Evaluation

Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT)

Published clinical mNGS workflow comparison; transcribed, not reproduced.

Evaluation results

1 evaluation · 18 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))
Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)Evaluation	7	4	3	10	5	5	84.1%	86.2%	76.9%	79.2%	88.9%	91.2%	42	40	52	37	25	10

All 18 result rows with coverage, uncertainty and sources

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Evaluation procedure

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

Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)
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)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: dna-pathogen-20261011-hu2026-protocol-cmt
dataset version: 62 residual BALF specimens (Hu et al. 2026)
split: Single clinical set
population: Organisms detected in the 62 BALF specimens by the workflow or the reference
inputs: DNA extracted from BALF
adaptation: Workflow as stated per configuration
metric implementation: Organism-level 2x2 counts; PPA and NPA
aggregation: All organism results in the specimen set
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Single clinical set
Adaptation: Workflow as stated per configuration
Scoring implementation: Organism-level 2x2 counts; PPA and NPA

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

38 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Workflow as stated per configuration Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Workflow as stated per configuration Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation All organism results in the specimen set Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation All organism results in the specimen set Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version 62 residual BALF specimens (Hu et al. 2026) Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version 62 residual BALF specimens (Hu et al. 2026) Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs DNA extracted from BALF Context-only references	Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Microbiology Spectrum 14(7):e03993-25, published 2026-06-03; PMC13339908 full-text XML Retrieved: 2026-10-11T21:37:24Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `555995fd870d878dd0e6c112064bbf1d2535a1cb1af17f70570ecc11774caa2d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs DNA extracted from BALF Context-only references	Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) Original source ↗ Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: spectrum.03993-25-s0001.docx as distributed with PMC13339908 Retrieved: 2026-10-11T21:41:40Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `7ab6c2cde30619e506a5e015ef5bbb253dfa6359ebd56140577eef136b153ed9` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261011-hu2026-eval-cmt-hdont

areas: microbes-communities
contexts: clinical_research
origin: author_reported
protocol: dna-pathogen-20261011-hu2026-protocol-cmt
version: Primary source as retrieved 2026-10-11
comparison: protocol id: dna-pathogen-20261011-hu2026-protocol-cmt; dataset version: 62 residual BALF specimens (Hu et al. 2026); split: Single clinical set; population: Organisms detected in the 62 BALF specimens by the workflow or the reference; inputs: DNA extracted from BALF; adaptation: Workflow as stated per configuration; metric implementation: Organism-level 2x2 counts; PPA and NPA; aggregation: All organism results in the specimen set; budget: Not reported
source locator: Table 2, block 'TGS', column group 'Clinical microbiological tests (CMT)'; Supplemental Tables S6 and S7, same block and column group
limitations: Organism-level agreement in 62 residual BALF specimens from lower respiratory tract infection; not plasma cell-free DNA and not patient-level diagnosis.; The two workflows differ in platform, library preparation, host depletion, aligner and positivity threshold together (MGISEQ-200 with BWA-MEM and RP20M >= 3; host-depleted ONT GridION with minimap2 and RP10K >= 1), so the comparison is of whole workflows, not of classifiers.; Both workflows used the same curated 20,484-genome reference database and lowest-common-ancestor assignment.; Eight of the listed authors, including co-corresponding author Lifeng Li, are affiliated with Genskey Medical Technology (Beijing), a clinical mNGS provider; the article states that the authors declare no conflict of interest. The workflows are the authors' own, so the evaluations are author_reported.

