Common sources of shiga toxin-producing Escherichia coli (STEC) O157 infection have been identified by investigating outbreaks and by case-control studies of sporadic infections. We conducted an analysis to attribute STEC O157 infections ascertained in 1996 and 1999 by the Foodborne Diseases Active Surveillance Network (FoodNet) to sources. Multivariable models from two case-control studies conducted in FoodNet and outbreak investigations that occurred during the study years were used to calculate the annual number of infections attributable to six sources. Using the results of the outbreak investigations alone, 27% and 15% of infections were attributed to a source in 1996 and 1999, respectively. Combining information from both data sources, 65% of infections in 1996 and 34% of infections in 1999 were attributed. The results suggest that methods to incorporate data from multiple surveillance systems and over several years are needed to improve estimation of the number of illnesses attributable to exposure sources.

In July 2011, a cluster of Yersinia enterocolitica infections was detected in southwestern Pennsylvania, USA. We investigated the outbreak's source and scope in order to prevent further transmission. Twenty-two persons were diagnosed with yersiniosis; 16 of whom reported consuming pasteurized dairy products from dairy A. Pasteurized milk and food samples were collected from this dairy. Y. enterocolitica was isolated from two products. Isolates from both food samples and available clinical isolates from nine dairy A consumers were indistinguishable by pulsed-field gel electrophoresis. Environmental and microbiological investigations were performed at dairy A and pasteurization deficiencies were noted. Because consumption of pasteurized milk is common and outbreaks have the potential to become large, public health interventions such as consumer advisories or closure of the dairy must be implemented quickly to prevent additional cases if epidemiological or laboratory evidence implicates pasteurized milk as the outbreak source.

Many infectious diseases exhibit repetitive or regular behaviour over time. Time-domain approaches, such as the seasonal autoregressive integrated moving average model, are often utilized to examine the cyclical behaviour of such diseases. The limitations for time-domain approaches include over-differencing and over-fitting; furthermore, the use of these approaches is inappropriate when the assumption of linearity may not hold. In this study, we implemented a simple and efficient procedure based on the fast Fourier transformation (FFT) approach to evaluate the epidemic dynamic of scarlet fever incidence (2004–2010) in China. This method demonstrated good internal and external validities and overcame some shortcomings of time-domain approaches. The procedure also elucidated the cycling behaviour in terms of environmental factors. We concluded that, under appropriate circumstances of data structure, spectral analysis based on the FFT approach may be applicable for the study of oscillating diseases.

The faecal-pat prevalence (as estimated by culture) of Campylobacter fetus from cattle and sheep on 19 farms in rural Lancashire was investigated using standard Campylobacter culture techniques and PCR during a 2-year longitudinal study. C. fetus was isolated from 9·48% [95% confidence interval (CI) 8·48–10·48] of cattle faecal pats and 7·29% (95% CI 6·21–9·62) of sheep faecal pats. There was evidence of significant differences in shedding prevalence between geographical regions; cows in geographical zone 3 had an increased risk of shedding C. fetus compared to cows in geographical zones 1 and 2 (OR 6·64, 95% CI 1·67–26·5, P = 0·007), as did cows at pasture (OR 1·66, 95% CI 1·01–2·73, P = 0·046) compared to when housed. Multiple logistic regression modelling demonstrated underlying seasonal periodicity in both species.

Water supply-associated cryptosporidiosis outbreaks have decreased in England since the application of risk reduction measures to public water supplies. We hypothesized that smaller outbreaks were occurring which could be better detected by enhanced surveillance. Rolling analysis of detailed questionnaire data was applied prospectively in a population of 2·2 million in the south of England in 2009 and 2010. Detection of spatiotemporal clusters using SaTScan was later undertaken retrospectively. Together these approaches identified eight outbreaks, compared to an expectation of less than one based on national surveillance data. These outbreaks were small and associated with swimming pool use or, less commonly, direct (e.g. petting-farm) contact with animals. These findings suggest that frequent small-scale transmission in swimming pools is an important contributor to disease burden. Identification of swimming pool-level risk factors may inform preventative measures. These findings and the approaches described may be applicable to many other populations and to some other diseases.

