Explify Respiratory Pathogens by Next-generation Sequencing

Each year, more than one million patients in the United States alone are admitted to the hospital and treated for pneumonia and related symptoms.

Respiratory Infections by Next-generation Sequencing

The laboratory work-up for pneumonia involves multiple tests, including cultures, microscopy, EIA, and PCR, the results of which may not be available for days or weeks. Current testing methods are limited to specific pathogens and can return negative results in up to 60 percent of pneumonia cases.

ARUP co-developed Explify Respiratory in collaboration with IDbyDNA, www.idbydna.com, as a new tool for diagnosing pneumonia that combines the latest genome science with cutting-edge computer search technologies to bring precision medicine to infectious disease.

Features

  • Detects more than 200 common, rare, and novel bacterial, viral, and fungal pathogens in respiratory specimens.
  • Includes detailed, user-friendly enhanced report to help guide therapeutic decisions.

Benefits

  • Identify pathogens PCR and culture can miss.
  • Enables hypothesis-free diagnosis.
  • Provides a new option for very ill patients, or patients with suspicion of infection, who resulted negative with traditional tests like culture and PCR.

Test Information

Test Number Test Name

2013694

Explify Respiratory Pathogens by Next Generation Sequencing
Collect Bronchoalveolar lavage (BAL)
Specimen Preparation
  • Specimen source required
  • Transfer 2 mL to a sterile container. (Min: 1.2 mL)
  • Place each specimen in an individually sealed bag.
Storage and Transport
  • Frozen
Stability
  • Ambient: Unacceptable
  • Refrigerated: 4 days
  • Frozen: 30 days

Limitations and Validated Organisms


Resources

Reports
Additional Information
Publications and References
  • S Flygare et al., “Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profling”, Genome Biol, 17, 111 (2016). PMID: 27224977.
  • EH Graf et al., “Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel”, J Clin Microbiol, 54, 1000–1007 (2016). PMID: 26818672.
Collaboration

Expert

  • Medical Director, Microbial Amplified Detection, Virology, and Fecal Chemistry Laboratories
    Assistant Medical Director, Virology and Molecular Infectious Disease Laboratories
    Dr. Schlaberg is an assistant professor of clinical pathology at the University of Utah School of Medicine. He received his MD and doctor medicinæ degrees at the Julius-Maximilians-University in Wuerzburg, Germany and his master of public health at the Mailman School of Public Health at Columbia University in New York City, where he also served as a postdoctoral fellow. Dr. Schlaberg trained in clinical pathology at the Columbia University College of Physicians & Surgeons, where he was the chief clinical pathology resident. He is certified in clinical pathology and medical microbiology by the American Board of Pathology. His research focuses on the use of next-generation sequencing for unbiased pathogen detection and host response-based diagnostics.