Emergence of the highly pathogenic avian influenza (HPAI) H5N1 virus in Egypt in mid-February 2006 caused significant losses for the poultry industry and constituted a potential threat to public health. Since late 2007, there has been increasing evidence that stable lineages of H5N1 viruses are being established in chickens and humans in Egypt. The virus has been detected in wild, feral and zoo birds and recently was found in donkeys and pigs. Most of the outbreaks in poultry and humans occurred in the highly populated Nile delta. The temporal pattern of the virus has changed since 2009 with outbreaks now occurring in the warmer months of the year. Challenges to control of endemic disease in Egypt are discussed. For the foreseeable future, unless a global collaboration exists, HPAI H5N1 virus in Egypt will continue to compromise the poultry industry, endanger public health and pose a serious pandemic threat.

Rates of herpes zoster (HZ) hospitalizations, antiviral prescriptions, and New South Wales emergency-department presentations for age groups <20, 20–39, 40–59 and ⩾60 years were investigated. Trends were analysed using Poisson regression to determine if rates increased following funding of varicella immunization in Australia in November 2005. The regression analysis revealed significantly increasing trends of between 2% and 6% per year in both antiviral prescriptions and emergency-department presentations in all except the <20 years age group. When considered together, the differential changes in rates observed by age group provides preliminary evidence to indicate that HZ incidence is increasing in adults aged >20 years. However, it is not possible to attribute the increasing trends in HZ observed directly to the varicella immunization programme, and continued monitoring and analyses of data for a longer duration, both pre- and post-vaccine introduction, is required.

Socioeconomic factors and the patterns of use of health services associated with influenza and pneumococcal vaccination were studied in people aged ⩾65 years admitted to three general hospitals in Spain between 2005 and 2007. The following data were collected: age, sex, risk of pneumonia, educational level, social class, type of household, physician visits, length of time with the same general practitioner, and influenza and pneumococcal vaccination (23vPPV). Associations between variables were assessed using multivariate logistic regression analysis. In total, 1702 patients were included; 59·9% had received 23vPPV and 65·6% influenza vaccine. Older age (OR 1·04, P<0·001), living with a partner (OR 1·72, P=0·003) and influenza vaccination during the last year (OR 6·64, P<0·001) were associated with 23vPPV. Male sex (OR 1·44, P=0·005), older age (OR 1·02, P=0·009), moderate risk of pneumonia (OR 1·58, P=0·001), living with a partner (OR 1·52, P=0·015) and frequent physician visits during the last year (1–6 annuals visits (OR 2·65, P<0·001); >6 visits (OR 3·83, P<0·001)) were associated with influenza vaccination. Coordination between public health and primary-care services may be necessary to improve vaccine uptake.

Genetic polymorphisms of the LMP/TAP gene coded by the HLA-II region may be associated with outcomes of HBV infection. We conducted a case-control study to test the hypothesis, including a persistent group of 155 patients with chronic hepatitis B and 36 healthy carriers, a recovered group of 165 individuals spontaneously recovered from HBV infection, and an uninfected group of 278 healthy normal controls. Genotypes of eight polymorphisms of the LMP/TAP gene were analysed by PCR–RFLP. A logistic regression model was used to analyse statistical differences in polymorphisms or haplotypes in different groups. Of the eight polymorphisms, two (TAP1 codon 637 and LMP7 codon 145) were observed to have statistically significant association with outcomes of HBV infection (P<0·05). The two-locus haplotype constructed with two such polymorphisms was analysed. The frequencies of haplotypes B (Asp-Lys), C (Gly-Gln), and D (Gly-Lys) were found to be increased significantly in the persistent group, compared to healthy controls (OR 2·26, 95% CI 1·62–3·15, P<0·001; OR 2·37, 95% CI 1·69–3·32, P<0·001; OR 4·38, 95% CI 1·78–10·77, P=0·001, respectively). The prevalence of haplotypes B (Asp-Lys), C (Gly-Gln), and D (Gly-Lys) were also significantly higher in the persistent infectious group than in the recovered group (OR 2·68, 95% CI 1·81–3·98, P<0·001; OR 2·40, 95% CI 1·62–3·55, P<0·001; OR 3·03, 95% CI 1·22–7·55, P=0·017, respectively). These findings indicated that genetic polymorphisms of the LMP/TAP gene might be an important factor in determining the outcome of HBV infection.

