This study aims to describe changes in incidence and risk factors for community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) infections upon admission to two New York City hospitals from 2006 to 2012. We examined the first hospitalization for adult patients using electronic health record and administrative data and determined the annual incidence/1000 admissions of total S. aureus, total MRSA, and CA-MRSA (within 48 h of admission) in clinical specimens over the study period. Logistic regression was used to identify factors associated with CA-MRSA in 2006 and 2012. In 137 350 admissions, the incidence of S. aureus, MRSA, and CA-MRSA/1000 admissions were 15·6, 7·0, and 3·5, respectively. The total S. aureus and MRSA isolations decreased significantly over the study period (27% and 25%, respectively) while CA-MRSA incidence was unchanged. CA-MRSA increased as a proportion of all MRSA between 2006 (46%) and 2012 (62%), and was most frequently isolated from respiratory (1·5/1000) and blood (0·7/1000) cultures. Logistic regression analysis of factors associated with isolation of CA-MRSA showed that age ⩾65 years [odds ratio (OR) 2·3, 95% confidence interval (CI) 1·2–4·5], male gender (OR 1·8, 95% CI 1·2–2·8) and history of renal failure (OR 2·6, 95% CI 1·6–4·2) were significant predictors of infection in 2006. No predictors were identified in 2012.

We determined prescribing rates of neuraminidase inhibitors (NIs) for influenza in UK primary care since 2009 in relation to national prescribing guidelines. All NI prescriptions issued during the influenza seasons between October 2010 and May 2013 were extracted from The Health Improvement Network (THIN), a large UK primary-care database. We calculated NI prescribing rates per 100 000 person-weeks (pw) by age group, sex, deprivation level, influenza season and presence of chronic conditions with 95% confidence intervals (CIs), and used negative binomial regression models to determine the independent association between these variables and NI prescribing. NI prescribing was rare. The prescribing rate was 1·7/100 000 pw (95% CI 1·7–1·8) during influenza-active periods, and 0·1/100 000 (95% CI 0·1–0·1) during non-active periods. Prescribing rates were highest in 25- to 44-year-olds in 2010/2011 and in persons aged ⩾85 years in 2011/2012 and 2012/2013. Individuals with chronic conditions had significantly higher prescribing rates than persons without (rate ratio 2·62, 95% CI 2·27–3·03). GPs are more likely to prescribe NIs to high-risk individuals and during influenza active periods, as per national guidelines. We could not assess the proportion of patients with influenza-like illness who were prescribed an NI.

This study describes epidemiological trends for acute rotavirus gastroenteritis (RVGE) in Belgium in children aged ⩽5 years during the period June 2007 to May 2014 after the introduction of routine rotavirus (RV) vaccination. This period encompassed the switch from lyophilized to the liquid formulation of Rotarix™ (GlaxoSmithKline, Belgium) in August 2011. Uptake of RV vaccine remained consistently high throughout the study period with Rotarix the brand most often used. RV was present in 9% (1139/12 511) of hospitalized cases with acute gastroenteritis included in the study. Epidemiological trends for hospital admissions for RVGE remained consistent throughout the study period, with no evidence of any change associated with the switch from lyophilized to liquid formulation of Rotarix. This suggests both formulations perform similarly, with the liquid formulation not inferior regarding ability to reduce hospital admissions for acute RVGE in children aged ⩽5 years. A strong seasonal effect was observed with most RVGE occurring in the winter months but with some variability in intensity, with highest incidence found in those aged 6–24 months. The main observation was the decreased number of hospital admissions for RVGE in Belgium that occurred during winter 2013/2014.

Historically, American Indian/Alaska Native (AI/AN) populations have suffered excess morbidity and mortality from influenza. We investigated the risk factors for death from 2009 pandemic influenza A(H1N1) in persons residing in five states with substantial AI/AN populations. We conducted a case-control investigation using pandemic influenza fatalities from 2009 in Alaska, Arizona, New Mexico, Oklahoma and Wyoming. Controls were outpatients with influenza. We reviewed medical records and interviewed case proxies and controls. We used multiple imputation to predict missing data and multivariable conditional logistic regression to determine risk factors. We included 145 fatal cases and 236 controls; 22% of cases were AI/AN. Risk factors (P < 0·05) included: older age [adjusted matched odds ratio (mOR) 3·2, for >45 years vs. <18 years], pre-existing medical conditions (mOR 7·1), smoking (mOR 3·0), delayed receipt of antivirals (mOR 6·5), and barriers to healthcare access (mOR 5·3). AI/AN race was not significantly associated with death. The increased influenza mortality in AI/AN individuals was due to factors other than racial status. Prevention of influenza deaths should focus on modifiable factors (smoking, early antiviral use, access to care) and identifying high-risk persons for immunization and prompt medical attention.

