This study aimed to describe the transmission dynamics, the serological and virus excretion patterns of Nipah virus (NiV) in Pteropus vampyrus bats. Bats in captivity were sampled every 7–21 days over a 1-year period. The data revealed five NiV serological patterns categorized as high and low positives, waning, decreasing and increasing, and negative in these individuals. The findings strongly suggest that NiV circulates in wild bat populations and that antibody could be maintained for long periods. The study also found that pup and juvenile bats from seropositive dams tested seropositive, indicating that maternal antibodies against NiV are transmitted passively, and in this study population may last up to 14 months. NiV was isolated from the urine of one bat, and within a few weeks, two other seronegative bats seroconverted. Based on the temporal cluster of seroconversion, we strongly believe that the NiV isolated was recrudesced and then transmitted horizontally between bats during the study period.

A prospective cohort study with a 1-year telephone follow-up was performed to estimate the incidence of surgical-site infections (SSIs) in hip and knee prostheses. Twenty-five public hospitals equipped with orthopaedic units in two Italian regions were involved. An 8-month surveillance period was set to obtain significant data at a regional level and data were collected by the infection control nurses of each centre. One-year follow-up was completed in 75% of cases. SSIs were recorded in 45 cases (incidence rate 1·9/100 person-years, 95% CI 1·4–2·5). Thirty-six percent of SSIs were diagnosed during hospitalization and 95·3% within 90 days post-operation. This incidence is similar to that reported by European and USA surveillance systems. The proposed investigative method proved to be reliable and feasible. A prolonged surveillance for at least 3 months post-operation yields a good estimate of SSI in joint replacements.

Salmonellosis is an internationally important disease of mammals and birds. Unique epidemics in New Zealand in the recent past include two Salmonella serovars: Salmonella enterica subsp. enterica serovar Typhimurium definitive type (DT) 160 (S. Typhimurium DT160) and S. Brandenburg. Although not a major threat internationally, in New Zealand S. Typhimurium DT160 has been the most common serovar isolated from humans, and continues to cause significant losses in wildlife. We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost identical to phage SE1 but has two regions not found in SE1 which are identical to the P22-like phage ST64T, suggesting that ST160 evolved from SE1 via two recombination events with ST64T. All of the New Zealand isolates of DT160 were identical indicating the clonal spread of this particular Salmonella. Some overseas isolates of S. Typhimurium DT160 differed from the New Zealand strain and contained SE1 phage rather than ST160. ST160 was also identified in New Zealand isolates of S. Typhimurium DT74 and S. Typhimurium RDNC-April06 and in S. Typhimurium DT160 isolates from the USA. The emergence of S. Typhimurium DT160 as a significant pathogen in New Zealand is postulated to have occurred due to the sensitivity of the Salmonella strains to the ST160 phage when S. Typhimurium DT160 first arrived.

This study aimed to evaluate the incidence of Staphylococcus aureus infections in different departments of Belcolle Hospital in Viterbo and the surrounding area between January 2003 and June 2008. Isolates of methicillin-resistant S. aureus (MRSA) recovered in this time interval were characterized by microbiological and molecular methods to evaluate the reliability of simple criteria to distinguish between hospital-acquired and community-acquired isolates. MRSA accounted for 33% of all S. aureus, with a significantly higher prevalence in isolates from nosocomial infections. MRSA isolates were assayed by PCR for the presence of 13 genes associated with virulence, agr type and SCCmec type. Cumulative data were analysed by partial least square discriminant analysis and a clear correlation was demonstrated between genetic profiles and classification of isolates as hospital or community acquired according to simple temporal criteria. Nosocomial MRSA isolates from blood samples showed significantly higher genetic diversity than other nosocomial isolates. Our data confirm the existence of significant differences between community- and hospital-acquired MRSA isolates.

This study investigated further the association between the Beijing family Mycobacterium tuberculosis circulating in rural China and anti-tuberculosis (TB) drug resistance. In total, 351 M. tuberculosis isolates were collected through a population-based epidemiological study, 223 (63·5%) of which were resistant to at least one anti-TB drug, including 53 (15·1%) multidrug-resistant (MDR) isolates. Spoligotyping found 243 isolates (69·2%) that belonged to the Beijing family. A major subgroup of the Beijing family identified by mycobacterial interspersed repetitive unit (MIRU) genotyping (223325173533), showed significantly higher frequencies of MDR (44·7% vs. 13·7%, OR 6·18, 95% CI 2·68–14·23), katG and rpoB mutations (31·6% vs. 9·3%, OR 4·27, 95% CI 1·86–9·80), and being clustered by IS6110 RFLP genotyping (60·5% vs. 21·0%, OR 6·14, 95% CI 2·82–13·37) in comparison with other Beijing family isolates. Our data suggest that MIRU genotype 223325173533 of the Beijing family is associated with MDR and increased transmissibility.

