Epidemics and emerging infectious diseases are becoming an increasing threat to global populations - challenging public health practitioners, decision makers and researchers to plan, prepare, identify and respond to outbreaks in near real-timeframes. The aim of this research is to evaluate the range of public domain and freely available software epidemic modelling tools. Twenty freely utilizable software tools underwent assessment of software usability, utility and key functionalities. Stochastic and agent based tools were found to be highly flexible, adaptable, had high utility and many features, but low usability. Deterministic tools were highly usable with average to good levels of utility.

Public health messaging about antimicrobial resistance (AMR) sometimes conveys the problem as an epidemic. We outline why AMR is a serious endemic problem manifested in hospital and community-acquired infections.

AMR is not an epidemic condition, but may complicate epidemics, which are characterized by sudden societal impact due to rapid rise in cases over a short timescale. Influenza, which causes direct viral effects, or secondary bacterial complications is the most likely cause of an epidemic or pandemic where AMR may be a problem. We discuss other possible causes of a pandemic with AMR, and present a risk assessment formula to estimate the impact of AMR during a pandemic. Finally, we flag the potential impact of genetic engineering of pathogens on global risk and how this could radically change the epidemiology of AMR as we know it.

Understanding the epidemiology of AMR is key to successfully addressing the problem. AMR is an endemic condition but can play a role in epidemics or pandemics, and we present a risk analysis method for assessing the impact of AMR in a pandemic.

Background: Zoonotic avian influenza poses a major risk to China, and other parts of the world. H5N1 has remained endemic in China and globally for nearly two decades, and in 2013, a novel zoonotic influenza A subtype H7N9 emerged in China. This study aimed to improve upon our current understanding of the spreading mechanisms of H7N9 and H5N1 by generating spatial risk profiles for each of the two virus subtypes across mainland China.

Methods and Findings: In this study, we (i) developed a refined data set of H5N1 and H7N9 locations with consideration of animal/animal environment case data, as well as spatial accuracy and precision; (ii) used this data set along with environmental variables to build species distribution models (SDMs) for each virus subtype in high resolution spatial units of 1km² cells using Maxent; (iii) developed a risk modelling framework which integrated the results from the SDMs with human and chicken population variables, which was done to quantify the risk of zoonotic transmission; and (iv) identified areas at high risk of H5N1 and H7N9 transmission. We produced high performing SDMs (6 of 8 models with AUC > 0.9) for both H5N1 and H7N9. In all our SDMs, H7N9 consistently showed higher AUC results compared to H5N1, suggesting H7N9 suitability could be better explained by environmental variables. For both subtypes, high risk areas were primarily located in south-eastern China, with H5N1 distributions found to be more diffuse and extending more inland compared to H7N9.

Conclusions: We provide projections of our risk models to public health policy makers so that specific high risk areas can be targeted for control measures. We recommend comparing H5N1 and H7N9 prevalence rates and survivability in the natural environment to better understand the role of animal and environmental transmission in human infections.

The 2014 Ebola virus disease (EVD) outbreak affected several countries worldwide, including six West African countries. It was the largest Ebola epidemic in the history and the first to affect multiple countries simultaneously. Significant national and international delay in response to the epidemic resulted in 28,652 cases and 11,325 deaths. The aim of this study was to develop a risk analysis framework to prioritize rapid response for situations of high risk. Based on findings from the literature, sociodemographic features of the affected countries, and documented epidemic data, a risk scoring framework using 18 criteria was developed. The framework includes measures of socioeconomics, health systems, geographical factors, cultural beliefs, and traditional practices. The three worst affected West African countries (Guinea, Sierra Leone, and Liberia) had the highest risk scores. The scores were much lower in developed countries that experienced Ebola compared to West African countries. A more complex risk analysis framework using 18 measures was compared with a simpler one with 10 measures, and both predicted risk equally well. A simple risk scoring system can incorporate measures of hazard and impact that may otherwise be neglected in prioritizing outbreak response. This framework can be used by public health personnel as a tool to prioritize outbreak investigation and flag outbreaks with potentially catastrophic outcomes for urgent response. Such a tool could mitigate costly delays in epidemic response.