The West African 2014 Ebola outbreak has highlighted the need for a better information network. Hybrid information networks, an integration of both hierarchical and formalized command control-driven and community-based, or ad hoc emerging networks, could assist in improving public health responses. By filling the missing gaps with social media use, the public health response could be more proactive rather than reactive in responding to such an outbreak of global concern. This article provides a review of the current social media use specifically in this outbreak by systematically collecting data from ProQuest Newsstand, Dow Jones Factiva, Program for Monitoring Emerging Diseases (ProMED) as well as Google Trends. The period studied is from 19 March 2014 (first request for information on ProMED) to 15 October 2014, a total of 31 weeks. The term ‘Ebola’ was used in the search for media reports. The outcome of the review shows positive results for social media use in effective surveillance response mechanisms – for improving the detection, preparedness and response of the outbreak – as a complement to traditional, filed, work-based surveillance approach.

Bartonellae are blood- and vector-borne Gram-negative bacteria, recognized as emerging pathogens. Whole-blood samples were collected from 58 free-ranging lions (Panthera leo) in South Africa and 17 cheetahs (Acinonyx jubatus) from Namibia. Blood samples were also collected from 11 cheetahs (more than once for some of them) at the San Diego Wildlife Safari Park. Bacteria were isolated from the blood of three (5%) lions, one (6%) Namibian cheetah and eight (73%) cheetahs from California. The lion Bartonella isolates were identified as B. henselae (two isolates) and B. koehlerae subsp. koehlerae. The Namibian cheetah strain was close but distinct from isolates from North American wild felids and clustered between B. henselae and B. koehlerae. It should be considered as a new subspecies of B. koehlerae. All the Californian semi-captive cheetah isolates were different from B. henselae or B. koehlerae subsp. koehlerae and from the Namibian cheetah isolate. They were also distinct from the strains isolated from Californian mountain lions (Felis concolor) and clustered with strains of B. koehlerae subsp. bothieri isolated from free-ranging bobcats (Lynx rufus) in California. Therefore, it is likely that these captive cheetahs became infected by an indigenous strain for which bobcats are the natural reservoir.

Healthcare workers (HCWs) reporting no history of varicella frequently receive varicella vaccination (vOka) if they test varicella-zoster virus (VZV) immunoglobulin G (IgG) negative. In this study, the utilities of VZV-IgG time-resolved fluorescence immunoassay (VZV-TRFIA) and a commercial VZV-IgG purified glycoprotein enzyme immunoassay (gpEIA) currently used in England for confirming VZV immunity have been compared to the fluorescent-antibody-to-membrane-antigen assay (FAMA). A total of 110 HCWs received two doses of vOka vaccine spaced 6 weeks apart and sera collected pre-vaccination (n = 100), at 6 weeks post-completion of vaccination (n = 86) and at 12–18 months follow-up (n = 73) were analysed. Pre-vaccination, by FAMA, 61·0% sera were VZV IgG negative, and compared to FAMA the sensitivities of VZV-TRFIA and gpEIA were 74·4% [95% confidence interval (CI) 57·9–87·0] and 46·2% (95% CI 30·1–62·8), respectively. Post-completion of vaccination the seroconversion rate by FAMA was 93·7% compared to rates of 95·8% and 70·8% determined by VZV-TRFIA and gpEIA, respectively. At 12–18 months follow-up seropositivity rates by FAMA, VZV-TRFIA and gpEIA were 78·1%, 74·0% and 47·9%, respectively. Compared to FAMA the sensitivities of VZV-TRFIA and gpEIA for measuring VZV IgG following vaccination were 96·4% (95% CI 91·7–98·8) and 74·6% (95% CI 66·5–81·6), respectively. Using both FAMA and VZV-TRFIA to identify healthy adult VZV susceptibles and measure seroconversion showed that vOka vaccination of HCWs is highly immunogenic.

