The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection

Table 1

Advantages and disadvantages of common pathogen detection methods.

Testing methods	Advantages	Disadvantages	Turnaround time	Reference
Culture	Easy to obtain, low cost, simple operation	Sensitivity is affected by antibiotics, limited use in fastidious organisms, time-consuming, unable to detect the gene mutation	Usually takes 5–7 days	[12, 13]
Polymerase chain reaction (PCR) (e.g., direct PCR and multiplex PCR)	Rapid, simple operation, accurate quantification, low cost	Limited to detection of known pathogens, depends on primer design, but the primer is not always effective, unable to detect the gene mutation	One to several hours	[14]
Targeted NGS	High throughput, potential for quantitation highly specific amplification of selected organism types, be able to detect gene mutation	PCR amplification is needed, complicated to operate and long time to result, limited to not covering the entire gene region, depends on hypothesis requiring primers that may not always work, accurate taxonomic identification depends on the quality and completeness of the reference databases	One to several days	[15–17]
Metagenomic NGS	High throughput, no amplification, no bias testing, direct application to clinical samples, potential for discovery of unknown pathogens, be able to detect gene mutation	High cost, long time to result, complicated to operate, vulnerable to human background pollution, difficult to analyze complex genome structure	One to several days	[16, 18]
Nanopore sequencing	Ultralong reads and real-time data, accurate species resolution, direct sequencing of DNA and RNA, high throughput and inexpensive, rapid, portable, and easy to operate, be able to parse complex genome structure, be able to detect gene mutation	Relatively high error rate, quality of sequencing is affected by library quality and sequencing inhibitors	Several hours	[19–21]