The objectives of our study were to identify and categorize primary research investigating swine/pork as a source of zoonotic hepatitis E virus (HEV) using the relatively new technique of scoping study, and to investigate the potential association between human exposure to swine/pork and HEV infection quantitatively using systematic review/meta-analysis methodology. From 1890 initially identified abstracts, 327 were considered for the review. Five study design types (cross-sectional, prevalence, genotyping, case-report and experimental transmission studies) were identified. A significant association between occupational exposure to swine and human HEV IgG seropositivity was reported in 10/13 cross-sectional studies. The association reported between pork consumption and HEV IgG seropositivity was inconsistent. The quantification of viral load in swine and retail pork, viral load required for infection in primates, cohort and case-control studies in humans, and formal risk assessment are recommended before specific public-health policy actions are taken.

Hepatitis E virus (HEV) infection is as an emerging disease of global importance because it is one of the major causes of acute hepatitis worldwide. There are few reports on the incidence of HEV in the USA. For better assessing the burden of primary HEV infection as well as understanding the epidemiology of HEV in the US population this analysis was conducted to estimate the force of infection of HEV in the USA. HEV force of infection in the general US population was calculated using catalytic models as cumulative markers of past infection from HEV seroprevalence data from the NHANES Survey. In the US population the force of infection was seven infections per 1000 susceptible persons per year. This study shows that in the USA HEV can be acquired locally and from developing countries. HEV is circulating more frequently in the non-Hispanic White racial/ethnic group and those who consume fish more frequently.

To determine the extent age, sex and co-infection affect morbidity in people infected with hepatitis C virus (HCV), we performed a population-based study linking HCV notifications in New South Wales, Australia with their hospital (July 2000 to June 2006), hepatitis B virus (HBV) and HIV notification, and death records. Poisson models were used to calculate hospitalization rate ratios (RRs) for all-cause, illicit drug and liver-related admissions. Co-infection RRs were used to estimate attributable risk (AR). The 86 501 people notified with HCV contributed 422 761 person-years of observation; 0·8% had HIV, 3·7% HBV, and 0·04% had both. RRs for males were equal to or lower than for females in younger ages, but higher in older ages (P for interaction ⩽0·013). HBV/HIV co-infection resulted in ARs of over 70% for liver disease and 30–60% otherwise. However, at the cohort level the impact was minimal (population ARs 1·3–8·7%). Our findings highlight the importance and success of public health measures, such as needle and syringe exchange programmes, which have helped to minimize the prevalence of co-infection in Australia. The findings also suggest that the age of study participants needs to be considered whenever the burden of HCV-related morbidity is reported by sex. The results are likely to be representative of patterns in hospital-related morbidity for the entire HCV-infected population in Australia and the ARs generalizable to other developed countries.

A universal hepatitis B vaccination programme has been conducted in Long An county since 1986. To investigate the epidemiological changes in hepatitis B virus (HBV) infection we conducted a serosurvey there in 2005. A total of 4686 subjects were enrolled and vaccination history and blood samples collected. HBV infective markers were determined by radioimmunoassay. The results were compared with the data of 1985. Our results show that the overall HBsAg prevalence was 7·5%, less than half of the prevalence reported in 1985. HBsAg and anti-HBc antibody prevalence in people born after 1985 decreased markedly. The gender difference in HBsAg prevalence was abolished in subjects aged <20 years. The administration of a first dose of vaccine within 24 h could reduce the HBsAg prevalence by half. In conclusion, the marked epidemiological changes in HBV prevalence found in this serosurvey indicate that the implementation of HBV vaccination was highly successful.

An unlinked anonymous survey was conducted to measure the prevalence of selected markers for HIV, hepatitis B and C infection in recruits to the UK Armed Forces to inform future screening and hepatitis B vaccination policies. During 2007, nearly 14 000 left-over samples taken from new recruits for blood typing were collected, unlinked from identifiers and anonymously tested for HIV, hepatitis C and current and past cleared hepatitis B infection. Overall, serological evidence of HIV and hepatitis C was found in 0·06% and 0·06% of recruits, respectively. Evidence of past cleared and current hepatitis B infection was found in 3·63% and 0·37% of recruits, respectively. Overall, prevalence rates were broadly consistent with UK population estimates of infection. However, HIV and hepatitis B prevalence was higher in recruits of African origin than in those from the UK (P<0·0001). Screening for these infections is an option that could be considered for those entering Services from high-prevalence countries.

The prevalence of antibodies to hepatitis A virus (HAV) was assessed in a nationwide sample (n=6229) in The Netherlands in 2006–2007, and compared to the seroprevalence in a similar study in 1995–1996 (n=7376). The overall seroprevalence increased from 34% in 1995–1996 to 39% in 2006–2007, mainly due to vaccination of travellers and an increased immigrant population. Risk factors remain travelling to, and originating from, endemic regions, and vaccination is targeted currently at these risk groups. Our results show a trend of increasing age of the susceptible population. These people would also benefit from HAV vaccination because they are likely to develop clinically serious symptoms after infection, and are increasingly at risk of exposure through imported viruses through foods or travellers. The cost-effectiveness of adding elderly people born after the Second World War as a target group for prophylactic vaccination to reduce morbidity and mortality after HAV infection should be assessed.

