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.

Economic analyses of cholera immunization programmes require estimates of the costs of cholera. The Diseases of the Most Impoverished programme measured the public, provider, and patient costs of culture-confirmed cholera in four study sites with endemic cholera using a combination of hospital- and community-based studies. Families with culture-proven cases were surveyed at home 7 and 14 days after confirmation of illness. Public costs were measured at local health facilities using a micro-costing methodology. Hospital-based studies found that the costs of severe cholera were US$32 and US$47 in Matlab and Beira. Community-based studies in North Jakarta and Kolkata found that cholera cases cost between US$28 and US$206, depending on hospitalization. Patients' cost of illness as a percentage of average monthly income were 21% and 65% for hospitalized cases in Kolkata and North Jakarta, respectively. This burden on families is not captured by studies that adopt a provider perspective.

In France surveillance underestimates the true burden of acute gastroenteritis (AG). We conducted a population-based, retrospective cross-sectional telephone survey between May 2009 and April 2010 in order to obtain more accurate estimates of the incidence and the burden of AG and to describe healthcare-seeking behaviour for AG. Of the 10 080 persons included in the survey, 260 respondents reported 263 episodes of AG. The incidence rate of AG was estimated at 0·33 cases/person-year (95% CI 0·28–0·37). It was highest in children aged <5 years and declined with age. Thirty-three percent (95% CI 27–40) of the AG cases consulted a physician and 76% (95% CI 70–82) used medication. Our results indicate that there are more than 21 million episodes of AG each year in France. These results allow a more accurate interpretation of the data derived from existing AG surveillance systems.

Serotyping, subtyping and genotyping are important tools for epidemiological studies of group B streptococci (GBS). We investigated the genotype distribution of 353 GBS isolates originating from vaginal or rectal carriage to identify capsular serotypes and subtypes based on the surface protein genes of the alpha-like protein (Alp) family. GBS were recovered from 30% of 1176 pregnant women during the period 2007–2009, with a predominance of capsular genotypes III (35%), Ia (20%), V (17%), II (15%), Ib (8%) and IV (5%). The most common Alp gene was epsilon (26%), followed by rib (22%), alp2 (21%), bca (17%) and alp3 (14%). Several protein genes were significantly associated (G2=249·635, P<0·0001) with particular serotypes: epsilon with Ia, Ib, IV; bca with Ib, II; rib with II, III; alp3 with V; alp2 with III. High genetic diversity within GBS strains was observed using DNA macrorestriction. Serotypes Ib, II and III demonstrated the greatest genetic heterogeneity and serotype V the lowest heterogeneity (relative frequency coefficient ⩾0·03 vs. −0·46, respectively). Macrolide-resistant strains with serotype V and alp3 gene, showed higher uniformity in genetic profile. The distribution of serotypes and surface proteins of GBS strains are necessary data to inform the design and formulation of new GBS vaccines for use in Poland and other countries.

There is currently no information regarding the genetic diversity of HPV-6 variants circulating in South Africa. The aim of this study was to determine the HPV-6 variants affecting patients with recurrent respiratory papillomatosis, to determine whether mutations correlate with disease severity and identify molecular determinants of virulence with prognostic relevance. HPV-6 variants were identified based on genome changes within the 712-991 bp region encompassing the non-coding region (URR) of the genome, with variations in length resulting from insertions and duplications, and the 453-bp gene encoding the E6 protein. Based on manual comparison of sequence data from the URR, the isolates were identified as HPV-6a and HPV-6vc variants. Three novel HPV-6 variants were identified: one based on a mutation in the E6 region; two based on changes in the URR including a unique substitution detected in three isolates and an insertion and 170-bp duplication in the URR genome in one patient, who had clinical features of severe disease.

We aimed to assess differences in the prevalence of hepatitis B virus (HBV) infection in The Netherlands between 1996 and 2007, and to identify risk factors for HBV infection in 2007. Representative samples of the Dutch population in 1996 and 2007 were tested for antibodies to hepatitis B core antigen (anti-HBc), hepatitis B surface antigen (HBsAg) and HBV-DNA. In 2007, the weighted anti-HBc prevalence was 3·5% (95% CI 2·2–5·5) and the HBsAg prevalence was 0·2% (95% CI 0·1–0·4). In indigenous Dutch participants, the anti-HBc prevalence was lower in 2007 than in 1996 (P=0·06). First-generation migrants (FGMs) had a 13-fold greater risk of being HBsAg- and/or HBV-DNA-positive than indigenous Dutch participants. In indigenous Dutch participants, risk factors for anti-HBc positivity were older age and having received a blood product before 1990. In FGMs, being of Asian origin was a risk factor. In second-generation migrants, having a foreign-born partner and injecting drug use were risk factors. FGMs are the main target group for secondary HBV prevention in The Netherlands.

