Towards a genomics-informed, real-time, global pathogen surveillance system.
Ontology highlight
ABSTRACT:
SUBMITTER: Gardy JL
PROVIDER: S-EPMC7097748 | biostudies-literature | 2018 Jan
REPOSITORIES: biostudies-literature
Publications
Towards a genomics-informed, real-time, global pathogen surveillance system.
Gardy Jennifer L JL Loman Nicholas J NJ
Nature reviews. Genetics 20171113 1
The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance ...[more]
Similar Datasets
Project description:It is time to shake up public health surveillance. New technologies for sequencing, aided by friction-free approaches to data sharing, could have an impact on public health efforts.
| S-EPMC4531805 | biostudies-literature
Project description:The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics.
| S-EPMC7906676 | biostudies-literature
Project description:The need for global data about the scale of antibiotic resistance (ABR) in a geographical explicit and timely manner has been identified by many stakeholders, including the World Health Organization. This primer should help defining the objectives, scale, scope, and structure of possible future efforts. Stakeholders and their expected information demands were identified to generate an inventory of surveillance objectives. For simplification, an original approach was chosen to bundle sets of objectives that represent common demands and can be addressed by common subject areas, which fall into three areas. Subject area I addresses clinical demands and focuses on patients; subject area II addresses public health demands by focusing on meta-populations; subject area III addresses infection control demands and focuses on pathogens. A division into these areas leads to a separation of surveillance activities suggesting a modular approach which can provide complementary information. Moreover, the modules address the conundrum of ABR at the complementary levels of 1) patient, 2) population, and 3) pathogen, which-rather conventionally-follow the operational and professional fault-lines of the main disciplines involved, namely clinical medicine, public health, and biology. Essential features that define different surveillance systems have been listed and taken into consideration when suggesting templates for future efforts. Putting ABR on the global health map is a daunting task as it requires acceptance, agreements, and engagement but also concessions at many different levels. Given the existing gaps in the global diagnostic service landscape only a step-wise approach which defines achievable aims, objectives, and milestones will succeed to produce a sustainable system of international co-operative surveillance of ABR.
| S-EPMC4034565 | biostudies-literature
Project description:Lack of disease surveillance in small companion animals worldwide has contributed to a deficit in our ability to detect and respond to outbreaks. In this paper we describe the first real-time syndromic surveillance system that conducts integrated spatio-temporal analysis of data from a national network of veterinary premises for the early detection of disease outbreaks in small animals. We illustrate the system's performance using data relating to gastrointestinal disease in dogs and cats. The data consist of approximately one million electronic health records for dogs and cats, collected from 458 UK veterinary premises between March 2014 and 2016. For this illustration, the system predicts the relative reporting rate of gastrointestinal disease amongst all presentations, and updates its predictions as new data accrue. The system was able to detect simulated outbreaks of varying spatial geometry, extent and severity. The system is flexible: it generates outcomes that are easily interpretable; the user can set their own outbreak detection thresholds. The system provides the foundation for prompt detection and control of health threats in companion animals.
| S-EPMC6882870 | biostudies-literature
Project description:BACKGROUND:Injury data and reports provide valuable information for both public and private organizations to guide programming, policy, and prevention, but in the increasingly complex and dangerous industry of US agriculture, the injury surveillance needed to produce this data is lacking. To address the gap, AgInjuryNews was established in 2015. The system includes fatal and nonfatal injury cases derived from publicly available reports, including occupational and nonoccupational injuries, occurring in the agricultural, forestry, and fishing (AFF) industry. OBJECTIVE:The study aimed to develop a stakeholder-engaged redesign of the interactive, up-to-date, and publicly available dataset of US AFF injury and fatality reports. METHODS:Instructor-led heuristic evaluations within a 15-student undergraduate course, data from 8 student participants of laboratory-based usability testing and 2016 and 2017 AgInjuryNews-registered user surveys, coupled with input from the National Steering Committee informed the development priorities for 2018. An interdisciplinary team employed an agile methodology of 2-week sprints developing in ASP.NET and Structured Query Language to deliver an intuitive frontend and a flexible, yet structured, backend, including a case report input form for capturing more than 50 data points on each injury report. RESULTS:AgInjuryNews produced 17,714 page views from 43 countries in 2018 captured via Google Analytics, whereas 623 injury reports were coded and loaded, totaling more than 31,000 data points. Newly designed features include customizable email alerts, an interactive map, and expanded search and filter options. User groups such as the Bureau of Labor Statistics and the Agricultural Safety and Health Council of America have endorsed the system within their networks. News media have cited or referenced the system in national outlets such as the New York Times, Politico, and the Washington Post. CONCLUSIONS:The new system's features, functions, and improved data granularity have sparked innovative lines of research and increased collaborative interest domestically and abroad. It is anticipated that this nontraditional sentinel surveillance system and its dataset will continue to serve many purposes for public and private agricultural safety and health stakeholders in the years to come.?.
