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 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.

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 purpose of this study was to determine whether pooling avian influenza (AI)-positive swabs with negative swabs has a detrimental effect on the sensitivity of AI real-time reverse transcription–polymerase chain reactions (rRT–PCRs). Cloacal and buccal swabs were sampled daily from 12 turkeys infected with A/goose/England/07(H2N2). For half the turkeys, each swab was mixed with four swabs from known AI-negative turkeys, and for the other half the swabs were tested individually. Bayesian modelling was used to (i) determine whether pooling the positive swabs compromised the cycle threshold (Ct) value obtained from the rRT–PCRs, and (ii) estimate the likelihood of detection of an H2N2 infected turkey flock via rRT–PCR for pooled and individually tested swabs (cloacal and buccal) vs. the number of days post-infection of the flock. Results indicated that there was no significant effect of compromising AI rRT–PCR sensitivity by pooling a weak positive swab with negative swabs on the Ct values which were obtained. Pooled sampling was able to widen the detection window compared to individual sampling, for the same number of rRT–PCR tests. This indicates that pooled sampling would be an effective method of reducing the number of tests to be performed to determine flock status during an AI outbreak and for surveillance.

The main Neisseria meningitidis adhesion molecules, type IV pili (Tfp) and Neisseria adhesion A (NadA), play important roles in the pathogenesis of invasive meningococcal disease. PilE is the major Tfp subunit. In this study, the prevalence and genetic diversity of pilE and nadA were investigated in the prevalent serogroups and clonal complexes (CC) of N. meningitidis isolated in China. All serogroup A strains belonging to CC1 and CC5 and all CC11 serogroup W135 strains were clustered into class II PilE clades. All serogroup C and most of serogroup B isolates except CC8 and ST5642 were class I PilE clades. Class II pilE sequences were highly conserved. All isolates belonging to class I PilE isolates were nadA negative. However, nadA-positive strains were exclusively found in CC5 and CC11 isolates (class II PilE). This study showed that PilE and NadA may be related to epidemic or endemic meningococcal disease.

Although immediate notification of a case is crucial for epidemic control, clinicians may delay notification due to uncertainties in diagnosis, reflecting a trade-off between timeliness and the accuracy of surveillance. We assessed this trade-off for four epidemic-prone diseases that require immediate notification of suspected cases: shigellosis, typhoid fever, paratyphoid fever, and cholera in the Korean National Notifiable Disease Surveillance System data for 2001–2007. Timeliness was measured as the time to registration (TR), being the time interval from symptom onset to notification by the clinician to the local public health centre. We introduced a new index, ‘time-accuracy trade-off ratio’ to indicate time saved by clinical vs. laboratory-based notifications. Clinical notifications comprised 34·4% of total notifications, and these showed a shorter median TR than laboratory-based notifications (1–4 days). The trade-off ratio was greatest for shigellosis (3·3 days), and smallest for typhoid fever (0·6 days). A higher trade-off ratio provides stronger evidence for clinical notification without waiting for laboratory confirmation.

We examined the uptake of HIV testing in black Africans living in England before the introduction of national testing guidelines. Analyses were conducted using data from an anonymous self-completed questionnaire linked to oral fluid samples to establish HIV status in black Africans attending community venues in England in 2004. Of 946 participants, 44% had ever been tested for HIV and 29% had been tested in the previous 24 months. Of those with undiagnosed HIV, 45% had previously had a negative HIV test. Almost a third of people tested in the UK had been at general practice. Uptake of HIV testing was not associated with perceived risk of HIV. These findings highlight the need for the implementation of national HIV testing guidelines in the UK, including the promotion of testing in general practice. Regular testing in black Africans living in the UK should be promoted regardless of their HIV test history.

This study aimed to determine the prevalence of serological markers for HIV-1/2, HBV, HCV, Treponema cruzi and T. pallidum infections. The association of these infections with risk factors in a population from Salvador, Bahia, Brazil was also analysed. Of the 780 enrolled individuals, 545 (70%) were female and 235 (30%) were male. Seroprevalence of 0·8% (6/702), 1·3% (9/678), 1·5% (10/684), 3·5% (23/663) and 11·5% (77/668) for HIV-1/2, HBV, HCV, T. cruzi and T. pallidum infections, respectively, was observed. The seroprevalence of T. pallidum was higher in males 20% (43/210) than in females 7% (34/458) (P < 0·01). An association between age and seroprevalence for T. cruzi (P = 0·02) and T. pallidum (P < 0·01) was observed. HBsAg was associated with having tattoos (3/37 vs. 6/623, P = 0·01) and not having a steady sexual partner (5/141 vs. 4/473, P = 0·04), while anti-HIV-1/2 was associated with having tattoos (2/39 vs. 4/647, P = 0·04); however, larger studies are needed to categorically state the relationship of these risk factors with infectious agents. The prevalence of serological markers for HIV-1/2, HBV, HCV and T. cruzi was consistent with other studies.

