Nipah virus (NiV) is a recently emerged zoonotic virus that causes severe disease in humans. The reservoir hosts for NiV, bats of the genus Pteropus (known as flying-foxes) are found across the Asia-Pacific including Australia. While NiV has not been detected in Australia, evidence for NiV infection has been found in flying-foxes in some of Australia's closest neighbours. A qualitative risk assessment was undertaken to assess the risk of NiV establishing in Australian flying-foxes through flying-fox movements from nearby regions. Events surrounding the emergence of new diseases are typically uncertain and in this study an expert opinion workshop was used to address gaps in knowledge. Given the difficulties in combining expert opinion, five different combination methods were analysed to assess their influence on the risk outcome. Under the baseline scenario where the median was used to combine opinions, the risk was estimated to be very low. However, this risk increased when the mean and linear opinion pooling combination methods were used. This assessment highlights the effects that different methods for combining expert opinion have on final risk estimates and the caution needed when interpreting these outcomes given the high degree of uncertainty in expert opinion. This work has provided a flexible model framework for assessing the risk of NiV establishment in Australian flying-foxes through bat movements which can be updated when new data become available.

In December 2004, the Department of Human Services investigated an outbreak of Q fever in South Australia. A case-control study tested an association between attending a local saleyard and human illness. A case was defined as a person with clinical illness and evidence of seroconversion or high phase II IgM. Controls were selected from a database of community controls matched on sex, age group and postcode. Matched analysis of the first 15 cases with 45 controls indicated that contracting Q fever was associated with attending the saleyard on one particular day (adjusted odds ratio 15·3, 95% confidence interval 1·7–undefined, P = 0·014). Saleyard conditions were windy and conducive for airborne dispersal of contaminated particles. In total, 25 cases were detected. Of these, 22 cases had attended a local saleyard on the same day. This outbreak suggests cases were probably infected by a single exposure at a saleyard from infected sheep and dust. The investigation resulted in an increase in the local uptake of Q fever vaccination and extension of the Australian national vaccination programme.

Mycoplasma infections are most frequently associated with disease in the urogenital or respiratory tracts and, in most cases, mycoplasmas infect the host persistently. In HIV-infected individuals the prevalence and role of genital mycoplasmas has not been well studied. To investigate the six species of Mycoplasma and the risk factors for infection in Jiangsu province, first-void urine and venous blood samples were collected and epidemiological questionnaires were administered after informed consent. A total of 1541 HIV/AIDS patients were recruited in this study. The overall infection rates of six Mycoplasma species were: Ureaplasma urealyticum (26·7%), Mycoplasma hominis (25·3%), M. fermentans (5·1%), M. genitalium (20·1%), M. penetrans (1·6%) and M. pirum (15·4%). The Mycoplasma infection rate in the unmarried group was lower than that of the married, divorced and widowed groups [adjusted odds ratio (aOR) 1·432, 95% confidence interval (CI) 1·077–1·904, P < 0·05]. The patients who refused highly active antiretroviral therapy (HAART) had a much higher risk of Mucoplasma infection (aOR 1·357, 95% CI 1·097–1·679, P < 0·05). Otherwise, a high CD4+ T cell count was a protective factor against Mycoplasma infection (aOR 0·576, 95% CI 0·460–0·719, P < 0·05). Further research will be required to confirm a causal relationship and to identify risk factors for Mycoplasma infection in HIV/AIDS populations.

Hand, foot and mouth disease (HFMD) associated with enterovirus 71 (EV71) is a growing public health concern. This study aimed to estimate the case-fatality of HFMD associated with EV71 on the basis of a meta-analysis. We searched PubMed, Cochrane, Web of Science, Elsevier, CNKI, Wanfang, and VIP databases. Two authors independently selected relevant studies. The pooled estimate of case-fatality was calculated using a random-effects model. Potential sources of heterogeneity were explored using subgroup analysis, sensitivity analysis and meta-regression. We identified 14 eligible studies with a total population of 112 546. The random-effects pooled case-fatality was 1·7% (95% confidence interval 1·2–2·4). The funnel plot was asymmetrical. The estimate of case-fatality was highest in mainland China (1·8%). Removal of eight local Chinese studies decreased the original estimate. The pooled case-fatality in the period of 1998–2007 (1·5%) was lower than that in the period 2008–2012 (1·8%). Control measures for HFMD associated with EV71 are essential because of the increased case-fatality over time, especially in East Asia.

