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.

Norovirus is a major cause of infectious intestinal disease, and a substantial prevalence of asymptomatic infection has been reported. We describe the prevalence, seasonality and characteristics of asymptomatic norovirus infection in England. Healthy individuals were recruited at random from the general population during the Study of Infectious Intestinal Disease (1993–1996). Norovirus was identified using real-time RT–PCR. The age-adjusted prevalence of asymptomatic norovirus infection was 12%; prevalence was highest in children aged <5 years and showed wintertime seasonality. More work is needed to understand whether asymptomatic infections are important for norovirus transmission leading to sporadic illness and outbreaks.

We analysed nosocomial MRSA cases between January 2004 and December 2006 in a retrospective case-control study in a 250-bed tertiary-care teaching hospital. During the study period, 265 nosocomial Staphylococcus aureus infections were identified in 231 patients. There was a significant increase in methicillin resistance in isolates (MRSA) from these infections with frequencies for 2004 of 39/88 (44·3%), 2005 (62/80, 77·5%), and 2006 (75/97, 77·3%) (P<0·001). Multivariate analysis showed that associated factors for nosocomial MRSA infection were prolonged hospitalization (OR 3·982, 95% CI 2·235–7·094, P<0·001), mechanical ventilation (OR 3·052, 95% CI 1·666–5·590, P<0·001), surgical operation (OR 2·032, 95% CI 1·102–3·748, P=0·023), and male sex (OR 2·000, 95% CI 1·081–3·699, P=0·027). The determination of associated factors for methicillin resistance in nosocomial S. aureus infections in hospitals will play an important role in efforts to reduce MRSA infection rates.

Salmonella Paratyphi A (SPA) is rapidly becoming a common cause of enteric fever in South East Asia. A large outbreak of SPA occurred in a boarding middle school in China in 2004. There were 394 suspected cases; 95·5% were students. The highest incidence was in the youngest children (7th grade). Forty-four of 151 (29%) blood cultures and 4/54 (7·4%) rectal swabs were positive for SPA; three were from kitchen workers. The geometric mean levels of serum IgG anti-lipopolysaccharide (anti-LPS) from patients was higher than from healthy individuals [35·25 vs. 5·20 ELISA units (EU), P<0·001]. A kitchen worker with a positive rectal swab, negative blood culture and a high level of serum IgG anti-LPS (529·65 EU), was identified as a possible SPA carrier. No SPA was isolated from water or food samples. A survey of students' habits indicated drinking unboiled water as being the main reason for contracting the disease. Hand washing was the second most important factor. A food handler with possible SPA carriage could also have been a risk factor. Attention to maintaining a safe water supply, enhancing food-handler hygiene and proper hand washing can help to prevent similar outbreaks in the future.

We measured the recall error, optimal recall length and factors associated with diarrhoea in a weekly survey. Data was taken from a year-long randomized controlled trial in which characteristics of diarrhoeal episodes were recorded weekly. We labelled the recall period as days 1–6; day 1 being the day before the visit. Recall error was the percentage difference between the number of episodes reported to begin on a particular day and the mean for days 1 and 2. Generalized estimating equations were used to determine associations. Recall error was 37% on day 3 and 51% on day 5. The error was less in younger children (by 10%), severe episodes (by 29%) and when blood was present in the stool (by 18%). Diarrhoea was underreported when the recall period extended beyond 2 days. Surveys that use longer recall periods risk underestimating diarrhoea incidence and selectively capturing more severe episodes.

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.

The clinical significance of different genetic subtypes or assemblages of Giardia lamblia is uncertain. Cases of giardiasis in south-west London between 1999 and 2005 were studied, comparing molecular-typing results with clinical and epidemiological findings from routine surveillance. We identified 819 cases, of whom 389 returned surveillance questionnaires. A subset of 267 faecal samples was submitted for typing by sequencing of the triose phosphate isomerase (tpi) and ribosomal RNA genes, and/or a separate duplex PCR of the tpi gene. Typing was successful in 199 (75%) samples by at least one of the molecular methods. Assemblage A accounted for 48 (24%) samples and Assemblage B for 145 (73%); six (3%) were mixed. Both assemblages had similar seasonality, age distribution and association with travel. Clinical features were available for 59 successfully typed cases: both assemblages caused similar illness, but Assemblage A was significantly more frequently associated with fever than Assemblage B.

