This study assessed changes in prevalence and distribution of HIV-1 non-subtype B viruses in Italian and immigrant patients over two decades in a province in Italy. All HIV-positive patients who underwent genotypic resistance testing were selected. Prevalence of non-subtype B viruses in 3-year periods was calculated. All sequences of non-subtype B and those provided by REGA as unassigned were analysed for phylogenetic relationships. In total, 250/1563 (16%) individuals were infected with a non-subtype B virus. Prevalence increased over time, reaching a peak (31·5%) in 2004–2006. In Italian patients, the most frequent subtypes were B (92·5%) and F1 (4%). F1 subtype was also prevalent in patients from South America (13·6%); in patients of African origin, CRF02_AG (54·9%) and G (12·3%) were the most frequent. HIV-1 non-subtype B infections in Italians were mostly found in patients who acquired HIV sexually. A phylogenetic relationship between F subtypes in Italian and representative HIV-1 sequences from Brazil was found. C subtypes in Italians were phylogenetically related to subtypes circulating in Brazil. Inter-subtype recombinants were also found in the latest years. The HIV-1 epidemic in Brescia province evolved to the point where about 1/3 patients recently diagnosed harboured non-B HIV subtypes. The distribution of HIV-1 non-B subtypes in Italian patients resembled that in South American patients and phylogenetic relatedness between some Italian and South American HIV-1 strains was found. The possible epidemiological link between these two populations would have been missed by looking only at risk factors for HIV acquisition declared by patients. The evidence of inter-subtype recombinants points to significant genetic assortment. Overall our results support phylogenetic analysis as a tool for epidemiological investigation in order to guide targeted prevention strategies.

Diarrhoea is a leading cause of morbidity and mortality yet diarrhoea specific incidence and mortality rates for older children, adolescents, and adults have not been systematically calculated for many countries. We conducted a systematic literature review to generate regional incidence rates by age and to summarize diarrhoea specific mortality rates for regions of the world with inadequate vital registration data. Diarrhoea morbidity rates range from 29·9 episodes/100 person-years for adults in the South East Asian region to 88·4 episodes/100 person-years in older children in the Eastern Mediterranean region and have remained unchanged in the last 30 years. Diarrhoea mortality rates decline as the child ages and remain relatively constant during adulthood. These data are critical for improving estimates worldwide and further highlight the need for improved diarrhoea specific morbidity and mortality data in these age groups.

We examined stool specimens for viral pathogens from 50 children referred to hospital due to acute gastroenteritis (AGE) resulting from consuming drinking water contaminated with sewage in a Finnish community using PCR methods. Rotavirus was detected in 33 (66%), human calicivirus in 31 (62%), and both in 40% of cases. Of the caliciviruses, 20/31 (65%) were noroviruses and 11 (35%) sapoviruses. Furthermore, Aichi virus was detected in 25 (50%), adenovirus in six (12%) and bocavirus in four (8%) cases. Campylobacter jejuni was present in 20 (61%) and Salmonella in four (12%) of the 33 stools cultured for bacteria. On a 20-point scale median severity score of AGE in the 28 hospitalized children was 17; the severity was similar regardless of viruses detected. Bloody diarrhoea occurred only when C. jejuni was present. To conclude, massive exposure to several AGE viruses caused mixed infections and severe AGE regardless of the aetiological agents.

The incidence of hospitalization for acute gastroenteritis (AGE) is a useful parameter to assess the utility of the new rotavirus vaccines in high-income countries. Children hospitalized for AGE were identified by searching hospital discharge data and the records of the microbiology laboratory of Hospital Donostia. Rotavirus antigen was investigated in 96·1% of the 1114 children aged 1 month to <5 years hospitalized for AGE in the study period. Nearly 40% were rotavirus positive (44·9% of the 798 children aged 1 month to <2 years), with G1[P8] being the predominant genotype. The mean annual incidence rate of hospitalization due to rotavirus AGE was 29·8 and 63·7 cases/10 000 inhabitants in the <5 and <2 years age groups, respectively, in 1996–1999, decreasing to 13·6 and 27·4 cases/10 000 inhabitants in <5 and <2 years age groups, respectively, in 2002–2005 (P<0·001). This decrease coincided with a significant increase in the consumption of oral rehydration solutions.

Traditionally, the routine artificial digestion test is applied to assess the presence of Trichinella larvae in pigs. However, this diagnostic method has a low sensitivity compared to serological tests. The results from artificial digestion tests in Switzerland were evaluated over a time period of 15 years to determine by when freedom from infection based on these data could be confirmed. Freedom was defined as a 95% probability that the prevalence of infection was below 0·0001%. Freedom was demonstrated after 12 years at the latest. A new risk-based surveillance approach was then developed based on serology. Risk-based surveillance was also assessed over 15 years, starting in 2010. It was shown that by using this design, the sample size could be reduced by at least a factor of 4 when compared with the traditional testing regimen, without lowering the level of confidence in the Trichinella-free status of the pig population.