We simulated the frequency of tuberculosis infection in healthcare workers in order to classify the risk of TB transmission for nine hospitals in Medellín, Colombia. We used a risk assessment approach to estimate the average number of infections in three risk groups of a cohort of 1082 workers exposed to potentially infectious patients over 10- and 20-day periods. The risk level of the hospitals was classified according to TB prevalence: two of the hospitals were ranked as being of very high priority, six as high priority and one as low priority. Consistent results were obtained when the simulation was validated in two hospitals by studying 408 healthcare workers using interferon gamma release assays and tuberculin skin testing. The latent infection prevalence using laboratory tests was 41% [95% confidence interval (CI) 34·3–47·7] and 44% (95% CI 36·4–51·0) in those hospitals, and in the simulation, it was 40·7% (95% CI 32·3–49·0) and 36% (95% CI 27·9–44·0), respectively. Simulation of risk may be useful as a tool to classify local and regional hospitals according to their risk of nosocomial TB transmission, and to facilitate the design of hospital infection control plans.

Paediatricians recognize that using the time-dependent community-acquired vs. hospital-acquired bloodstream infection (BSI) dichotomy to guide empirical treatment no longer distinguishes between causative pathogens due to the emergence of healthcare-associated BSIs. However, paediatric epidemiological evidence of the aetiology of BSIs in relation to hospital admission in England is lacking. For 12 common BSI-causing pathogens in England, timing of laboratory reports of positive paediatric (3 months to 5 years) bacterial blood isolates were linked to in-patient hospital data and plotted in relation to hospital admission. The majority (88·6%) of linked pathogens were isolated <2 days after hospital admission, including pathogens widely regarded as hospital acquired: Enterococcus spp. (67·2%) and Klebsiella spp. (88·9%). Neisseria meningitidis, Streptococcus pneumoniae, group A streptococcus and Salmonella spp. were unlikely to cause hospital-acquired BSI. Pathogens commonly associated with hospital-acquired BSI are being isolated <2 days after hospital admission alongside pathogens commonly associated with community-acquired BSI. We confirm that timing of blood samples alone does not differentiate between bacterial pathogens. Additional factors including clinical patient characteristics and healthcare contact should be considered to help predict the causative pathogen and guide empirical antibiotic therapy.

Toxoplasma gondii is a globally distributed parasitic protozoan that infects most warm-blooded animals. We incorporated a bead coupled with recombinant SAG2A protein into our Neglected Tropical Disease (NTD) multiplex bead assay (MBA) panel and used it to determine Toxoplasma infection rates in two studies in Haiti. In a longitudinal cohort study of children aged 0–11 years, the infection rate varied with age reaching a maximum of 0·131 infections/year in children aged 3 years [95% confidence interval (CI) 0·065–0·204]. The median time to seroconversion was estimated to be 9·7 years (95% CI 7·6–∞). In a cross-sectional, community-wide survey of residents of all ages, we determined an overall seroprevalence of 28·2%. The seroprevalence age curve from the cross-sectional study also suggested that the force of infection varied with age and peaked at 0·057 infections/year (95% CI 0·033–0·080) at age 2·6 years. Integration of the Toxoplasma MBA into NTD surveys may allow for better estimates of the potential burden of congenital toxoplasmosis in underserved regions.

Previous studies have shown the association between the polymorphisms serine (S) or aspartic acid (D) at codon 146 of the PRNP gene and resistance to scrapie. All goats aged >12 months (a total of 1075 animals) from four herds with the highest prevalence of scrapie in the country were culled and tested, of which 234 (21·7%) were positive by either the rapid test or immunohistochemistry (IHC) for any of the tissues tested. The odds of scrapie infection occurring in NN146 goats was 101 [95% credible interval (CrI) 19–2938] times higher than for non-NN146 or unknown genotypes. IHC applied to lymphoreticular tissue produced the highest sensitivity (94%, 95% CrI 90–97). The presence of putatively resistant non-NN146 alleles in the Cypriot goat population, severely affected by scrapie, provides a potential tool to reduce/eradicate scrapie provided that coordinated nationwide breeding programmes are implemented and maintained over time.

Arboviral infections are emerging among tourists travelling to (sub)tropical regions. This study aims to describe the importation of chikungunya virus (CHIKV) and West Nile virus (WNV) into Belgium over a 6-year period from 2007 to 2012. Clinical samples were obtained from travellers presenting at the outpatient clinic of the Institute of Tropical Medicine (ITM), Antwerp, Belgium or submitted to the Central Laboratory for Clinical Biology of the ITM. Testing was performed by serology and/or by real-time reverse transcriptase–polymerase chain reaction. A total of 1288 returning travellers were investigated for CHIKV infection resulting in 34 confirmed and two probable diagnoses (2·80%). Out of 899 patients, four confirmed and one probable imported WNV infections were diagnosed (0·55%). No locally acquired cases have been registered in Belgium until now and the geographical origin of the imported infections reflects the global locations where the viruses are circulating.

