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Diagnostics Technology and innovation, Microbiology and immunology, Clinical care, Genetics and epigenetics, Omics

Diagnosis Ex Machina

At a Glance

  • Infectious diseases are one of the world’s biggest killers, but doctors still lack rapid, conclusive ways of identifying pathogens 
  • Current methods may be time- consuming, inconclusive, have limited scope, or require equipment and skills not available in all settings 
  • A new type of software, Taxonomer, may be able to speed up clinical diagnostics by examining pathogens’ genetic material 
  • Unbiased pathogen detection combined with fast, accurate, and easy-to-use data analysis will, in the future, provide rapid answers to the question, “What’s wrong with my patient?” 

When faced with an unidentified infection, doctors typically pursue two approaches – they apply treatment (for instance, a broad- spectrum antibiotic) based on the suspected cause of disease, or they can proceed with diagnostic testing to determine the cause of the infection, and therefore the best treatment. Both approaches have limitations. The former might result in inadequate treatment and risks prescribing antibiotics where none are needed. The latter is often time-consuming, delaying the patient’s treatment, and may provide inconclusive results, hampering decisive action. This lack of good options becomes even more unconscionable when one considers the high morbidity and mortality from infectious diseases, especially in the elderly, young children, the seriously ill, and in resource-limited settings. My colleagues and I felt it was clear that a better solution was needed – so to tackle the problem, we developed methods that use next- generation DNA sequencing for the rapid, unbiased detection of all known pathogens. These efforts led to the development of Taxonomer (1,2), an ultra-fast NGS data analysis software package that can identify pathogens from millions of DNA sequences within minutes.

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About the Author

Robert Schlaberg

Robert Schlaberg is Medical Director of the Microbial Amplified Detection, Virology and Fecal Chemistry Laboratories and Assistant Medical Director of the Virology and Molecular Infectious Disease Laboratories at ARUP Laboratories, Salt Lake City, USA. He is also an Assistant Professor of Pathology at the University of Utah School of Medicine and a co-founder of IDbyDNA Inc.

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