MICROBIOLOGY | NGS for Microbiology

Enhancing and Improving Diagnostic Microbiology with qPCR + NGS

Expand clinical impact through enhanced diagnostic power

Mystery Microbes?

At Dr. James Snyder’s mycology laboratory at the University of Louisville Hospital, a mold would not sporulate using conventional methods despite repeated attempts. A sample was submitted to MicroGenDX for qPCR+NGS, which identified the isolate as a rare fungus in just four days, and the patient’s symptoms resolved with an appropriate antifungal therapy. View Dr. Snyder video

In another example of NGS diagnostic efficacy, a landmark 15-center study demonstrated 68.6% of revision failures following two-stage exchange were due to untreated or undertreated pathogens missed by culture, but detected by NGS at the time of initial resection. Only 8.6% of failures had negative NGS results at the time of revision surgery. Read about study

12 years of 16S/ITS NGS testing quality and reliability

With over 500,000 qPCR+NGS samples processed, referencing against a validated microbial database of 50,000+ microbes, MicroGenDX ensures representation of a comprehensive and growing library of infective organisms. This precise and expanding identification has been consistently confirmed by a 99.2% CAP proficiency average from more than 1,000 blinded specimens. MicroGenDX has also been a trusted research partnership lab for the FDA, NASA, and the CDC. View CAP data

Attentive customer service

MicroGenDX accepts the largest selection of media and specimen types, offers a 3.5 day turnaround time for NGS reports and a 24-48 hour turnaround for identification of antimicrobial resistance genes, and provides custom capabilities and validation of lab developed tests in collaboration with customers.

Industry leader in reference laboratory affordability

  • $100 for direct colony identification
  • Less than $300 for specimen identification

NGS supports physicians with culture-negative infection management

Originally described in 1982, it is now believed that any environmental stressor could send a community into this non-culturable but still viable state (VNBC). Known human pathogens such as E. coli, .E faecalis, P. aeruginosa and S. aureus are all capable of entering and resuscitating from a VBNC state without losing their virulence. During the VBNC state, the microbes maintain their cellular structure and biology (allowing detection with molecular testing) along with significant gene expression, but they are non-culturable by ‘standard’ laboratory methods.

NGS supports direct colony identification from culture

MicroGenDX offers direct colony identification from agar and broth media for bacteria, mycobacteria and fungi using a curated database of 50,000+ microbes. MicroGenDX NGS results have demonstrated 96% concordance with traditional culture based on a study by Dr. Javad Parvizi at Thomas Jefferson University and published in the Bone and Joint Journal, 2018.


  1. Tarabichi M, Shohat N, Goswami K, et al. Diagnosis of Periprosthetic Joint Infection: The Potential of Next-Generation Sequencing. The Journal of Bone and Joint Surgery. DOI: 10.2106/JBJS.17.00434 , 2018.
  2. https://www.odtmag.com/contents/view_breaking-news/2020-09-16/next-generation-sequencing-predicts-failure-in-total-joint-arthroplasty/
  3. 2009 - 2019 College of American Pathology proficiency results
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