In a Belgian wool-processing factory, living anthrax spores were found in raw goat hair and air dust, but confirmed anthrax cases had never been reported. Anthrax vaccines are not licensed nor recommended in Belgium. We conducted a B. anthracis seroprevalence study to investigate risk factors associated with positive serology and advise on protective measures. Overall 12·1% (8/66) employees were seropositive; 30% of persons processing raw goat hair and 20% of persons sorting raw goat hair were seropositive compared to 3% in less exposed jobs [adjusted prevalence ratio (aPR) 44·4, P=0·001; aPR 14·5, P=0·016, respectively). The number of masks used per day was protective (aPR 0·3, P=0·015). Results suggest a dose–response association for those processing raw goat hair. Host-related factors probably played a role as antibody response varied from person to person within an exposure group. Workers exposed to raw goat hair should be offered higher protection against anthrax and have access to anthrax vaccines.

Twenty-two confirmed cases of Salmonella Infantis were identified in 70 residents of high-level care areas of a residential aged care facility in Sydney in April 2010 during an outbreak of gastroenteritis. A retrospective cohort study was conducted to identify a possible cause. Consuming a soft diet, puréed diet, or thickened fluid were each independently associated with illness. A logistic regression showed consumption of thickened fluid to be the only significant exposure associated with illness (adjusted odds ratio 11·8, 95% confidence interval 1·9–75·9). It was postulated that the thickened fluid had been contaminated by chicken mince, a sample of which also cultured S. Infantis. This finding reinforces the need to educate food-handlers on the risk of potential cross-contamination; it also highlights the need to consider all dietary components, such as thickened fluids, as potential vehicles for transmission in an outbreak.

Laboratory data are the cornerstone in surveillance of infectious disease. We investigated whether changes in reported incidence of Campylobacter and Salmonella infection might be explained by changes in stool sampling rates. Data were extracted from a national database on 585 843 patient stool samples tested by microbiology laboratories in Wales between 1998 and 2008. Salmonella incidence fell from 43 to 19 episodes/100 000 population but Campylobacter incidence after declining from 111/100 000 in 1998 to 84/100 000 in 2003 rose to 119/100 000 in 2008. The proportion of the population sampled rose from 2·0% in 1998 to 2·8% in 2008, mostly due to increases in samples from hospital patients and older adults. The proportion of positive samples declined for both Salmonella and Campylobacter from 3·1% to 1·1% and from 8·9% to 7·5%, respectively. The decline in Salmonella incidence is so substantial that it is not masked even by increased stool sampling, but the recent rise in Campylobacter incidence may be a surveillance artefact largely due to the increase in stool sampling in older people.

The state of Queensland has the highest incidence of Q fever in Australia. In recent years, there has been an increase in human cases where no contacts with the typical reservoir animals or occupations were reported. The aim of this study was to determine the seroprevalence of Coxiella burnetii in Australian native animals and introduced animals in northern and southeastern Queensland. Australian native marsupials sampled included the brushtail possum (Trichosurus vulpecula) and common northern bandicoot (Isoodon macrourus). Introduced species sampled included dingoes (Canis lupus dingo), cats (Felis catus), foxes (Vulpes vulpes) and pigs (Sus scrofa). Serum samples were tested by ELISA for both phase II and phase I antigens of the organism using an Australian isolate. The serological evidence of C. burnetii infection demonstrated in these species has public health implications due to their increasing movement into residential areas in regional Queensland. This study is the first known investigation of C. burnetii seroprevalence in these species in northern Queensland.

Despite recent improvements, New Zealand still has one of the highest per-capita incidence rates of campylobacteriosis in the world. To reduce the incidence, a thorough understanding of the epidemiology of infection is needed. This retrospective analysis of 36 000 notified human cases during a high-risk period between 2001 and 2007 explored the spatial and temporal determinants of Campylobacter notifications at a fine spatial scale in order to improve understanding of the complex epidemiology. Social deprivation was associated with a decreased risk of notification, whereas urban residence was associated with an increased risk. However, for young children rural residence was a risk factor. High dairy cattle density was associated with an increased risk of notification in two of the three regions investigated. Campylobacter notification patterns exhibit large temporal variations; however, few factors were associated with periods of increased risk, in particular temperature did not appear to drive the seasonality in campylobacteriosis.

