Coccidioidomycosis results from inhaling spores of the fungus Coccidioides spp. in soil or airborne dust in endemic areas. We investigated an outbreak of coccidioidomycosis in a 12-person civilian construction crew that excavated soil during an underground pipe installation on Camp Roberts Military Base, California in October 2007. Ten (83·3%) workers developed symptoms of coccidioidomycosis; eight (66·7%) had serologically confirmed disease, seven had abnormal chest radiographs, and one developed disseminated infection; none used respiratory protection. A diagnosis of coccidioidomycosis in an eleventh worker followed his exposure to the outbreak site in 2008. Although episodic clusters of infections have occurred at Camp Roberts, the general area is not associated with the high disease rates found in California's San Joaquin Valley. Measures to minimize exposure to airborne spores during soil-disrupting activities should be taken before work begins in any coccidioides-endemic area, including regions with only historic evidence of disease activity.

In Finland, rabies in bats was suspected for the first time in 1985 when a bat researcher, who had multiple bat bites, died in Helsinki. The virus isolated from the researcher proved to be antigenically related to rabies viruses previously detected in German bats. Later, the virus was typed as EBLV-2b. Despite an epidemiological study in bats 1986 and subsequent rabies surveillance, rabies in bats was not detected in Finland until the first case in a Daubenton's bat (Myotis daubentonii) was confirmed in August 2009. The bat was paralysed, occasionally crying, and biting when approached; it subsequently tested positive for rabies. The virus was genetically typed as EBLV-2. This is the northernmost case of bat rabies ever detected in Europe. Phylogenetic analyses showed that the EBLV-2b isolate from the human case in 1985 and the isolate from the bat in 2009 were genetically closely related, demonstrating that EBLV-2 may have been circulating in Finland for many years.

Highly pathogenic avian influenza (HPAI) subtype H5N1 remains a public health threat as long as it circulates in wild and domestic birds. Information on the transmissibility of H5N1 HPAI from wild birds is needed for evidence-based public health advice. We investigated if transmission of H5N1 HPAI had taken place in people that had unprotected contact with infected wild mute swans during an incident at the Abbotsbury Swannery in Dorset, England. Thirteen people who had been exposed to infected swans were contacted and actively followed up for symptoms. Serology was taken after 30 days. We did not find evidence of transmission of H5N1 HPAI to humans during the incident. The incident provided a rare opportunity to study the transmissibility of the virus from wild birds to humans.

Bangladesh faced two epidemic waves of highly pathogenic avian influenza (HPAI) H5N1 in two consecutive years. The peaks of the waves were observed in February–July 2007 and January–April 2008, respectively. We examined the spatial and temporal patterns of the 293 outbreaks in 143 subdistricts in 2007 and 2008. Global clustering assessed by K-function was seen at distances 150–300 km between subdistricts. Significant local clusters were detected by space–time scan statistics. In both waves, significant primary clusters of HPAI outbreaks were identified in the central part of the country dominated by commercial production systems and in the northwestern part primarily in backyard production systems. Secondary clusters varied from the northwestern part in 2007 and the southern part in 2008. The findings are highly relevant for the successful planning and implementation of control, prevention and surveillance strategies by highlighting areas where detailed investigations should be initiated.

The relationship between flock management and histomoniasis, a re-emergent infection in poultry, was investigated by statistical techniques used in veterinary epidemiology to deal with various problems including: multicollinearity, confounding, interaction or sample size. Associations between the variables describing flock management were examined by multivariate descriptive analysis to reduce the number of independent variables, prior to investigating associations with the disease. No homogenous groups of farms were found in the 44 free-range turkey flocks sampled in France. Histomonas meleagridis was identified in 26/38 flocks and histomoniasis was confirmed in 19 flocks. Cleanliness of the building, wet litter and diarrhoea were linked with H. meleagridis and severity of histomoniasis. Sharing outdoor fields simultaneously with chickens was related to serious macroscopic lesions determined by post-mortem examinations. Contrary to general belief, acidification of drinking water with organic acid had consistent association with the presence of H. meleagridis in turkey caeca. These results confirm previous findings and provide several new hypotheses on the effects of hygiene and water management on H. meleagridis and histomoniasis.

