During 2007–2009 a UK-wide, 3-year stratified randomized survey of UK chicken broiler flocks was conducted to estimate the prevalence of Campylobacter-infected batches of birds at slaughter. Thirty-seven abattoirs, processing 88·3% of the total UK slaughter throughput, were recruited at the beginning of the survey. Of the 1174 slaughter batches sampled, 79·2% were found to be colonized with Campylobacter, the majority of isolates being C. jejuni. Previous partial depopulation of the flock [odds ratio (OR) 5·21], slaughter in the summer months (categorized as June, July and August; OR 14·27) or autumn months (categorized as September, October and November; OR 1·70) increasing bird age (40–41 days, OR 3·18; 42–45 days, OR 3·56; ⩾46 days, OR 13·43) and higher recent mortality level in the flock (1·00–1·49% mortality, OR 1·57; ⩾1·49% mortality, OR 2·74) were all identified as significant risk factors for Campylobacter colonization of the birds at slaughter. Time in transit to the slaughterhouse of more than 2·5 h was identified as a protective factor (OR 0·52).

Yersinia enterocolitica is an important cause of acute gastrointestinal disease and post-infectious complications. In Germany, incidence of reported yersiniosis is relatively high compared with other countries of the European Union. Children aged <5 years are most frequently affected. The aim of our study was to identify risk factors for sporadic yersiniosis in Germany. A population-based case-control study was conducted in five federal states of Germany from April 2009 to June 2010. Cases exhibiting gastrointestinal symptoms were notified to the local health department with a Yersinia enterocolitica infection culture-confirmed from stool. Controls were selected from population registries and frequency-matched on age group and state of residency. Cases and controls received a questionnaire on possible risk factors by mail. Multivariable logistic regression modelling was used to identify risk factors and to calculate adjusted odds ratios (aORs). Population attributable fractions (PAFs) were estimated for exposures associated with yersiniosis. We analysed data on 571 case patients and 1798 controls. Consumption of raw minced pork, a dish frequently consumed even by young children in Germany, was the main risk factor for disease (aOR 4·7, 95% confidence interval (CI) 3·5–6·3, PAF 30%). This association varied by age group and, unexpectedly, was strongest for children aged <2 years (aOR 17·5, 95% CI 6·0–51·2). Other independent risk factors included recent preparation of minced pork in the household (aOR 1·4, 95% CI 1·1–1·9, PAF 21%), playing in a sandbox (aOR 1·7, 95% CI 1·3–2·4, PAF 17%), and contact with birds (aOR 1·7, 95% CI 1·1–2·6, PAF 4%). Prevention efforts should specifically target parents and caregivers of young children and focus on the high infection risk associated with consumption of raw minced pork.

Seventy-five individuals with Salmonella infection were identified in the Portsmouth area during August and September 2009, predominantly Salmonella Enteritidis phage type 8. Five patients were admitted to hospital. A case-case comparison study showed that a local restaurant was the most likely source of the infection with a risk of illness among its customers 25-fold higher than that of those who did not attend the restaurant. A case-control study conducted to investigate specific risk factors for infection at the restaurant showed that eating salad was associated with a threefold increase in probability of illness. Changing from using ready washed lettuces to lettuces requiring washing and not adhering strictly to the 48 hours exclusion policy for food handlers with diarrhoea were likely to have contributed to the initiation and propagation of this outbreak. Possibilities for cross-contamination and environmental contamination were identified in the restaurant.

Salmonella Enteritidis has emerged as the most prevalent cause of human salmonellosis in Canada. Recent trends of S. Enteritidis subtypes and their potential sources were described by integrating Salmonella data from several Canadian surveillance and monitoring programmes. A threefold increase in S. Enteritidis cases from 2003 to 2009 was identified to be primarily associated with phage types 13, 8 and 13a. Other common phage types (4, 1, 6a) showed winter seasonality and were more likely to be associated with cases linked to international travel. Conversely, phage types 13, 8 and 13a had summer seasonal peaks and were associated with cases of domestically acquired infections. During agri-food surveillance, S. Enteritidis was detected in various commodities, most frequently in chicken (with PT13, PT8 and PT13a predominating). Antimicrobial resistance was low in human and non-human isolates. Continued integrated surveillance and collaborative prevention and control efforts are required to mitigate future illness.