Haematopoietic stem cell transplant (HSCT) recipients lose immune memory of exposure to infectious agents and vaccines accumulated throughout their lifetime and therefore need to be revaccinated. We aimed to evaluate the influence of different factors on hepatitis A virus (HAV) immunity in both child and adult HSCT recipients living in an intermediate endemic region, Turkey. Eighty patients (age range 2·5–57 years) who had HAV serology prior to HSCT were evaluated. The prevalence of HAV seropositivity was 85% (n=68) before HSCT. There was no history of HAV vaccination before HSCT in children and HAV vaccine was not available in Turkey 10 years ago, so it was assumed that all seropositive patients reflected natural immunity. After the exclusion of six patients with autologous HSCT, the remaining 62 seropositive and allogeneic patients were included in this retrospective study. The duration of HAV seropositivity was estimated using the Kaplan–Meier method, log-rank analysis and Cox regression models. Estimated mean time to loss of HAV seropositivity was 48·6 months after transplantation. Patients who were older (⩾18 years) at transplantation and who had older (⩾18 years) donors became seronegative later (P<0·05). Cox backward-stepwise regression confirmed that older age of recipient at transplantation was the only significant parameter for HAV seropositivity (P<0·05). HAV-inactivated vaccine might be recommended later to older HSCT recipients in intermediate endemic regions.

Systematic national surveillance of foodborne disease outbreaks effectively serves the development of public health policy on food safety. The Health Protection Agency has maintained a collaborative surveillance system for foodborne outbreaks in England and Wales since 1992. Up to 2008, 2429 foodborne outbreaks were identified, described and analysed for changes over time. Salmonella spp. accounted for half of the outbreaks, although the proportion of these decreased over the surveillance period. Similarly, the proportion of outbreaks caused by Clostridium perfringens decreased, while those attributed to Campylobacter spp. and Vero cytotoxin-producing Escherichia coli O157 increased. Although poultry meat was the most frequently implicated food vehicle in outbreaks followed by miscellaneous foods and red meats, the proportion of outbreaks attributed to meats in fact decreased over time but those linked to miscellaneous foods did not. Over the surveillance period, the proportion of outbreaks linked to eggs and S. Enteritidis non-phage-type 4, particularly in food service establishments, increased, highlighting the importance of this organism/setting/vehicle association. Contributory factors in most outbreaks were cross-contamination, inadequate heat treatment, and inappropriate food storage. This study describes the overall decline in foodborne outbreaks, providing evidence that the introduction and adherence to effective control measures provide the best means of minimizing the risk of foodborne infection.

In order to monitor epidemiological trends, Cryptosporidium-positive samples (n=4509) from diarrhoeic patients were typed. Compared to the previous 4 years, the proportion of Cryptosporidium hominis cases in 2004–2006 increased to 57·3%, while 38·5% were C. parvum. The remaining 4·2% cases included mixed C. parvum and C. hominis infections, C. meleagridis, C. felis, C. ubiquitum and a novel genotype. When the typing results were combined with enhanced surveillance data to monitor risk exposures, C. hominis was linked to urban dwelling, previous diarrhoea in the household, any travel especially abroad, and using a swimming or paddling pool. C. parvum was linked to having a private water supply, contact with surface water, visiting or living on a farm, and contact with farm animal faeces. The proportion of laboratory-confirmed indigenous cases acquired from direct contact with farm animals was estimated to be 25% for C. parvum and 10% of all reported Cryptosporidium cases.

In July and August 2007, a giardiasis outbreak affected attendees of a private recreational camp in California. Twenty-six persons had laboratory-confirmed giardiasis; another 24 had giardiasis-like illness with no stool test. A retrospective cohort study determined that showering was associated with illness (adjusted odds ratio 3·1, 95% confidence interval 1·1–9·3). Two days before the outbreak began, the camp had installed a slow-sand water filtration system that included unsterilized sand. Review of historical water-quality data identified substantially elevated total coliform and turbidity levels in sand-filtered spring water used for showering during the suspected exposure period. Unfiltered spring water tested at the same time had acceptable coliform and turbidity levels, implicating the filtration system as the most likely contamination source. To prevent waterborne illness, slow-sand water filtration systems should use sterilized sand, and slow-sand-filtered water should not be used for any purpose where inadvertent ingestion could occur until testing confirms its potability.

Contamination of locally produced, ready-to-eat meats by Listeria spp. has been previously reported at one processing plant in Trinidad. However, the status of this pathogen in locally produced products sold at retail outlets is unknown. This study was conducted to establish whether there is a risk to consumers of locally processed meats caused by the presence of Listeria spp., and whether a link exists between the presence of the pathogen in retail products and the manufacturing plant of one brand (B). Four hundred and eighty ready-to-eat meat products of two popular local brands (A and B) were collected from retail outlets and analysed for the presence of Listeria spp. together with food samples and surfaces from one manufacturing plant (B). Eighty-eight of the retail products (18·3%) were contaminated with Listeria spp., of which, 52·3% were L. innocua, 44·3% were L. monocytogenes and 3·4% belonged to the L. seeligeri–L. welshimeri–L. ivanovii (Siwi) group. L. innocua was found in 15 in-process food samples and on three surfaces of equipment at plant B. Four in-process food samples were also contaminated with Siwi isolates. Repetitive extragenic palindromic PCR DNA fingerprinting showed a possible association between strains of different Listeria spp. and brand as well as with manufacturing plant B.

