Since Ebola virus was discovered in 1970s, the virus has persisted in Africa and sporadic fatal outbreaks in humans and non-human primates have been reported. However, the evolutionary history of Ebola virus remains unclear. In this study, 27 Ebola virus strains with complete glycoprotein genes, including five species (Zaire, Sudan, Reston, Tai Forest, Bundibugyo), were analysed. Here, we propose a hypothesis of the evolutionary history of Ebola virus which will be helpful to investigate the molecular evolution of these viruses.

Historically, the highest incidence rates of invasive Haemophilus influenzae disease in the world were found in North American and Australian Indigenous children. Although immunization against H. influenzae type b (Hib) led to a marked decrease in invasive Hib disease in countries where it was implemented, this disease has not been eliminated and its rates in Indigenous communities remain higher than in the general North American population. In this literature review, we examined the epidemiology of invasive H. influenzae disease in the pre-Hib vaccine era, effect of carriage on disease epidemiology, immune response to H. influenzae infection and Hib vaccination in Indigenous and Caucasian children, and the changing epidemiology after Hib conjugate vaccine has been in use for more than two decades in North America. We also explored reasons behind the continued high rates of invasive H. influenzae disease in Indigenous populations in North America. H. influenzae type a (Hia) has emerged as a significant cause of severe disease in North American Indigenous communities. More research is needed to define the genotypic diversity of Hia and the disease burden that it causes in order to determine if a Hia vaccine is required to protect the vulnerable populations.

Setting priorities in the field of infectious diseases requires evidence-based and robust baseline estimates of disease burden. Therefore, the European Centre for Disease Prevention and Control initiated the Burden of Communicable Diseases in Europe (BCoDE) project. The project uses an incidence- and pathogen-based approach to measure the impact of both acute illness and sequelae of infectious diseases expressed in disability-adjusted life years (DALYs). This study presents first estimates of disease burden for four pathogens in Germany. The number of reported incident cases adjusted for underestimation served as model input. For the study period 2005–2007, the average disease burden was estimated at 33 116 DALYs/year for influenza virus, 19 115 DALYs/year for Salmonella spp., 8708 DALYs/year for hepatitis B virus and 740 DALYs/year for measles virus. This methodology highlights the importance of sequelae, particularly for hepatitis B and salmonellosis, because if omitted, the burden would have been underestimated by 98% and 56%, respectively.

Community-onset methicillin resistant Staphylococcus aureus (CO-MRSA) became a prominent cause of infection in North America in 2003, with a peak in the epidemic noted by multiple groups in the USA between 2005 and 2007. We reviewed rates of MRSA in two hospitals in Vancouver, Canada, to observe changes in epidemiology from 2003 to 2011. Episodes of emergency department (ED) MRSA bacteraemia and wounds were extracted from the laboratory database, with rates calculated per 10 000 ED visits. All cases were assumed to be community onset, as they were diagnosed in the ED. A peak in ED MRSA bacteraemias occurred in 2005, at 7·8/10 000 ED visits. By 2011, rates of ED bacteraemia declined significantly to 3·3/10 000 ED visits (P⩽0·03). MRSA wound rates peaked at 82·2 cases/10 000 ED visits in 2007 with a subsequent significant decline to 34·3 cases in 2011 (P = 0·04). We have demonstrated a significant decline in CO-MRSA within our population, consistent with reports from the USA, suggesting a substantial change in the epidemiology of CO-MRSA in certain North American cities.

A new surveillance system for outbreaks of norovirus in English hospitals, the hospital norovirus outbreak reporting system (HNORS), was launched in January 2009. On site investigators were enabled to enter data on outbreaks of norovirus directly onto a tailored system via an internet-based front end. A standard dataset was designed to collect information describing the key epidemiological characteristics of each outbreak. In the period 1992–2008, 1817 suspected and confirmed outbreaks of norovirus in English hospitals were reported to national surveillance. After introduction of the new system there were 3980 reports of outbreaks of suspected and confirmed norovirus received in the years 2009–2011. Data from the new reporting system demonstrates that transmission of norovirus levies a heavy burden on English hospitals. On average, reported outbreaks are associated with 13 000 patients and 3400 staff becoming ill, 8900 days of ward closure and the loss of over 15 500 bed-days annually.

