| 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] |
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