The increasing prevalence of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) strains together with their disease impact on hospital patients and individuals in the community has posed a major challenge to healthcare workers. This study examined the prevalence of S. aureus nasal carriage, antimicrobial susceptibility patterns, and possible risk factors in the community. Of 500 studied subjects (aged from 6 to 65 years) in Lebanon, the overall S. aureus nasal carriage rate was 38·4%, the highest (57·1%) being in children aged 6–10 years. Only eight individuals (1·6%) were carriers of MRSA. Risk factors for S. aureus nasal colonization were male gender, young age, contact with healthcare workers, use of needle injections, and having asthma. A significant decrease in colonization rate was associated with nasal wash with water, use of nasal sprays, and the presence of acne. These findings may assist in better understanding of control measures to decrease nasal colonization with S. aureus in Lebanon and elsewhere.

We estimated the extent of undiagnosed hepatitis C virus (HCV) infection in injecting drug users (IDUs) in Scotland. We used record-linkage to determine HCV diagnosis status for 41 062 current/former IDUs attending drug treatment and support services between 1 April 1995 and 31 March 2006; the extent of undiagnosed HCV infection was estimated by comparing the number HCV-diagnosed to the number HCV-infected (estimated from an unlinked anonymous testing survey of 2141 current/former IDUs). In all, 9145 IDUs (22%) were diagnosed HCV antibody-positive since first attendance at drug services (diagnosis rate of 33·6/1000 person-years, 95% CI 32·7–34·4). By 31 March 2006, of the 19 632 current/former IDUs who had attended drug services and were determined to be living with HCV, an estimated 58% (95% CI 45–62) had not been HCV-diagnosed. It is essential that the deployment of resources for identifying at-risk IDUs with a view to offering antiviral therapy is guided by evidence.

The extent of hantavirus seroprevalence in the healthy population from Bosnia and Herzegovina has not yet been investigated; therefore, the aim of this study was to assess the hantavirus seroprevalence in the population from different regions of Bosnia and Herzegovina and in different risk groups. The serosurvey included 1331 subjects from endemic and non-endemic regions in Bosnia and Herzegovina. All sera samples were examined using IgG ELISA, and Western blot (Bunyavirus IgG) tests. Hantavirus seroprevalence was 7·4% in the endemic region and 2·4% in the non-endemic region (P<0·05). Former soldiers from the endemic region had significantly the highest seroprevalence (16·1%) compared to the general population from the endemic region (6·2%), the occupational risk group from the non-endemic region (5·6%) and the general population from the non-endemic region (0·8%) (P<0·01). No difference in hantavirus seroprevalence between gender or age groups was observed. Hantavirus seroprevalence in different populations in Bosnia and Herzegovina was found to be highest compared to other central European countries.

Participating researchers and public health personnel at a Canadian workshop in 2007, noted considerable gaps in current understanding of community-associated Clostridium difficile infection (CA-CDI), specifically infection sources and risk factors. A disease transmission model for CA-CDI was requested as an initial step towards a risk assessment, to analyse infection sources and risk factors, addressing priority research areas. The developed model contains eight infection states (susceptible, gastrointestinal exposure, colonized, diseased, deceased, clinically resolved colonized, relapse diseased, and cleared) and notes directional transfers between the states. Most published research used focused on hospital-associated C. difficile infection (HA-CDI) and further studies are needed to substantiate the use of HA-CDI knowledge in the transmission of CA-CDI. The aim was to provide a consistent framework for researchers, and provide a theoretical basis for future quantitative risk assessment of CA-CDI.

In a 2-year longitudinal study of adult animals on 15 dairy farms and four sheep farms in Lancashire, UK. C. jejuni was isolated from all farms, although not on every occasion. Faecal samples were collected and cultured using standard techniques for isolation of Campylobacter. Assignment to species was via PCR assays. Peak prevalence of C. jejuni in both cattle and sheep was observed during the summer and in cattle this apparent seasonality was associated with grazing pasture [odds ratio (OR) 2·14], while in sheep it was independent of grazing. Increased prevalence was associated with increased milk yield (OR 1·05) and herd size (OR 1·01) in dairy cattle, and with increased stocking density (OR 1·29) and pasture quality (OR 2·16) in sheep. There was considerable variation in prevalence between farms but no evidence of large-scale spatial variation. The association between C. jejuni prevalence and diet in dairy cattle deserves further investigation.

