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The advent of high throughput human DNA sequencing capability has allowed a crossover for sequencing infectious diseases. The same technologies that allow us to query the human genome for cancer mutations, pharmacogenomics, and inherited genetic errors now allow a more in-depth analysis of human samples for evidence of infectious disease. Next Generation DNA sequencing (NGS) for infectious disease holds the promise of accuracy with greater sensitivity and specificity than culture, serologic and PCR methods. NGS allows for better discrimination between strains, species, detection of novel variants and new organisms, detection of an ever-growing array of uncultivable organisms, and the ability to detect eukaryotes that were previously undetectable. NGS also may soon provide the ability to determine drug resistance and sensitivity information. The following describes the Rapid Infectious Disease Identification System (RIDI™) and its practical use. Application of the RIDI™ system is discussed in four case reports with patients suffering from chronic malaise, rheumatoid arthritis, osteoarthritis, and chronic fatigue syndrome.
Keywords: next-generation sequencing for infectious disease, RIDI™, chronic fatigue syndrome, osteoarthritis, rheumatoid arthritis, Funneliformis mosseae, Saccharomyces cerevisiae, Toxoplasma gondii
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