Trichinella nativa infection (trichinellosis) is highly prevalent in Arctic wildlife, but the human burden of trichinellosis in present-day Greenland is unknown. The study aimed to determine Trichinella seroprevalence in an eastern Greenlandic hunting community and to evaluate risk factors for seropositivity. Overall, 998 inhabitants aged ⩾10 years in the Ammassalik municipality were tested for Trichinella-specific IgG antibodies. Background information was obtained from questionnaires. Seropositivity was 1·4% in persons aged <40 years and increased to >12% in those aged ⩾60 years. Older age, occupation as hunter or fisherman, and consumption of polar bear meat significantly increased the risk of Trichinella seropositivity. The seropositivity age pattern probably reflects changes in dietary preferences, but could also reflect mandatory meat inspection since 1966. However, preventive measures against Trichinella infection should be strengthened in Greenland.

Knowledge of the factors affecting the presence of Toxoplasma gondii in wildlife is limited. Here we analyse which local landscape characteristics are associated with the presence of toxoplasmosis in wild boar, Sus scrofa, on the island of Corsica, France. Meat juice samples from 1399 wild boars collected during two hunting seasons were tested for T. gondii antibodies using the modified agglutination test (titre 1:4). The overall seroprevalence was 0·55 (95% CI 0·50–0·59) for the first year and 0·33 (95% CI 0·29–0·35) for the second year. Seroprevalence varied according to age and county. At the county level, seropositivity in adults was related to farm density during year 1, and to habitat fragmentation, farm density and altitude during year 2. The exposure of wild boar to T. gondii is thus variable according to landscape characteristics and probably results in a variable risk of transmission of toxoplasmosis to humans.

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.

In 2006 an outbreak of avian influenza A(H5N1) in Turkey caused 12 human infections, including four deaths. We conducted a serological survey to determine the extent of subclinical infection caused by the outbreak. Single serum samples were collected from five individuals with avian influenza whose nasopharyngeal swabs tested positive for H5 RNA by polymerase chain reaction, 28 family contacts of the cases, 95 poultry cullers, 75 individuals known to have had contact with diseased chickens and 81 individuals living in the region with no known contact with infected chickens and/or patients. Paired serum samples were collected from 97 healthcare workers. All sera were tested for the presence of neutralizing antibodies by enzyme-linked immunoassay, haemagglutination inhibition and microneutralization assays. Only one serum sample, from a parent of an avian influenza patient, tested positive for H5N1 by microneutralization assay. This survey shows that there was minimal subclinical H5N1 infection among contacts of human cases and infected poultry in Turkey in 2006. Further, the low rate of subclinical infection following contact with diseased poultry gave further support to the reported low infectivity of the virus.

Statins reduce cardiovascular mortality and related risks associated with pneumonia suggesting potentially beneficial use in influenza pandemics. We investigated the effect of current statin use on acute respiratory infections in primary care. Data from anonymized electronic medical records of persons aged ⩾45 years were examined for statin use, chronic morbidity, respiratory diagnoses, vaccination procedures, and immune suppression. Logistic regression models were used to calculate odds ratios (ORs) for statin users vs. non-users in respiratory infection outcomes. A total of 329 881 person-year observations included 18% statin users and 46% influenza vaccinees. Adjusted ORs for statin users vs. non-users were: influenza-like illness, 1·05 (95% CI 0·92–1·20); acute bronchitis, 1·08 (95% CI 1·01–1·15); pneumonia, 0·91 (95% CI 0·73–1·13); all acute respiratory infections, 1·03 (95% CI 0·98–1·07); and urinary tract infections, 0·91 (95% CI 0·85–0·98). We found no benefit in respiratory infection outcomes attributable to statin use, although uniformly higher ORs in non-vaccinated statin users might suggest synergism between statins and influenza vaccination.

Schistosoma japonicum infection associated with a rectal carcinoid in an asymptomatic 44-year-old female from the Philippines is described. A systematic review of the literature could not identify similar reports, suggesting a rare coincidence. However, epidemiological data on the frequency of both conditions as well as published results of a colorectal screening programme from China indicate that underreporting of this concurrence is likely. Moreover, several studies suggest a causal link between schistosomiasis caused by S. japonicum and more common gastrointestinal malignancies such as colorectal carcinoma. Hence the presented case and the apparent neglect of this observation in the current literature allow speculation on a role of S. japonicum in the pathogenesis of rare gastrointestinal neoplasms such as carcinoid tumours as well. Future reports on similar observations could help to determine the need for systematic investigations and are strongly encouraged.

Japanese encephalitis (JE) has been found to be endemic in Bali, Indonesia. A case-control study was conducted to identify factors associated with JE infection. All 94 serologically confirmed JE cases (cases) and 163 cases of encephalitis or aseptic meningitis without JE (controls) identified in Bali during 2001–2004 were included in the study. Potential risk factors were surveyed at hospital admission. Univariate analyses revealed the following factors to be associated with JE: older age, referral from sub-district health centre or private hospital, playing outdoors after dinner, use of mosquito repellent or spraying, proximity of the residence to rice fields, and pig ownership by the family or next-door neighbours. Multivariate analysis identified proximity to rice fields (OR 2·93, 95% CI 1·57–5·45), pig ownership (OR 2·24, 95% CI 1·17–4·26), and older age (OR 1·21, 95% CI 1·09–1·33) as being independently associated with the risk of JE. Because rice cultivation and pig rearing are essential to the economy of Bali, JE immunization is the best intervention for prevention of JE in Bali.

