The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

Abstract

Whole 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 highperformance 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 . CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/381830 doi: bioRxiv preprint first posted online Jul. 31, 2018; 3 "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 bett...

Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype

“…NextSeq has previously been used successfully for WGS of Salmonella 4,[5],12:i:- isolates [ 36 ]. Whole genome sequencing was therefore performed by 150 bp paired-end read sequencing on the Illumina NextSeq platform using NextSeq 500/550 Mid Output kits and sequence reads were deposited in the appropriate IRIDA Platform Beta Release databases (ngs-archive.corefacility.ca/irida) [ 37 ].…”

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

“…Nextera XT libraries were sequenced on a MiSeq system (Illumina) using 2×300 bp paired-end reads. A minimum raw sequence coverage of 40× based on an estimated genome size of 5 Mb was calculated using the Integrated Rapid Infectious Analysis (IRIDA) platform [40]. Sequence quality was assessed using BioNumerics v7.6.2 with the following parameters: AvgQuality ≥30, N50 ≥100 000, NrContigs <200, length 4.5 to 5.5 Mb, NrConsensus (congruent allele calls by assembly-based and assembly-free algorithms) >3800, NrDifferent 0 (alleles with no overlap between assembly-based and assembly-free algorithms), core per cent ≥90 %.…”

Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens

“…Demand grew for older resources such as BioNumerics (Applied Maths, Sint-Martens-Latem, Belgium), used by the PulseNet community [ 21 ], to allow users to submit their WGS data to NCBI, as well as the capability to download NCBI data into BioNumerics to perform local, customized analyses. As a result of building interoperable systems, researchers can now use public data from the INSDC in conjunction with private data from individual or industry labs, using platforms such as Integrated Rapid Infectious Disease Analysis (IRIDA) [ 22 ], INNUENDO [ 23 ], PathogenWatch [ 24 ] NextStrain [ 13 ], IDseq [ 25 ], and CGE Evergreen [ 26 ]. And finally, for FDA-specific missions, open source tools to support genomic epidemiology (GalaxyTrakr) [ 27 ], AMR surveillance (Resistome Tracker) [ 28 ], and risk assessment (GenomeGraphR) [ 29 ] have been created.…”