INFECTIOUS DISEASE | Reading The NGS Report

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.

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References

Corona P S, et al. General Assembly, Diagnosis, Pathogen Isolation: Proceedings of International Consensus on Orthopedic Infections. The Journal of Arthroplasty. 34 (2019) S207eS214. https://doi.org/10.1016/j.arth.2018.09.072

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What do these results tell us?

The combined synovial CRP, WBC, and PMN scoring represent 2018 ICM diagnostic criteria guidelines for PJI.
Cutibacterium acnes was detected by qPCR.
NGS offers a complete list of microbes detected in the sample that are potentially contributing to the joint infection confirmed by biomarkers – even when culture is negative – as recommended by a 2018 ICM consensus. These included Escherichia coli and Enterococcus faecalis , which were detected by NGS. The microbial abundance distribution informs treatment decisions.
Antimicrobial resistance genes reveal the in vivo resistance potential within the sample’s microbial community.
Patient scoring according to the 2018 ICM diagnostic criteria guidelines for PJI. The higher the scores, the stronger the indication of infection.
“Cumulative Patient Score” represents a supportive diagnostic conclusion that, in combination with culture results and sinus tract observations, provides a more complete and actionable periprosthetic joint infection assessment.

What do these results tell us?

Antimicrobial resistance genes reveal the resistance potential within a sample’s microbial community, indicating which antimicrobials’ effects would be reduced.
Bacterial Load represents the number of viable DNA copies per mL.
A complete list of clinically-relevant microbes detected in the sample:
1. Pseudomonas and Enterococcus were detected by qPCR;
2. The more dominant E. coli and B. fragilis were only detected by NGS;
3. The microbial abundance distribution informs treatment decisions.
Evidence-based antimicrobials for consideration, based on Sanford Guide and Johns Hopkins Guides (Infectious Disease consultations also available). Not determined by phenotypic susceptibility analysis.