A retrospective study of clinical characteristics, outcome and prognostic factors of patients with cryptococcosis was undertaken in intensive care units (ICUs) of a medical centre for the period 2000–2005. Twenty-six patients with Cryptococcus neoformans var. grubii infection were identified (16 males, median age 58 years). The most frequent underlying diseases were liver cirrhosis (38·5%), diabetes mellitus (26·9%) and HIV infection (19·2%). The most frequently identified sites of infection were blood (61·5%), cerebrospinal fluid (38·5%) and airways (34·6%). The mean Acute Physiologic and Chronic Health Evaluation II score at ICU admission was 22·46. The ICU mortality rate in these patients was 73·1% (19/26) and there were a further two mortalities recorded after discharge from ICU, reaching a total mortality rate of 80·8% (21/26). Patients with ICU survival >2 weeks had lower rates of HIV infection (P=0·004), less use of inotropic agents during ICU stay (P<0·001) and lower white blood cell counts (P=0·01). After adjusting for clinical variables in the multivariate Cox regression model, diabetes and cryptococcal infection after ICU admission were independent predictors of good long-term prognosis (P=0·015) and HIV infectious status was associated with poor outcome (P=0·012).

Understanding age-specific differences in infection rates can be important in predicting the magnitude of and mortality in outbreaks and targeting age groups for vaccination programmes. Standard methods to estimate age-specific rates assume that the age-specific force of infection is constant in time. However, this assumption may easily be violated in the face of a highly variable outbreak history, as recently observed for acute immunizing infections like measles, in strongly seasonal settings. Here we investigate the biases that result from ignoring such fluctuations in incidence and present a correction based on the epidemic history. We apply the method to data from a measles outbreak in Niamey, Niger and show that, despite a bimodal age distribution of cases, the estimated age-specific force of infection is unimodal and concentrated in young children (<5 years) consistent with previous analyses of age-specific rates in the region.

The screening of 2000 women of childbearing age in Cork between 2004 and 2006 produced 37 erythromycin-resistant group B streptococcus (GBS) isolates. PCR analysis was performed to determine the basis for erythromycin resistance. The ermTR gene was most frequently expressed (n=19), followed by the ermB gene (n=8). Four isolates harboured the mefA gene. Six isolates yielded no PCR products. Some phenotype–genotype correlation was observed. All isolates expressing the mefA gene displayed the M phenotype whilst all those expressing ermB displayed the constitutive macrolide resistance (cMLSB) phenotype. Of 19 isolates that expressed the ermTR gene, 16 displayed the inducible macrolide resistance (iMLSB) phenotype. Serotype analysis revealed that serotypes III and V predominated in these isolates. The identification of two erythromycin-resistant serotype VIII isolates among this collection represents the first reported finding of erythromycin resistance in this serotype. A single isolate was non-typable using two latex agglutination serotyping kits.

Streptococcus pneumoniae is a common cause of community-acquired pneumonia (CAP) but existing diagnostic tools have limited sensitivity and specificity. We enrolled adults undergoing chest radiography at three Indian Health Service clinics in the Southwestern United States and collected acute and convalescent serum for measurement of PsaA and PspA titres and urine for pneumococcal antigen detection. Blood and sputum cultures were obtained at the discretion of treating physicians. We compared findings in clinical and radiographic CAP patients to those in controls without CAP. Urine antigen testing showed the largest differential between CAP patients and controls (clinical CAP 13%, radiographic CAP 17%, control groups 2%). Serological results were mixed, with significant differences between CAP patients and controls for some, but not all changes in titre. Based on urine antigen and blood culture results, we estimated that 11% of clinical and 15% of radiographic CAP cases were due to pneumococcus in this population.

