Clinical Pathoscope: Rapid Alignment and Filtration for Accurate Pathogen Identification in Clinical Samples Using Unassembled Sequencing Data

• Activity Number: 611
• Type: Contributed
• Date/Time: Thursday, August 7, 2014 : 8:30 AM to 10:20 AM
• Sponsor: Section on Medical Devices and Diagnostics
• Author(s): Joseph Perez-Rogers*+ and Allyson Byrd and W. Evan Johnson
• Companies: Boston University and Boston University and Boston University School of Medicine
• Keywords: Sequencing ; Diagnostic ; Pathogen ; Pipeline ; Clinical ; Microbiome

Abstract

The use of sequencing technologies to investigate the microbiome of a sample can positively impact patient healthcare by providing therapeutic targets for personalized disease treatment. However, these samples contain genomic sequences from various sources that complicate the identification of pathogens. Here we present Clinical PathoScope, a pipeline to rapidly and accurately remove host contamination, isolate microbial reads, and identify potential disease-causing pathogens. Our optimized framework employs a computational subtraction methodology in concordance with read trimming and ambiguous read reassignment. Using real clinical sequencing data, we have demonstrated the ability of our approach to identify multiple pathogens in a single clinical sample, accurately identify pathogens at the subspecies level, and determine the nearest phylogenetic neighbor of novel or highly mutated pathogens. Clinical PathoScope is the only pathogen identification method currently available that can identify multiple pathogens from mixed samples and distinguish between very closely related species with very little coverage of the genome.