Although norovirus infection is generally known to be a mild disease, there is some evidence for severe outcome. An outbreak in a Dutch psychiatric institution, originating from pilgrims returning from Lourdes (France), provided an opportunity for performing a retrospective cohort study in order to identify risk factors for norovirus disease and excess mortality. Relative risks (RR) including 95% confidence intervals (CI) showed that attending the pilgrimage (RR 2·0, 95% CI 1·4–3·0) and age >70 (RR 1·7, 95% CI 1·2–2·2) were risk factors for symptomatic infection. In a subset of patients, for whom more detailed information was available, the use of statins was associated with norovirus disease when adjusted for underlying condition (adjusted odds ratio 3·9, 95% CI 1·2–13·0). Mortality was higher in cases infected during the pilgrimage compared to other residents (RR 20·9, 95% CI 4·7–93·8). Norovirus disease can lead to severe outcome. The newly identified risk of statins for contracting norovirus disease may have considerable consequences for the Western world and needs prospective confirmation.

A cross-sectional study was conducted to investigate risk factors for sporadic Cryptosporidium infection in a paediatric population in Nigeria. Of 692 children, 134 (19·4%) were infected with Cryptosporidium oocysts. Cryptosporidium spp. were identified in 49 positive samples using PCR–restriction fragment length polymorphism and direct sequencing of the glycoprotein60 (GP60) gene. Generalized linear mixed-effects models were used to identify risk factors for all Cryptosporidium infections, as well as for C. hominis and C. parvum both together and separately. Risk factors identified for all Cryptosporidium infections included malaria infection and a lack of Ascaris infection. For C. hominis infections, stunting and younger age were highlighted as risk factors, while stunting and malaria infection were identified as risk factors for C. parvum infection.

We examined the association between water exposures and acute diarrhoeal illness (ADI) in children under non-outbreak conditions in a major US metropolitan area. We used a nested case-control study of children seen in an urban/suburban emergency department. Cases were those seen for a complaint of diarrhoea, while controls were age-matched children with a non-gastrointestinal complaint. Parents of subjects completed a validated water-use survey. Stratum-specific adjusted odds ratios (aOR) were calculated for the three main water effects: water source [surface vs. ground (well)], drinking-water type (tap vs. bottled), and use of water filters. Of 2472 subjects, 45% drank mostly or only bottled water. Well-water use was associated with increased odds of ADI compared to surface water [aOR 1·38, 95% confidence interval (CI) 1·01–1·87]. Use of bottled water did not affect the odds of ADI in well-water users, but increased the odds of ADI for surface-water users (aOR 1·27, 95% CI 1·02–1·57). We conclude that well-water use and bottled-water use are associated with increased odds of ADI in children.

Within Europe, Ireland has one of the highest reported infection rates with the diarrhoeal protozoan pathogen Cryptosporidium. In this study 249 Cryptosporidium parvum isolates collected from Irish patients between 2000 and 2009 were subtyped by sequence analysis of the GP60 locus. A subsample of 127 isolates was also typed at the MS1 and ML1 loci. GP60 subtype IIaA18G3R1 was the predominant subtype in every year and every season throughout the country. Over the 10-year period there was no evidence that host immunity to the predominant subtype caused a shift in its prevalence. Length frequency distributions of the GP60 TCA/TCG repeats compiled from published data, showed distinct patterns for countries with predominantly zoonotic or anthroponotic transmission cycles, respectively. Although considered to be mostly affected by zoonotic cryptosporidiosis, the GP60 fragment length of Irish C. parvum isolates mirrored that of countries with predominantly human-to-human transmission, indicating more complex routes of infection between livestock and humans. Due to their homogeneity, ML1 and MS1 were not considered useful loci for subtyping C. parvum strains in Ireland.