We used a national survey of 7578 randomly selected respondents in 2008–2009 to identify the period prevalence of acute respiratory infection (ARI) by season and state, and to estimate the incidence of ARI in the Australian community. A case was defined as any episode of cold or flu with at least one of the following symptoms: fever, chills, sore throat, running nose, or cough in the past 4 weeks. Frequency data were weighted to the Australian population. The response rate to the survey was 49%, and 19·9% (1505/7578) of respondents reported an ARI in the previous 4 weeks, which extrapolated to 68·9 million cases [95% confidence interval (CI) 65·1–72·7] of ARI in Australia annually. The incidence was 3·2 (95% CI 3·0–3·4) cases of ARI/person per year, and was highest in young children and lowest in older people. ARI imposes a significant burden on Australian society.

Pertussis or whooping cough has persisted and resurged in the face of vaccination and has become one of the most prevalent vaccine-preventable diseases in Western countries. The high circulation rate of Bordetella pertussis poses a threat to infants that have not been (completely) vaccinated and for whom pertussis is a severe, life-threatening, disease. The increase in pertussis is mainly found in age groups in which immunity has waned and this has resulted in the perception that waning immunity is the main or exclusive cause for the resurgence of pertussis. However, significant changes in B. pertussis populations have been observed after the introduction of vaccinations, suggesting a role for pathogen adaptation in the persistence and resurgence of pertussis. These changes include antigenic divergence with vaccine strains and increased production of pertussis toxin. Antigenic divergence will affect both memory recall and the efficacy of antibodies, while higher levels of pertussis toxin may increase suppression of the innate and acquired immune system. We propose these adaptations of B. pertussis have decreased the period in which pertussis vaccines are effective and thus enhanced the waning of immunity. We plead for a more integrated approach to the pertussis problem which includes the characteristics of the vaccines, the B. pertussis populations and the interaction between the two.

Isolates of Listeria monocytogenes (n = 932) isolated in Sweden during 1958–2010 from human patients with invasive listeriosis were characterized by serotyping and pulsed-field gel electrophoresis (PFGE) (AscI). Of the 932 isolates, 183 different PFGE types were identified, of which 83 were each represented by only one isolate. In all, 483 serovar 1/2a isolates were distributed over 114 PFGE types; 90 serovar 1/2b isolates gave 32 PFGE types; 21 serovar 1/2c isolates gave nine PFGE types; three serovar 3b isolates gave one PFGE type; and, 335 serovar 4b isolates gave 31 PFGE types. During the 1980s in Sweden, several serovar 4b cases were associated with the consumption of European raw soft cheese. However, as cheese-production hygiene has improved, the number of 4b cases has decreased. Since 1996, serovar 1/2a has been the dominant L. monocytogenes serovar in human listeriosis in Sweden. Therefore, based on current serovars and PFGE types, an association between human cases of listeriosis and the consumption of vacuum-packed gravad and cold-smoked salmon is suggested.

Crimean-Congo haemorrhagic fever (CCHF) is endemic in Turkey, and since 2004 many cases have been reported from different regions of Turkey. There are limited data about the seroprevalence of the disease in household members of patients or persons sharing the same environment. We evaluated seroprevalence of CCHF in the immediate neighbourhood and in household members of patients living in the same environment as confirmed cases of CCHF in an endemic area of Turkey. A total of 625 healthy subjects [mean (s.d.) age: 42·3 (18·4) years, 58·7% females] without a past history of CCHF infection included in this case-control, retrospective study were evaluated in terms of sociodemographic characteristics, risk factors for CCHF via a study questionnaire, while serum analysis for CCHF virus (CCHFV) IgG antibodies was performed by ELISA. Anti-CCHFV IgG antibodies were positive in 85 (13·6%) participants. None of the seropositive individuals had a history of symptomatic infection. Regression analysis revealed that animal husbandry [odds ratio (OR) 1·84, 95% confidence interval (CI) 1·09–3·11], contact with animals (OR 2·31, 95% CI 1·08–5·10), contact with ticks (OR 3·45, 95% CI 1·87–6·46), removing ticks from animals by hand (OR 2·48, 95% CI 1·48–4·18) and living in a rural area (OR 4·05, 95% CI 1·65–10·56) were associated with increased odds of having IgG seropositivity, while being a household member of a patient with prior CCHF infection had no influence on seropositivity rates. This result also supports the idea that CCHF is not transmitted person-to-person by the airborne route.

