A retrospective cohort study was conducted from 1 January 2006 to 31 December 2009 in Michigan to estimate the prevalence of HIV and hepatitis co-infection and identify associated factors. The prevalence of co-infection was 4·1% [95% confidence interval (CI) 3·8–4·5]. Multivariable logistic regression analysis revealed a significant association between co-infection and being male and: of Black race [odds ratio (OR) 2·0, 95% CI 1·2–3·6] and of Other race (OR 3·5, 95% CI 1·7–7·0) compared to Hispanic race. A significant association was found between co-infection and risk categories of blood products (OR 11·1, 95% CI 6·2–20·2), injecting drug user (IDU) (OR 3·6, 95% CI 2·7–4·8) and men who have sex with men/IDU (OR 3·4, 95% CI 2·4–4·9) in addition to two interactions; one between sex and current HIV status and the other between current HIV status and age at HIV diagnosis. Our results document the changing epidemiology of HIV–hepatitis co-infection which can guide preventive measures and interventions to reduce the prevalence of hepatitis co-infection.

A review of the annual prevalence of Pseudomonas aeruginosa at a regional hospital in Taiwan revealed a significant increase in the incidence of extensive drug-resistant P. aeruginosa (XDRPA) from 2·1% in 2003 to 5·8% in 2007. The first XDRPA isolate was recovered in 2001 from the emergency ward. The widespread dissemination of XDRPA isolates to more than 10 other wards was discovered the following year. Six pulsotypes of 67 XDRPA isolates from 2006 onwards were identified and 91% were a single strain, suggesting the existence of a hidden outbreak. Prior to the recognition of the outbreak, the majority of cases were not considered to be healthcare-associated infections until molecular evidence was provided. A cohort measure was launched by the infection control practitioners that effectively controlled the outbreak. Patients with XDRPA were mostly referred from neighbouring long-term care facilities, which may have been the reservoir of the XDRPA clone.

The prevalence of natural carriage and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS) isolates in a Jordanian community were investigated. The MRSA nasal carriage rate in 227 healthy volunteers was 7·5% and the majority (81%) of MRSA harboured the resistance element SCCmec type IVe and were of a novel spa type t9519 (76%); other significant spa gene types were t223 (14·7%) and t044 (5·9%). All MRSA isolates were susceptible to other classes of antibiotics, and tested positive for at least three virulence factor encoding genes, but only two harboured the pvl gene. MR-CoNS carriage was 54·2% and these isolates were characterized by single, double and untypable SCCmec elements, with Staphylococcus epidermidis SCCmec type IVa predominating. Of eight subjects with nasal co-colonization of MR-CoNS + MRSA, three shared SCCmec type IV in both groups of organisms. This is the first report of methicillin-resistant staphylococci carriage in a Jordanian community and its findings are important for epidemiological study and infection control measures of these organisms.

This study was conducted during the 2008–2009 respiratory syncytial virus (RSV) season in France to compare hospitalization rates for bronchiolitis (RSV-confirmed and all types) between very preterm infants (<33 weeks' gestational age, WGA) without bronchopulmonary dysplasia and full-term infants (39–41 WGA) matched for date of birth, gender and birth location, and to evaluate the country-specific risk factors for bronchiolitis hospitalization. Data on hospitalizations were collected both retrospectively and prospectively for 498 matched infants (249 per group) aged <6 months at the beginning of the RSV season. Compared to full-term infants, preterm infants had a fourfold [95% confidence interval (CI) 1·36–11·80] and a sevenfold (95% CI 2·79–17·57) higher risk of being hospitalized for bronchiolitis, RSV-confirmed and all types, respectively. Prematurity was the only factor that significantly increased the risk of being hospitalized for bronchiolitis. The risk of multiple hospitalizations for bronchiolitis in the same infant significantly increased with male gender and the presence of siblings aged ⩾2 years.

A 15-h stay in a paediatric intensive care unit by a girl with generalized dermal lesions superinfected with Streptococcus pyogenes led to four streptococcal infections in healthcare workers. Phenotypic and molecular analyses of the strains revealed that four isolates, characterized as emm87/ST62/T28, were identical to the isolate obtained from the index case. The occurrence of this outbreak, despite of the girl's brief hospital stay and appropriate patient management, highlights the high transmissibility of this pathogen.

