Interpreting Your NGS + Biomarker Report

Why was E. coli not detected by qPCR alone?

MicroGenDX has E. coli in its qPCR panel. However, in this sample report, E. coli was not detected in the qPCR panel, and was subsequently detected with NGS. Why? Because qPCR uses very precise primers, so that deviations and mutations can go undetected. According to our analysis, E. coli is missed by qPCR but detected by NGS 18% of the time. In addition, microbial inclusion on a qPCR panel reflects a traditional culture bias, underrepresenting anaerobes and fastidious organisms. The role of these organisms in polymicrobial infection are gaining recognition due to NGS-based research. NGS can accommodate microbe mutation variabilities and is not limited by panel size. Using NGS, physicians receive a true representation of microbial community in the sample.


  1. Corona P S, et al. General Assembly, Diagnosis, Pathogen Isolation: Proceedings of International Consensus on Orthopedic Infections.  The Journal of Arthroplasty. 34 (2019) S207eS214.
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