The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

AbstractWhole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine public health microbiology laboratories is impeded by a lack of user-friendly automated and semi-automated pipelines, restrictive jurisdictional data sharing policies, and the proliferation of non-interoperable analytical and reporting systems. To address these issues, we developed the Integrated Rapid Infectious Disease Analysis (IRIDA) platform (irida.ca), a user-friendly, decentralized, open-source bioinformatics and analytical web platform to support real-time infectious disease outbreak investigations using WGS data. Instances can be independently installed on local high-performance computing infrastructure, enabling private and secure data management and analyses according to organizational policies and governance. IRIDA’s data management capabilities enable secure upload, storage and sharing of all WGS data and metadata. The core platform currently includes pipelines for quality control, assembly, annotation, variant detection, phylogenetic analysis, in silico serotyping, multi-locus sequence typing, and genome distance calculation. Analysis pipeline results can be visualized within the platform through dynamic line lists and integrated phylogenomic clustering for research and discovery, and for enhancing decision-making support and hypothesis generation in epidemiological investigations. Communication and data exchange between instances are provided through customizable access controls. IRIDA complements centralized systems, empowering local analytics and visualizations for genomics-based microbial pathogen investigations. IRIDA is currently transforming the Canadian public health ecosystem and is freely available at https://github.com/phac-nml/irida and www.irida.ca.Impact StatementWhole genome sequencing (WGS) is revolutionizing infectious disease analysis and surveillance due to its cost effectiveness, utility, and improved analytical power. To date, no “one-size-fits-all” genomics platform has been universally adopted, owing to differences in national (and regional) health information systems, data sharing policies, computational infrastructures, lack of interoperability and prohibitive costs. The Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, decentralized, open-source bioinformatics and analytical web platform developed to support real-time infectious disease outbreak investigations using WGS data. IRIDA empowers public health, regulatory and clinical microbiology laboratory personnel to better incorporate WGS technology into routine operations by shielding them from the computational and analytical complexities of big data genomics. IRIDA is now routinely used as part of a validated suite of tools to support outbreak investigations in Canada. While IRIDA was designed to serve the needs of the Canadian public health system, it is generally applicable to any public health and multi-jurisdictional environment. IRIDA enables localized analyses but provides mechanisms and standard outputs to enable data sharing. This approach can help overcome pervasive challenges in real-time global infectious disease surveillance, investigation and control, resulting in faster responses, and ultimately, better public health outcomes.DATA SUMMARYData used to generate some of the figures in this manuscript can be found in the NCBI BioProject PRJNA305824.

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The use of hospital emergency department chief complaint data as a "Near" real-time marker for assessing public health risk of infectious disease outbreak

Journal of Urban Health ◽

10.1007/bf02416905 ◽

2003 ◽

Vol 80 (S1) ◽

pp. i121-i121 ◽

Cited By ~ 1

Author(s):

Ronald J. Shannon ◽

Michael Davisson ◽

Trang Nguyen ◽

Carolyn Stetson ◽

Kevin Jones

Keyword(s):

Public Health ◽

Infectious Disease ◽

Emergency Department ◽

Health Risk ◽

Disease Outbreak ◽

Chief Complaint ◽

Hospital Emergency Department ◽

Hospital Emergency ◽

Infectious Disease Outbreak ◽

Time Marker

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Examination of Hospital Workers’ Emotional Responses to an Infectious Disease Outbreak: Lessons From the 2015 MERS Co-V Outbreak in South Korea

Disaster Medicine and Public Health Preparedness ◽

10.1017/dmp.2018.95 ◽

2018 ◽

Vol 13 (03) ◽

pp. 504-510 ◽

Cited By ~ 8

Author(s):

Heejung Son ◽

Wang Jun Lee ◽

Hyun Soo Kim ◽

Kkot Sil Lee ◽

Myoungsoon You

Keyword(s):