RSV is the most important viral cause of pneumonia and bronchiolitis in children worldwide and has been associated with significant disease burden. With the renewed interest in RSV vaccines, we provide realistic estimates on duration, and influencing factors on RSV shedding which are required to better understand the impact of vaccination on the virus transmission dynamics. The data arise from a prospective study of 47 households (493 individuals) in rural Kenya, followed through a 6-month period of an RSV seasonal outbreak. Deep nasopharyngeal swabs were collected twice each week from all household members, irrespective of symptoms, and tested for RSV by multiplex PCR. The RSV G gene was sequenced. A total of 205 RSV infection episodes were detected in 179 individuals from 40 different households. The infection data were interval censored and assuming a random event time between observations, the average duration of virus shedding was 11·2 (95% confidence interval 10·1–12·3) days. The shedding durations were longer than previous estimates (3·9–7·4 days) based on immunofluorescence antigen detection or viral culture, and were shown to be strongly associated with age, severity of infection, and revealed potential interaction with other respiratory viruses. These findings are key to our understanding of the spread of this important virus and are relevant in the design of control programmes.

During the last few years, several cases of West Nile virus (WNV) infection in humans have been reported in Tunisia. However, detailed information on WNV infection in wild birds, the primary amplifying host of WNV, are lacking. In this work, we investigated the exposure of wild sparrows (hybrid Passer domesticus × hispaniolensis) living in two oases in southern Tunisia (Gabès and Kébili oases) to WNV, through the detection of WNV-specific antibodies by using ELISA and microneutralization tests. In total, 208 birds were sampled (54 from Kébili, 154 from Gabès). Anti-WNV antibodies were detected in two birds, corresponding to an overall seroprevalence of 1%. There was no significant difference between the two sampled populations [1·85% (1/54) in Kébili, 0·65% (1/154) in Gabès]. These data provide indirect evidence of the exposure of resident sparrows in southern Tunisia to WNV.

The goal of this study was to determine the reduction in risk of infection by viruses with the use of an alcohol-based hand sanitizer, used in addition to routine hand washing, in family members in households. A quantitative microbial risk model was used to determine the probability of infection from the concentration of virus on the hands. The model incorporated variation in hand size, frequency of touching orifices (nose, mouth, eyes), and percent transfer to the site of infection, as well as, dose-response for each virus. Data on the occurrence of virus on household members' hands from an intervention study using MS-2 coliphage was used to determine the reduction of viruses on the hands pre- and post-intervention. It was found that the risk of rhinovirus, rotavirus or norovirus infection after the intervention was reduced by 47–98% depending upon the initial concentration of virus on the hands.

The health status of the Irish Traveller ethnic minority is low compared to the general population in Ireland in terms of infant mortality rates and life expectancies. Respiratory disease is an area of health disparity manifested as excess mortalities in Traveller males and females. In this study, we examined the available data with regard to tuberculosis (TB) notifications in Ireland from 2002 to 2013. We found an increase in TB notifications in Irish Travellers from 2010 onwards. This resulted in a crude incidence rate for TB in Irish Travellers that was approximately threefold higher than that of the white Irish-born population in 2011 and 2012. An outbreak of TB in Irish Travellers in 2013 increased this differential further, but when outbreak-linked cases were excluded, a higher incidence rate was still observed in Irish Travellers relative to the general population and to white Irish-born. The mean age of a TB patient was 26 years in Irish Travellers compared to 43 years in the general population, and 49 years in white Irish-born. Based on available data, Irish Travellers exhibit a higher incidence rate and younger age distribution of TB compared to white Irish-born and the general population. These observations emphasize the importance of routine use of ethnicity identifiers in the management of TB and other notifiable communicable illnesses in Ireland. They also have implications for the orientation of preventive services to address health disparities in Irish Travellers and other ethnic minority groups.

The objectives of this study were to characterize methicillin-resistant Staphylococcus aureus (MRSA) blood culture isolates and to determine their relative importance in both nosocomial and community-acquired infections. A total of 535 MRSA blood culture isolates were analysed. In vitro susceptibility to 14 agents was determined. The genes nuc, mecA and coding for PVL toxin were identified by PCR. All isolates were characterized by PFGE or spa typing to assess their genomic relationships. Most MRSA isolates were retrieved from nosocomial bloodstream infections (474, 89%) and were of the CMRSA2 genotype. Healthcare-associated (HA)-MRSA bloodstream infections were associated with older age (70–89 years, P = 0·002) and most often secondary to central line infections (P = 0·005). Among MRSA strains associated with community-acquired (CA)-MRSA, 28·8% were isolated in intravenous drug users. CA-MRSA genotypes were more frequently found in young adults (20–39 years, P < 0·0001) with skin/soft tissue as the primary sources of infection (P = 0·006). CMRSA10 genotype was the predominant CA-MRSA strain. All MRSA isolates were susceptible to doxycycline, tigecycline, trimethoprim/sulfamethoxazole and vancomycin. Both the presence of the genes coding for PVL toxin (89·8%) and susceptibility to clindamycin (86·5%) were predictive of CA-MRSA genotypes. Whereas in the USA, HA-MRSA have been replaced by USA300 (CMRSA10) clone as the predominant MRSA strain type in positive blood cultures from hospitalized patients, this phenomenon has not been observed in the province of Quebec.