Plague, which is most often caused by the bite of Yersinia pestis-infected fleas, is a rapidly progressing, serious disease that can be fatal without prompt antibiotic treatment. In late December 2007, an outbreak of acute gastroenteritis occurred in Nimroz Province of southern Afghanistan. Of the 83 probable cases of illness, 17 died (case fatality 20·5%). Being a case was associated with consumption or handling of camel meat (adjusted odds ratio 4·4, 95% confidence interval 2·2–8·8, P<0·001). Molecular testing of patient clinical samples and of tissue from the camel using PCR/electrospray ionization–mass spectrometry revealed DNA signatures consistent with Yersinia pestis. Confirmatory testing using real-time PCR and immunological seroconversion of one of the patients confirmed that the outbreak was caused by plague, with a rare gastrointestinal presentation. The study highlights the challenges of identifying infectious agents in low-resource settings; it is the first reported occurrence of plague in Afghanistan.

Non-typhic Salmonella is one of the major bacterial pathogens that cause foodborne infections as well as economic losses for the food production industry. There is therefore a need to improve early detection to prevent the emergence and spread of Salmonella within the agro-food chain. The passive laboratory-based surveillance system of the Salmonella network has been integrated into the French Food Safety Agency's working plan. The objective of this study was to evaluate the ability of this network to detect unusual Salmonella contamination as early as possible in the agro-food chain. Three statistical methods were used to detect unusual events from the time-series of counts. After an experimental period of more than 1 year, this approach detected several unusual events linked to contamination in the agro-food chain that were confirmed in a timely manner at national or regional levels. This evaluation also reinforced the position of the Salmonella network as an integral part of the national public health surveillance system.

This is the first study comparing societal costs of acute illness with Salmonella Typhimurium (ST) and Salmonella Enteritidis (SE) in the UK. It included the cost and severity of the illness and explored the impact of each Salmonella serovar on the patients, their families, the NHS, and the wider economy. The study ascertained confirmed cases of ST and SE between July and November 2008. The mean costs per case were £1282 (ST) and £993 (SE). The indirect costs associated with the work-time lost by the case, parents, or carers were £409 (ST) and £228 (SE); this difference was statistically significant. The aggregate cost of ST and SE identified using laboratory test results for the UK as a whole was estimated as £6.5 million. Work-time lost and caring activities are cost categories that are not frequently investigated within the infectious intestinal disease literature, although they represent an important societal cost.

Targets for maximum acceptable levels of Salmonella in pigs and pork are to be decided. A stochastic simulation model accounting for herd and abattoir information was used to evaluate food safety and economic consequences of different surveillance and control strategies, based among others on Danish surveillance data. An epidemiological module simulated the Salmonella carcass prevalence for different scenarios. Cost-effectiveness analysis was used to compare the costs of the different scenarios with their expected effectiveness. Herd interventions were not found sufficient to attain Salmonella carcass prevalence <1%. The cost-effectiveness of abattoir interventions changed with abattoir size. The most cost-effective strategy included the use of steam vacuum and steam ultrasound. Given uncertainty of the effect of steam vacuum and steam ultrasound, model results should be updated as more information becomes available. This framework contributes to informed decision-making for a more cost-effective surveillance and control of Salmonella in pigs and pork.

A cross-sectional study on 32 different Belgian broiler farms was performed in 2007 and 2008 to identify risk factors for ceftiofur resistance in Escherichia coli. On each farm, one E. coli colony was isolated from 30 random birds. Following susceptibility testing of 14 antimicrobials, an on-farm questionnaire was used to obtain information on risk factors. Using a multilevel logistic regression model two factors were identified at the animal level: resistance to amoxicillin and to trimethoprim–sulfonamide. On the farm level, besides antimicrobial use, seven management factors were found to be associated with the occurrence of ceftiofur resistance in E. coli from broilers: poor hygienic condition of the medicinal treatment reservoir, no acidification of drinking water, more than three feed changes during the production cycle, hatchery of origin, breed, litter material used, and treatment with amoxicillin. This study confirms that not only on-farm antimicrobial therapy, but also management- and hatchery-related factors influence the occurrence of antimicrobial resistance.