Assessing the overall burden of disease which can be attributed to hospital-acquired infections (HAIs) remains a challenge. A matched cohort study was performed to estimate excess mortality, length of stay and costs attributable to HAIs in Belgian acute-care hospitals, using six matching factors (hospital, diagnosis-related group, age, ward, Charlson score, estimated length of stay prior to infection). Information was combined from different sources on the epidemiology and burden of HAIs to estimate the impact at national level. The total number of patients affected by a HAI each year was 125 000 (per 10·9 million inhabitants). The excess mortality was 2·8% and excess length of stay was 7·3 days, corresponding to a public healthcare cost of €290 million. A large burden was observed outside the intensive-care unit setting (87% of patients infected and extra costs, 73% of excess deaths).

Infectious diarrhoea caused by bacterial pathogens contributes to the high level of mortality in developing countries like Bangladesh. Following standard bacteriological procedures, a total of 14 428 bacterial pathogens were isolated from 56 132 stool samples and rectal swabs collected from diarrhoeal patients between 2005 and 2008. The rate of isolation and antimicrobial susceptibility data were retrospectively analysed for these isolates and among them Vibrio spp. (42·9%) were the most predominant, followed by Shigella spp. (20·3%), Aeromonas spp. (12·8%) and Salmonella spp. (6·4%). A decreasing trend in isolation of Vibrio spp. (P<0·001) and Salmonella spp. (P<0·001) was observed. While Vibrio cholerae isolates remained susceptible to ciprofloxacin, an increase in resistance was observed in Campylobacter spp. and Shigella flexneri. Variations in susceptibility to other tested antibiotics were observed among the isolated pathogens. Access to this current data will help in understanding the local burden of diarrhoeal disease and contribute to better design of prevention programmes.

The effectiveness of influenza vaccination programmes is seldom known during an epidemic. We developed an internet-based system to record influenza-like symptoms and response to infection in a participating cohort. Using self-reports of influenza-like symptoms and of influenza vaccine history and uptake, we estimated vaccine effectiveness (VE) without the need for individuals to seek healthcare. We found that vaccination with the 2010 seasonal influenza vaccine was significantly protective against influenza-like illness (ILI) during the 2010–2011 influenza season (VE 52%, 95% CI 27–68). VE for individuals who received both the 2010 seasonal and 2009 pandemic influenza vaccines was 59% (95% CI 27–77), slightly higher than VE for those vaccinated in 2010 alone (VE 46%, 95% CI 9–68). Vaccinated individuals with ILI reported taking less time off work than unvaccinated individuals with ILI (3·4 days vs. 5·3 days, P<0·001).

New variants of Vibrio cholerae O1 have appeared in different time-frames in various endemic regions, especially in Asia and Africa. Sixty-nine strains of V. cholerae O1 isolated in Zambia between 1996 and 2004 were investigated by various genotypic techniques to determine the lineage of virulence signatures and clonality. All strains were positive for Vibrio seventh pandemic Islands (VSP)-I and VSP-II and repeat toxin (RTX) gene clusters attesting their El Tor lineage. Interestingly, strains isolated in recent times (2003–2004) were identified as an altered variant (El Tor biotype that harbours El Tor type rstR but produce classical ctxB) that replaced completely the progenitor El Tor strains prevalent in 1996–1997. Recent altered variant strains differed from prototype El Tor strains isolated earlier in that these strains lacked two ORFs, VC0493 and VC0498, in the VSP-II region. PFGE analysis revealed two major clonal lineages in the strains; cluster A represented the strains isolated before 2003 and cluster B the altered strains isolated in 2003–2004. Cluster A was closely related to prototype El Tor reference strain isolated in Bangladesh in 1971. Cluster B was found to be matched with Bangladeshi altered strains but was different from the hybrid strains isolated from Mozambique and Bangladesh. This report provides important information on the genesis of altered strains of V. cholerae O1 isolated in Zambia and emphasizes the need for further studies to follow the trends of evolutionary changes.