This paper summarizes influenza activity in the European Union/European Economic Area (EU/EEA) in 2012–2013. The influenza season 2012–2013 in Europe lasted from early December to late April. Overall the severity of the season could be described as moderate, based on the ILI/ARI consultation rates and the percentage of sentinel specimens positive for influenza compared to previous seasons. Both influenza A and B viruses circulating accounted for 47% and 53% of positive sentinel specimens, respectively, with both A(H1) and A(H3) varying for dominance. Compared to outpatients, the proportion of laboratory-confirmed influenza hospitalized cases infected by A(H1N1)pdm09 was significantly higher in middle-aged patients (33% vs. 17%, χ 2 = 66·6, P < 0·01). Despite a relatively good match between vaccine and circulating strains, vaccine effectiveness was estimated to be moderate.

This study examined the epidemiological and clinical characteristics of measles in Wenzhou, China. From 2000 to 2010, a total of 13271 measles cases were reported in Wenzhou, with epidemics occurring every 3-4 years. Forty-five per cent of the cases were aged <1 year and 27·2% were aged >14 years. Of 2262 hospitalized measles cases, 66·3% were diagnosed with pneumonia, and three cases died from respiratory failure. The number of measles cases of infants requiring hospitalization increased from birth to age 8 months and declined thereafter. Measurement of serum measles antibody levels in normal infants indicates that over 80% of infants in Wenzhou may be susceptible to measles by age 6 months. The existence of a sufficient pool of unvaccinated children and the decreased level of passively transferred measles antibodies in infants from vaccinated mothers contributed to the sustained transmission observed in Wenzhou.

We present a basic mathematical model of Staphylococcus aureus transmission in the USA based on natural history of infection and nationally representative data. We employed a Susceptible-Colonized-Infected-Recovered-Susceptible compartmental modelling framework with two different phenotypes of S. aureus: methicillin-susceptible (MSSA) and methicillin-resistant (MRSA). The model is dynamic and accounts for the US population growth. For model calibration/validation, we used published 1999–2005 S. aureus infection data in conjunction with the 2001–2004 National Health and Nutrition Examination Survey colonization data. Baseline model projections illustrated how MRSA might continue to expand and gradually replace MSSA over time, in the absence of intervention, if there is strong competition for colonization. The model-based estimate of the basic reproduction number (R0) highlights the need for infection control. We illustrate the potential population-level impact of intervention with a hypothetical S. aureus vaccination component.

We investigated the seasonality of tuberculosis (TB) in Wuhan, China, to evaluate the increased risk of disease transmission during each season and to develop an effective TB control strategy. We applied spectral analysis to the weekly prevalence data of sputum smear positive (SSP) and sputum smear negative (SSN) pulmonary TB reported from 2006 to 2010. Cases of both SSP and SSN feature 1·0- and 0·5-year periodic modes. The least squares method was used to fit curves to the two periodic modes for SSP and SSN data. The curves demonstrated dominant peaks in spring similar to cases reported previously for other locations. Notably for SSP, dominant peaks were also observed in summer. The spring peaks of SSP and SSN were explained in terms of poorly ventilated and humid rooms and vitamin D deficiency. For the summer peaks of SSP, summer influenza epidemics in Wuhan may contribute to the increase in TB prevalence.

Invasive meningococcal disease (IMD) reported to the Massachusetts Department of Public Health from 1988 to 2011 was reviewed. The average annual incidence of IMD/100 000 decreased from 1·57 [95% confidence interval (CI) 1·42–1·73] for 1988–1991 to 0·22 (95% CI 0·17–0·29) for 2008–2011. The pattern of decreasing incidence over time differed by age group. There was a decrease in IMD/100 000 in the 0–4 years age group after 1991 from 10·92 (95% CI 8·08–14·70) in 1991 to 5·76 (95% CI 3·78–8·72) in 1992. Incidence in the 0–4 years age group remained below 5/100 000 per year on average thereafter. A substantial reduction in incidence in all age groups was observed between 2000 and 2009, which began before the introduction of conjugate meningococcal vaccine in 2005. Marked reductions in incidence of IMD in Massachusetts, and elsewhere, deserve further investigation with respect to potential factors that go beyond the introduction and deployment of improved meningococcal vaccines.

