Bloodstream infections (BSIs) are a major cause of morbidity and mortality. Although population-based studies have been proposed as an optimal means to define their epidemiology, the merit of these designs has not been well documented. This report investigated the potential value of using population-based designs in defining the epidemiology of BSIs. Population-based BSI surveillance was conducted in Calgary, Canada (population 1·24 million) and illustrative comparisons were made between the overall and selected subgroup cohorts within five main themes. The value of population denominator data, and age and gender standardization for calculation and comparison of incidence rates were demonstrated. In addition, a number of biases including those related to differential admission rates, selected hospital admission, and referral bias were highlighted in non-population-based cohorts. Due to their comprehensive nature and intrinsic minimization of bias, population-based designs should be considered the gold standard means of defining the epidemiology of an infectious disease.

Toxoplasma gondii and Bartonella spp. are zoonotic pathogens of cats. Feline immunodeficiency virus (FIV), and feline leukaemia virus (FeLV) are immunosuppressive viruses of cats that can affect T. gondii oocyst shedding. In this study, the prevalence of antibodies to T. gondii, Bartonella spp., FIV, as well as FeLV antigens were determined in sera from feral cats (Felis catus) from Addis Ababa, Ethiopia. Using the modified agglutination test, IgG antibodies to T. gondii were found in 41 (85·4%) of the 48 cats with titres of 1:25 in one, 1:50 in one, 1:200 in six, 1:400 in six, 1:800 in six, 1:1600 in eight, and 1:3200 in 13 cats. Toxoplasma gondii IgM antibodies were found in 11/46 cats tested by ELISA, suggesting recent infection. Antibodies to Bartonella spp. were found in five (11%) of 46 cats tested. Antibodies to FIV or FeLV antigen were not detected in any of the 41 cats tested. The results indicate a high prevalence of T. gondii and a low prevalence of Bartonella spp. infection in cats in Ethiopia.

Socioeconomic and culturally defined social contact patterns are expected to be an important determinant in the continuing transmission of Mycobacterium leprae in leprosy-endemic areas. In a case-control study in two districts in Bangladesh, we assessed the association between social contact patterns and the risk of acquiring clinical leprosy. Social contacts of 90 recently diagnosed patients were compared to those of 199 controls. Leprosy was associated with a more intensive social contact pattern in the home [odds ratio (OR) 1·09, 95% confidence interval (CI) 1·00–1·19, P = 0·043] and in the nearby neighbourhood (OR 1·07, 95% CI 1·03–1·11, P = 0·001). Although it is known that M. leprae spreads most easily within households of infected persons, in endemic areas social contacts within the neighbourhood, village or urban ward, also appear to be important for transmission. We advise that disease control measures in leprosy-endemic areas should not be limited to households, but include high-risk groups in the nearby neighbourhood of patients.

We describe trends in incidence rates of methicillin-resistant Staphylococcus aureus (MRSA) in HIV-infected and HIV-uninfected patients enrolled in a large northern California Health Plan, and the ratio of MRSA to methicillin-susceptible S. aureus (MSSA) case counts. Between 1995 and 2010, 1549 MRSA infections were diagnosed in 14060 HIV-infected patients (11·0%) compared to 89546 MRSA infections in 6597396 HIV-uninfected patients (1·4%) (P = 0·00). A steady rise in MRSA infection rates began in 1995 in HIV-uninfected patients, peaking at 396·5 infections/100000 person-years in 2007. A more rapid rise in MRSA infection rates occurred in the HIV-infected group after 2000, peaking at 3592·8 infections/100000 in 2005. A declining trend in MRSA rates may have begun in 2008–2009. Comparing the ratio of MRSA to MSSA case counts, we observed that HIV-infected patients shouldered a greater burden of MRSA infection during most years of study follow-up compared to HIV-uninfected patients.

This longitudinal field study investigated the hypothesis that persistently high antibody levels indicate a high risk of Salmonella Dublin shedding in animals in 14 endemically infected dairy herds. A hierarchical multivariable logistic regression was used to analyse 6614 paired faecal cultures and four types of temporal antibody profiles from cattle aged ≥180 days. Age and repeated measurements on animals nested within herds were taken into account. Overall, the prevalence of faecal shedders was low (0·3% and 2·8% in the lowest and highest risk groups, respectively). An important predictor of faecal shedding was young age. There was a significant, but modest increase in risk in cattle with persistently high or recently increased antibody levels, but no difference between these two groups. Contrary to previous recommendations, the detection of carriers by the use of repeated antibody testing is not likely to be a plausible control option in most Salmonella Dublin-infected dairy herds.

