DNA detection with the greatest clinical utility

MicroGenDX combines qPCR with targeted 16S/ITS NGS to deliver timely, highly accurate, actionable diagnostic information for infections. Matching samples against a curated database of over 50,000 microbial species, MicroGenDX’s qPCR+NGS results identify all potentially pathogenic microbial taxa, along with their clinically relevant distribution in the sample, in 3.5 days, at a low cost. In contrast, the strain-level resolution and discovery power of shotgun metagenomics does not provide any greater diagnostic utility for most infections* — and shotgun is also slower and more expensive, with lower sensitivity and accuracy than targeted NGS. For clinical applications, qPCR and targeted NGS offer a clear advantage for optimal treatment strategies.

Comparison of DNA sequencing technologies

qPCRTargeted 16S/ITS NGSShotgun Metagenomics**

  • Amplifies the target gene if found in the specimen

  • Inclusion of specific primers/probes enables detection of those specific microbes

  • Amplifies and sequences a universal target gene within the microbe genome — not limited by a targeted primer mix like qPCR

  • 16S ribosomal RNA is a highly conserved primer binding site for bacteria and contains species-specific sequences in its hypervariable regions

  • The ITS1 region is a commonly used DNA marker for identifying fungal species in metagenomic samples

  • Shears the entire genome into random fragments, then sequences the fragments and aligns them back to the entire microbe genome

  • Human host DNA is sequenced at the same time as the microbial DNA, because no target genes are selected as they are in qPCR and NGS


  • High sensitivity

  • Fastest processing speed

  • High sequencing depth enables high sensitivity

  • High discovery power

  • High mutation resolution

  • High relative processing speed

  • Base-by-base view of the genome, capturing both large and small variants

  • Provides strain-level information most relevant for viral typing, as well as epidemiology tracing and research


  • Can only interrogate a limited set of mutations

  • No discovery power beyond the primer set

  • Cannot detect viruses or parasites

  • No strain level specificity

  • Longest sequencing and data processing time

  • Most expensive

  • Sequence library is much smaller
  • Lowest overall sensitivity

  • Requires the largest amount of nucleic acid

*Shotgun metagenomics may discover additional resistance genes, but MicroGenDX qPCR detects a total of 17 resistance genes from among all main classes of antimicrobials.

**MicroGenDX is also able to provide shotgun metagenomics offered by its RTL Genomics research division.


  1. Mitchell SL, Simner PJ. Next-Generation Sequencing in Clinical Microbiology: Are We There Yet? Clin Lab Med. 2019 Sep;39(3):405-418.doi: 10.1016/j.cll.2019.05.003.

  2. https://www.illumina.com/content/dam/illumina-marketing/documents/gated/10143_Shotgun_Metagenomics_Methods_Guide.pdf
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