The Netherlands experienced an unprecedented outbreak of Q fever between 2007 and 2010. The Jeroen Bosch Hospital (JBH) in 's-Hertogenbosch is located in the centre of the epidemic area. Based on Q fever screening programmes, seroprevalence of IgG phase II antibodies to Coxiella burnetii in the JBH catchment area was 10·7% [785 tested, 84 seropositive, 95% confidence interval (CI) 8·5–12·9]. Seroprevalence appeared not to be influenced by age, gender or area of residence. Extrapolating these data, an estimated 40 600 persons (95% CI 32 200–48 900) in the JBH catchment area have been infected by C. burnetii and are, therefore, potentially at risk for chronic Q fever. This figure by far exceeds the nationwide number of notified symptomatic acute Q fever patients and illustrates the magnitude of the Dutch Q fever outbreak. Clinicians in epidemic Q fever areas should be alert for chronic Q fever, even if no acute Q fever is reported.

Wildlife reservoir hosts of bovine tuberculosis (bTB) include Eurasian badgers (Meles meles) and brushtail possum (Trichosurus vulpecula) in the UK and New Zealand, respectively. Similar species warrant further investigation in the northern lower peninsula of Michigan, USA due to the continued presence of bTB on cattle farms. Most research in Michigan, USA has focused on interactions between white-tailed deer (Odocoileus virginianus) and cattle (Bos taurus) for the transmission of the infectious agent of bTB, Mycobacterium bovis, due to high deer densities and feeding practices. However, limited data are available on medium-sized mammals such as Virginia opossum (Didelphis virginiana; hereafter referred to as opossum) and their movements and home range in Michigan near cattle farms. We conducted surveillance of medium-sized mammals on previously depopulated cattle farms for presence of M. bovis infections and equipped opossum with Global Positioning System (GPS) technology to assess potential differences in home range between farms inside and outside the bTB core area that has had cattle test positive for M. bovis. On farms inside the bTB core area, prevalence in opossum was comparable [6%, 95% confidence interval (CI) 2·0–11·0] to prevalence in raccoon (Procyon lotor; 4%, 95% CI 1·0–9·0, P = 0·439) whereas only a single opossum tested positive for M. bovis on farms outside the bTB core area. The prevalence in opossum occupying farms that had cattle test positive for M. bovis was higher (6·4%) than for opossum occupying farms that never had cattle test positive for M. bovis (0·9%, P = 0·01). Mean size of home range for 50% and 95% estimates were similar by sex (P = 0·791) both inside or outside the bTB core area (P = 0·218). Although surveillance efforts and home range were not assessed on the same farms, opossum use of farms near structures was apparent as was selection for farms over surrounding forested habitats. The use of farms, stored feed, and structures by opossum, their ability to serve as vectors of M. bovis, and their propensity to ingest contaminated sources of M. bovis requires additional research in Michigan, USA.

Prevalence monitoring of avian influenza in wild bird populations is important to estimate risks for the occurrence of potentially zoonotic and economically disastrous outbreaks of highly pathogenic avian influenza virus (AIV) in poultry worldwide. A targeted, cost-effective monitoring method for AIV in wild birds was developed, which is based on monitoring results for AIV in Germany and information on the distribution and abundance of wild bird species in selected habitat types. Spatial data were combined with virological and outbreak data for the period of 1 January 2006 to 31 December 2010. Using Germany as an example, we identified 11 indicator species. By concentrating monitoring efforts on these species in spatially confined locations, we propose a targeted and more cost-effective risk-based AIV monitoring approach that can be adapted universally for the identification of wild bird indicator species worldwide with the perspective of reducing sample sizes (and costs) without impairing the validity of the results.

A recent resurgence of mumps in doubly vaccinated cohorts has been observed, identifying genotype G as the current predominant genotype. In this study, the neutralization efficacy of guinea pig sera immunized with three vaccine viruses: L-Zagreb, Urabe AM9 and JL5, was tested against seven mumps viruses: three vaccine strains and four wild-type strains (two of genotype G, one of genotype C, one of genotype D) isolated during 1998–2011. All sera neutralized all viruses although at different levels. The neutralization efficiency of sera decreases several fold by temporal order of virus isolation. Therefore, we concluded that gradual evolution of mumps viruses, rather than belonging to a certain genotype, results in an antigenic divergence from the vaccine strains that decrease the neutralization capacity of vaccine-induced antibodies. Moreover, the amino-acid sequence alignment revealed three new potentially relevant regions for escape from neutralization, i.e. 113–130, 375–403 and 440–443.