Related records

system: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)
assessment: Organism-level agreement with clinical microbiological tests (CMT), 62 BALF specimens (Hu et al. 2026)
data: 62 residual BALF specimens with culture results (Hu et al. 2026)
evaluation: hu2026 cmt hdont all false-negative-count
evaluation: hu2026 cmt hdont all false-positive-count
evaluation: hu2026 cmt hdont all specificity
evaluation: hu2026 cmt hdont all recall
evaluation: hu2026 cmt hdont all true-negative-count
evaluation: hu2026 cmt hdont all true-positive-count
evaluation: hu2026 cmt hdont bacteria false-negative-count
evaluation: hu2026 cmt hdont bacteria false-positive-count
evaluation: hu2026 cmt hdont bacteria specificity
evaluation: hu2026 cmt hdont bacteria recall
evaluation: hu2026 cmt hdont bacteria true-negative-count
evaluation: hu2026 cmt hdont bacteria true-positive-count
evaluation: hu2026 cmt hdont fungi false-negative-count
evaluation: hu2026 cmt hdont fungi false-positive-count
evaluation: hu2026 cmt hdont fungi specificity
evaluation: hu2026 cmt hdont fungi recall
evaluation: hu2026 cmt hdont fungi true-negative-count
evaluation: hu2026 cmt hdont fungi true-positive-count

Suggest a correction

Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	7 False negatives (sequencing negative, comparator positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "TGS", column group "Clinical microbiological tests (CMT)", row "−" (sequencing negative), column "＋" (comparator positive)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	10 False positives (sequencing positive, comparator negative; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "TGS", column group "Clinical microbiological tests (CMT)", row "＋" (sequencing positive), column "−" (comparator negative)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	79.2% Specificity (negative percent agreement; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "TGS", column group "Clinical microbiological tests (CMT)", row "NPA"
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	84.1% Recall (positive percent agreement; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "TGS", column group "Clinical microbiological tests (CMT)", row "PPA"
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	42 True negatives (concordant negative; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "TGS", column group "Clinical microbiological tests (CMT)", row "−" (sequencing negative), column "−" (comparator negative)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	37 True positives (concordant positive; organism level; organisms: all organisms; reference: clinical microbiological tests (CMT)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy · Table 2, block "TGS", column group "Clinical microbiological tests (CMT)", row "＋" (sequencing positive), column "＋" (comparator positive)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	4 False negatives (sequencing negative, comparator positive; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "TGS", column group "Clinical microbiological tests (CMT)", row "−" (sequencing negative), column "＋" (comparator positive)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	5 False positives (sequencing positive, comparator negative; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "TGS", column group "Clinical microbiological tests (CMT)", row "＋" (sequencing positive), column "−" (comparator negative)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	88.9% Specificity (negative percent agreement; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "TGS", column group "Clinical microbiological tests (CMT)", row "NPA"
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	86.2% Recall (positive percent agreement; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "TGS", column group "Clinical microbiological tests (CMT)", row "PPA"
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	40 True negatives (concordant negative; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "TGS", column group "Clinical microbiological tests (CMT)", row "−" (sequencing negative), column "−" (comparator negative)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	25 True positives (concordant positive; organism level; organisms: bacteria; reference: clinical microbiological tests (CMT)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 6, block "TGS", column group "Clinical microbiological tests (CMT)", row "＋" (sequencing positive), column "＋" (comparator positive)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	3 False negatives (sequencing negative, comparator positive; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Clinical microbiological tests (CMT)", row "−" (sequencing negative), column "＋" (comparator positive)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	5 False positives (sequencing positive, comparator negative; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Clinical microbiological tests (CMT)", row "＋" (sequencing positive), column "−" (comparator negative)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	91.2% Specificity (negative percent agreement; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Clinical microbiological tests (CMT)", row "NPA"
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	76.9% Recall (positive percent agreement; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Clinical microbiological tests (CMT)", row "PPA"
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	52 True negatives (concordant negative; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Clinical microbiological tests (CMT)", row "−" (sequencing negative), column "−" (comparator negative)
Configuration: Host-depleted ONT GridION mNGS workflow (Hu et al. 2026)	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)	10 True positives (concordant positive; organism level; organisms: fungi; reference: clinical microbiological tests (CMT)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Host-depleted ONT GridION mNGS workflow (Hu et al. 2026) against clinical microbiological tests (CMT) dna-pathogen-20261011-hu2026-protocol-cmt Aggregation: Not reported Hu et al. 2026 Supplemental Tables S1 to S4, S6 and S7 (spectrum.03993-25-s0001.docx) · Supplemental Table 7, block "TGS", column group "Clinical microbiological tests (CMT)", row "＋" (sequencing positive), column "＋" (comparator positive)