In Ontario, Canada, the number of Salmonella Enteritidis (SE) cases increased over the years 2005–2010. A population-based case-control study was undertaken from January to August 2011 for the purpose of identifying risk factors for acquiring illness due to SE within Ontario. A total of 199 cases and 241 controls were enrolled. After adjustment for confounders, consuming any poultry meat [adjusted odds ratio (aOR) 2·24, 95% confidence interval (CI) 1·31–3·83], processed chicken (aOR 3·32, 95% CI 1·26–8·76) and not washing hands following handling of raw eggs (OR 2·82, 95% CI 1·48–5·37) were significantly associated with SE infection. The population attributable fraction was 46% for any poultry meat consumption and 10% for processed chicken. Poultry meat continues to be identified as a risk factor for SE illness. Control of SE at source, as well as proper food handling practices, are required to reduce the number of SE cases.

We developed a new phage-typing method and evaluated its application in combination with XbaI macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) as a useful tool for the long-term epidemiology of Salmonella enterica serovar Infantis. In this study, we investigated 1008 S. Infantis isolates recovered from humans, various animal species and food products from 1973 to 2009. The typing scheme is based on 17 typing phages, defining 61 different patterns within the strain collection. The experiments showed that phage typing is a reliable method for differentiation of outbreaks and sporadic clinical cases as well as for elucidation of chains of transmission. The combined analysis of phage typing and PFGE revealed the existence of epidemic clones with a high stability over time like PT29/XB27 which was identified in nosocomial salmonellosis, community outbreaks as well as in broiler chickens from 2002 to 2009.

We investigated norovirus (NoV) concentrations and genotypes in oyster and faecal samples associated with two separate oyster-related outbreaks of gastroenteritis in Ireland. Quantitative analysis was performed using real-time quantitative reverse transcription polymerase chain reaction and phylogenetic analysis was conducted to establish the NoV genotypes present. For both outbreaks, the NoV concentration in oysters was >1000 genome copies/g digestive tissue and multiple genotypes were identified. In faecal samples, GII.13 was the only genotype detected for outbreak 1, whereas multiple genotypes were detected in outbreak 2 following the application of cloning procedures. While various genotypes were identified in oyster samples, not all were successful in causing infection in consumers. In outbreak 2 NoV GII.1 was identified in all four faecal samples analysed and NoV GII concentrations in faecal samples were >108 copies/g. This study demonstrates that a range of NoV genotypes can be present in highly contaminated oysters responsible for gastroenteritis outbreaks.

During a 5-year (2007–2011) surveillance period a total of 435 (15·34%) of 2834 stool specimens from children aged <14 years with acute gastroenteritis tested positive for norovirus and 217 strains were characterized upon partial sequence analysis of the polymerase gene as either genogroup (G)I or GII. Of the noroviruses, 99·2% were GII with the GII.P4 genotype being predominant (80%). GII.P4 variants (Yerseke 2006a, Den Haag 2006b, Apeldoorn 2008, New Orleans 2009) emerged sequentially during the study period. Sequence analysis of the capsid gene of 57 noroviruses revealed that 7·8% were recombinant (ORF1/ORF2) viruses including GII.P7_GII.6, GII.P16_GII.3, GII.P16_GII.13, GII.Pe_GII.2, and GII.Pe_GII.4, never identified before in Italy. GII.P1_GII.1, GII.P2_GII.1, GII.P3_GII.3 and GII.P6_GII.6 strains were also detected. Starting in 2011 a novel GII.4 norovirus with 3–4% nucleotide difference in the polymerase and capsid genes from variant GII.4 New Orleans 2009 was monitored in the local population. Since the epidemiology of norovirus changes rapidly, continuous surveillance is necessary to promptly identify the onset of novel types/variants.

Salmonella Hadar ranks in the top ten serovars reported from humans in Switzerland. In this study, all 64 S. Hadar strains isolated from different patients from 2005 to 2010 in Switzerland were characterized by (i) assessing phenotypic antimicrobial resistance profiles using the disk diffusion method and (ii) by genotyping using pulsed-field gel electrophoresis (PFGE) in order to evaluate the relationship of the strains. The annual incidences varied between 0·32/100 000 in 2005 (highest incidence) and 0·065/100 000 in 2007 (lowest incidence). In total 71·8% of the isolates were resistant to nalidixic acid. Although 40·6% of the strains were resistant to the β-lactam antibiotic ampicillin, they remained susceptible to the third-generation cephalosporin cefotaxime. Genotyping revealed a primary cluster consisting of 42 strains, sharing a similarity of >92%, with a subcluster of 18 strains with indistinguishable patterns. Resistance profiles allowed further differentiation within this subcluster providing a link of two strains to an outbreak in Spain.