We determined the prevalence of microsporidia Enterocytozoon (Ent.) bieneusi and Encephalitozoon (E.) intestinalis infection in patients with chronic diarrhoea and hepatocellular carcinoma (HCC). A total of 330 stool samples were examined from 171 (52%) patients with chronic diarrhoea, 18 (5%) with HCC while 141 (43%) were controls. Stool microscopy, polymerase chain reaction (PCR) with species-specific primers for Ent. bieneusi and E. intestinalis and sequencing were carried out. Microsporidia were found by trichrome staining in 11/330 (3%) and E. intestinalis by PCR in 13/330 (4%) while Ent. bieneusi was not detected. PCR for E. intestinalis was positive in 8/171 (5%) stool samples from patients with chronic diarrhoea, 2/141 (1·4%) samples from healthy controls and in 3/18 (17%) samples from patients with HCC. In the chronic diarrhoea group, E. intestinalis was positive in 4/171 (2·3%) (P=0·69) stool samples compared to 2/18 (11%) (P=0·06) in the HCC group and 2/141 (1·4%) from healthy controls. E. intestinalis infection was significantly associated with chronic diarrhoea and HCC in these patients who were negative for HIV. Stool examination with trichrome or species-specific PCR for microsporidia may help establish the cause of chronic diarrhoea.

Infectious gastroenteritis causes a considerable burden of disease worldwide. Effective control should be targeted at diseases with the highest burden and costs. Therefore, an accurate understanding of the relative importance of the different microorganisms is needed. The objective of this study was to determine the incidence and aetiology of gastroenteritis in adults requiring hospital admission in The Netherlands. Five hospitals enrolled patients admitted with gastroenteritis for about 1 year during the period May 2008 to November 2009. Participants completed questionnaires and provided a faecal sample. The hospital completed a clinical questionnaire. In total, 44 adults hospitalized for gastroenteritis were included in the study. The cases had serious symptoms, with 31% subsequently developing kidney failure. One or more pathogens were found in 59% of cases. Overall, rotavirus (22%) was the most common infection. Co-infections were observed relatively often (22%). This study emphasizes that rotavirus can also cause serious illness in adults.

Between 2000 and 2009, the total number of patients with Clostridium difficile infections increased considerably in Southeastern Germany. A clear seasonality was observed with a higher number of affected patients occurring in the winter months (January–March). Moxifloxacin and erythromycin-resistant C. difficile PCR ribotypes 001 (72%) and 027 (4·6%) were the most commonly isolated strains.

The objective of this study was to investigate the genetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC) 398 using pulsed-field gel electrophoresis (PFGE). Dust and pigs at five age groups were sampled in six Danish MRSA-positive pig farms. MRSA CC398 was isolated from 284 of the 391 samples tested, including 230 (74%) animal and 54 (68%) environmental samples. PFGE analysis of a subset of 48 isolates, including the six strains previously isolated from farm workers, revealed the existence of farm-specific pulsotypes. With a single exception, human, environmental and porcine isolates originating from the same farm clustered together in the PFGE cluster analysis, indicating that spread of MRSA CC398 in Danish pig farms is mainly due to clonal dissemination of farm-specific lineages that can be discriminated by PFGE. This finding has important implications for planning future epidemiological studies investigating the spread of CC398 in pig farming.

Prevalence of and risk factors associated with MRSA-ST398 carriage in 1872 (response 70%) farmers and neighbouring residents in a pig- and poultry-dense area in Germany were investigated using a cross-sectional study and self-sampling nasal swabs. In the population, 1% without occupational livestock contact and 24% with occupational livestock contact tested positive for MRSA-ST398. The group without occupational livestock contact was 3·8 times [95% confidence interval (CI) 1·5–9·3] more likely to be colonized if a household member had livestock contact and 3·2 times (95% CI 1·4–7·4) more likely if they regularly made private farm visits (e.g. to buy eggs or milk). In the group with occupational livestock contact, pig contact had an odds ratio of 7·1 (95% CI 2·9–17·2) for MRSA-ST398 acquisition. This is the first study to associate private farm visits with acquisition of MRSA; more research to explore the exact transmission routes is necessary.