Pathogen detection and genetic characterization has dramatically changed in recent years. Clinical laboratories are transitioning from traditional culture and primer-specific sequencing to more robust and rapid nucleic acid testing such as real-time PCR and meta-genomic characterization, respectively. Specimen collection is the first step in any downstream molecular diagnostic procedure. PrimeStore Molecular Transport Medium (MTM) is an optimized blend of nucleic acid stabilizing reagents that includes a non-specific internal positive control that can be amplified using real-time RT–PCR for tracking the integrity of a specimen from the point of collection to detection. PrimeStore MTM is shown here to effectively kill pathogens, including highly pathogenic H5 influenza virus, inactivate nucleases and to protect and preserve released RNA at ambient temperature for up to 30 days for downstream real-time and traditional RT–PCR detection and genetic characterization. PrimeStore MTM is also compatible with a variety of commercial extraction kits. PrimeStore is suited for routine clinical specimens and has added utility for field collection in remote areas, triage centres, border crossings and during pandemics where cold-chain, transport, and dissemination of potentially infectious pathogens are a concern.

Shiga toxin-producing Escherichia coli (STEC), an important foodborne pathogen, can cause mild to severe bloody diarrhoea (BD), sometimes followed by life-threatening complications such as haemolytic uraemic syndrome (HUS). A total of 44 O157 strains isolated from different patients from 2000 through 2009 in Switzerland were further characterized and linked to medical history data. Non-bloody diarrhoea was experienced by 15·9%, BD by 61·4% of the patients, and 29·5% developed HUS. All strains belonged to MLST type 11, were positive for stx2 variants (stx2 and/or stx2c), eae and ehxA, and only two strains showed antibiotic resistance. Of the 44 strains, nine phage types (PTs) were detected the most frequent being PT32 (43·2%) and PT8 (18·2%). By PFGE, 39 different patterns were found. This high genetic diversity within the strains leads to the conclusion that STEC O157 infections in Switzerland most often occur as sporadic cases.

Q fever (Coxiella burnetii) is a zoonotic disease of increasing public health importance. The objective of this study was to estimate the prevalence of, and risk factors associated with, exposure to C. burnetii in cattle in the Republic of Ireland. Bulk-tank milk samples from 290 dairy herds and 1659 sera from 332 dairy and beef herds, randomly sampled, were tested by indirect ELISA to detect antibodies to C. burnetii. In total, 37·9% of bulk-milk sample herds and 1·8% of sera (from 6·9% of herds) were antibody positive. Of risk factors tested using logistic regression analysis, only large herd size (bulk-milk analysis) and dairy breed (serum analysis) significantly increased the odds of being positive for antibodies to C. burnetii. Herds with positive milk or serum samples were randomly distributed throughout the Republic of Ireland and no clustering was observed. The use of an ELISA to test bulk-milk samples collected by randomized stratified sampling is a cost-effective method by which national herd prevalence can be estimated by active surveillance.

The epidemiology and clinical features of invasive group A streptococcal (iGAS) disease in Queensland children was investigated in response to anecdotal evidence of an increase in frequency and severity of this condition. A retrospective review of clinical records of all cases of iGAS disease notified to Queensland Health aged 0–18 years during a 5-year period was conducted. The annualized incidence of iGAS was 3·5/100 000 for the total population aged 0–18 and 13·2/100 000 for the Indigenous population of similar age. The annualized incidence was highest in Indigenous infants but no increase in frequency or severity of iGAS infections was observed. Findings included an increased prevalence in Indigenous children particularly in those aged <1 year, a significant male preponderance, lack of seasonal variation and an association with blunt trauma. Further studies are required to confirm and investigate these findings and to define specific risk factors in high-risk groups.

An inappropriate cross-connection between sewage- and drinking-water pipelines contaminated tap water in a Finnish town, resulting in an extensive waterborne gastroenteritis outbreak in this developed country. According to a database and a line-list, altogether 1222 subjects sought medical care as a result of this exposure. Seven pathogens were found in patient samples of those who sought treatment. To establish the true disease burden from this exposure, we undertook a population-based questionnaire investigation with a control population, infrequently used to study waterborne outbreaks. The study covered three areas, contaminated and uncontaminated parts of the town and a control town. An estimated 8453 residents fell ill during the outbreak, the excess number of illnesses being 6501. Attack rates were 53% [95% confidence interval (CI) 49·5–56·4] in the contaminated area, 15·6% (95% CI 13·1–18·5) in the uncontaminated area and 6·5% (95% CI 4·8–8·8) in the control population. Using a control population allowed us to differentiate baseline morbidity from the observed morbidity caused by the water contamination, thus enabling a more accurate estimate of the disease burden of this outbreak.