In August 2012, an outbreak of gastroenteritis occurred among 88 persons attending a wedding reception at a resort/activity centre in Ylöjärvi, Finland. Of 39 interviewed guests, 23 met the case definition. Two persons were hospitalized. Epidemiological, laboratory and environmental investigations were conducted to characterize the outbreak and to recommend control measures. Investigation confirmed the presence of a new strain of norovirus GII.4 Sydney variant in stool specimens obtained from two wedding guests and on several environmental surfaces in the centre. In the questionnaire study, none of the foods or beverages served during the reception were significantly associated with the illness. Additional cases of gastroenteritis that occurred at the centre before and after the wedding reception supported the hypothesis of environmental transmission of norovirus. After thorough cleansing and disinfection and 1 week's quarantine, no new cases with symptoms typical for norovirus infection were identified at the centre.

The objective of this study was to determine the distribution of Shiga toxin-producing Escherichia coli (STEC) virulence markers (stx1, stx2, eae, ehxA) in E. coli strains isolated from young calves aged fewer than 7 days (bobby calves). In total, 299 recto-anal mucosal swabs were collected from animals at two slaughter plants and inoculated onto tryptone bile X-glucuronide and sorbitol MacConkey agar supplemented with cefixime and potassium tellurite. Isolates were analysed using multiplex polymerase chain reaction to detect stx1, stx2, eae and ehxA genes. The most common combination of virulence markers were eae, ehxA (n = 35) followed by eae (n = 9). In total, STEC and atypical enteropathogenic E. coli (aEPEC) were isolated from 8/299 (2·6%) and 37/299 (12·3%) calves, respectively. All the isolates could be assigned to 15 genotype clusters with >70% similarity cut-off using XbaI pulsed-field gel electrophoresis. It may be concluded that healthy calves from the dairy industry are asymptomatic carriers of a diverse population of STEC and aEPEC in New Zealand.

Both case-ascertained household studies, in which households are recruited after an ‘index case’ is identified, and household cohort studies, where a household is enrolled before the start of the epidemic, may be used to test and estimate the protective effect of interventions used to prevent influenza transmission. A simulation approach parameterized with empirical data from household studies was used to evaluate and compare the statistical power of four study designs: a cohort study with routine virological testing of household contacts of infected index case, a cohort study where only household contacts with acute respiratory illness (ARI) are sampled for virological testing, a case-ascertained study with routine virological testing of household contacts, and a case-ascertained study where only household contacts with ARI are sampled for virological testing. We found that a case-ascertained study with ARI-triggered testing would be the most powerful design while a cohort design only testing household contacts with ARI was the least powerful. Sensitivity analysis demonstrated that these conclusions varied by model parameters including the serial interval and the risk of influenza virus infection from outside the household.

Although post-weaning mortality (PWM) in pig farming is mainly due to the effect of pathogens, farm type or swine management are also directly or indirectly involved. In this work, we used null models and the partial least squares approach (PLS) to structural equation modelling, also known as PLS path modelling (PLS-PM), to explore whether farm type, swine management and pathogens, including porcine circovirus type 2, swine influenza virus, porcine reproductive and respiratory syndrome virus and Aujeszky's disease virus, directly or indirectly influenced PWM in 42 Spanish indoor pig farms. The null model analysis revealed that contact with multiple combinations of viruses could occur by chance. On the other hand, PLS-PM showed that farm characteristics do not influence virus infections, and thus neither farm type nor associated management practices shaped PWM due to pathogens. Accordingly, preventive programmes aimed at controlling PWM in intensive farming should prioritize the control of major pig pathogens.