Five cases of STEC O157 phage type (PT) 21/28 reported consumption of raw cows' drinking milk (RDM) produced at a dairy farm in the South West of England. STEC O157 PT21/28 was isolated from faecal specimens from milking cows on the implicated farm. Whole genome sequencing (WGS) showed that human and cattle isolates were the same strain. Further analysis of WGS data confirmed that sequences of isolates from an additional four cases (who did not report consumption of RDM when first questioned) fell within the same five single nucleotide polymorphism cluster as the initial five cases epidemiologically linked to the consumption of RDM. These four additional cases identified by WGS were investigated further and were, ultimately, associated with the implicated farm. The RDM outbreak strain encoded stx2a, which is associated with increased pathogenicity and severity of symptoms. Further epidemiological analysis showed that 70% of isolates within a wider cluster containing the outbreak strain were from cases residing in, or linked to, the same geographical region of England. During this RDM outbreak, use of WGS improved case ascertainment and provided insights into the evolution of a highly pathogenic clade of STEC O157 PT21/28 stx2a associated with the South West of England.

Salmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

The rapid rise in syphilis cases has prompted a number of public health campaigns to assist men who have sex with men (MSM) recognize and present early with symptoms. This study aimed to investigate the temporal trend of the duration of self-report symptoms and titre of rapid plasma reagin (RPR) in MSM with infectious syphilis. Seven hundred and sixty-one syphilis cases in MSM diagnosed at the Melbourne Sexual Health Centre (MSHC) from 2007–2013 were reviewed. Median duration of symptoms and RPR titres in each year were calculated. The median durations of symptoms with primary and secondary syphilis were 9 [interquartile range (IQR) 6–14] days and 14 (IQR 7–30) days, respectively. The overall median titre of RPR in secondary syphilis (median 128, IQR 64–256) was higher than in primary syphilis (median 4, IQR 1–32) and in early latent syphilis (median 32, IQR 4–64). The median duration of symptoms for primary syphilis, secondary syphilis and titre of RPR level did not change over time. Public health campaigns were not associated with a significant shorter time from onset of symptoms to treatment. Alternative strategies such as more frequent testing of MSM should be promoted to control the syphilis epidemic in Australia.

Repeat rectal chlamydia infection is common in men who have sex with men (MSM) following treatment with 1 g azithromycin. This study describes the association between organism load and repeat rectal chlamydia infection, genovar distribution, and efficacy of azithromycin in asymptomatic MSM. Stored rectal chlamydia-positive samples from MSM were analysed for organism load and genotyped to assist differentiation between reinfection and treatment failure. Included men had follow-up tests within 100 days of index infection. Lymphogranuloma venereum and proctitis diagnosed symptomatically were excluded. Factors associated with repeat infection, treatment failure and reinfection were investigated. In total, 227 MSM were included – 64 with repeat infections [28·2%, 95% confidence interval (CI) 22·4–34·5]. Repeat positivity was associated with increased pre-treatment organism load [odds ratio (OR) 1·7, 95% CI 1·4–2·2]. Of 64 repeat infections, 29 (12·8%, 95% CI 8·7–17·8) were treatment failures and 35 (15·4%, 95% CI 11·0–20·8) were reinfections, 11 (17·2%, 95% CI 8·9–28·7) of which were definite reinfections. Treatment failure and reinfection were both associated with increased load (OR 2·0, 95% CI 1·4–2·7 and 1·6, 95% CI 1·2–2·2, respectively). The most prevalent genovars were G, D and J. Treatment efficacy for 1 g azithromycin was 83·6% (95% CI 77·2–88·8). Repeat positivity was associated with high pre-treatment organism load. Randomized controlled trials are urgently needed to evaluate azithromycin's efficacy and whether extended doses can overcome rectal infections with high organism load.

Sexual transmission has become the primary route of HIV transmission in China. Therefore, a comprehensive overview of HIV-1 subtype distribution is necessary for the prevention and control of the HIV epidemic. The present study aimed to provide a comprehensive prevalence estimate of different HIV-1 subtypes in sexual transmission in China. We conducted a systematic literature review for studies of HIV-1 subtypes in English and Chinese through several databases. Eligible articles were screened and selected by two authors independently. Random-effects model were applied to calculate the pooled prevalence of different HIV-1 subtypes, and subgroup analyses examined prevalence estimates across time, locations, and populations. A total of 130 eligible studies were identified, including 18 752 successfully genotyped samples. The pooled prevalence of CRF01_AE, subtype B, CRF07_BC, CRF08_BC, and subtype C were 44·54% (95% CI 40·81–48·30), 18·31% (95% CI 14·71–22·17), 16·45% (95% CI 13·82–19·25), 2·55% (95% CI 1·56–3·73), 0·37% (95% CI 0·11–0·72), respectively. The prevalence of subtype B in sexual transmission decreased, while the prevalence of CRF01_AE and CRF07_BC in sexual transmission, and CRF08_BC in heterosexual transmission increased. There is significant variation in HIV-1 subtype distribution between regions. The distribution of HIV-1 subtypes and circulating recombinant forms have changed significantly. The high genetic variability of HIV-1 poses a significant challenge for disease control and surveillance in China.

Hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) is becoming increasingly established in Asian hospitals. The primary aim of this study was to decompose the risk factors for HA-MRSA based on conceptual clinical pathways. The secondary aim was to show the amount of effect attributable to antibiotic exposure and total length of stay before outcome (LBO) so that institutions can manage at-risk patients accordingly. A case-control study consisting of 1200 inpatients was conducted in a large tertiary hospital in Singapore between January and December 2006. Results from the generalized structural equation model (GSEM) show that LBO [adjusted odds ratio (aOR) 14·9, 95% confidence interval (CI) 8·7–25·5], prior hospitalization (aOR 6·2, 95% CI 3·3–11·5), and cumulative antibiotic exposure (aOR 3·5, 95% CI 2·3–5·3), directly affected HA-MRSA acquisition. LBO accounted for the majority of the effects due to age (100%), immunosuppression (67%), and surgery (96%), and to a lesser extent for male gender (22%). Our model enabled us to account and quantify effects of intermediaries. LBO was found to be an important mediator of age, immunosuppression and surgery on MRSA infection. Traditional regression approaches will not only give different conclusions but also underestimate the effects. Hospitals should minimize the hospital stay when possible to reduce the risk of MRSA.

Hand, foot, and mouth disease (HFMD) has caused public health concerns worldwide. We aimed to investigate the effect of meteorological factors on the HFMD epidemic in Qingdao, a port city in China. A total of 78641 cases were reported in Qingdao between January 2007 and December 2014. Of those, 71084 (90·39%) occurred in children aged 0–5 years, with an incidence of 1691·2/100000. The incidence increased from early spring, peaked between spring and summer, and decreased in late summer. Aetiological agents in all severe cases and selected mild cases were characterized by examining throat swabs. Except for enterovirus 71 (EV71) and coxsackievirus A16 (CA16), other EVs caused >50% of the HFMD cases between 2011 and 2014. EV71 was more frequent in the off-peak months than in the peak months and prone to causing more severe cases compared to CA16 (χ2 = 46·3, P < 0·001). CA10 caused more severe HFMD than did CA6 (χ2 = 20·49, P < 0·001) and all non-CA10 EVs (χ2 = 41·01, P < 0·001). Community-derived HFMD cases accounted for 65·11%. Spearman rank correlation analysis showed that HFMD incidence in children aged 0–5 years was positively correlated with atmospheric temperature (rs = 0·77, P < 0·001), relative humidity (rs = 0·507, P < 0·001), and precipitation (rs = 0·328, P < 0·001). Climate changes and CA10 surveillance in communities should be integrated into the current prophylactic programme.

The value of Google Flu Trends (GFT) remains unclear after it overestimated the proportion of physician visits related to influenza-like illness (ILI) in the United States in 2012–2013. However, GFT estimates (%GFT) have not been examined nationally in Canada nor compared with positivity for respiratory viruses other than influenza. For 2010–2014, we compared %GFT for Canada to Public Health Agency of Canada ILI consultation rates (%PHAC) and to positivity for influenza A and B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and rhinoviruses. %GFT correlated well with %PHAC (ρ = 0·77–0·90) and influenza A positivity (ρ = 0·64–0·96) and overestimated the 2012–2013 %PHAC peak by 0·99 percentage points. %GFT peaks corresponded temporally with peaks in positivity for influenza A and rhinoviruses (all seasons) and RSV and hMPV when their peaks preceded influenza peaks. In Canada, %GFT represented traditional surveillance data and corresponded temporally with patterns in circulating respiratory viruses.