| S-EPMC6696853 | biostudies-literature
Project description:We propose a simple real-time index of global human-induced warming and assess its robustness to uncertainties in climate forcing and short-term climate fluctuations. This index provides improved scientific context for temperature stabilisation targets and has the potential to decrease the volatility of climate policy. We quantify uncertainties arising from temperature observations, climate radiative forcings, internal variability and the model response. Our index and the associated rate of human-induced warming is compatible with a range of other more sophisticated methods to estimate the human contribution to observed global temperature change.
| S-EPMC5684339 | biostudies-literature
Project description:BackgroundUnderstanding nosocomial acquisition, outbreaks, and transmission chains in real time will be fundamental to ensuring infection-prevention measures are effective in controlling coronavirus disease 2019 (COVID-19) in healthcare. We report the design and implementation of a hospital-onset COVID-19 infection (HOCI) surveillance system for an acute healthcare setting to target prevention interventions.MethodsThe study took place in a large teaching hospital group in London, United Kingdom. All patients tested for SARS-CoV-2 between 4 March and 14 April 2020 were included. Utilizing data routinely collected through electronic healthcare systems we developed a novel surveillance system for determining and reporting HOCI incidence and providing real-time network analysis. We provided daily reports on incidence and trends over time to support HOCI investigation and generated geotemporal reports using network analysis to interrogate admission pathways for common epidemiological links to infer transmission chains. By working with stakeholders the reports were co-designed for end users.ResultsReal-time surveillance reports revealed changing rates of HOCI throughout the course of the COVID-19 epidemic, key wards fueling probable transmission events, HOCIs overrepresented in particular specialties managing high-risk patients, the importance of integrating analysis of individual prior pathways, and the value of co-design in producing data visualization. Our surveillance system can effectively support national surveillance.ConclusionsThrough early analysis of the novel surveillance system we have provided a description of HOCI rates and trends over time using real-time shifting denominator data. We demonstrate the importance of including the analysis of patient pathways and networks in characterizing risk of transmission and targeting infection-control interventions.
| S-EPMC7454383 | biostudies-literature
Project description:The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
| S-EPMC4817224 | biostudies-literature
Project description:Fast, minimally invasive, high-resolution intravascular imaging is essential for identifying vascular pathological features and for developing novel diagnostic tools and treatments. Intravascular magnetic resonance imaging (MRI) with active internal probes offers high sensitivity to pathological features without ionizing radiation or the limited luminal views of conventional X-rays, but has been unable to provide a high-speed, high-resolution, endoscopic view. Herein, real-time MRI endoscopy is introduced for performing MRI from a viewpoint intrinsically locked to a miniature active, internal transmitter-receiver in a clinical 3.0-T MRI scanner. Real-time MRI endoscopy at up to 2 frames/s depicts vascular wall morphological features, atherosclerosis, and calcification at 80 to 300 ?m resolution during probe advancement through diseased human iliac artery specimens and atherosclerotic rabbit aortas in vivo. MRI endoscopy offers the potential for fast, minimally invasive, transluminal, high-resolution imaging of vascular disease on a common clinical platform suitable for evaluating and targeting atherosclerosis in both experimental and clinical settings.
| S-EPMC3064492 | biostudies-literature
Project description:This work presents the first simulation of a large-scale, bio-physically constrained cerebellum model performed on neuromorphic hardware. A model containing 97,000 neurons and 4.2 million synapses is simulated on the SpiNNaker neuromorphic system. Results are validated against a baseline simulation of the same model executed with NEST, a popular spiking neural network simulator using generic computational resources and double precision floating point arithmetic. Individual cell and network-level spiking activity is validated in terms of average spike rates, relative lead or lag of spike times, and membrane potential dynamics of individual neurons, and SpiNNaker is shown to produce results in agreement with NEST. Once validated, the model is used to investigate how to accelerate the simulation speed of the network on the SpiNNaker system, with the future goal of creating a real-time neuromorphic cerebellum. Through detailed communication profiling, peak network activity is identified as one of the main challenges for simulation speed-up. Propagation of spiking activity through the network is measured, and will inform the future development of accelerated execution strategies for cerebellum models on neuromorphic hardware. The large ratio of granule cells to other cell types in the model results in high levels of activity converging onto few cells, with those cells having relatively larger time costs associated with the processing of communication. Organizing cells on SpiNNaker in accordance with their spatial position is shown to reduce the peak communication load by 41%. It is hoped that these insights, together with alternative parallelization strategies, will pave the way for real-time execution of large-scale, bio-physically constrained cerebellum models on SpiNNaker. This in turn will enable exploration of cerebellum-inspired controllers for neurorobotic applications, and execution of extended duration simulations over timescales that would currently be prohibitive using conventional computational platforms.
| S-EPMC8202688 | biostudies-literature