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Review
. 2023 Nov;27(6):685-701.
doi: 10.1007/s40291-023-00669-8. Epub 2023 Aug 11.

Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections

Jie Chen  1 , Feng Xu  2
Affiliations
Review

Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections

Jie Chen et al. Mol Diagn Ther. 2023 Nov.

Abstract

This review provides an in-depth discussion of the development, principles and utility of nanopore sequencing technology and its diverse applications in the identification of various pulmonary pathogens. We examined the emergence and advancements of nanopore sequencing as a significant player in this field. We illustrate the challenges faced in diagnosing mixed infections and further scrutinize the use of nanopore sequencing in the identification of single pathogens, including viruses (with a focus on its use in epidemiology, outbreak investigation, and viral resistance), bacteria (emphasizing 16S targeted sequencing, rare bacterial lung infections, and antimicrobial resistance studies), fungi (employing internal transcribed spacer sequencing), tuberculosis, and atypical pathogens. Furthermore, we discuss the role of nanopore sequencing in metagenomics and its potential for unbiased detection of all pathogens in a clinical setting, emphasizing its advantages in sequencing genome repeat areas and structural variant regions. We discuss the limitations in dealing with host DNA removal, the inherent high error rate of nanopore sequencing technology, along with the complexity of operation and processing, while acknowledging the possibilities provided by recent technological improvements. We compared nanopore sequencing with the BioFire system, a rapid molecular diagnostic system based on polymerase chain reaction. Although the BioFire system serves well for the rapid screening of known and common pathogens, it falls short in the identification of unknown or rare pathogens and in providing comprehensive genome analysis. As technological advancements continue, it is anticipated that the role of nanopore sequencing technology in diagnosing and treating lung infections will become increasingly significant.

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Conflict of interest statement

The authors FX and JC have no conflicts of interest that are directly relevant to the content of this article.

Figures

Fig. 1
Fig. 1
Principle of nanopore sequencing. Nanopore sequencing technology is based on the utilization of nanoscale protein pores, referred to as nanopores, as biosensors embedded within an insulating polymer membrane. By applying a constant voltage across the polymer membrane, negatively charged single-stranded DNA or RNA molecules are driven from the negatively charged side (cis) to the positively charged side (trans) of the membrane. The motor protein possesses helicase activity that unwinds the double-stranded DNA or DNA–RNA duplex into single strands that pass through the nanopore. The migration rate of the nucleic acid strands within the nanopore is also controlled by the motor protein. As the nucleic acid strand translocates through the nanopore, different bases induce different changes in the electric current. These changes are read by the signal receptor within the nanopore, and subsequent base recognition is accomplished via computational algorithms
See this image and copyright information in PMC

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