Evidence claim

Relevance of patient-level detection of causative pathogens in blood against the final clinical diagnosis (Huang et al. 2026 Table 2) to "Select a DNA pathogen-identification workflow for diagnostic testing"

Use case: Select a DNA pathogen-identification workflow for diagnostic testing
Assessed by: Patient-level detection of causative pathogens in blood against the final clinical diagnosis (Huang et al. 2026 Table 2)
Relevance: Proxy evidence
Endpoint: Patient-level sensitivity, specificity, PPV, NPV and accuracy (95% intervals) of blood bstNGS, blood mNGS, conventional tests and blood culture against the adjudicated clinical diagnosis in 122 ICU patients, overall and for gram-positive, gram-negative and fungal pneumonia

Two DNA sequencing workflows on blood (targeted probe-capture bstNGS and untargeted mNGS) and two conventional tests are scored on the same 122 patients against an adjudicated clinical diagnosis, which bears directly on the use case's question of which DNA workflow detects clinically relevant pathogens from blood. It is proxy evidence: the reference incorporates NGS results, the cohort is retrospective, the specimens are plasma microbial cell-free DNA in pneumonia-associated sepsis, and the targeted assay detects only its 1,872-organism panel.

4 reviewed evaluations

Evidence

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Evidence table

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20 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
Citation locations 1 values source id dna-pathogen-20261011-huang2026-source locator Table 2; Methods 'Clinical diagnosis' and 'bstNGS assay workflow and mNGS steps' Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group huang2026-blood-sepsis Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Blood targeted and untargeted sequencing against clinical diagnosis in pneumonia-associated sepsis (Huang et al. 2026) Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator and preserved limitations before citing a result. Do not combine these results with another protocol's results; reference standards, specimens and scoring units differ between sources. Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Patient-level sensitivity, specificity, PPV, NPV and accuracy (95% intervals) of blood bstNGS, blood mNGS, conventional tests and blood culture against the adjudicated clinical diagnosis in 122 ICU patients, overall and for gram-positive, gram-negative and fungal pneumonia Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:dna-pathogen-20261011-huang2026-protocol-clinical-diagnosis Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric recall Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 6 values Incorporation bias: the reference was established primarily from BALF mNGS and CMT results (Methods 'Sample enrollment and standard-of-care microbiology testing' paragraph 3; Table 2 footnote), with clinical adjudication. CMTs is scored against a reference that contains it, which favours CMTs, and BALF mNGS is a sequencing assay on a different specimen. Retrospective single-centre cohort; 61 of 183 screened patients excluded. Few patients are reference-negative: the count is not printed, and the specificity intervals are wide (44.44% for bstNGS, 24.56% to 66.28%). Targeted panel: bstNGS cannot detect organisms outside its 1,872 probes, which bears on the use case's question of organisms absent from the reference. Blood culture PPV in fungal pneumonia is printed 0.00% with a zero denominator (result source_anomaly). Commercial assay with two co-authors from its supplier (Geneplus-Beijing); no competing interests declared. Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 8af50ff68cde77b114f9f0e6c3400a6f3b9f7cef1faf309470f92aaf9be19fdc record id dna-pathogen-20261011-huang2026-source fields status attributes.artifact_sha256 sha256 9de12591b7a075a2b2001998bbee57faaf3d4541c5b65c49fcf48a096f771c8a record id use-case-diagnostic-dna-pathogen-identification fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 fc133441f475bb23dafd0c0c55f4e16cd20302f9148b21b98de31077dfe16338 Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale Two DNA sequencing workflows on blood (targeted probe-capture bstNGS and untargeted mNGS) and two conventional tests are scored on the same 122 patients against an adjudicated clinical diagnosis, which bears directly on the use case's question of which DNA workflow detects clinically relevant pathogens from blood. It is proxy evidence: the reference incorporates NGS results, the cohort is retrospective, the specimens are plasma microbial cell-free DNA in pneumonia-associated sepsis, and the targeted assay detects only its 1,872-organism panel. Context-only references	Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis Original source ↗ dna-pathogen-20261011-huang2026-source: Table 2 Version: Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML Retrieved: 2026-10-11T22:07:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