We examined non-pregnancy-related listeriosis cases in England and Wales reported to the Health Protection Agency between 1990 and 2009 (n=1864) using unconditional multivariate logistic regression analysis to identify factors independently associated with mortality. A subset analysis of cases between 2005 and 2009 (n=694) investigated the additional effect of antibiotic therapy on survival. In these cases particular malignancies, alcoholism, cardiovascular disease, increasing age, and treatment to reduce gastric acid secretion were positively associated with mortality. The absence of a concurrent condition and presence of autoimmune disease had a protective effect. The subset analysis identified illness in winter or spring as a risk factor and antibiotic therapy as a protective factor for mortality. The impact of antibiotic therapy, seasonality and reduced gastric acid status on survival should be further investigated. Policy-makers and clinicians need to more broadly advise those at risk of contracting this disease and dying as a consequence.

Norovirus (NoV) is a leading cause of outbreaks of gastroenteritis worldwide, and a major burden for healthcare facilities. This study investigated the NoV genotypes responsible for outbreaks in Edinburgh healthcare facilities between June 2008 and July 2011, and studied their temporal distribution to enable a better understanding of the epidemiology of the outbreaks. A total of 287 samples positive for NoV genogroup II (GII) RNA by reverse transcription–polymerase chain reaction (RT–PCR) during routine diagnostic testing were investigated. Nested RT–PCR (nRT–PCR) and sequencing was used to genotype the NoV strains. Overall, a total of 69 NoV strains belonging to six different genoclusters (GII.1, GII.2, GII.3, GII.4, GII.6, GII.13) were detected. The predominant genotype was GII.4 that included four variants, GII.4 2006a, GII.4 2006b, GII.4 2007 and GII.4 2010. Importantly, increases in NoV activity coincided with the emergence of new GII.4 strains, highlighting the need for an active surveillance system to allow the rapid identification of new strains.

A pandemic influenza A(H1N1) 2009 outbreak in a summer school affected 117/276 (42%) students. Residential social contact was associated with risk of infection, and there was no evidence for transmission associated with the classroom setting. Although the summer school had new admissions each week, which provided susceptible students the outbreak was controlled using routine infection control measures (isolation of cases, basic hygiene measures and avoidance of particularly high-risk social events) and prompt treatment of cases. This was in the absence of chemoprophylaxis or vaccination and without altering the basic educational activities of the school. Modelling of the outbreak allowed estimation of the impact of interventions on transmission. These models and follow-up surveillance supported the effectiveness of routine infection control measures to stop the spread of influenza even in this high-risk setting for transmission.

A seroepidemiological study of Brucella infections in multiple livestock species in the Borana pastoral system of Ethiopia was performed between December 2007 and October 2008. A cross-sectional multi-stage sampling technique was employed to select 575 cattle, 1073 camels and 1248 goats from the target populations. Sera were collected from the animals, and serially tested using Rose Bengal test and complement fixation test. Overall prevalence and prevalence with respect to explanatory variables were established, and potential risk factors for seropositivity were analysed using a multivariable logistic regression. The results showed that 8·0% (95% CI 6·0–10·6), 1·8% (95% CI 1·1–2·8) and 1·6% (95% CI 1·0–2·5) of the tested cattle, camels and goats, respectively, had antibodies to Brucella antigen. Positive reactors were found in 93·8% of the villages with more frequent detection of positive cattle (93·3%) than camels (56·3%) and goats (37·5%). Risk factors identified for cattle were: keeping more livestock species at household level (OR 4·1, 95% CI 1·9–8·9), increasing age of the animal (OR 2·8, 95% CI 1·3–6·0) and wet season (OR 3·3, 95% CI 1·6–6·9). Increase in household-level species composition (OR 4·1, 95% CI 1·2–14·2) and wet season (OR 3·7, 95% CI 1·5–9·1) were found to be risk factors for seropositivity in camels and goats, respectively. Existence of more than one seroreactor animal species in most villages and association of increased livestock species composition with seropositivity may add more credence to the possibility of cross-species transmission of Brucella infections. Although no attempt to isolate Brucella spp. was made, our results suggest that cattle are more likely maintenance hosts of Brucella abortus which has spread to goats and camels. This should be substantiated by further isolation and identification of Brucella organisms to trace the source of infection and transmission dynamics in various hosts kept under mixed conditions. In conclusion, the present study suggests the need for investigating a feasible control intervention and raising public awareness on prevention methods of human exposure to brucellosis.

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.