Reduced vancomycin susceptibility (RVS) may lead to poor clinical outcomes in Staphylococcus aureus bacteraemia. We conducted a cohort study of 392 patients with S. aureus bacteraemia within a university health system. The association between RVS, as defined by both Etest [vancomycin minimum inhibitory concentration (MIC) >1·0 μg/ml] and broth microdilution (vancomycin MIC ⩾1·0 μg/ml), and patient and clinical variables were evaluated to create separate predictive models for RVS. In total, 134 (34·2%) and 73 (18·6%) patients had S. aureus isolates with RVS by Etest and broth microdilution, respectively. The final model for RVS by Etest included methicillin resistance [odds ratio (OR) 1·51, 95% confidence interval (CI) 0·97–2·34], non-white race (OR 0·67, 95% CI 0·42–1·07), healthcare-associated infection (OR 0·56, 95% CI 0·32–0·96), and receipt of any antimicrobial therapy ⩽30 days prior to the culture date (OR 3·06, 95% CI 1·72–5·44). The final model for RVS by broth microdilution included methicillin resistance (OR 2·45, 95% CI 1·42–4·24), admission through the emergency department (OR 0·54, 95% CI 0·32–0·92), presence of an intravascular device (OR 2·24, 95% CI 1·30–3·86), and malignancy (OR 0·51, 95% CI 0·26–1·00). The availability of an easy and rapid clinical prediction rule for early identification of RVS can be used to help guide the timely and individualized management of these serious infections.

A total of 2475 animals from Germany, both captive and wild, were tested for antibodies against Francisella tularensis to obtain more knowledge about the presence of this pathogen in Germany. An indirect and a competitive ELISA served as screening methods, positive and inconclusive samples were confirmed by Western blot. Of the zoo animals sampled between 1992 and 2007 (n = 1122), three (0·3%) were seropositive. The seroconversion of a hippopotamus in Berlin Zoo was documented. From 1353 serum samples of wild foxes (Vulpes vulpes), raccoon dogs (Nyctereutes procyonoides) and wild boars (Sus scrofa), collected between 2005 and 2009 in the federal state of Brandenburg (surrounding Berlin), a total of 101 (7·5%) tested positive for antibodies to F. tularensis lipopolysaccharide. Our results indicate a higher seroprevalence of F. tularensis in wildlife in eastern Germany than commonly assumed. Furthermore, we found foxes and raccoon dogs to be biological indicators for tularaemia.

We studied seasonal patterns of swine hepatitis E virus (HEV) infection in China. From 2008 to 2011, 4200 swine bile specimens were collected for the detection of HEV RNA. A total of 92/2400 (3·83%) specimens in eastern China and 47/1800 (2·61%) specimens in southwestern China were positive for HEV. Seasonal patterns differing by geographical area were suggested. In eastern China, the major peak of HEV RNA prevalence was during March–April, with a minor peak during September–October, and a dip during July–August. In southwestern China, the peak was during September–October and the dip during March–April. The majority of subtype 4a cases (63/82, 76·83%) were detected in the first half of the year, while the majority of subtype 4b cases (26/29, 89·66%) were concentrated in the second half of the year, suggesting that different subtypes contribute to different peaks. Our results indicate that the distribution of HEV subtypes is associated with seasonal patterns.

There are still questions about the importance of different animal reservoirs and environmental factors that played a role in the large Q fever epidemic in The Netherlands. We therefore investigated the spatial association between reported Q fever cases and different livestock and environmental factors at the national level. A spatial regression analysis was performed, with four-digit postal code areas as the unit of analysis. High level of particulate matter (⩾24·5 μg/m3) with an aerodynamic diameter <10 μm (PM10) was by far the strongest risk factor for human Q fever with an odds ratio of 10·4 (95% confidence interval 7·0–15·6) using PM10 <24·5 μg/m3 as reference, in logistic regression analysis, controlling for differences in animal densities, vegetation and other risk factors. Particulate matter seems to play an important role in the transmission of Q fever from infected animals to humans and should be a focus for further studies on zoonotic infectious diseases and decision-making.

The emergence of epidemic cholera in post-earthquake Haiti portended a public health disaster of uncertain magnitude. In order to coordinate relief efforts in an environment with limited healthcare infrastructure and stretched resources, timely and realistic projections of the extent of the cholera outbreak were crucial. Projections were shared with Government and partner organizations beginning 5 days after the first reported case and were updated using progressively more advanced methods as more surveillance data became available. The first projection estimated that 105 000 cholera cases would occur in the first year. Subsequent projections using different methods estimated up to 652 000 cases and 163 000–247 000 hospitalizations during the first year. Current surveillance data show these projections to have provided reasonable approximations of the observed epidemic. Providing the real-time projections allowed Haitian ministries and external aid organizations to better plan and implement response measures during the evolving epidemic.