A cross-sectional study into risk factors for Salmonella was undertaken using data gathered from 252 fattening turkey flocks in the UK. The data was derived from the EU baseline survey conducted during 2006 and 2007, in addition to a voluntary questionnaire. Multivariate logistic regression models identified significant risk factors for Salmonella spp. and Salmonella Typhimurium. A decreased risk of Salmonella spp. infection was associated with a history of intestinal illness in the sampled flock (OR 0·17), the use of wood shavings as litter (OR 0·21), use of disinfectant in the cleaning process (OR 0·25), incineration of dead birds on farm (OR 0·29), seasonal production (OR 0·31), farm staff also working with cattle (OR 0·31), and the presence of pigs on neighbouring farms (OR 0·38). The risk of isolating Salmonella spp. varied according to the company from which the poults were sourced. A reduced risk of S. Typhimurium infection was associated with the use of wax blocks to control rodents (OR 0·09), using mains water (OR 0·19) and having a Salmonella test programme (OR 0·23). An increased risk of S. Typhimurium infection was associated with storage of items around the turkey house (OR 5·20), evidence of mice (OR 4·71) and a soil surface surrounding the turkey house (OR 2·70). This study therefore identifies a number of important practical measures which can be implemented by farmers and veterinarians within the turkey industry to assist in the control of salmonellosis at the farm level.

In February 2008, three white-nosed coatis (Nasua narica) were found dead in a recreational park in Cancun, Mexico. The diagnosis of rabies virus (RABV) infection was confirmed by direct immunofluorescence test. The phylogenetic analysis performed with the complete RABV nucleoprotein gene positioned this isolate close to a sequence of a human rabies case reported during 2008 from Oaxaca, Mexico, sharing 93% similarity. In turn, these two variants are related to another variant found in rabid Tadarida brasiliensis mexicana bats across North America. Anti-RABV neutralizing activity (1·3 IU/ml) was found in the serum of one white-nosed coati captured with another five that cohabited with the dead animals. Enhanced rabies surveillance and pathogenesis studies should be conducted in coatis and insectivorous bats of the region to clarify the role of these species as potential emergent or long-term unidentified RABV reservoirs.

In England, there is no surveillance system for vaccines offered to healthcare workers apart from that in place annually for the seasonal influenza vaccine. To inform the feasibility of a general vaccine uptake surveillance system and to understand which policies are currently in place, we conducted a survey in the 162 National Health Service Foundation and Acute Hospital trusts in England, by submitting a questionnaire to their occupational health departments on immunization policies and methods of storing vaccine uptake data. In total, 104 hospital trusts (64·2%) responded. All responders offer hepatitis B, tuberculosis, measles-mumps-rubella, and influenza vaccines to healthcare workers; 0·9% reported not offering varicella and 13·5% not offering tetanus-diphtheria-polio; 66·4% record staff eligible for immunizations and 68·2% record staff they have immunized. Our study suggests that setting up a surveillance system to monitor vaccine uptake in healthcare workers is possible but would be challenging, given the variation in current systems.

Birth cohort has been shown to be related to morbidity and mortality from other diseases and conditions, yet little is known about the potential for birth cohort in its relation to pneumonia and influenza (P&I) outcomes. This issue is particularly important in older adults, who experience the highest disease burden and most severe complications from these largely preventable diseases. The objective of this analysis is to assess P&I patterns in US seniors with respect to age, time, and birth cohort. All Medicare hospitalizations due to P&I (ICD-9CM codes 480-487) were abstracted and categorized by single-year of age and influenza year. These counts were then divided by intercensal estimates of age-specific population levels extracted from the US Census Bureau to obtain age- and season-specific rates. Rates were log-transformed and linear models were used to assess the relationships in P&I rates and age, influenza year, and cohort. The increase in disease rates with age accounted for most of the variability by age and influenza season. Consistent relationships between disease rates and birth cohorts remained, even after controlling for age. Seasonal associations were stronger for influenza than for pneumonia. These findings suggest that there may be a set of unmeasured characteristics or events people of certain ages experienced contemporaneously that may account for the observed differences in P&I rates in birth cohorts. Further understanding of these circumstances and those resulting age and cohort groups most vulnerable to P&I may help to target health services towards those most at risk of disease.