Legionnaires' disease (LD) is caused by the inhalation of aerosols containing Legionella, a Gram-negative bacteria. Previous national- or regional-level studies have suggested an impact of climate on LD incidence. The objective of this study was to investigate the effect of temperature, rainfall, and atmospheric pressure on short-term variations in LD notification rate. EU/EEA Member States report their LD surveillance data to the European Centre for Disease Prevention and Control. Community-acquired LD cases reported by Denmark, Germany, Italy, and The Netherlands with onset date in 2007–2012 were aggregated by onset week and region of residence. Weather variables were extracted from the European Climate Assessment & Dataset project. We fitted Poisson regression models to estimate the association between meteorological variables and the weekly number of community-acquired LD cases. Temperature, rainfall and atmospheric pressure were all associated with LD risk with higher risk associated with simultaneous increase in temperature and rainfall. Temperatures >20 °C were not associated with a higher risk for LD. LD cases occurring during wintertime may be associated with sources less influenced by meteorological conditions.

Despite the availability of inexpensive antimicrobial treatment, syphilis remains prevalent worldwide, affecting millions of individuals. Furthermore, syphilis infection is suspected of increasing both susceptibility to, and tendency to transmit, HIV. Development of a syphilis vaccine would be a potentially promising step towards control, but the value of dedicating resources to vaccine development should be evaluated in the context of the anticipated benefits. Here, we use a detailed mathematical model to explore the potential impact of rolling out a hypothetical syphilis vaccine on morbidity from both syphilis and HIV and compare it to the impact of expanded ‘screen and treat’ programmes using existing treatments. Our results suggest that an efficacious vaccine has the potential to sharply reduce syphilis prevalence under a wide range of scenarios, while expanded treatment interventions are likely to be substantially less effective. Our modelled interventions in our simulated study populations are expected to have little effect on HIV, and in some scenarios lead to small increases in HIV incidence, suggesting that interventions against syphilis should be accompanied with interventions against other sexually transmitted infections to prevent the possibility that lower morbidity or lower perceived risk from syphilis could lead to increases in other sexually transmitted diseases.

Cytomegalovirus (CMV) is the leading cause of congenital infection and non-genetic sensorineural hearing loss in children. There are no recent data on the incidence of CMV infection during pregnancy in Canada. This present study was undertaken to determine the seroprevalence of CMV IgG antibodies and the rate of seroconversion in a cohort of pregnant women in the province of Québec, Canada. We used serum samples and questionnaire data collected as part of the 3D Pregnancy and Birth Cohort Study (2010–2013) conducted in Québec, Canada. CMV IgG antibodies were determined in serum samples collected at the first and third trimesters. Associations between independent variables and seroprevalence were assessed using logistic regression, and associations with seroconversions, by Poisson regression. Of 1938 pregnant women tested, 40·4% were seropositive for CMV at baseline. Previous CMV infection was associated with: working as a daycare educator, lower education, lower income, having had children, first language other than French or English, and being born outside Canada or the United States. Of the 1122 initially seronegative women, 24 (2·1%) seroconverted between their first and third trimesters. The seroconversion rate was 1·4 [95% confidence interval (CI) 0·9–2·1]/10 000 person-days at risk or 3·9 (95% CI 2·5–5·9)/100 pregnancies (assuming a 280-day gestation). The high proportion of pregnant women susceptible to CMV infection (nearly 60%) and the subsequent rate of seroconversion are of concern.

In Germany tularemia is a re-emerging zoonotic disease. Therefore, we investigated wild animals and environmental water samples for the presence and phylogenetic diversity of Francisella tularensis in the poorly studied Berlin/Brandenburg region. The phylogenomic analysis of three isolates from wild animals revealed three new subclades within the phylogenetic tree of F. tularensis [B.71 from a raccoon dog (Nyctereutes procyonoides); B.74 from a red fox (Vulpes vulpes), and B.75 from a Eurasian beaver (Castor fiber albicus)]. The results from histological, PCR, and genomic investigations on the dead beaver showed that the animal suffered from a systemic infection. Indications were found that the bacteria were released from the beaver carcass into the surrounding environment. We demonstrated unexpectedly high and novel phylogenetic diversity of F. tularensis in Germany and the fact that the bacteria persist in the environment for at least one climatic season. These findings support a broader host species diversity than previously known regarding Germany. Our data further support the assumption derived from previous serological studies of an underestimated frequency of occurrence of the pathogen in the environment and in wild animals. F. tularensis was isolated from animal species not previously reported as natural hosts in Germany.