The aims of this study were to define the basic epidemiology of serologically confirmed acute Q fever in patients tested via the Townsville Hospital laboratory from 2000 to 2010 and to determine the impact of geographical location and seasonality on the incidence of acute cases in the Townsville region. Seven Statistical Local Areas (SLA) were identified as having an incidence higher than the average Queensland incidence over the study period. The SLA with the highest incidence was Woodstock-Ross with 24·9 cases/100 000. A clear seasonal peak was found, with the greatest number of cases observed in May, 3 months following the peak in rainfall in February. We hypothesize that an increase in wildlife numbers and drier conditions seen immediately following the wet season is the reason for the seasonal peak of human acute Q fever cases in Townsville.

We undertook a national paediatric seroprevalence survey of measles, mumps and rubella (MMR) in Singapore to assess the impact of the national childhood immunization programme against these three diseases after introduction of the trivalent MMR vaccine in 1990. The survey involved 1200 residual sera of Singapore residents aged 1–17 years collected from two hospitals between 2008 and 2010. The overall prevalence of antibodies against measles, mumps and rubella was 83·1% [95% confidence interval (CI) 80·9–85·1], 71·8% (95% CI 69·1–74·2) and 88·5% (95% CI 86·6–90·2), respectively. For all three diseases, the lowest prevalence was in children aged 1 year (47·8–62·3%). The seroprevalence of the vaccinated children declined over time. The national MMR immunization programme is effective in raising the herd immunity of the childhood population, although certain age groups are more susceptible to infection, in particular, those who are not eligible for vaccination at age <15 months.

Very few Pacific islands escaped the 1918–1919 influenza pandemic. Subsequent influenza epidemics in the established colonial outposts of American Samoa and New Caledonia infected many but killed very few persons whereas the extraordinarily isolated Niue, Rotuma, Jaliut and Yule islands experienced high mortality influenza epidemics (>3% of population) following 1918. These dichotomous outcomes indicate that previous influenza exposure and degree of epidemiological isolation were important mortality risk factors during influenza epidemics on Pacific islands.

A cross-sectional study was conducted from 10 January to 9 April 2012, to determine the seroprevalence of tuberculosis (TB) of all captive Asian elephants and their handlers in six locations in Peninsular Malaysia. In addition, trunk-wash samples were examined for tubercle bacillus by culture and polymerase chain reaction (PCR). For 63 elephants and 149 elephant handlers, TB seroprevalence was estimated at 20·4% and 24·8%, respectively. From 151 trunk-wash samples, 24 acid-fast isolates were obtained, 23 of which were identified by hsp65-based sequencing as non-tuberculous mycobacteria. The Mycobacterium tuberculosis-specific PCR was positive in the trunk-wash samples from three elephants which were also seropositive. Conversely, the trunk wash from seven seropositive elephants were PCR negative. Hence, there was evidence of active and latent TB in the elephants and the high seroprevalence in the elephants and their handlers suggests frequent, close contact, two-way transmission between animals and humans within confined workplaces.

We investigated the virulence gene carriage and molecular type characteristics of Staphylococcus aureus isolates from bloodstream infections (BSIs) and skin and soft tissue infections (SSTIs) in children. A total of 71 isolates, 16 of which were methicillin-resistant S. aureus (MRSA), were investigated by PCR for virulence-associated gene profiles, sequence type and spa type. This revealed that 76·7% and 53·7% of the SSTI and BSI isolates, respectively, exhibited simultaneous carriage of ⩾10 virulence genes. Compared to BSI isolates, carriage rates for hla, hlb, cna, clfA, seb, sec and pvl genes were significantly higher in SSTI isolates. By contrast, carriage of eta, etb and sea was significantly higher for BSI isolates. Thirty-four sequence types (STs) and 36 spa types were identified in the 71 isolates and included 14 novel STs and four novel spa types. ST59-MRSA-IV/V-t437 was the most common clone in the MRSA isolates. We concluded that virulence determinants are widely distributed in isolates of S. aureus strains from children with BSIs and SSTIs, with an unexpectedly high rate in SSTI isolates. Future profiling of S. aureus virulence determinants may allow the prediction of severity and outcome for children with these infections.