The incidence of bacteraemia has increased considerably during the last decades. This may be related to population ageing, increased use of invasive procedures, and increased ascertainment of bacteraemia. Generalized additive and generalized linear models were used to analyse the impact of four successive improvements in blood culture methodology on the recovery of prevalent blood culture isolates while simultaneously controlling for underlying time trend and seasonal variation. Between 1981 and 2006, 20 091 bacteraemias comprising 22 800 blood culture isolates were diagnosed. The changes in methodology increased the recovery of some bacterial groups; the greatest impact was observed for Enterobacteriaceae, pneumococci and Staphylococcus aureus whereas recovery of β-haemolytic streptococci, Pseudomonas aeruginosa, other Gram-negative aerobes, and fungi was not affected. Changes in blood culture methodology should be taken into account when assessing time trends of bacteraemia.

A prospective cohort study with a 1-year telephone follow-up was performed to estimate the incidence of surgical-site infections (SSIs) in hip and knee prostheses. Twenty-five public hospitals equipped with orthopaedic units in two Italian regions were involved. An 8-month surveillance period was set to obtain significant data at a regional level and data were collected by the infection control nurses of each centre. One-year follow-up was completed in 75% of cases. SSIs were recorded in 45 cases (incidence rate 1·9/100 person-years, 95% CI 1·4–2·5). Thirty-six percent of SSIs were diagnosed during hospitalization and 95·3% within 90 days post-operation. This incidence is similar to that reported by European and USA surveillance systems. The proposed investigative method proved to be reliable and feasible. A prolonged surveillance for at least 3 months post-operation yields a good estimate of SSI in joint replacements.

The 7-valent pneumococcal conjugate vaccine (PCV7) was included in the routine infant immunization schedule in Ireland in September 2008. We determined the serotype of 977 S. pneumoniae isolates causing invasive disease between 2000–2002 and 2007–2008, assessed for the presence of the recently described serotype 6C and determined the susceptibility of isolates during 2007–2008 to penicillin and cefotaxime. Serotype 14 was the most common serotype during both periods and 7·7% of isolates previously typed as serotype 6A were serotype 6C. During 2000–2002 and 2007–2008, PCV7 could potentially have prevented 85% and 74% of invasive pneumococcal disease in the target population (i.e. children aged <2 years), respectively. The level of penicillin non-susceptibility was 17% in 2007–2008. Ongoing surveillance of serotypes is required to determine the impact of PCV7 in the Irish population and to assess the potential of new vaccines with expanded valency.

Population-based studies of Gram-negative bloodstream infection (BSI) in children are lacking. Therefore, we performed this population-based investigation in Olmsted County, Minnesota, to determine the incidence rate, site of acquisition, and outcome of Gram-negative BSI in children aged ⩽18 years. We used Kaplan–Meier method and Cox proportional hazard regression for mortality analysis. We identified 56 unique children with Gram-negative BSI during the past decade. The gender-adjusted incidence rate of Gram-negative BSI per 100 000 person-years was 129·7 [95% confidence interval (CI) 77·8–181·6]) in infants, with a sharp decline to 14·6 (95% CI 6·0–23·2) and 7·6 (95% CI 4·3–10·9) in children aged 1–4 and 5–18 years, respectively. The urinary tract was the most commonly identified source of infection (34%) and Escherichia coli was the most common pathogen isolated (38%). Over two-thirds (68%) of children had underlying medical conditions that predisposed to Gram-negative BSI. The overall 28-day and 1-year all-cause mortality rates were 11% (95% CI 3–18) and 18% (95% CI 8–28), respectively. Younger age and number of underlying medical conditions were associated with 28-day and 1-year mortality, respectively. Nosocomial or healthcare-associated acquisition was associated with both 28-day and 1-year mortality.

This study estimated the frequency of exposure of meat workers to carcasses infected with Leptospira serovars Hardjobovis or Pomona in a sheep-only abattoir in New Zealand. A stochastic spreadsheet model was developed to assess the daily risk of exposure of eviscerators, meat inspectors and offal handlers to live leptospires in sheep carcasses from May to November 2004 (high-risk period), and from December 2004 to June 2005 (low-risk period). The average sheep processed per day were 225 for an eviscerator, 374 for a meat inspector, and 1123 for an offal handler. The median daily exposures during high- and low-risk periods were 11 [95% distribution interval (DI) 5–19] and three (95% DI 1–8) infected carcasses/day for eviscerators, 18 (95% DI 9–29) and six (95% DI 2–12) for meat inspectors, and 54 (95% DI 32–83) and 18 (95% DI 8–31) for offal handlers, respectively. Stochastic risk modelling provided evidence that processing of sheep carcasses exposed meat workers regularly to live leptospires with substantial seasonal variation.