A cluster of methicillin-resistant Staphylococcus aureus (MRSA) breast abscesses in women who had given birth at a hospital in Mumbai, India was investigated retrospectively. Nineteen of 20 cases were caused by a single clone: pvl-positive, spa type 648 (Ridom t852), ccrB:dru subtype 3:0, ST22-MRSA-IV. Despite the presence of pvl and SCCmec type IV, which are common genetic markers in community-associated MRSA, this outbreak was caused by a healthcare-associated, community-onset MRSA that was common in the hospital environment. Thus, infection control practices may have an important role in limiting the spread of this virulent clone.

The incidence of hepatitis A in England has declined in recent years, but travel-related cases and imported infections remain a challenge. We report an outbreak of hepatitis A in an extended family where two primary cases were infected while in Pakistan and two secondary cases were infected in England. All four were infected by the same genotype IIIA virus. Testing of the children in the extended family by dried blood spots (DBS) determined that three had evidence of recent past infections (anti-HAV IgM positive), one had a current asymptomatic infection (anti-HAV IgM and HAV RNA positive) and one was incubating the virus (anti-HAV IgM negative, HAV RNA positive). HAV RNA from the DBS was identical to the adult cases. This outbreak demonstrates secondary spread of hepatitis A by asymptomatic children after importation from abroad and highlights the importance of preventing travel-associated hepatitis A infection.

We investigated an unprecedented outbreak of fulminant hepatitis B virus (HBV) that occurred in Modasa, Gujarat (India) in 2009. Genomic analysis of all fulminant hepatic failure cases confirmed exclusive predominance of subgenotype D1. A1762T, G1764A basal core promoter (BCP) mutations, insertion of isoleucine after nt 1843, stop codon mutation G1896A, G1862T transversion plus seven other mutations in the core gene caused inhibition of HBeAg expression implicating them as circulating precore/BCP mutant virus. Two rare mutations at amino acids 89 (Ile→Ala) and 119 (Leu→Ser) in addition to other mutations in the polymerase (pol) gene may have caused some alteration in either of four pol gene domains to affect encapsidation of pregenomic RNA to enhance pathogenicity. Sequence similarity among patients' sequences suggested an involvement of a single hepatitis B mutant strain/source to corroborate the finding of gross and continued usage of HBV mutant-contaminated syringes/needles by a physician which resulted in this unprecedented outbreak of fulminant hepatitis B. The fulminant exacerbation of the disease might be attributed to mutations in the BCP/precore/core and pol genes that may have occurred due to selection pressure during rapid spread/mutation of the virus.

In a cohort of 272 treatment-naive individuals with chronic hepatitis C infection acquired on a known date who were enrolled in the UK HCV National Register, a progressive improvement in response to treatment was found with the evolution of antiviral therapies from 20% (25/122) for interferon monotherapy to 63% (55/88) for pegylated interferon+ribavirin therapy. Multivariable analysis results showed increasing age to be associated with poorer response to therapy [odds ratio (OR) 0·84, 95% confidence interval (CI) 0·72–0·99, P=0·03] whereas time since infection was not associated with response (OR 0·93, 95% CI 0·44–1·98, P=0·85). Other factors significantly associated with a positive response were non-type 1 genotype (P<0·0001) and combination therapies (P<0·0001). During the first two decades of chronic HCV infection, treatment at a younger age was found to be more influential in achieving a sustained viral response than treating earlier in the course of infection.

Hepatitis E virus (HEV) is now considered an endemic pathogen in industrialized countries, leading to acute and sometimes chronic hepatitis, mostly in vulnerable people. The endemic sources are unclear. A survey in The Netherlands in 2006–2007 showed a 1·9% seroprevalence of HEV antibodies measured by ELISA and confirmed by immunoblot in a nationwide sample. Overall, in 134/7072 (1·9%) seropositive individuals, older age (P<0·01), being male (P<0·01), working with patients (P=0·03), working with animals (P=0·07), recent diarrhoeal complaints (P=0·07) and adhering to a religion that considers pigs unclean (P<0·01) were independently associated with seropositivity in multivariate analysis. Sub-analysis of 59/4022 (1·5%) anti-HEV antibody-positive subjects with probable endemic exposure showed independent association with youngest household member being aged <5 years or between 19 and <65 years (P=0·05) in multivariate analysis. These findings may contribute to a better understanding of the sources of endemic HEV exposure, and also highlight the need for systematic epidemiological and serological evaluation of new cases.