An outbreak of infective mastitis due to Enterococcus faecalis occurred in an intensive sheep farm in north Sardinia (Italy). E. faecalis, which is only rarely isolated from sheep milk, was unexpectedly found in 22·3% of positive samples at microbiological examination. Forty-five out of the 48 E. faecalis isolates showed the same multi-drug resistance pattern (cloxacillin, streptomycin, kanamycin, clindamycin, oxytetracycline). E. faecalis isolates were analysed by pulsed-field gel electrophoresis, and all 45 multi-drug resistant strains showed an indistinguishable macrorestiction profile, indicating their clonal origin. To our knowledge, this is the first report of an outbreak of mastitis in sheep caused by E. faecalis.

In spring 2008, an influenza A subtype H3N2 outbreak occurred in a long stay psycho-geriatric ward and two wards in the intellectual disability services (IDS), part of a large psychiatric hospital. The attack rate in the index ward was 90% (18/20) for patients and 35% (7/20) for staff. It was 14% (1/7) and 17% (2/12) in the affected IDS wards for patients and 0% (0/20) and 4% (1/25) for staff. Many of the laboratory-confirmed cases did not have a fever >38 °C, a typical sign of influenza. Control measures included oseltamivir treatment for cases and prophylaxis for contacts, standard and droplet infection control precautions, active surveillance for early detection and isolation of potential cases. As a result, the outbreak did not spread throughout the hospital. Although the staff vaccination rate (10%) prior to the outbreak was low, we observed a much lower vaccine effectiveness rate in the patients (11%) than in the staff (100%) in the index ward. Vaccination of residents and staff of such facilities remains the key influenza prevention strategy.

In order to estimate influenza-associated excess mortality in southern Brazil, we applied Serfling regression models to monthly mortality data from 1980 to 2008 for pneumonia/influenza- and respiratory/circulatory-coded deaths for all ages and for those aged ⩾60 years. According to viral data, 73·5% of influenza viruses were detected between April and August in southern Brazil. There was no clear influenza season for northern Brazil. In southern Brazil, influenza-associated excess mortality was 1·4/100 000 for all ages and 9·2/100 000 person-years for persons aged ⩾60 years using underlying pneumonia/influenza-coded deaths and 10·0/100 000 for all ages and 86·6/100 000 person-years for persons aged ⩾60 years using underlying respiratory/circulatory-coded deaths. Influenza-associated excess mortality rates for southern Brazil are similar to those published for other countries. Our data support the need for continued influenza surveillance to guide vaccination campaigns to age groups most affected by this virus in Brazil.

Mycobacterium tuberculosis is primarily a pathogen of humans. Infections have been reported in animal species and it is emerging as a significant disease of elephants in the care of humans. With the close association between humans and animals, transmission can occur. In November 2010, a clinically healthy Asian elephant in an Australian zoo was found to be shedding M. tuberculosis; in September 2011, a sick chimpanzee at the same zoo was diagnosed with tuberculosis caused by an indistinguishable strain of M. tuberculosis. Investigations included staff and animal screening. Four staff had tuberculin skin test conversions associated with spending at least 10 hours within the elephant enclosure; none had disease. Six chimpanzees had suspected infection. A pathway of transmission between the animals could not be confirmed. Tuberculosis in an elephant can be transmissible to people in close contact and to other animals more remotely. The mechanism for transmission from elephants requires further investigation.

The prevalence and epidemiological traits of human immunodeficiency virus (HIV)/hepatitis B virus (HBV) infections in high-risk populations (HRPs) remained unclarified in Japan. We determined the prevalence of HIV, HBV and Treponema pallidum (TP) and the viral genotypes in HRPs who attended primary sexually transmitted infection (STI) clinics in Osaka province during 2006–2011. Of 7898 specimens, 133 (1·7%) were HIV positive, which was significantly higher than the figures reported by Japanese Red Cross (0·0019%) and public health centres (0·27%) in Japan. The frequency of HIV-1 subtype B was 88·7%, followed by CRF01_AE (2·3%) and C (0·8%), which were almost identical to the national trend. HBV seroprevalence was surprisingly high in the HIV-positive group (63·2%), which was significantly higher than that in the HIV-negative group (25·6%). By contrast, there was no statistical correlation between HIV and TP infection. Interestingly, the distinct HBV genotypes Ae and G were prevalent in the HIV-positive population (60·0% and 20·0%, respectively), although both were rarely detected during nationwide surveillance. The transmission of HIV and HBV appeared to occur largely within a closed community early in life. Of note, about one-quarter of HIV-positive cases would have remained untested if health professionals had not motivated individuals to undergo HIV testing. This is the first evidence-based assessment of HIV positivity and HIV/HBV co-infection in HRPs at primary STIs in Japan and the effect of the involvement of health professionals in the diagnosis of HIV infections in asymptomatic carriers. The genotyping of HBV provided valuable information for understanding HIV epidemical traits.