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Comparative analysis of next-generation versus third-generation sequencing for pathogen detection in clinical
Chenyan Yuan1, Ting Zhang2, Juan Huo2
1Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, 210009, China.
World Journal of Microbiology & Biotechnology
|May 8, 2026
Summary
Next-generation sequencing (NGS) offers higher sensitivity for pathogen detection, especially for viruses and fungi, while third-generation sequencing (TGS) provides faster, more specific results. Both technologies have complementary roles in clinical diagnostics.
Area of Science:
- Clinical microbiology
- Genomic technologies
- Infectious disease diagnostics
Background:
- Accurate pathogen identification is vital for managing infectious diseases.
- Next-generation sequencing (NGS) and third-generation sequencing (TGS) are advanced molecular techniques for pathogen detection.
- TGS offers real-time analysis and long-read capabilities, complementing NGS.
Purpose of the Study:
- To compare the diagnostic performance of NGS and TGS in identifying pathogens.
- To evaluate sensitivity, specificity, and turnaround time of both sequencing technologies.
- To determine the optimal application of NGS and TGS in clinical settings.
Main Methods:
- A prospective diagnostic accuracy study was conducted on 105 clinical samples.
- Samples included bronchoalveolar lavage fluid, whole blood, and other body fluids from patients with suspected infections.
- Both NGS (BGI platform) and TGS (Nanopore platform) were used, with results compared against a composite reference standard.
Main Results:
- NGS showed significantly higher sensitivity (95.9%) than TGS (82.4%) (p < 0.001).
- TGS demonstrated superior specificity (87.1%) compared to NGS (64.5%) (p = 0.012).
- NGS excelled in viral and fungal detection, while TGS offered a significantly shorter turnaround time (8 h vs. 30 h, p < 0.001).
Conclusions:
- NGS and TGS possess complementary strengths for clinical pathogen detection.
- NGS is suitable for comprehensive diagnostics due to its high sensitivity and broad pathogen detection.
- TGS is advantageous for time-critical decisions due to its speed and specificity, suggesting combined approaches may optimize diagnostics.
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