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Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis · Original source · Respiratory Research 27:357, published 2026-06-24; PMC13584460 full-text XML

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-dna-pathogen-20261011-huang2026-clinical-diagnosis

field: links:assessed_by:dna-pathogen-20261011-huang2026-protocol-clinical-diagnosis
value: dna-pathogen-20261011-huang2026-protocol-clinical-diagnosis
relevance: proxy
endpoint: Patient-level sensitivity, specificity, PPV, NPV and accuracy (95% intervals) of blood bstNGS, blood mNGS, conventional tests and blood culture against the adjudicated clinical diagnosis in 122 ICU patients, overall and for gram-positive, gram-negative and fungal pneumonia
rationale: Two DNA sequencing workflows on blood (targeted probe-capture bstNGS and untargeted mNGS) and two conventional tests are scored on the same 122 patients against an adjudicated clinical diagnosis, which bears directly on the use case's question of which DNA workflow detects clinically relevant pathogens from blood. It is proxy evidence: the reference incorporates NGS results, the cohort is retrospective, the specimens are plasma microbial cell-free DNA in pneumonia-associated sepsis, and the targeted assay detects only its 1,872-organism panel.
constraints: Inspect every linked evaluation's source locator and preserved limitations before citing a result.; Do not combine these results with another protocol's results; reference standards, specimens and scoring units differ between sources.
limitations: Incorporation bias: the reference was established primarily from BALF mNGS and CMT results (Methods 'Sample enrollment and standard-of-care microbiology testing' paragraph 3; Table 2 footnote), with clinical adjudication. CMTs is scored against a reference that contains it, which favours CMTs, and BALF mNGS is a sequencing assay on a different specimen.; Retrospective single-centre cohort; 61 of 183 screened patients excluded.; Few patients are reference-negative: the count is not printed, and the specificity intervals are wide (44.44% for bstNGS, 24.56% to 66.28%).; Targeted panel: bstNGS cannot detect organisms outside its 1,872 probes, which bears on the use case's question of organisms absent from the reference.; Blood culture PPV in fungal pneumonia is printed 0.00% with a zero denominator (result source_anomaly).; Commercial assay with two co-authors from its supplier (Geneplus-Beijing); no competing interests declared.
citation locators: source id: dna-pathogen-20261011-huang2026-source; locator: Table 2; Methods 'Clinical diagnosis' and 'bstNGS assay workflow and mNGS steps'
source locator: dna-pathogen-20261011-huang2026-source: Table 2
revision: 1
reason: Recorded from the 2026-10-11 DNA pathogen-identification literature pass (data/omics/use-case-coverage-dna-pathogen-20261011-huang2026). Independently reviewed in docs/reviews/use-cases/pathogen-use-cases-2026-10-11.md.
comparison group: huang2026-blood-sepsis
comparison title: Blood targeted and untargeted sequencing against clinical diagnosis in pneumonia-associated sepsis (Huang et al. 2026)
headline metric: recall
stratum label: 122 ICU patients
stratum order: 1
review: method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Separate Claude review agent (reviewer-path), independent of the extractor; no human review claimed; date: 2026-10-11; artifact sha256: 79b237d733d9ad3af33722c30013afb0539adf03098ca1e1c2f18344bcc4a67d; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13584460/fullTextXML; method note: Judgement drafted by the extracting agent from the pinned article.; note: Re-downloaded the pinned artifact and matched its SHA-256; compared every value with a separate stdlib parser written for this review (the extractor's script was not run) and checked a stratified sample by hand against the rendered table.
reviewed evaluations: dna-pathogen-20261011-huang2026-eval-bstngs; dna-pathogen-20261011-huang2026-eval-cmt; dna-pathogen-20261011-huang2026-eval-culture; dna-pathogen-20261011-huang2026-eval-mngs
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