The incidence of nosocomial candidaemia was evaluated in a retrospective study in a Turkish tertiary-care hospital. Over a 12-year period (1996–2007), a total of 743 episodes of candidaemia occurred in 743 patients, accounting for an average incidence of 1·9 episodes/1000 admissions and 2·9 episodes/10 000 patient-days per year. The annual incidence was almost constant during the study period except for 1996 when it was significantly higher in comparison with other years (P<0·05). The most common species isolated was Candida albicans (45%), followed by C. parapsilosis (26%), C. tropicalis (7%), C. krusei (7%), and C. glabrata (3·5%). A significant increase in C. albicans isolates causing candidaemia linked to a decrease in C. parapsilosis isolates in adult patients and C. krusei isolates in children was found between the two 6-year study periods. This trend reflects improved infection control at Uludağ University Hospital. Ninety percent of isolates were susceptible to fluconazole (⩽8 μg/ml) and resistance was found only in C. glabrata and C. parapsilosis isolates. Regular local surveillance of Candida spp. is important in order to develop empirical treatment protocols to reduce the incidence and mortality of candidaemia.

We report on a measles outbreak originating in an anthroposophic community in Austria, 2008. A total of 394 (94·9%) cases fulfilled the outbreak case definition including 168 cases affiliated to the anthroposophic community. The source case was a school pupil from Switzerland. The Austrian outbreak strain was genotype D5, indistinguishable from the Swiss outbreak strain. A school-based retrospective cohort study in the anthroposophic school demonstrated a vaccine effectiveness of 97·3% in pupils who had received a single dose of measles-containing vaccine and 100% in those who had received two doses. The vaccination coverage of the cases in the anthroposophic community was 0·6%. Of the 226 outbreak cases not belonging to the anthroposophic community, the 10–24 years age group was the most affected. Our findings underline the epidemiological significance of suboptimal vaccination coverage in anthroposophic communities and in older age groups of the general population in facilitating measles virus circulation. The findings of this outbreak investigation suggest that the WHO European Region is unlikely to achieve its 2010 target for measles and rubella elimination.

Puumala hantavirus (PUUV) is apparently transmitted to humans by inhalation of aerosolized secretions of carrier rodents (bank voles). The means of transmission and the associated risk factors are poorly defined. An epidemiological study during the peak of an epidemic season in Finland was conducted based on 282 acute clinical PUUV infections and 204 controls without PUUV infection or immunity. The main risk factors adjusted by age, sex and living environment were cigarette smoking [odds ratio (OR) 3·6, 95% confidence interval (CI) 2·1–5·9, P<0·0001] and buildings with holes allowing rodents to enter (OR 3·3, 95% CI 2·0–5·6); these results were similar in two subsets. Further, use of rodent traps (OR3·5, 95% CI 2·2–5·7) and handling firewood (OR 2·7, 95% CI 1·6–4·4) were associated with a risk. The risk attributed to smoking also remained high using simulated population controls with average smoking habits. The results suggest that hantavirus transmission occurs by inhalation mainly indoors and is dependent on the condition of the respiratory tract.

Recurrence of peste des petits ruminants (PPR) was diagnosed in the United Arabian Emirates in several wild ruminants confirmed by morphological, immunohistochemical, serological and molecular findings. Phylogenetic analysis revealed that the virus strain belongs to lineage IV, which is different to some previously isolated PPR strains from the Arabian Peninsula. This study shows that wild ruminants may play an important epidemiological role as virus source for domestic small ruminants.

To assess the burden of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in a high-risk population, the monthly incidence of laboratory-confirmed MRSA in service members/trainees stationed at Fort Benning, Georgia, USA without hospitalization or surgery documented 30 days prior to infection was calculated for calendar years 2002–2007. Clinical management and antibiotic susceptibility patterns were also evaluated. By 2007, ~67% of S. aureus strains were MRSA, and ~82% of these were community-associated, primarily in trainees. In total, 3531 CA-MRSA infections were identified. Rates appeared to be seasonal, peaking at 42 cases/1000 soldiers in 2005, with rates remaining above 35/1000 soldiers thereafter. Increased prescription of effective antibiotics was documented. Susceptibility to clindamycin, ciprofloxacin, and levofloxacin decreased from 2002 to 2007 by 6%, 17%, and 14%, respectively. The sustained high prevalence of CA-MRSA observed highlights the need for more vigilant population-based counter-measures at military training installations.

