Table 1_A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.docx

Across six published clinical cohorts, CMGD achieved 91.0% detection concordance with BLAST-NT and a strong read-count correlation (R² = 0.97). In 30 retrospective samples, CMGD and NT showed strong correlations for total mapped reads (R² = 0.99) and uniquely mapped reads (R² = 0.89), with concordance correlation coefficients of 0.99 and 0.92, respectively. High sequence-mapping accuracy did not ensure reliable species-level discrimination for highly homologous taxa such as Escherichia coli and Shigella flexneri.</p>Discussion<p>Clinically stratified database curation improves the analytical performance, computational efficiency, and interpretability of mNGS-based pathogen detection.

Species-complex-level reporting may be more appropriate when species-level discriminatory evidence is insufficient. Prospective multicenter validation is required to establish clinical diagnostic utility.</p>