The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection

Table 2

Nanopore sequencing can quickly identify pathogens in various clinical samples.

Sample type	Nucleic acid type	Diagnosis	Sequencing methods	Turnaround time	Pathogen
Blackbird brain tissues	DNA	—	—	—	Usutu virus [21]
Whole blood	RNA	—	—	<24 h	Ebola virus [20]
Plasma	RNA	—	Metagenomic sequencing	<6 h	Chikungunya virus [29]
Whole blood	RNA	—	Metagenomic sequencing	<6 h	Ebola virus [29]
Serum	RNA	—	Metagenomic sequencing	<6 h	Hepatitis C virus [29]
Cerebrospinal fluid	DNA	Bacterial meningitis	16S sequencing	3 h	L. monocytogenes: S. pneumoniae, P. aeruginosa: K. pneumoniae, etc. [34]
Sputum	DNA	Community-acquired pneumonia	16S sequencing	5 h	Haemophilus influenzae pneumonia [30]
Faeces	DNA	Necrotizing enterocolitis	Shotgun metagenomic sequencing	<5 h	Klebsiella pneumoniae and Enterobacter cloacae [28]
Sonication fluid	DNA	Prosthetic joint infections	Metagenomic sequencing	—	Staphylococcus aureus, Cutibacterium acnes, Staphylococcus epidermidis, etc. [35]

—, not given.