On 13 November 2009, the authorities of Flemish Brabant, Belgium, received an alert concerning a potential outbreak of Shigella sonnei at a public institution. A study was conducted to assess the extent, discover the source and to implement further measures. We performed a matched case-control study to test an association between shigellosis and canteen-food consumption. Water samples and food handlers' faecal samples were tested. The reference laboratory characterized the retrospectively collected Shigella specimens. We found 52 cases distributed over space (25/35 departments) and time (2 months). We found a matched odds ratio of 3·84 (95% confidence interval 1·02–14·44) for canteen-food consumption. A food handler had travelled to Morocco shortly before detection of the first laboratory-confirmed case. Water samples and food handlers' faecal samples tested negative for Shigella. Confirmed cases presented PFGE profiles, highly similar to archived isolates from Morocco. Foodborne transmission associated with the canteen was strongly suspected.

Past studies exploring risk factors for fluoroquinolone (FQ) resistance in urinary tract infections (UTIs) focused only on UTIs caused by Gram-negative pathogens. The epidemiology of FQ resistance in enterococcal UTIs has not been studied. We conducted a case-control study at two medical centres within the University of Pennsylvania Health System in order to identify risk factors for FQ resistance in enterococcal UTIs. Subjects with positive urine cultures for enterococci and meeting CDC criteria for healthcare-acquired UTI were eligible. Cases were subjects with FQ-resistant enterococcal UTI. Controls were subjects with FQ-susceptible enterococcal UTI and were frequency matched to cases by month of isolation. A total of 136 cases and 139 controls were included from 1 January 2003 to 31 March 2005. Independent risk factors [adjusted OR (95% CI)] for FQ resistance included cardiovascular diseases [2·24 (1·05–4·79), P=0·037], hospitalization within the past 2 weeks [2·08 (1·05–4·11), P=0·035], hospitalization on a medicine service [2·15 (1·08–4·30), P<0·030], recent exposure to β-lactamase inhibitors (BLIs) [14·98 (2·92–76·99), P<0·001], extended spectrum cephalosporins [9·82 (3·37–28·60), P<0·001], FQs [5·36 (2·20–13·05), P<0·001] and clindamycin [13·90 (1·21–10·49), P=0·035]. Use of BLIs, extended spectrum cephalosporins, FQs and clindamycin was associated with FQ resistance in enterococcal uropathogens. Efforts to curb FQ resistance should focus on optimizing use of these agents.

The 7-valent pneumococcal conjugate vaccine (PCV7) was included in the routine infant immunization schedule in Ireland in September 2008. We determined the serotype of 977 S. pneumoniae isolates causing invasive disease between 2000–2002 and 2007–2008, assessed for the presence of the recently described serotype 6C and determined the susceptibility of isolates during 2007–2008 to penicillin and cefotaxime. Serotype 14 was the most common serotype during both periods and 7·7% of isolates previously typed as serotype 6A were serotype 6C. During 2000–2002 and 2007–2008, PCV7 could potentially have prevented 85% and 74% of invasive pneumococcal disease in the target population (i.e. children aged <2 years), respectively. The level of penicillin non-susceptibility was 17% in 2007–2008. Ongoing surveillance of serotypes is required to determine the impact of PCV7 in the Irish population and to assess the potential of new vaccines with expanded valency.

We investigated an international outbreak of Salmonella Agona with a distinct PFGE pattern associated with an Irish Food company (company X) producing pre-cooked meat products sold in various food outlet chains in Europe. The outbreak was first detected in Ireland. We undertook national and international case-finding, food traceback and microbiological investigation of human, food and environmental samples. We undertook a matched case-control study on Irish cases. In total, 163 cases in seven European countries were laboratory-confirmed. Consumption of food from food outlet chains supplied by company X was significantly associated with being a confirmed case (mOR 18·3, 95% CI 2·2–149·2) in the case-control study. The outbreak strain was isolated from the company's pre-cooked meat products and production premises. Sufficient evidence was gathered to infer the vehicles of infection and sources of the outbreak and to justify the control measures taken, which were plant closure and food recall.

Active pulmonary tuberculosis was diagnosed in a 4-month-old infant 16 days after hospitalization; 186 exposed individuals were traced and one conversion detected. Although the risk of tuberculosis transmission in paediatric hospitals is low, paediatricians in low-incidence countries should maintain a high level of alert for timely identification of cases.