Background: Bacterial colonization of the respiratory tract is commonly described and usually thought to be of no clinical significance. The aim of this study was to examine the presence and significance of bacteria and viruses in the upper respiratory tract of healthcare workers (HCWs), and association with respiratory symptoms.

Methods: A prospective cohort study was conducted in China and 223 HCWs were recruited from fever clinics and respiratory, paediatric, emergency/Intensive medication wards. Participants were followed over 4 weeks (7th May 2015 to 4th June 2015) for development of clinical respiratory illness (CRI). Nasopharyngeal swabs were obtained at baseline and at the end of the study. The primary endpoints were laboratory-confirmed bacterial colonization and viral respiratory infection. Rates of the following infections in symptomatic and asymptomatic participants were compared at the start or end of the study; 1) all bacterial/viral infections, 2) bacterial infection and bacterial-viral co-infections, excluding virus only infections, and 3) only bacterial infections.

Results: Bacterial colonization was identified in 88% (196/223) of participants at the start or end of the study. Among these participants, 66% (148/223) had only bacterial colonization while 22% (48/223) had co-infection with a virus. Bacteria were isolated from 170 (76.2%) participants at baseline and 127 (57%) participants at the end of the study. Laboratory confirmed viral infections were identified in 53 (23.8%) participants - 35 (15.7%) at the baseline and 20 (9.0%) at the end of the study. CRI symptoms were recorded in 12 participants (4.5%) and all had a positive bacterium isolation at baseline (n = 11) or end of the study (n = 1). Among asymptomatic participants, 187 (87%) had bacterial colonization or bacterial/viral co-infection at baseline or end of the study. Viruses were also isolated from 5 (2.4%) asymptomatic cases. Rates of all infection outcomes were higher in symptomatic participants, however differences were not statistically significant.

Conclusion: We isolated high rates of bacteria and viruses in the upper respiratory tract of hospital HCWs, which may reflect greater exposure to respiratory infections in the hospital. Although respiratory infections are mostly symptomatic, the association between bacterial colonization and symptomatic illness is not clear. In the healthcare setting, HCWs may acquire and transmit infection to patients and other HCWs around them. Larger studies are required to explore ongoing occupational risk of respiratory infection in hospitals HCWs.

Rationale: Medical masks are commonly used by sick individuals with influenza-like illness (ILI) to prevent spread of infections to others, but clinical efficacy data are absent.

Objective: Determine whether medical mask use by sick individuals with ILI protects well contacts from related respiratory infections.

Setting: 6 major hospitals in 2 districts of Beijing, China.

Design: Cluster randomised controlled trial.

Participants: 245 index cases with ILI.

Intervention: Index cases with ILI were randomly allocated to medical mask (n=123) and control arms (n=122). Since 43 index cases in the control arm also used a mask during the study period, an as-treated post hoc analysis was performed by comparing outcomes among household members of index cases who used a mask (mask group) with household members of index cases who did not use a mask (no-mask group).

Main Outcome Measure: Primary outcomes measured in household members were clinical respiratory illness, ILI and laboratory-confirmed viral respiratory infection.

Results: In an intention-to-treat analysis, rates of clinical respiratory illness (relative risk (RR) 0.61, 95% CI 0.18 to 2.13), ILI (RR 0.32, 95% CI 0.03 to 3.13) and laboratory-confirmed viral infections (RR 0.97, 95% CI 0.06 to 15.54) were consistently lower in the mask arm compared with control, although not statistically significant. A post hoc comparison between the mask versus no-mask groups showed a protective effect against clinical respiratory illness, but not against ILI and laboratory-confirmed viral respiratory infections.

Conclusions: The study indicates a potential benefit of medical masks for source control, but is limited by small sample size and low secondary attack rates. Larger trials are needed to confirm efficacy of medical masks as source control.