Public Health ◽

Infectious Disease ◽

South Korea ◽

Disease Transmission ◽

Negative Emotions ◽

Emotional Responses ◽

Disease Outbreaks ◽

Disease Outbreak ◽

Hospital Workers ◽

Infectious Disease Outbreak

ABSTRACTHospital workers are critical for a successful response to an infectious disease outbreak and for preventing disease transmission to the community. Therefore, hospital crisis management should implement efforts to improve hospital workers’ preparedness in responding to public health emergencies caused by infectious diseases. Traditionally, preparedness and skill of hospital workers have been emphasized, but awareness of the importance of the emotional mindset of hospital workers in dealing with disease outbreaks has only recently increased; therefore, empirical approaches to examining emotional responses of hospital workers has been limited. This study analyzed qualitative data of the 2015 Middle East Respiratory Syndrome outbreak in South Korea. In particular, negative emotions and stress experienced by hospital workers who treated patients were characterized, as were the events that triggered such experiences. These events were categorized into four themes (eg,Mistake, Missing, Delay Due to Communication Failure). Identifying events that trigger negative emotions in hospital workers has important implications for hospitals’ management guidance in relation to an infectious disease outbreak. (Disaster Med Public Health Preparedness.2019;13:504-510)

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Detecting Emerging Infectious Diseases: An Overview of the Laboratory Response Network for Biological Threats

Public Health Reports ◽

10.1177/0033354919874354 ◽

2019 ◽

Vol 134 (2_suppl) ◽

pp. 16S-21S ◽

Cited By ~ 3

Author(s):

Julie Villanueva ◽

Beth Schweitzer ◽

Marcella Odle ◽

Tricia Aden

Keyword(s):

Public Health ◽

Infectious Disease ◽

Infectious Diseases ◽

Emerging Infectious Diseases ◽

Data Entry ◽

Disease Outbreak ◽

Infectious Disease Outbreak ◽

Public Health Emergencies ◽

Response Network ◽

Biosecurity Practices

The Laboratory Response Network (LRN) was established in 1999 to ensure an effective laboratory response to high-priority public health threats. The LRN for biological threats (LRN-B) provides a laboratory infrastructure to respond to emerging infectious diseases. Since 2012, the LRN-B has been involved in 3 emerging infectious disease outbreak responses. We evaluated the LRN-B role in these responses and identified areas for improvement. LRN-B laboratories tested 1097 specimens during the 2014 Middle East Respiratory Syndrome Coronavirus outbreak, 180 specimens during the 2014-2015 Ebola outbreak, and 92 686 specimens during the 2016-2017 Zika virus outbreak. During the 2014-2015 Ebola outbreak, the LRN-B uncovered important gaps in biosafety and biosecurity practices. During the 2016-2017 Zika outbreak, the LRN-B identified the data entry bottleneck as a hindrance to timely reporting of results. Addressing areas for improvement may help LRN-B reference laboratories improve the response to future public health emergencies.

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Real-time Estimation of Epidemiologic Parameters from Contact Tracing Data During an Emerging Infectious Disease Outbreak

Epidemiology ◽

10.1097/ede.0000000000000776 ◽

2018 ◽

Vol 29 (2) ◽

pp. 230-236 ◽

Cited By ~ 5

Author(s):

Loes Soetens ◽

Don Klinkenberg ◽

Corien Swaan ◽

Susan Hahné ◽

Jacco Wallinga

Keyword(s):

Infectious Disease ◽

Real Time ◽

Time Estimation ◽

Disease Outbreak ◽

Emerging Infectious Disease ◽

Contact Tracing ◽

Infectious Disease Outbreak ◽

Real Time Estimation

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An approach to and web-based tool for infectious disease outbreak intervention analysis

Scientific Reports ◽

10.1038/srep46076 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 7

Author(s):

Ashlynn R. Daughton ◽

Nicholas Generous ◽

Reid Priedhorsky ◽

Alina Deshpande

Keyword(s):

Public Health ◽

Infectious Disease ◽

Infectious Diseases ◽

Disease Outbreak ◽

Control Measures ◽

Infectious Disease Outbreak ◽

Web Based ◽

The Public ◽

Health Community ◽

Parameter Ranges

Abstract Infectious diseases are a leading cause of death globally. Decisions surrounding how to control an infectious disease outbreak currently rely on a subjective process involving surveillance and expert opinion. However, there are many situations where neither may be available. Modeling can fill gaps in the decision making process by using available data to provide quantitative estimates of outbreak trajectories. Effective reduction of the spread of infectious diseases can be achieved through collaboration between the modeling community and public health policy community. However, such collaboration is rare, resulting in a lack of models that meet the needs of the public health community. Here we show a Susceptible-Infectious-Recovered (SIR) model modified to include control measures that allows parameter ranges, rather than parameter point estimates, and includes a web user interface for broad adoption. We apply the model to three diseases, measles, norovirus and influenza, to show the feasibility of its use and describe a research agenda to further promote interactions between decision makers and the modeling community.

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