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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Bartonella spp. are increasingly implicated in infectious endocarditis cases in the UK. Herein, we attempted to quantify their role in this syndrome and explored the epidemiology of Bartonella-associated endocarditis in the UK. Between November 2005 and October 2010, samples from 685 endocarditis patients were submitted to the Health Protection Agency for Bartonella serology. Serological evidence of infection was obtained for 57 (8·3%) patients. PCR-based evidence of infection was obtained from 13 out of 14 patients for whom heart valve tissue was available, with Bartonella quintana implicated in 12 cases and B. henselae in one. Six patients with B. quintana endocarditis were recent immigrants into the UK, of whom four lived in poor socioeconomic conditions. These results indicate that Bartonella is a not uncommon cause of endocarditis in the UK and should be considered particularly in patients raised in eastern Europe and/or with a history of homelessness or alcoholism.

Although community-onset bloodstream infection (BSI) is recognized as a major cause of morbidity and mortality, its epidemiology has not been well defined in non-selected populations. We conducted population-based laboratory surveillance in the Victoria area, Canada during 1998–2005 in order to determine the burden associated with community-onset BSI. A total of 2785 episodes were identified for an overall annual incidence of 101·2/100 000. Males and the very young and the elderly were at highest risk. Overall 1980 (71%) episodes resulted in hospital admission for a median length of stay of 8 days; the total days of acute hospitalization associated with community-onset BSI was 28 442 days or 1034 days/100 000 population per year. The in-hospital case-fatality rate was 13%. Community-onset BSI is associated with a major burden of illness. These data support ongoing and future preventative and research efforts aimed at reducing the major impact of these infections.

The potential for direct transmission of type A influenza viruses from wild waterfowl to humans is undefined. This study estimated exposure of hunters to avian influenza virus (AIV) resulting from direct contact with potentially infected waterfowl in Georgia (GA), Louisiana (LA) and Minnesota (MN), and demonstrated variation in the risk of exposure to AIV by hunting location and time. Hunting begins earlier in MN, starting in October, and later in GA and LA, usually starting in November. In addition, the numbers of hunters and birds harvested varies considerably in each state, with LA hosting the largest harvest in the USA Temporal effects resulted in variation of the exposure risk per hunter-day, with a higher risk associated with the earlier months of the hunting season. Exposure risk in locations varied due to AIV prevalence during each hunting season, average bird harvest per hunter-day, and ratio of juveniles/adult birds harvested (higher risk associated with higher ratios). Population risk is discussed based on the exposure risk and number of active hunters in each state per month. The risk of human exposure to AIV was also shown to be temporally distinct from the time of greatest risk of human influenza A infection during circulation of seasonal human influenza viruses, making recombination events due to co-infection unlikely.