In August 2012, an explosive outbreak of severe lower respiratory tract infection (LRTI) due to Streptococcus pneumoniae serotype-8 occurred in a highly vaccinated elderly institutionalized population in England. Fifteen of 23 residents developed LRTI over 4 days (attack rate 65%); 11 had confirmed S. pneumoniae serotype-8 disease, and two died. Following amoxicillin chemoprophylaxis and pneumococcal polysaccharide vaccine (PPV) re-vaccination no further cases occurred in the following 2 months. No association was found between being an outbreak-associated case and age (P = 0·36), underlying comorbidities [relative risk (RR) 0·84 95% confidence interval (CI) 0·34–2·09], or prior receipt of PPV (RR 1·4, 95% CI 0·60–3·33). However, the median number of years since PPV was significantly higher for cases (n = 15, 10·2 years, range 7·3–17·9 years) than non-cases (n = 8, 7·2 years, range 6·8–12·8 years) (P = 0·045), provided evidence of waning immunity. Alternative vaccination strategies should be considered to prevent future S. pneumoniae outbreaks in institutionalized elderly populations.

This study examined recent trends in type-specific HPV infection rates in women referred for HPV typing as part of cervical cancer screening in the United States. HPV analyses were performed from March 2004 to March 2011. Women were aged 21–65 years at testing. The 18 most prevalent HPV types were analysed. Type-specific HPV infection rates were estimated in 3-month blocks. Lowess smoothing was used to examine time trends in infection rates for each HPV type, both combined, and separated by age group (younger women 21–30 years, older women 31–64 years). A total of 220914 women were included in the final analysis. The number of HPV tests performed on the younger age group increased, with the number of HPV infections and multiple type HPV infections decreasing. When separated by HPV type-specific analysis, the majority of HPV infection rates decreased; however, HPV types 61 and 83 increased. When analysing the older age group, there was a marked increase of the number of HPV tests. Overall, the rates of any HPV infection, as well as multiple type infections, were lower compared to the younger age group. The change in type-specific HPV rates in the older age group was minimal, with many rates remaining the same. In this population of women, overall rates of HPV infection decreased, while the number of HPV tests increased. Younger women had a more marked decrease in HPV infection rates, while for older women type-specific HPV infection rates appear consistent.

This study describes the incidence rate of reported lymphogranuloma venereum (LGV) in men who have sex with men (MSM) in Barcelona from 2007 to 2012. Epidemiological, clinical and sexual behaviour characteristics of LGV cases are described. Seroadaptive behaviours as a transmission risk factor were assessed by a telephone questionnaire during 2012. Data were handled on a strictly confidential basis. LGV annual rate ratios in MSM were compared with cases from 2007. Differences were statistically analysed with a Poisson test. The incidence rate of LGV in MSM aged 15–69 years ranged from 32·1/105 MSM per year in 2007 to 182·7/105 MSM per year in 2012. In 2012, 31/51 LGV cases (61%) answered the telephone questionnaire, of which 84% (26/31) were HIV positive, 39% (12/31) reported having sex according to their partners’ serostatus and 7% (2/31) used strategic positioning. The incidence of LGV has increased since 2007 and mainly affects HIV-positive MSM. It is probable that seroadaptation has facilitated LGV transmission.

The objective of this study was to estimate the direct financial costs of hospital care for management of invasive group A streptococcal (GAS) infections using hospital records for cases diagnosed in England. We linked laboratory-confirmed cases (n = 3696) identified through national surveillance to hospital episode statistics and reimbursement codes. From these codes we estimated the direct hospital costs of admissions. Almost all notified invasive GAS cases (92% of 3696) were successfully matched to a primary hospital admission. Of these, secondary admissions (within 30 days of primary admission) were further identified for 593 (17%). After exclusion of nosocomial cases (12%), the median costs of primary and secondary hospital admissions were estimated by subgroup analysis as £1984–£2212 per case, totalling £4·43–£6·34 million per year in England. With adjustment for unmatched cases this equated to £4·84–£6·93 million per year. Adults aged 16–64 years accounted for 48% of costs but only 40% of cases, largely due to an increased number of surgical procedures. The direct costs of hospital admissions for invasive GAS infection are substantial. These estimated costs will contribute to a full assessment of the total economic burden of invasive GAS infection as a means to assess potential savings through prevention measures.