Protocol

Organism-level agreement with clinical microbiological tests (CMT), 62 BALF specimens (Hu et al. 2026)

Positive and negative percent agreement of each workflow's organism calls against clinical microbiological tests (CMT), for all organisms (Table 2), bacteria (Supplemental Table 6) and fungi (Supplemental Table 7).

2 evaluations · 36 results

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2 recorded evaluations, 36 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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2 evaluations · 36 results. Different protocols are not a single leaderboard.

Protocol: Organism-level agreement with clinical microbiological tests (CMT), 62 BALF specimens (Hu et al. 2026) · Dataset: 62 residual BALF specimens with culture results (Hu et al. 2026)

Sorted by False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT))	False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT))	False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: clinical microbiological tests (CMT))	False positives (sequencing positive, comparator negative; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT))	False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT))	False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: clinical microbiological tests (CMT))	Recall (positive percent agreement; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT))	Recall (positive percent agreement; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT))	Recall (positive percent agreement; organism level; organisms: fungi; reference: clinical microbiological tests (CMT))	Specificity (negative percent agreement; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT))	Specificity (negative percent agreement; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT))	Specificity (negative percent agreement; organism level; organisms: fungi; reference: clinical microbiological tests (CMT))	True negatives (concordant negative; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT))	True negatives (concordant negative; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT))	True negatives (concordant negative; organism level; organisms: fungi; reference: clinical microbiological tests (CMT))	True positives (concordant positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT))	True positives (concordant positive; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT))	True positives (concordant positive; organism level; organisms: fungi; reference: clinical microbiological tests (CMT))
MGISEQ-200 short-read mNGS workflow (Hu et al. 2026)Evaluation	5 (best in column)	3 (best in column)	2 (best in column)	13	10	4 (best in column)	88.6% (best in column)	89.7% (best in column)	84.6% (best in column)	75%	80%	92.9% (best in column)	39	40 (best in column)	52 (best in column)	39 (best in column)	26 (best in column)	11 (best in column)
Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)Evaluation	7	4	3	10 (best in column)	5 (best in column)	5	84.1%	86.2%	76.9%	79.2% (best in column)	88.9% (best in column)	91.2%	42 (best in column)	40 (best in column)	52 (best in column)	37	25	10

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Original source · Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML
Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Original source · spectrum.03993-25-s0001.docx as distributed with PMC13339908

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261011-hu2026-protocol-cmt

areas: microbes-communities
contexts: clinical_research
protocol: Reference: Culture plus additional verification: organism-specific qPCR, or Xpert MTB/RIF for M. tuberculosis complex, on discordant organisms where residual BALF allowed. Each organism result is concordant positive, sequencing positive and comparator negative, sequencing negative and comparator positive, or concordant negative; PPA = TP/(TP+FN) and NPA = TN/(TN+FP). Supplemental Tables S6 and S7 label the culture column 'Sensitivity' and 'Specificity'.
version: Table 2; Supplemental Tables S6 and S7
source locator: Methods 'Clinical performance evaluation and reference standards' paragraphs 1-3; Table 2 footnote
limitations: Organism-level agreement; a specimen contributes one comparison per organism detected by either side.; Discrepant analysis: confirmatory qPCR or GeneXpert was run on discordant sequencing-positive findings where residual BALF allowed (19 NGS-positive and 17 TGS-positive findings confirmed), so the CMT reference depends partly on the sequencing results and favours the sequencing workflows.

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