Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

J Clin Microbiol. 2019 Dec 23;58(1):e01315-19. doi: 10.1128/JCM.01315-19. Print 2019 Dec 23.


Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.

Keywords: infectious disease diagnostics; nanopore sequencing; third-generation sequencing.

Publication types

  • Review

MeSH terms

  • Clinical Laboratory Services* / standards
  • Clinical Laboratory Techniques*
  • Communicable Diseases / diagnosis*
  • Communicable Diseases / etiology
  • High-Throughput Nucleotide Sequencing* / methods
  • High-Throughput Nucleotide Sequencing* / standards
  • Humans
  • Nanopore Sequencing* / methods
  • Nanopore Sequencing* / standards