Residential locations of cases are often used as proxy measures for the likely place of exposure and this assumption may result in biases affecting both surveillance and epidemiological studies. This study aimed to describe the importance of domestic travel in cases of human campylobacteriosis reported during routine surveillance in Iceland from 2001 to 2005. Various measures of disease frequency were calculated based upon the cases' region of residence, adjusting location of domestic travel cases to their travel region, as well as separate estimations for travellers and non-travellers. Of the 376 cases included in the analysis, 37% had travelled domestically during their incubation period. Five of the eight regions were identified as high-risk when considering domestic travel whereas there were no high-risk regions when considering only region of residence. The change in regional representation of disease occurrence indicates the importance of collecting domestic travel information in ongoing surveillance activities.

We propose an age-structured mathematical model for respiratory syncytial virus in which children aged <1 year are especially considered. Real data on hospitalized children in the Spanish region of Valencia were used in order to determine some seasonal parameters of the model. Weekly predictions of the number of children aged <1 year that will be hospitalized in the following years in Valencia are presented using this model. Results are applied to estimate the regional cost of paediatric hospitalizations and to perform a cost-effectiveness analysis of possible vaccination strategies.

Expert opinion was elicited to undertake a qualitative risk assessment to estimate the current and future risks to the European Union (EU) from five vector-borne viruses listed by the World Organization for Animal Health. It was predicted that climate change will increase the risk of incursions of African horse sickness virus (AHSV), Crimean-Congo haemorrhagic fever virus (CCHFV) and Rift Valley fever virus (RVFV) into the EU from other parts of the world, with African swine fever virus (ASFV) and West Nile virus (WNV) being less affected. Currently the predicted risks of incursion were lowest for RVFV and highest for ASFV. Risks of incursion were considered for six routes of entry (namely vectors, livestock, meat products, wildlife, pets and people). Climate change was predicted to increase the risk of incursion from entry of vectors for all five viruses to some degree, the strongest effects being predicted for AHSV, CCHFV and WNV. This work will facilitate identification of appropriate risk management options in relation to adaptations to climate change.

There are few data on circulatory pro-inflammatory cytokine levels and cytokine gene polymorphisms in H. pylori-positive patients. A cross-sectional study was conducted to examine the effects of H. pylori infection, gastric atrophy, and the IL-8 T-251A polymorphism on plasma IL-8 levels in 98 Japanese adults. Seventy-one subjects were positive for H. pylori infection. The geometric mean of plasma IL-8 concentration was significantly higher in subjects with H. pylori infection than in those without (P=0·001). The development of atrophy was negatively associated with IL-8 levels in the H. pylori-positive subjects, although not significantly. Plasma IL-8 levels in the T/T genotype were associated with H. pylori infection and atrophy status (P=0·016). Our findings suggested that circulating IL-8 levels were associated with H. pylori infection. The effect of H. pylori infection on plasma IL-8 levels was not clearly modified by the IL-8 T-251A polymorphism.

Chlamydia pneumoniae infection is said to be associated with obesity. We studied the association between C. pneumoniae infection and inflammation and increased BMI in 891 Finnish military recruits. IgG seropositivity in arrival and departure serum samples during 6–12 months of military service was considered as persistence of antibodies and a possible indication of chronic infection. Persistently high C-reactive protein (CRP) level (elevated on arrival and departure) (OR 2·2, 95% CI 1·3–3·9), and persistent C. pneumoniae antibodies (OR 2·1, 95% CI 1·5–2·8) were significant risk factors for overweight (BMI ⩾25 kg/m2). In addition, those who had persistent antibodies and persistently elevated CRP levels, or those who had either of them, had a significantly higher BMI (kg/m2) compared to those who had neither of them (25·8 vs. 24·6 vs. 23·5, respectively; P<0·001). These results provide new information about the association between possible chronic C. pneumoniae infection and obesity in young men.

One thousand adults aged between 18 and 35 years were investigated for nasal colonization with community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA). Each volunteer completed a questionnaire to assess the presence or absence of risk factors for hospital-acquired MRSA (HA-MRSA) carriage. All MRSA isolated were characterized by microbiological and molecular methods. A S. aureus carriage rate of 22% and a MRSA carriage rate of 0·7% were observed. Analysis of the questionnaires revealed 121 individuals with HA-MRSA risk factors. Subsequently two MRSA infections with associated risk factors were excluded from calculation of the true carriage rate and an adjusted rate of 0·57% (5/879) was established. All seven MRSA isolates expressed the genotypic profile ST22-MRSA-IV, were PVL negative, agr type 1, and differed only by their antimicrobial susceptibility patterns. ST22-MRSA-IV (EMRSA-15) has shown worldwide spread in the hospital setting but has not been previously documented in isolation in the community.

