Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience

Abstract

Background

The use of 16S/18S rRNA targeted next-generation sequencing (tNGS) has improved microbial diagnostics, however, the use of tNGS in a routine clinical setting requires further elucidation. We retrospectively evaluated the diagnostic accuracy and clinical utility of 16S/18S tNGS, routinely used in the North Denmark Region between 2017 and 2021.

Methods

We retrieved 544 tNGS results from 491 patients hospitalised with suspected infection (e.g. meningitis, pneumonia, intraabdominal abscess, osteomyelitis and joint infection). The tNGS assays was performed using the Illumina MiSeq desktop sequencer, and BION software for annotation. The patients’ diagnosis and clinical management was evaluated by medical chart review. We calculated sensitivity and specificity, and determined the diagnostic accuracy of tNGS by defining results as true positive, true negative, false positive, and false negative.

Results

Overall, tNGS had a sensitivity of 56% and a specificity of 97%. tNGS was more frequently true positive compared to culture (32% vs 18%), and tNGS detected a greater variety of bacteria and fungi, and was more frequently polymicrobial. However, the total diagnostic turnaround time was 16 days, and although 73% of tNGS results were true positive or true negative, only 4.4% of results led to changes in clinical management.

Conclusions

As a supplement to culture, tNGS improves identification of pathogenic microorganisms in a broad range of clinical specimens. However, the long turnaround time of tNGS in our setting may have contributed to a limited clinical utility. An improved turnaround time can be the key to improved clinical utility in a future setting.

Keywords:

• 16S rRNA gene sequencing
• 18S rRNA gene sequencing
• Targeted next-generation sequencing (tNGS)
• Next-generation sequencing (NGS)
• Diagnostic accuracy
• Clinical utility

Acknowledgments

The authors thank the laboratory technicians and clinical microbiologists at the SSI and the Aalborg DCM for their most diligent work and contributions to databases accessed during this study. The authors are also grateful for the cooperation between SSI and the DCM at Aalborg UH.

Author contributions

HLN devised the project, the main conceptual ideas and design. SHP reviewed the medical charts, performed the primary analysis and drafted the manuscript including all tables. KF handled the tNGS data at the SSI. KKS and HLN verified the analytical methods and supervised the findings of this work. All Authors revised the manuscript critically and approved the final version.

Disclosure statement

The authors report there are no competing interests to declare.