There are limited data examining whether outcomes of methicillin-resistant Staphylococcus aureus (MRSA) healthcare-associated infections (HAIs) are worse when caused by community-associated (CA) strains compared to HA strains. We reviewed all patients’ charts at our institution from 1999 to 2009 that had MRSA first isolated only after 72 h of hospitalization (n = 724). Of these, 384 patients had a MRSA-HAI according to CDC criteria. Treatment failure was similar in those infected with a phenotypically CA-MRSA strain compared to a phenotypically HA-MRSA strain (23% vs. 15%, P = 0·10) as was 30-day mortality (16% vs. 19%, P = 0·57). Independent risk factors associated with (P < 0·05) treatment failure were higher Charlson Comorbidity Index, higher APACHE II score, and no anti-MRSA treatment. These factors were also associated with 30-day mortality, as were female gender, older age, MRSA bloodstream infection, MRSA pneumonia, and HIV. Our findings suggest that clinical and host factors, not MRSA strain type, predict treatment failure and death in hospitalized patients with MRSA-HAIs.

Surveillance is integral for the monitoring and control of infectious diseases. We conducted prospective laboratory surveillance of methicillin-resistant Staphylococcus aureus (MRSA) in five Singaporean public-sector hospitals from 2006 to 2010, using WHONET 5.6 for data compilation and analysis. Molecular profiling using multilocus variable-number tandem-repeat analysis, staphylococcal cassette chromosome mec classification and multilocus sequence typing was performed for a random selection of isolates. Our results showed overall stable rates of infection and bacteraemia, although there was significant variance among the individual hospitals, with MRSA rates increasing in two smaller hospitals and showing a trend towards decreasing in the two largest hospitals. The proportion of blood isolates that are EMRSA-15 (ST22-IV) continued to increase over time, slowly replacing the multi-resistant ST239-III. A new MRSA clone – ST45-IV – is now responsible for a small subset of hospital infections locally. More effort is required in Singaporean hospitals in order to reduce the rates of MRSA infection significantly.

Pulsed-field gel electrophoresis genotypes of Campylobacter isolates from 603 human patients were compared with 485 isolates from retail offal (primarily chicken and lamb) to identify temporal clusters and possible sources of campylobacteriosis. Detailed epidemiological information was collected from 364 of the patients, and when combined with genotyping data allowed a putative transmission pathway of campylobacteriosis to be assigned for 88% of patients. The sources of infection were 47% food, 28% direct animal contact, 7% overseas travel, 4% person-to-person transmission and 3% water-related. A significant summer increase in campylobacteriosis cases was primarily attributed to an increase in food-related cases. Genotyping of isolates was essential for identifying the likely cause of infection for individuals. However, a more rapid and cheaper typing tool for Campylobacter is needed, which if applied to human and animal isolates on a routine basis could advance greatly our understanding of the ongoing problem of Campylobacter infection in New Zealand.

Monitoring injecting drug users' (IDUs) health is challenging because IDUs form a difficult to reach population. We examined the impact of recruitment setting on hepatitis C prevalence. Individual datasets from 12 studies were merged. Predictors of HCV positivity were sought through a multilevel analysis using a mixed-effects logistic model, with study identifier as random intercept. HCV prevalence ranged from 21% to 86% across the studies. Overall, HCV prevalence was higher in IDUs recruited in drug treatment centres compared to those recruited in low-threshold settings (74% and 42%, respectively, P < 0·001). Recruitment setting remained significantly associated with HCV prevalence after adjustment for duration of injecting and recent injection (adjusted odds ratio 0·7, 95% confidence interval 0·6–0·8, P = 0·05). Recruitment setting may have an impact on HCV prevalence estimates of IDUs in Europe. Assessing the impact of mixed recruitment strategies, including respondent-driven sampling, on HCV prevalence estimates, would be valuable.

Tuberculosis (TB) due to infection with Mycobacterium bovis is transmitted between cattle and badgers (Meles meles) in the UK and Ireland but it is unclear where or when transmission occurs. We investigated direct and indirect interactions between badgers and cattle using automated proximity loggers on animals and at badger latrines located on pasture, in an area of south-west England with a high-density badger population. Direct contacts (interactions within 1·4 m) between badgers and cattle at pasture were very rare (four out of >500 000 recorded animal-to-animal contacts) despite ample opportunity for interactions to occur. Indirect interactions (visits to badger latrines by badgers and cattle) were two orders of magnitude more frequent than direct contacts: 400 visits by badgers and 1700 visits by cattle were recorded. This suggests that indirect contacts might be more important than direct contacts in terms of disease transmission at pasture. The TB infection status of individual badgers (ascribed with 93% accuracy using three diagnostic tests) did not affect the frequency or duration of their visits to latrines located on pasture grazed by cattle. Nevertheless, there was wide variation in contact behaviour between individuals, which highlights the importance of understanding heterogeneity in contact patterns when developing strategies to control disease spread in wildlife and livestock.

