Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.

Comparative benchmark of NGS (Illumina/MGI) vs TGS (Nanopore) on mock communities and 62 clinical bronchoalveolar lavage samples for pathogen detection

Next-generation sequencing (NGS, short-read: Illumina/MGI) and third-generation sequencing (TGS, long-read: Nanopore) are compared on defined mock communities and 62 clinical bronchoalveolar lavage (BAL) samples for pathogen detection. NGS and TGS achieve comparable overall sensitivity (93.3% vs 90.7%), but long-read provides better resolution of co-infections and faster turnaround. The authors provide quantitative criteria for technology selection based on clinical context.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

This benchmark informs a frequent decision in clinical microbiology: short-read or long-read for diagnostic metagenomics? Comparable overall performance but long-read superiority for co-infections argues for a hybrid approach in complex cases. Generalization to non-pulmonary samples remains to be established.

Clinical impact: 2/3 · Evidence strength: 3/3 · Novelty: 1/2 · Sample size: 1/1 · Publication status: 0/1 → Total: 7/10