In February 2007 an outbreak of Nipah virus (NiV) encephalitis in Thakurgaon District of northwest Bangladesh affected seven people, three of whom died. All subsequent cases developed illness 7–14 days after close physical contact with the index case while he was ill. Cases were more likely than controls to have been in the same room (100% vs. 9·5%, OR undefined, P<0·001) and to have touched him (83% vs. 0%, OR undefined, P<0·001). Although the source of infection for the index case was not identified, 50% of Pteropus bats sampled from near the outbreak area 1 month after the outbreak had antibodies to NiV confirming the presence of the virus in the area. The outbreak was spread by person-to-person transmission. Risk of NiV infection in family caregivers highlights the need for infection control practices to limit transmission of potentially infectious body secretions.

In South Africa, for the years 2003–2007, the Enteric Diseases Reference Unit received 510 human isolates of Salmonella Typhi, of which 27 were nalidixic acid-resistant [minimum inhibitory concentrations (MICs) 128–512 μg/ml] with reduced susceptibility to ciprofloxacin (MICs 0·125–0·5 μg/ml). Pulsed-field gel electrophoresis analysis of 19 available isolates differentiated them into five DNA pattern types; multiple-locus variable-number tandem repeat analysis differentiated the isolates into 10 types. This level of genetic diversity suggested that resistant strains usually emerged independently of one another. A 16- to 32-fold decrease in nalidixic acid MIC and a 2- to 8-fold decrease in ciprofloxacin MIC, was observed in the presence of an efflux pump inhibitor. All isolates were negative by PCR screening for qnr genes. Seven resistant isolates were further analysed for mutations in the quinolone resistance-determining region of gyrA, gyrB, parC and parE. No amino-acid mutations were identified in GyrB and ParE; all isolates showed amino-acid mutations in both GyrA and ParC. We conclude that amino-acid mutations in GyrA and ParC in combination with active efflux of antibiotic out of the bacterial cell are the probable mechanisms conferring quinolone resistance.

Few reports exist regarding the association between onychomadesis and an enterovirus infection presenting clinically as hand, foot, and mouth disease (HFMD). In February 2009, an outbreak of HFMD occurred in a Spanish nursery school, followed by onychomadesis 36–69 days later. Twelve of 17 children with HFMD developed nail shedding; enterovirus was detected in stool samples from eight (47%) of the 17. However, in only three of the children could an enterovirus serotype coxsackievirus B1 be identified. The epidemiological results of this study confirm onychomadesis as a complication in HFMD. In future outbreaks, molecular characterization of enterovirus from appropriate clinical samples should be studied.

To analyse sociodemographic, viroimmunological and clinical parameters in different HIV-transmission categories at baseline and during treatment, 3039 patients were followed up for 12 months after the initiation of a nelfinavir-based regimen. Multiple baseline parameters were significantly different in the diverse categories, including CD4 counts (P<0·0001) and viral load (P=0·02). There were differences in the groups regarding the CD4 response (P=0·01), but not the virological response (P=0·4), to therapy over time. Multivariate analyses revealed that transmission categories were significantly related to baseline CD4 counts (P=0·01), viral load at 12 months (P=0·0006), poorer adherence to therapy of injecting drug users (IDUs) vs. each of the other groups (P<0·001) and failure to complete the 12-month evaluation of IDU vs. heterosexual (P=0·003) and men who have sex with men (MSM) groups (P=0·02). We conclude that transmission categories had a significant influence on several baseline parameters and viroimmunological outcomes following highly active antiretroviral therapy (HAART), as well as on adherence to therapy and to medical appointments.