Though largely controlled in developed countries, measles remains a major global public health issue. Regional and local transmission patterns are rooted in human mixing behaviour across spatial scales. Identifying spatial interactions that contribute to recurring epidemics helps define and predict outbreak patterns. Using spatially explicit reported cases from measles outbreaks in Niger, we explored how regional variations in movement and contact patterns relate to patterns of measles incidence. Because we expected to see lower rates of re-introductions in small, compared to large, populations, we measured the population-size corrected proportion of weeks with zero cases across districts to understand relative rates of measles re-introductions. We found that critical elements of spatial disease dynamics in Niger are agricultural seasonality, transnational contact clusters, and roads networks that facilitate host movement and connectivity. These results highlight the need to understand local patterns of seasonality, demographic characteristics, and spatial heterogeneities to inform vaccination policy.

We assessed recent trends in hepatitis C virus (HCV) prevalence in pregnant women with HIV using data from a large national study. Based on 1240 pregnancies, we observed a 3·4-fold decline in HCV seroprevalence in pregnant women with HIV between 2001 (29·3%) and 2008 (8·6%). This decline was the net result of two components: a progressively declining HCV seroprevalence in non-African women (from 35·7% in 2001 to 16·7% in 2008), sustained by a parallel reduction in history of injecting drug use (IDU) in this population, and a significantly growing presence (from 21·2% in 2001 to 48·6% in 2008) of women of African origin, at very low risk of being HCV-infected [average HCV prevalence 1%, adjusted odds ratio (aOR) for HCV 0·09, 95% CI 0·03–0·29]. Previous IDU was the stronger determinant of HCV co-infection in pregnant women with HIV (aOR 30·9, 95% CI 18·8–51·1). The observed trend is expected to translate into a reduced number of cases of vertical HCV transmission.

Clostridium difficile and staphylococcal infections are associated with increased morbidity, mortality and healthcare costs. Vitamin D deficiency may also contribute to increased healthcare costs. There is increasing evidence that vitamin D may have an antimicrobial role. We examined the relationship of serum 25(OH)D levels to staphylococcal and C. difficile infections to determine if vitamin D deficiency was associated with adverse outcomes. In the outpatient setting, vitamin D deficiency in patients with C. difficile and staphylococcal infections were associated with significantly increased total outpatients costs and fee-based consultation. Laboratory expenses had a trend towards higher costs in the vitamin D-deficient group but did not reach statistical significance. The differences were most clearly seen in the in-patient group with enhanced laboratory, pharmacy and radiology costs. These differences resulted in vitamin D-deficient patients with C. difficile or staphylococcal infections having costs more than five times higher than the non-deficient patients. The total length of hospital stay was four times greater in the vitamin D-deficient group. In addition, the total number of hospitalizations was also significantly greater in the vitamin D-deficient group. Surgery costs demonstrated a tendency to be higher in the vitamin D-deficient group but failed to reach statistical significance. Vitamin D deficiency is intimately linked to adverse health outcomes and costs in Veterans with staphylococcal and C. difficile infections in North East Tennessee. We recommend that vitamin D status be checked in patients with these infections and appropriate therapy be instituted to restore vitamin D level to normal in an expeditious manner.

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.

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.

Burkholderia pseudomallei, the causative agent of melioidosis is associated with soil. This study used a geographic information system (GIS) to determine the spatial distribution of clinical cases of melioidosis in the endemic suburban region of Townsville in Australia. A total of 65 cases over the period 1996–2008 were plotted using residential address. Two distinct groupings were found. One was around the base of a hill in the city centre and the other followed the old course of a major waterway in the region. Both groups (accounting for 43 of the 65 cases examined) are in areas expected to have particularly wet topsoils following intense rainfall, due to soil type or landscape position.

Pneumococcal meningitis is a subgroup of invasive pneumococcal disease with a case-fatality rate of up to 30% and long-term sequelae in more than 50% of cases in adults in developed countries. We aimed to determine risk factors for this particular form of pneumococcal disease. We conducted a prospective population-based laboratory study of invasive pneumococcal disease in adults in North-Rhine-Westphalia, Germany from February 2001 to August 2006. All isolates underwent serotyping and susceptibility testing at the National Reference Centre for Streptococci in Aachen, Germany. Data were analysed using multiple linear regression. A total of 1043 isolates from bacteraemia and 131 isolates from meningitis were included into the study. Serotype 23F and being female were independent risk factors for pneumococcal meningitis. Being ⩾60 years and serotype 1 were associated with a reduced odds ratio. Season, penicillin and macrolide resistance were not statistically associated with CNS involvement.