In March 2012, a second outbreak of Cryptosporidium parvum affected children following a stay at a holiday farm in Norway; the first outbreak occurred in 2009. We studied a cohort of 145 schoolchildren who had visited the farm, of which 40 (28%) were cases. Cryptosporidium oocysts were detected in faecal samples from humans, goat kids and lambs. Molecular studies revealed C. parvum subtype IIa A19G1R1 in all samples including human samples from the 2009 outbreak. A dose–response relationship was found between the number of optional sessions with animals and illness, increasing from two sessions [risk ratio (RR) 2·7, 95% confidence interval (CI) 0·6–11·5] to six sessions (RR 8·0, 95% CI 1·7–37·7). The occurrence of two outbreaks 3 years apart, with the same subtype of C. parvum, suggests that the parasite is established in the farm's environment. We recommend greater emphasis on hand hygiene and routines related to animal contact.

For the purpose of developing a national system for outbreak surveillance, local outbreak signals were compared in three sources of syndromic data – telephone triage of acute gastroenteritis, web queries about symptoms of gastrointestinal illness, and over-the-counter (OTC) pharmacy sales of antidiarrhoeal medication. The data sources were compared against nine known waterborne and foodborne outbreaks in Sweden in 2007–2011. Outbreak signals were identified for the four largest outbreaks in the telephone triage data and the two largest outbreaks in the data on OTC sales of antidiarrhoeal medication. No signals could be identified in the data on web queries. The signal magnitude for the fourth largest outbreak indicated a tenfold larger outbreak than officially reported, supporting the use of telephone triage data for situational awareness. For the two largest outbreaks, telephone triage data on adult diarrhoea provided outbreak signals at an early stage, weeks and months in advance, respectively, potentially serving the purpose of early event detection. In conclusion, telephone triage data provided the most promising source for surveillance of point-source outbreaks.

It has been suggested that mortality is higher in patients admitted to hospitals during the weekend. The objective of this study was to compare outcomes in patients with E. coli urinary tract infection (UTI) depending on the hospital admission day. For this purpose, a secondary analysis of data from a prospective cohort of patients with E. coli UTI was conducted. Weekend diagnosis of UTI was not associated with higher mortality. However, mortality was associated with sepsis, sepsis-induced hypotension and intensive care unit (ICU) admission. Sepsis-induced hypotension and ICU admission were independent determinants of mortality. The results indicate that indicators of severity of illness are associated with higher mortality in patients with UTI rather than the time of diagnosis.

The occurrence of Anaplasma phagocytophilum was investigated in spleen and serum samples from Swedish moose (Alces alces) in southern Sweden (island and mainland). Samples were analysed for presence of A. phagocytophilum DNA by real-time PCR (n = 263), and for Anaplasma antibodies with ELISA serology (n = 234). All serum samples had antibodies against A. phagocytophilum. The mean DNA-based prevalence was 26·3%, and significant (P < 0·01) temporal, and spatial variation was found. Island moose had significantly (P < 0·001) higher prevalence of A. phagocytophilum DNA than moose from the mainland areas. Two samples were sequenced to determine genetic variation in the 16S rRNA and groESL genes. Genetic sequence similarity with the human granulocytic anaplasmosis agent, equine granulocytic ehrlichiosis agent, and different wildlife-associated A. phagocytophilum variants were observed in the 16S rRNA and groESL genes. Our study shows that moose are exposed to A. phagocytophilum in Sweden, and represent a potential wildlife reservoir of the pathogen.

The aim of this study was to investigate the epidemiology of influenza A virus infection in Cyprus from the 2009 pandemic until 2013. Pandemic influenza A(H1N1)2009 virus infections outnumbered infections with other respiratory viruses until the end of 2009. The pandemic virus was also the prevalent influenza strain during influenza season 2010–2011; however, it was completely replaced by H3N2 subtype in the next season. During the most recent influenza season, 2012–2013, the pandemic strain was once again the only influenza A virus circulating in Cyprus. Full-length neuraminidase gene sequencing revealed mutations that had previously been identified as permissive. No significant difference in the expression of the IFN-inducible genes OAS and IFIT1 were observed. The phylogenetic analysis of the neuraminidase gene sequences revealed a picture of continuous importation of influenza strains in the island of Cyprus with local circulation playing only a minor role in determining the prevalent strain of the next influenza season.