Mathematical models of influenza pandemics are sensitive to changes in contact rates between individuals. We conducted population-based telephone surveys in four North Carolina counties to determine the number of social interactions between individuals during the 2007–2008 influenza season. Influenza activity was monitored through sentinel medical practices. Among 3845 adults, the number of social contacts varied with age, was lower on weekends than on weekdays, and further decreased during school holiday periods. Adults with influenza-like illnesses had fewer social contacts. Adults' contacts in the community setting increased during periods of peak influenza activity. Among 290 children, potential contacts (i.e. other people in the same location) were lowest among preschool-age children and decreased on weekends and during school holidays. In adjusted analyses, children's potential social contacts did not change during periods of peak influenza activity. These results should be useful for modelling influenza epidemics and pandemics and in planning mitigation and response strategies.

Phylogenetic analysis was performed on the haemagglutinin and neuraminidase subtype N2 genes of low-pathogenic avian influenza viruses (LPAIVs) detected in Ireland between 2003 and 2007. Nucleotide sequences were compared to previously published sequences from the National Centre for Biotechnology Information. Sequences from viruses of the same subtype isolated in different years were compared to examine the possibility that LPAIVs may have been maintained in Ireland from year to year. All viruses had closest identity with published sequences of European lineage, supporting the conclusion that LPAIVs had been introduced to Ireland by dabbling ducks that had migrated from Europe. The data suggested that different subtypes of virus had been introduced each year. However, there was evidence that some LPAIVs may have been maintained in the sedentary waterfowl population for consecutive seasons. Furthermore, almost identical H6 and H10 sequences with different N types were found in isolates from the same season, suggesting that reassortment had occurred.

In France, the surveillance of hospitalized cases of pandemic influenza was implemented in July 2009 and restricted to intensive-care unit (ICU) patients in November. We described the characteristics of the 1065 adult patients admitted to ICUs and analysed risk factors for severe outcome (mechanical ventilation or death). Eighty-seven percent of cases were aged 15–64 years. The case-fatality ratio was 20%. The risk for severe outcome increased with age and obesity while this association was negative for chronic respiratory disease. Late antiviral therapy was associated with a severe outcome in ICU patients with risk factors (adjusted OR 2·0, 95% CI 1·4–3·0). This study confirms the considerable contribution of young adults to A(H1N1) 2009 mortality. It shows the role of obesity as an independent risk factor for severe disease, and of early antiviral therapy as a protective factor, at least in patients with risk factors.

Understanding seasonal changes in age-related incidence of infections can be revealing for disentangling how host heterogeneities affect transmission and how to control the spread of infections between social groups. Seasonal forcing has been well documented in human childhood diseases but the mechanisms responsible for age-related transmission in free-living and socially structured animal populations are still poorly known. Here we studied the seasonal dynamics of Bordetella bronchiseptica in a free-living rabbit population over 5 years and discuss the possible mechanisms of infection. This bacterium has been isolated in livestock and wildlife where it causes respiratory infections that rapidly spread between individuals and persist as subclinical infections. Sera were collected from rabbits sampled monthly and examined using an ELISA. Findings revealed that B. bronchiseptica circulates in the rabbit population with annual prevalence ranging between 88% and 97%. Both seroprevalence and antibody optical density index exhibited 1-year cycles, indicating that disease outbreaks were seasonal and suggesting that long-lasting antibody protection was transient. Intra-annual dynamics showed a strong seasonal signature associated with the recruitment of naive offspring during the breeding period. Infection appeared to be mainly driven by mother-to-litter contacts rather than by interactions with other members of the community. By age 2 months, 65% of the kittens were seropositive.

Bovine tuberculosis (TB) is primarily a disease of cattle. In both Ireland and the UK, badgers (Meles meles) are an important wildlife reservoir of infection. This paper examined the hypothesis that TB is spatially correlated in cattle herds, established the range of correlation and the effect, if any, of proactive badger removal on this. We also re-analysed data from the Four Area Project in Ireland, a large-scale intervention study aimed at assessing the effect of proactive badger culling on bovine TB incidence in cattle herds, taking possible spatial correlation into account. We established that infected herds are spatially correlated (the scale of spatial correlation is presented), but at a scale that varies with time and in different areas. Spatial correlation persists following proactive badger removal.

