Background: We are transforming the field of infectious disease diagnostics with the development of the Sample Prep for Infectious Disease Recognition With EDGE Bioinformatics (SPIDR-WEB). SPIDR-WEB is a sample-to-result biotechnology platform that enables efficient use of next generation sequencing (NGS) for pathogen detection in clinical samples. NGS has become a powerful tool for detection and characterization of both known and emerging pathogens. The main advantage of NGS is its non-biased approach that identifies all organisms in a sample. This is in contrast to traditional molecular assays that force us to look for a set of specific pathogens. In most clinical samples, the relative abundance of pathogen nucleic acids (DNA or RNA) is vanishingly small. Therefore, vast amounts of sequence data must be generated and analyzed to identify rare pathogen sequences. SPIDR-WEB is a sample-to-result process that relies on efficient laboratory and in silico steps.
Methods & Materials: Clinical samples mostly comprise non-informative host RNAs or abundant housekeeping gene transcripts. SPIDR-WEB incorporates removal of non-informative RNAs (RNR), thereby enriching all other RNAs, including those from pathogens. This step enables either higher sensitivity and specificity, or less expensive and faster sequencing. Our custom EDGE bioinformatics data analysis platform provides rapid read classification at all taxonomic levels, and reliably detects all organisms present in a sample. EDGE is an efficient process, as it uses databases with pre-computed signatures, instead of aligning sequencing reads to the entire Genbank. In addition to RNR and EDGE, SPIDR-WEB includes robust, inexpensive and rapid sample lysis, RNA extraction, and library preparation steps.
Results: We will describe SPIDR-WEB technology and show clinically-relevant results obtained from human blood, stool, respiratory, and other sample types.
Conclusion: We are implementing SPIDR-WEB in both research and clinical settings to support a multitude of applications, such as discovery of novel mechanisms and biomarkers, study host-pathogen interactions, improve vaccines and therapeutics, and complement current diagnostic tools and help improve their utility.
© 2016 Published by Elsevier Inc.