner, and S. aureus colonization. In a cross-sectional study, nasal carriage and antibiotic susceptibility of S. aureus was determined for 830 dogs and 736 owners. Relatedness of isolates was investigated using antibiograms and pulsed-field gel electrophoresis (PFGE). Associations between carriage and demographics or amount of contact between owners and dogs were documented. S. aureus was isolated in 24% of humans and 8·8% of dogs. Antibiotic resistance was significantly more common in canine isolates. Of 17 owner/dog colonized pairs, six were indistinguishable by PFGE. Colonization of dogs was not associated with close human contact, but was strongly associated with health-care occupations (OR 3·29, 95% CI 1·49–7·26, P=0·002). In outbreak situations health-care workers' pets should be considered as a source of S. aureus. High rates of resistance indicate increased monitoring of antibiotic use in veterinary practice is needed.

Individuals belonging to five families, 12 genera, and 19 different species of bats from dengue endemic areas in the Gulf and Pacific coasts of Mexico were examined by ELISA, RT–PCR, and for the presence of dengue virus (DV) NS1 protein. Nine individuals from four species were seropositive by ELISA: three insectivorous, Myotis nigricans (four positives/12 examined), Pteronotus parnellii (3/19), and Natalus stramineus (1/4), and one frugivorous Artibeus jamaicensis (1/35) (12·86% seroprevalence in positive species). DV serotype 2 was detected by RT–PCR in four samples from three species (all from the Gulf coast – rainy season): two frugivorous, A. jamaicensis (2/9), and Carollia brevicauda (1/2), and one insectivorous, M. nigricans (1/11). The latter was simultaneously positive for NS1 protein. DV RT–PCR positive animals were all antibody seronegative. M. nigricans showed positive individuals for all three tests. This is the first evidence suggesting the presence of DV in bats from Mexico.