In patients receiving anti-neoplastic chemotherapy, the impact of influenza on the incidence of invasive pulmonary aspergillosis (IPA) remains unknown. We matched data of the Cologne Cohort of Neutropenic Patients (CoCoNut) with records from the Institute for Virology and compared the findings to historical data. During the pandemic, we diagnosed influenza A(H1N1) in five patients with malignancies and febrile neutropenia refractory to antibiotic therapy. Probable IPA was diagnosed in three of these patients on the grounds of typical computed tomography morphology and microbiological results. Three of five patients receiving remission-induction chemotherapy for acute myeloid leukaemia developed aspergillosis although receiving posaconazole prophylaxis. In the 3 years before the influenza pandemic, only 2/77 patients of this group developed infection. Infection with influenza A(H1N1) may increase the risk for invasive aspergillosis in neutropenic patients. Pulmonary aspergillosis is an important additional differential diagnosis in neutropenic influenza patients with pneumonia.

Aimed at assessing the circulation of Mycobacterium tuberculosis in a highly endemic prison, this 13-month prospective study was performed on strains isolated from tuberculosis (TB) cases detected passively and actively. We used X-ray screening of newly admitted inmates and mass screening at the beginning of the study and again 1 year later. Of the 94 strains genotyped by restriction fragment-length polymorphism, 79 (84·0%) belonged to one of the 12 identified clusters (2–21 strains each), including two main clusters (18 and 21 cases, respectively). A history of TB treatment was reported in 22/79 (27·8%) clustered cases. Time–space distribution of clustered cases was predominantly consistent with transmission, in micro-epidemics. Given the dominant pattern of exogenous infection and the extensive strain circulation, effective TB control should emphasize reduction of overcrowding and improvement of environmental measures as a complement to detection and treatment of cases.

We present a mathematical transmission model of tuberculosis in the USA. The model is calibrated to recent trends of declining incidence in the US-born and foreign-born populations and is used in assessing relative impacts of treatment of latently infected individuals on elimination time, where elimination is defined as annual incidence <1 case/million. Provided current control efforts are maintained, elimination in the US-born population can be achieved before the end of this century. However, elimination in the foreign-born population is unlikely in this timeframe even with higher rates of targeted testing and treatment of residents of and immigrants to the USA with latent tuberculosis infection. Cutting transmission of disease as an interim step would shorten the time to elimination in the US-born population but foreign-born rates would remain above the elimination target.

This study used linked national tuberculosis (TB) and HIV surveillance data to investigate recent trends and factors associated with HIV co-infection (TB-HIV) in healthcare workers (HCWs) with TB in England and Wales. Methods applied were the χ2 trend test and logistic regression. Overall 14% (231/1627) of HCWs with TB were co-infected with HIV, increasing from 8% in 1999 to 14% in 2005 (P<0·001). Most (78%) HCWs were non-UK born and 74% of these developed TB ⩾2 years post-entry. Being born in Sub-Saharan Africa was an independent predictor for TB-HIV, especially for female HCWs (odds ratio 66·5, 95% confidence interval 16·3–271·1), who also had a lower median CD4 count than other co-infected women (106/mm3, interquartile range 40–200, P<0·01). Voluntary HIV testing of new HCWs should be encouraged as an opportunity for early diagnosis. Post-entry, a high index of clinical suspicion for TB in those most at risk remains important.

We conducted an epidemic investigation to discover the route of transmission and the host factors of an outbreak of post-injection abscesses. Of the 2984 patients who visited a single clinic, 77 cases were identified and 208 age- and sex-matched controls were selected for analysis. Injected medications per se were not found to be responsible, and a deviation from safe injection practice suggested the likelihood of diluent contamination. Therefore the injected medications were classified according to whether there was a need for a diluent, and two medications showed a statistically significant association, i.e. injection with pheniramine [adjusted odds ratios (aOR) 5·93, 95% confidence interval (CI) 2·97–11·87] and ribostamycin (aOR 47·95, 95% CI 11·08–207·53). However, when considered concurrently, pheniramine lost statistical significance (aOR 8·71, 95% CI 0·44–171·61) suggesting that normal saline was the causative agent of this outbreak. Epidemiological evidence strongly suggested that this post-injection outbreak was caused by saline contaminated with Mycobacterium massiliense without direct microbiological evidence.