Group B streptococcus (GBS) is a leading cause of neonatal sepsis and is usually acquired via the woman's birth canal. GBS serotypes isolated from 200 pregnant women were determined. Serotypes V (19%) and VI (17%) were the most frequent followed by serotypes III (12%), Ia (11·5%) and IV (10%); 17% of the strains were non-typable. All isolates were susceptible to penicillin, 96% to erythromycin and 97·5% to clindamycin. The emergence of new GBS serotypes has important implications for vaccine prevention strategies.

Hong Kong has a subtropical climate and an influenza seasonality lying approximately mid-way (March–June) between those of the Northern (November–March) and Southern (June–September) hemispheres. Respiratory syncytial virus (RSV) shares a similar seasonality to that of influenza in Hong Kong and is another important respiratory infection of childhood. Daily virus incidence data from public hospitals in Hong Kong's New Territory East Cluster, together with Hong Kong climate data were obtained for 2000–2007. Statistical time-series analysis using monthly time windows showed that influenza A and RSV incidence increased with higher environmental relative humidity, whereas influenza B incidence decreased with higher environmental temperatures. The other climate variables (including vapour pressure as a measure of absolute humidity) were not significantly related to the incidence of these respiratory viruses. Data from this study further reinforces the concept that the relationship between climate factors and respiratory virus incidence differ between subtropical/tropical and temperate countries.

The burden of pneumococcal carriage is largest in developing countries from which, however, detailed studies on pneumococcal transmission are missing. In this study we followed nasopharyngeal carriage in Bangladeshi infants (n=99) from birth, with 2-week sampling intervals until age 4 months, and monthly thereafter until age 1 year, and also their family members at the same intervals. We assessed the dependence of pneumococcal acquisition rates on age, serotype, serotype-specific exposure (i.e. transmission) and current state of carriage (yes/no). A statistical model of pneumococcal transmission, taking into account incompletely observed data, was applied to estimate rates of acquisition and clearance for a large number of serotypes at the same time. Serotypes that were common in the study population were more often acquired from the community than rarer serotypes. However, when conditioning on serotype-specific exposure within the family, transmission rates were similar between different serotypes. Exposure within families signified more than tenfold increase in the rate of acquisition.

An innovative and well-adapted statistical method, called multiblock redundancy analysis, is proposed for a complex health-event analysis to account for the thematic block organization of variables. The outcome block contained the condemnation rates of 404 broiler chicken flocks, distinguishing infectious and traumatic condemnation categories. Explanatory variables were organized in blocks related to the different production stages (farm structure and routine husbandry practices; on-farm flock history and characteristics; catching, transport and lairage conditions; slaughterhouse and inspection features). The aim was to determine risk factors for both condemnation categories, and the relative impact of the different production stages on the whole condemnation rate. Results showed that significant factors were either specific to one condemnation category or related to both categories, and each of the explanatory blocks was involved in the explanation of infectious and traumatic condemnation rates. On-farm flock information explained 40% of the overall condemnation process whereas the other explanatory blocks had similar relative impacts.

Streptococcus pyogenes group A (GAS) is a primary human pathogen. We performed genetic emm sequence and serological T-antigen typing of 819 mostly invasive GAS isolates recovered in Israel during 1996–2005. Of the 72 emm types found, the six most prevalent types (1, 81, 89, 14, 28, 5) comprised 30·2% of all isolates, and emm-type changes were observed over the years. The predicted coverage of the 26-valent S. pyogenes vaccine formulated for usage in the USA was predicted to be only ~60%. On the basis of different emm–T antigen type associations, some Israeli strains are probably different clonal types than those found in USA. About 2% of GAS had emm types that were originally associated with S. dysgalactiae subsp. equisimilis emm genes. Therefore, routine emm typing allows meaningful GAS strain surveillance, and provides data relevant to better vaccine coverage.