The emergence of human and animal rabies in Bali since November 2008 has attracted local, national and international interest. The potential origin and time of introduction of rabies virus to Bali is described. The nucleoprotein (N) gene of rabies virus from dog brain and human clinical specimens was sequenced using an automated DNA sequencer. Phylogenetic inference with Bayesian Markov Chain Monte Carlo (MCMC) analysis using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) v. 1.7.5 software confirmed that the outbreak of rabies in Bali was caused by an Indonesian lineage virus following a single introduction. The ancestor of Bali viruses was the descendant of a virus from Kalimantan. Contact tracing showed that the event most likely occurred in early 2008. The introduction of rabies into a large unvaccinated dog population in Bali clearly demonstrates the risk of disease transmission for government agencies and should lead to an increased preparedness and efforts for sustained risk reduction to prevent such events from occurring in future.

Information is lacking in Canada on the frequency of exposures of healthy people to enteric pathogen sources (i.e. water, food, animal contact) at the community level. This information is critical to develop more robust risk assessments and prioritize control measures. A 12-month-long cross-sectional telephone survey of 1200 healthy individuals in a sentinel community was performed. Survey respondents were divided into three recall period groups (3, 7, 14 days). The occurrence of 46 exposures (including water, animal contact, environmental contact and high-risk foods) was assessed per recall period. Effect of age, gender, and season on exposures was modelled and frequencies of exposure were extrapolated. Thirty-five exposures had similar occurrences across recall periods. Age was significant for 23 exposures, season for 18, and gender for three. Exposures that vary by age and season (i.e. bottled water, swimming, etc.) warrant consideration when investigating and analysing cases of enteric illness.

In 2010, a marked increase in listeriosis incidence was observed in Finland. Listeria monocytogenes PFGE profile 96 was responsible for one-fifth of the reported cases and a cluster of PFGE profile 62 was also detected. Investigations revealed two fishery production plants with persistent Listeria contamination. It appears likely that the plants were at least partly responsible for the increase of listeriosis. Epidemiological investigation revealed that 57% (31/54) of cases with underlying immunosuppressive condition or medication reported eating gravad or cold-smoked fish. Two public notices were issued by THL and Evira informing which groups were most at risk from the effects of listeriosis and should therefore be cautious in consuming certain products. Systematic sampling of foods and adequate epidemiological investigation methods are required to identify the sources of Listeria infections. Continuous control measures at fishery production plants producing risk products are essential.

Although the compartmentalization of poultry industry components has substantial economic implications, and is therefore a concept with huge significance to poultry industries worldwide, the current requirements for compartment status are generic to all OIE member countries. We examined the consequences for potential outbreaks of highly pathogenic avian influenza in the British poultry industry using a metapopulation modelling framework. This framework was used to assess the effectiveness of compartmentalization relative to zoning control, utilizing empirical data to inform the structure of potential epidemiological contacts within the British poultry industry via network links and spatial proximity. Conditions were identified where, despite the efficient isolation of poultry compartments through the removal of network-mediated links, spatially mediated airborne spread enabled spillover of infection with nearby premises making compartmentalization a more ‘risky’ option than zoning control. However, when zoning control did not effectively inhibit long-distance network links, compartmentalization became a relatively more effective control measure than zoning. With better knowledge of likely distance ranges for airborne spread, our approach could help define an appropriate minimum inter-farm distance to provide more specific guidelines for compartmentalization in Great Britain.

We investigated whether straight-line distance from residential compounds to healthcare facilities influenced mortality, the incidence of pneumonia and vaccine efficacy against pneumonia in rural Gambia. Clinical surveillance for pneumonia was conducted on 6938 children living in the catchment areas of the two largest healthcare facilities. Deaths were monitored by three-monthly home visits. Children living >5 km from the two largest healthcare facilities had a 2·78 [95% confidence interval (CI) 1·74–4·43] times higher risk of all-cause mortality compared to children living within 2 km of these facilities. The observed rate of clinical and radiological pneumonia was lower in children living >5 km from these facilities compared to those living within 2 km [rate ratios 0·65 (95% CI 0·57–0·73) and 0·74 (95% CI 0·55–0·98), respectively]. There was no association between distance and estimated pneumococcal vaccine efficacy. Geographical access to healthcare services is an important determinant of survival and pneumonia in children in rural Gambia.