A cross-sectional study based on a questionnaire survey was conducted to determine the distribution of lumpy skin disease (LSD) and associated risk factors in three main agro-climatic zones of Ethiopia. A total of 330 questionnaire surveys were collected from 44 peasant associations (PA) distributed in 15 districts. Across agro-climate zones, herd-level LSD prevalence in the midland agro-climate was significantly higher 55·2% [95% confidence interval (CI) 47·5–62·6] than in highland and lowland agro-climate zones. Overall observed LSD prevalence at animal-level was 8·1% (95% CI 7·3–8·9) and observed mortality was 2·12% (95% CI 1·73–2·6). The odds ratio (OR) of LSD occurrence in midland vs. highland and lowland vs. highland zones was 3·86 (95% CI 2·61–5·11) and 4·85 (95% CI 2·59–7·1), respectively. Significantly high risk of LSD occurrence was associated with communal grazing and watering management (OR 4·1, 95% CI 2·02–6·18) and introduction of new cattle (OR 8·5, 95% CI 6·0–11·0). Our findings describe the distribution of LSD in different agro-climates in Ethiopia along with associated risk factors, and can help shed light on the epidemiology of LSD in other African countries suffering from the disease.

Large-scale population-based studies have reported a significant increase in invasive pneumococcal disease (IPD) in those with underlying haematological or solid-organ malignancy, but limited condition-specific data are available on rates of IPD in the adult population. A retrospective chart review of all patients with IPD (identified prospectively) in the province of Alberta, Canada (population ~3·3 million) was conducted from 2000 to 2004 to study the epidemiology of IPD. Rates of IPD in patients with various haematological and solid-organ malignancies were determined by obtaining the number of these patients at risk from the provincial cancer registry. Compared to the attack rate of IPD in the adult population aged ⩾18 years (11·0 cases/100 000 per year, 95% CI 10·44–11·65), there were significantly increased rates of IPD in those with lung cancer (143·6 cases/100 000 per year, OR 13·4, 95% CI 9·3–19·4, P<0·001) and multiple myeloma (673·9 cases/100 000 per year, OR 62·8, 95% CI 39·6–99·8, P<0·001). More modestly increased rates of IPD were found in those with chronic lymphocytic leukaemia, acute myeloid leukaemia, acute lymphoblastic leukaemia, and Hodgkin's and non-Hodgkin's lymphoma. There was an increased prevalence of serotype 6A in those with these underlying malignancies, but no other serotypes predominated. Fifty-three percent (48/83) of cases were caused by serotypes in the investigational 13-valent pneumococcal conjugate vaccine (PCV13), and 57/83 (69%) of the cases were caused by serotypes in the 23-valent pneumococcal polysaccharide vaccine (PPV23). The incidence of IPD in adults with certain haematological and solid-organ malignancies is significantly greater than the overall adult population. Such patients should be routinely given pneumococcal polysaccharide vaccine; this population could also be targeted for an expanded valency conjugate vaccine.

In July 2008, office workers in Dublin complained of influenza-like illness preceding and interspersing two cases of notified Legionnaires' disease. Legionella pneumophila serogroup 1 was identified in both cooling towers supplying the office. A retrospective cohort study was undertaken to investigate possible Pontiac fever (PF). Forty-seven employees (23%) met the clinical case definition for PF but confirmatory testing was negative. Exposure to the smoking area situated beside the cooling towers was associated with an increased risk of PF (RR 2·4, 95% CI 1·5–3·8). The diagnosis of PF should be considered when many persons exposed to a possible reservoir of Legionella spp. present with flu-like symptoms. More sensitive microbiological tests would allow better confirmation and more comprehensive reporting of PF. Early detection is vital to prevent potentially severe illness and outbreaks of PF or Legionnaires' disease.