This study attempted to examine the relatedness between RAPD–PCR, PFGE and VcA VNTR results with those of conventional phage typing of V. cholerae strains and to evaluate VcA VNTR as an indispensable molecular-typing tool that accomplishes the urgent need for effective epidemiological surveillance. All the O1 El Tor strains were predominantly clustered into phage type T27 with the new phage-typing scheme. Using RAPD–PCR, a total of 69 O1 El Tor strains were grouped under 16 different electrophoretic patterns. A total of 33 pulsotypes were identified in these strains by PFGE. VcA VNTR revealed high VcA polymorphism in all V. cholerae strains incorporated in this study. Our results underline the considerable potential of VcA VNTR analysis as a tool for molecular typing of V. cholerae.

A cross-sectional study was carried out in injecting drug users (IDUs) from Greece to assess the seroprevalence of human herpesvirus 8 (HHV-8) and to identify potentially associated risk factors. A total of 288 IDUs were tested for K8.1 antibodies to HHV-8 lytic antigen. Associations between HHV-8 serostatus and potential risk factors were examined using univariate and multivariate logistic regression analysis. Seroprevalence of HHV-8 was 24·3% (95% CI 19·5–29·7), increasing with age from 19·4% in those aged <30 years to 52·9% in those aged ⩾40 years (P for trend=0·003). No statistically significant associations between HHV-8-positive status and gender, educational level, age at first drug injection, needle sharing, number of imprisonments, complications from drug overdose, HIV and HCV were observed. In the multivariate logistic regression analysis, older age (⩾40 vs. <40 years, OR 3·30, 95% CI 1·14–9·56) and report of septicaemia/abscess (yes vs. no, OR 1·80, 95% CI 1·01–3·18) were each independently associated with higher HHV-8 seroprevalence. HHV-8 is highly prevalent in the IDU population in Greece. The independent association between HHV-8 and reported abscess or septicaemia supports the hypothesis that poor hygiene conditions in the setting of drug injection may contribute to HHV-8 transmission.

We investigated the incidence of cases of nosocomial pathogens and risk factors in an intensive treatment unit ward to determine if the number of cases is dependent on location of patients and the colonization/infection history of the ward. A clustering approach method was developed to investigate the patterns of spread of cases through time for five microorganisms [methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter spp., Klebsiella spp., Candida spp., and Pseudomonas aeruginosa] using hospital microbiological monitoring data and ward records of patient-bed use. Cases of colonization/infection by MRSA, Candida and Pseudomonas were clustered in beds and through time while cases of Klebsiella and Acinetobacter were not. We used structural equation modelling to analyse interacting risk factors and the potential pathways of transmission in the ward. Prior nurse contact with colonized/infected patients, mediated by the number of patient-bed movements, were important predictors for all cases, except for those of Pseudomonas. General health and invasive surgery were significant predictors of cases of Candida and Klebsiella. We suggest that isolation and bed movement as a strategy to manage MRSA infections is likely to impact upon the incidence of cases of other opportunist pathogens.

We aimed to characterize an environmental niche driving the distribution of Crimean-Congo haemorrhagic fever (CCHF) in Turkey, using a georeferenced collection of cases reported between 2003 and 2008 and a set of climate and vegetation features. We used mean monthly air temperatures and Normalized Derived Vegetation Index (NDVI) values, at a resolution of 0·1°, as well as climate features at and below the surface. We computed significant differences in monthly variables between positive and negative sites, within the range of distribution of the tick vector. Seasonal climate (growth season and summer length, accumulated temperatures in winter) and vegetation components (anomalies in NDVI data) were analysed. Fragmentation of habitat was obtained from NDVI monthly data at a resolution of 1 km. Neither single climate or vegetation variables, nor any individual seasonal component, accounted in both space and time for the delineation of areas of disease although accumulated temperatures in winter consistently showed lower values in areas where the disease was reported. Coherent and significant differences between disease-containing and disease-free sites were found when habitat fragmentation and connectivity were examined. High fragmentation and connectivity were unambiguously associated with sites where disease is reported and accounted for the spatial spread of cases in 2003–2008. CCHF cases were always associated with areas of highly fragmented and well-connected patches within the range of the tick vector, while there were no reports from areas with low fragmentation. There was a linear relationship between degree of fragmentation and case incidence. The implications of these findings are discussed with reference to the concept of disease spread through networks of connected spots with high densities of infected vectors and social factors driving different human activities in sites of high fragmentation.