In Bangladesh from 1 July to 30 September 2010 there were 104 animal cases of anthrax and 607 associated human cases. This investigation was conducted in Sirajganj district in December 2010, on eight farms where animal cases had occurred. Bacillus anthracis was recovered from soil samples and turbinate bones on six farms. Canonical single nucleotide polymorphism (SNP) analysis showed that all the isolates belonged to the major lineage A, sublineage A.Br.001/002 of China and South East Asia while a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) with 15 VNTRs demonstrated three unique genotypes. The single nucleotide repeat (SNR) analyses showed two SNR types in 97 out of 99 isolates; nevertheless, due to its higher discriminatory power the presence of two isolates with different SNR-type polymorphisms were detected within two MLVA genotypes. The epidemic occurred during the monsoon season, a time of extensive flooding, suggesting that the source was contaminated feed, not grazing, which is supported by the genetic variance.

In August 2008 an outbreak of Salmonella Typhimurium DT104 occurred in South West London. Sixteen cases were identified with a particular multilocus variable number tandem repeat analysis (MLVA) pattern. In a matched case-control study 14 primary cases were included. These were defined as individuals with gastrointestinal symptoms and Salmonella Typhimurium DT104 isolated from a stool specimen, with a characteristic antibiotic resistance profile and MLVA pattern, and diagnosed in a local laboratory. Four controls per case were matched on age, gender and area of residence. Cases were 26 times more likely than controls to have eaten beef biltong, a South African speciality meat product (odds ratio 25·83, 95% confidence interval 4·92–135·59, P < 0·01). Although environmental investigation failed to identify Salmonella in the food product we conclude that beef biltong consumption led to this outbreak. This conclusion has importance in informing the ongoing risk assessment relating to uncontrolled foodstuffs.

Tuberculosis is emerging/re-emerging in captive elephant populations, where it causes morbidity and deaths, although no case of TB in wild African elephants has been reported. In this paper we report the first case of fatal TB in an African elephant in the wild. The infection with Mycobacterium tuberculosis was confirmed by post-mortem and histological examinations of a female sub-adult elephant aged >12 years that died in Tsavo East National Park, Kenya, while under treatment. This case is unique in that during its lifetime the elephant had contact with both humans and wild elephants. The source of the infection was unclear because the elephant could have acquired the infection in the orphanage or in the wild. However, our results show that wild elephants can maintain human TB in the wild and that the infection can be fatal.

The transmission of human metapneumovirus (hMPV) among family members is not well understood. We identified 15 families in which multiple members were diagnosed with hMPV infection by real-time PCR in 2008 and 2010. Index patients ranged in age from 2 years to 11 years (median 5 years), and all 15 index cases were children who attended primary school, kindergarten, or nursery school. Contact patients ranged in age from 2 months to 46 years (median 6 years). Excluding five adult cases, contact patients were significantly younger than index patients (P = 0·0389). Of the 12 contact children, seven (58%) were infants who were taken care of at home. The serial interval between the onset of symptoms in an index patient and the onset of symptoms in a contact patient was estimated to be 5 days. These results suggest that the control of school-based outbreaks is important for preventing hMPV infection in infants.

Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to have an increased burden of disease in the late spring due to strains of non-chicken origin (e.g. ruminant and wild bird strains from environmental sources). In contrast the adult population had an extended summer peak associated with chicken strains. Travel abroad and UK mainland travel were associated with up to 17% and 18% of cases, respectively. International strains were associated with chicken, had a higher diversity than indigenous strains and a different spectrum of MLST types representative of these countries. Integrating empirical epidemiology and molecular subtyping can successfully elucidate the seasonal components of human campylobacteriosis. The findings will enable public health officials to focus strategies to reduce the disease burden.