This study was performed to investigate space–time patterns of Campylobacter spp. colonization in broiler flocks in Norway. Data on the Campylobacter spp. status at the time of slaughter of 16 054 broiler flocks from 580 farms between 2002 and 2006 was included in the study. Spatial relative risk maps together with maps of space–time clustering were generated, the latter by using spatial scan statistics. These maps identified the same areas almost every year where there was a higher risk for a broiler flock to test positive for Campylobacter spp. during the summer months. A modified K-function analysis showed significant clustering at distances between 2·5 and 4 km within different years. The identification of geographical areas with higher risk for Campylobacter spp. colonization in broilers indicates that there are risk factors associated with Campylobacter spp. colonization in broiler flocks varying with region and time, e.g. climate, landscape or geography. These need to be further explored. The results also showed clustering at shorter distances indicating that there are risk factors for Campylobacter spp. acting in a more narrow scale as well.

All bacterial isolates from 7058 patients admitted to haemato-oncology wards at National Taiwan University Hospital between 2002 and 2006 were characterized. In total 1307 non-duplicate bloodstream isolates were made from all patients with haematological malignancy; 853 (65%) of these were from neutropenic patients. Gram-negative bacteria predominated (60%) in neutropenic isolates with Escherichia coli (12%), Klebsiella pneumoniae (10%), Acinetobacter calcoaceticus-baumannii complex (6%), and Stenotrophomonas maltophilia (6%) the most frequent. Coagulase-negative staphylococci (19%) and Staphylococcus aureus (4%) were the most common Gram-positive pathogens. Resistance to ciprofloxacin was found in 50% of E. coli and 20% of K. pneumoniae isolates from neutropenic patients. Extensively drug-resistant A. calcoaceticus-baumannii complex and vancomycin-resistant enterococci were also found during the study period. Emerging antimicrobial resistant pathogens are an increasing threat to neutropenic cancer patients.

Puumala virus (PUUV) causes mild haemorrhagic fever with renal syndrome, a rodent-borne zoonosis. To evaluate the disease burden of PUUV infections in Finland, we analysed data reported by laboratories to the National Infectious Disease Registry during 1995–2008 and compared these with data from other national registries (death, 1998–2007; hospital discharge, 1996–2007; occupational diseases, 1995–2006). A total of 22 681 cases were reported (average annual incidence 31/100 000 population); 85% were in persons aged 20–64 years and 62% were males. There was an increasing trend in incidence, and the rates varied widely by season and region. We observed 13 deaths attributable to PUUV infection (case-fatality proportion 0·08%). Of all cases, 9599 (52%) were hospitalized. Only 590 cases (3%) were registered as occupational disease, of which most were related to farming and forestry. The wide seasonal and geographical variation is probably related to rodent density and human behaviour.

Comparing pertussis epidemiology over time and between countries is confounded by differences in diagnostic and notification practices. Standardized serological methods applied to population-based samples enhance comparability. Population prevalence of different levels of pertussis toxin IgG (PT IgG) antibody, measured by standardized methods, were compared by age group and region of Australia between 1997/1998 and 2002. The proportion of 5- to 9-year-olds with presumptive recent pertussis infection (based on IgG levels ⩾62·5 ELISA units/ml) significantly decreased in 2002, consistent with notification data for the same period and improved uptake of booster vaccines following the schedule change from whole-cell to acellular vaccine. In contrast, recent presumptive infection significantly increased in adults aged 35–49 years. Population-based serosurveillance using standardized PT IgG antibody assays has the potential to aid interpretation of trends in pertussis incidence in relation to vaccine programmes and between countries.

This study was performed to test the hypothesis that there are ‘hotspots’, i.e. geographical heterogeneity, of dengue transmission. Data from two repeat serosurveys in two villages in Vietnam were used to identify incident infections and to relate these to prevalence at baseline and thus assess geographical heterogeneity, i.e. clustering, in dengue transmission. A total of 400 households were surveyed; serological data from 521 children at baseline and from 119 children at follow-up were included in a spatial analysis. Geographical heterogeneity of dengue transmission was explored using a permutation null distribution test. This showed for the first time evidence of clustering of dengue virus transmission at the household level in asymptomatic children. Risk areas could be identified by seroprevalence surveys combined with mapping. Control of dengue virus transmission could be supported by identification and control of hotspots.