Rodents are a potential source of pathogenic Yersinia enterocolitica and Y. pseudotuberculosis. In order to study this, 190 rodents were captured and sampled on seven pig farms (n=110), five chicken farms (n=55) and six other locations (n=25) in Sweden. Pigs from three of the pig farms were also sampled (n=60). Pathogenic Y. enterocolitica was detected by TaqMan PCR in about 5% of rodent samples and 18% of pig samples. Only rodents caught on pig farms tested positive for the pathogen. Y. enterocolitica bioserotype 4/O:3 strains isolated from the rodent and pig samples were compared by pulsed-field gel electrophoresis and revealed a high degree of similarity, which was confirmed by random amplified polymorphic DNA. Y. pseudotuberculosis was only detected in one rodent sample. Thus, rodents may be vectors for the transmission of pathogenic Y. enterocolitica to pigs, acting as carriers rather than a reservoir, and should therefore remain an important issue in hygiene control measures on farms.

In 2005, over 600 clinically diagnosed typhoid fever cases occurred in South Africa, where an outbreak had been previously described in 1993. Case-control and molecular investigations, including Salmonella enterica serovar Typhi (S. Typhi) isolates from that area from 1993, 2005 and later, were undertaken. Controls were significantly older than cases (P=0·003), possibly due to immunity from previous infection, and a significantly larger proportion had attended a gathering (P=0·035). Exposure to commercial food outlets and person-to-person transmission was not significant. Pulsed-field gel electrophoresis and multi-locus tandem repeat analysis revealed common clusters of S. Typhi strains identified in 1993 and 2005 as well as in 2007 and 2009. This outbreak probably occurred in a non-immune population due to faecally contaminated water. S. Typhi strains appeared to be related to strains from 1993; failure to address unsafe water may lead to further outbreaks in the area if the current population immunity wanes or is lost.

The aim of this study was to identify the sources of sporadic domestic Salmonella cases in Sweden and to evaluate the usefulness of a source-attribution model in a country in which food animals are virtually free from Salmonella. The model allocates human sporadic domestic Salmonella cases to different sources according to distribution of Salmonella subtypes in the different sources. Sporadic domestic human Salmonella cases (n=1086) reported between July 2004 and June 2006 were attributed to nine food-animal and wildlife sources. Of all Salmonella cases, 82% were acquired abroad and 2·9% were associated with outbreaks. We estimated that 6·4% were associated with imported food, 0·5% with food-producing animals, and 0·6% with wildlife. Overall, 7·7% could not be attributed to any source. We concluded that domestic food-producing animals are not an important source for Salmonella in humans in Sweden, and that the adapted model is useful also in low-prevalence countries.

In December 2008 an increase of tetracycline-resistant Salmonella Typhimurium definitive phage-type 191a (DT191a) was identified in England and Wales by the reference laboratory. This was confirmed to have a phage-typing pattern that had not previously been seen. Strong statistical evidence for an association between illness and keeping reptiles was demonstrated by a matched case-case study (mOR 16·82, 95% CI 2·78–∞). Questionnaires revealed an association with frozen reptile feeder mice, and mice representing 80% of the UK supply lines were tested for the presence of Salmonella. DT191a was found in three pools of sampled mice, which were traced back to a single supplier in the USA. Imports from this supplier were halted, and tighter regulations are now in place. A leaflet detailing how to prevent contracting Salmonella from pet reptiles has been published as well as updated advice on the Health Protection Agency's website.

Salmonellosis is an internationally important disease of mammals and birds. Unique epidemics in New Zealand in the recent past include two Salmonella serovars: Salmonella enterica subsp. enterica serovar Typhimurium definitive type (DT) 160 (S. Typhimurium DT160) and S. Brandenburg. Although not a major threat internationally, in New Zealand S. Typhimurium DT160 has been the most common serovar isolated from humans, and continues to cause significant losses in wildlife. We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost identical to phage SE1 but has two regions not found in SE1 which are identical to the P22-like phage ST64T, suggesting that ST160 evolved from SE1 via two recombination events with ST64T. All of the New Zealand isolates of DT160 were identical indicating the clonal spread of this particular Salmonella. Some overseas isolates of S. Typhimurium DT160 differed from the New Zealand strain and contained SE1 phage rather than ST160. ST160 was also identified in New Zealand isolates of S. Typhimurium DT74 and S. Typhimurium RDNC-April06 and in S. Typhimurium DT160 isolates from the USA. The emergence of S. Typhimurium DT160 as a significant pathogen in New Zealand is postulated to have occurred due to the sensitivity of the Salmonella strains to the ST160 phage when S. Typhimurium DT160 first arrived.

We investigated an international outbreak of Salmonella Agona with a distinct PFGE pattern associated with an Irish Food company (company X) producing pre-cooked meat products sold in various food outlet chains in Europe. The outbreak was first detected in Ireland. We undertook national and international case-finding, food traceback and microbiological investigation of human, food and environmental samples. We undertook a matched case-control study on Irish cases. In total, 163 cases in seven European countries were laboratory-confirmed. Consumption of food from food outlet chains supplied by company X was significantly associated with being a confirmed case (mOR 18·3, 95% CI 2·2–149·2) in the case-control study. The outbreak strain was isolated from the company's pre-cooked meat products and production premises. Sufficient evidence was gathered to infer the vehicles of infection and sources of the outbreak and to justify the control measures taken, which were plant closure and food recall.