The 7-valent pneumococcal conjugate vaccine (PCV7) has been included in the routine childhood immunization programme in the UK since September 2006. A population-based study of serotypes causing invasive pneumococcal disease (IPD) post-PCV7 in North East England was conducted using data from a regional enhanced IPD surveillance system. Overall, there was a 20% reduction [95% confidence interval (CI) 5–32] from 12·1 cases/100 000 population in 2006/2007 to 9·7 in 2009/2010. There was a fall in IPD caused by PCV7 serotypes in all age groups, with reductions of 90% (95% CI 61–99) in children aged <5 years, 50% (95% CI 4–75) in persons aged 5–64 years and 66% (95% CI 40–82) in adults aged ⩾65 years. There was a non-significant increase in IPD caused by non-PCV7 serotypes in children aged <5 years of 88% (95% CI −10 to 312) and adults aged ⩾65 years of 12% (95% CI −19 to 50), which was largely caused by serotypes 7F, 19A and 22F. Replacement disease appears to have reduced the benefits of PCV7 in North East England.

Chemotherapy and/or radiotherapy used as conditioning regimens before autologous or allogeneic haematopoietic cell transplantations (HCTs) cause neutropenia, which is the main reason for bloodstream infections. Autologous HCTs are considered to be superior to allogeneic HCTs in terms of infection outcome. A previous analysis suggested that patients with allogeneic HCTs are exposed to a reduced infection hazard and that an unfavourable infection outcome of allogeneic HCTs may be mediated through prolonged neutropenia. Therefore, we investigated whether allogeneic HCTs initially lead to fewer infections. We evaluated data from a prospective non-randomized multi-centre cohort study, with a total of 1616 patients. Of these, 703 patients received autologous and 913 patients received allogeneic HCTs from January 2000 to June 2004. The retrospective analysis used simultaneous confidence bands for the cumulative infection probability in the presence of competing risks. Patients with allogeneic HCTs experienced fewer infections during the early phase of neutropenia. As patients with autologous HCTs are not necessarily subject to antibiotic prophylaxis, a future study should investigate this policy. A limitation of the analysis is that it did not find the effect of crossing cumulative infection probabilities to be significant.

Children with sickle cell anaemia (SCA) might carry hospital-associated bacterial lineages due to frequent hospital stays and antibiotic treatments. In this study we compared Staphylococcus aureus from SCA patients (n = 73) and healthy children (n = 143) in a cross-sectional study in Gabon. S. aureus carriage did not differ between children with SCA (n = 34, 46·6%) and controls matched for age, residence and sex (n = 67, 46·9%). Both groups shared similar S. aureus genotypes. This finding points towards a transmission of S. aureus between both groups in the community. We conclude that resistance rates from population-based studies with healthy participants could therefore also be used to guide treatment and prophylaxis of endogenous infections in children with SCA despite a different selection pressure.

Japan experienced dengue outbreaks vectored by Aedes albopictus during the Second World War. The probable vector density that caused the largest dengue outbreak in Nagasaki in 1942 was estimated using a mathematical simulation model. The estimated vector density was 15·0–558·0 per person when various assumptions of uncertain parameters were applied, such as proportion of symptomatic cases, vector mortality, and human biting rate of A. albopictus. When the most favourable disease spread conditions, such as a combination of the exclusive human biting rate and the longest vector survival were assumed, the vector density was 15–25 mosquitoes per person. Unusually high vector density due to wartime practices, and the traditional Japanese lifestyle were presumably responsible for the earlier dengue outbreak. If an outbreak occurs in present-day Japan, it is unlikely to spread as much as the previous one, as environmental conditions and human behaviour have changed in a protective manner.

A 3-year longitudinal study was conducted on a multi-site farrow-to-finish production system. For each of 18 cohorts at three finishing sites, 50 pigs were randomly selected. Faecal samples were collected every 2 weeks for 16 weeks. Salmonella was cultured from 453 (6·6%) of 6836 faecal samples. The pig-level incidence of Salmonella was 20·8% (187/899 pigs). Salmonella prevalence varied between cohorts and within pigs. The adjusted Salmonella prevalence decreased over the finishing period from 6·4% to 0·8%. Intermittent detection of Salmonella was found in more than 50% of pigs that were positive at more than one collection. The finding that the majority of pigs shed intermittently has implications for surveillance and research study design when determining Salmonella status. The variability in shedding over time, as well as between and within cohorts and pigs suggests that there may be time-variant risk factors for Salmonella shedding in swine.