In the incidence patterns of cholera, diphtheria and croup during the past when they were of epidemic proportions, we document a set of cycles (periods), one of which was reported and discussed by A. L. Chizhevsky in the same data with emphasis on the mirroring in human disease of the ∼11-year sunspot cycle. The data in this study are based on Chizhevsky's book The Terrestrial Echo of Solar Storms and on records from the World Health Organization. For meta-analysis, we used the extended linear and nonlinear cosinor. We found a geographically selective assortment of various cycles characterizing the epidemiology of infections, which is the documented novel topic of this paper, complementing the earlier finding in the 21st century or shortly before, of a geographically selective assortment of cycles characterizing human sudden cardiac death. Solar effects, if any, interact with geophysical processes in contributing to this assortment.

The notification rate of Legionnaires' disease (LD) in France was 2·4/100 000 population in 2010, varying across regions with an increasing rate from west to east. Two sources [mandatory notifications (MN) and a survey of hospital laboratories] were used in a capture–recapture study to estimate the number of LD cases and the sensitivity of the MN system at national and regional levels in 2010. The number of missed cases was estimated using Chapman's method. The estimated sensitivity of MN was 88·5% (95% CI 88·0–89·0) and ranged from 70% to 100% by region. The estimated incidence was 2·7/100 000 population. Sensitivity of the MN system improved since the previous capture–recapture estimates (10% in 1995, 33% in 1998). This study confirmed that the observed west–east gradient is not related to regional notification disparities. Ecological studies should be conducted to better understand the observed spatial variations in LD incidence.

The aim of this study was to characterize updated HIV subtypes in Yunnan to determine their origins and distribution within the population. RT–PCR of both the gag and env genes were sequenced from Yunnan province inhabitants newly diagnosed with HIV-1. Sequence data from 290 samples were used for statistical analysis of subtype distribution and phylogenetic tree construction. Distribution data were adjusted to account for different geographical distributions of HIV-1 subtypes in the population. Phylogenetic analysis revealed six HIV-1 subtypes in Yunnan, including eight types of unique recombination forms (URFs). The most prevalent subtypes in this province, CRF07_BC (18·9%), CRF08_BC (39·1%), CRF01_AE (22·4%), and URFs (subtype C, 5·9% and subtype B, 4·5%), were all recombinants. We found significant differences in the distribution of these HIV-1 subtypes not only geographically, but also between various ethnic groups and with respect to transmission routes. Our findings indicate a complex population of HIV-1 subtypes, URFs, and recombinant subtypes in Yunnan province. This diversity could make the prevention and control of HIV infection in Yunnan more difficult due to the possibility of virus recombination or infection by multiple subtypes.

West Nile virus (WNV) was first recognized in the USA in 1999. We estimated the cumulative incidence of WNV infection in the USA from 1999 to 2010 using recently derived age- and sex-stratified ratios of infections to WNV neuroinvasive disease (WNND) and the number of WNND cases reported to national surveillance. We estimate that over 3 million persons have been infected with WNV in the USA, with the highest incidence rates in the central plains states. These 3 million infections would have resulted in about 780 000 illnesses. A substantial number of WNV infections and illnesses have occurred during the virus' first decade in the USA.

Antivirals are an important defence against novel strains of influenza. However, the impact of widespread drug usage on strain circulation across multiple epidemic waves – via their impact on host immunity – is unknown despite antivirals having the likelihood of extensive use during a pandemic. To explore how drug usage by individuals affects population strain dynamics, we embedded a two-strain model of within-host dynamics within an epidemic model. We found that when 40% of hosts took drugs early during the infectious period, transmission was reduced by 30% and average levels of immunity by 2·9-fold (comparable to antibody concentrations), relative to 14% and 1·5-fold reductions when drugs were taken late. The novel strain was more successful relative to the resident strain when drugs were not taken, and an intermediate level of drug coverage minimized incidence in subsequent waves. We discuss how drug regimens, coverage and R0 could impact pandemic preparedness.

The serotype distribution and susceptibility to 14 antimicrobial agents of 526 isolates of Shigella spp. from four hospitals in Sun county, Henan province, China during 2001–2008, were analysed to identify associations of serotypes with resistance trends. S. flexneri was the most frequent species (92·4%), the remainder was S. sonnei. The prevalent serotype of S. flexneri was 2a (26·7%). Almost all (>99%) isolates were resistant to tetracycline, nalidixic acid and pipemidic acid; >80% were resistant to chloramphenicol, amoxicillin and co-trimoxazole but less than 5% were resistant to polymyxin B, furazolidone, cefotaxime and gentamicin. S. flexneri showed statistically significant higher resistance than S. sonnei to amoxicillin, ampicillin, chloramphenicol and ciprofloxacin but resistance to co-trimoxazole was more common in S. sonnei than in S. flexneri. These results emphasize that monitoring of emerging resistance in Shigella isolates is essential for timely and appropriate recommendations for antimicrobial therapy.