{"doi":"10.1183/13993003.02443-2024","title":"Cystic Fibrosis Microbiome-directed Antibiotic Therapy Trial in Exacerbations Results Stratified (CFMATTERS): results of a multicentre randomised controlled trial","abstract":"Background This study explores the effectiveness and safety of microbiome-directed antimicrobial therapy versus usual antimicrobial therapy in adult cystic fibrosis pulmonary exacerbations. Methods A multicentre two-arm parallel randomised control trial conducted across Europe/North-America enrolled 223 participants (January 2015 to August 2017). All participants were chronically colonised with Pseudomonas aeruginosa and were randomised 1:1 into two study arms. The “usual therapy” group received 2 weeks of intravenous ceftazidime 3 g thrice daily (for allergies: aztreonam 2 g thrice daily) and tobramycin 5–10 mg·kg −1 once daily. The “microbiome-directed” group received the same usual therapy plus an additional antibiotic with greatest presumed activity against the second, third and fourth most abundant genera present in the sputum microbiome, selected by a consensus expert treatment panel. The primary outcome was change in percentage of predicted forced expiratory volume in 1 s (ppFEV 1 ) at 14 days post initiation of antibiotics. Secondary outcomes examined ppFEV 1 at 7 days, 28 days and 3 months; time to next exacerbation; symptom burden at 7 days; health-related quality of life (HRQoL) at 28 days; and number of exacerbations and i.v. antibiotic days at 12 months. Results 149 participants had an eligible exacerbation (usual therapy n=83, microbiome-directed therapy n=66). There was no difference between the groups for ppFEV 1 at day 14 (−1.1%, 95% CI −3.9–1.7%; p=0.46), or ppFEV 1 measured at other time points, or for time to next exacerbation (microbiome-directed versus usual therapy hazard ratio 0.91, 95% CI 0.60–1.38; p=0.66). The microbiome-directed group trended to have more i.v. days (median 42 days versus 28 days; p=0.08) and more subsequent exacerbations (median three versus two; p=0.044) the following year. There were no appreciable differences in symptom burden; however, HRQoL subscores were consistently worse in the microbiome-directed group (−4.3 points versus usual therapy, 95% CI −8.3–−0.3 points; p=0.033). Conclusion The addition of a third antibiotic based on sputum microbiome sequencing analysis did not result in improved clinical outcomes.","journal":"European Respiratory Journal","year":2025,"id":521409,"datarank":0.29916441428574125,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.030400493901533005,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.030400493901533005,"corpus_percentile":44.86733194089889,"corpus_rank":7128,"citation_count":5,"citer_count":4,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5268,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":56.25,"fair_percentile":71.90461632528279,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":592349,"name":"G.G. Einarsson","orcid":"0000-0003-1353-950X","position":1,"is_corresponding":false},{"id":1391763,"name":"K. Deasy","orcid":"0000-0002-1685-249X","position":2,"is_corresponding":false},{"id":104021,"name":"Darren Dahly","orcid":"0000-0003-0110-324X","position":3,"is_corresponding":false},{"id":499479,"name":"Pradeep K. Singh","orcid":"0000-0001-9281-0219","position":4,"is_corresponding":false},{"id":1391764,"name":"Peter Barry","orcid":"0000-0001-6326-4431","position":5,"is_corresponding":false},{"id":460724,"name":"Christopher H. Goss","orcid":"0000-0001-8602-0309","position":6,"is_corresponding":false},{"id":486166,"name":"Isabelle Fajac","orcid":"0000-0002-1532-1486","position":7,"is_corresponding":false},{"id":1391765,"name":"Tamara Vagg","orcid":"0000-0002-6582-2975","position":8,"is_corresponding":false},{"id":1391766,"name":"I. Durieu","orcid":"0000-0002-3874-5580","position":9,"is_corresponding":false},{"id":1391767,"name":"Evelyn Flanagan","orcid":"0009-0005-4443-6740","position":10,"is_corresponding":false},{"id":1392274,"name":"Grace O’Callaghan","orcid":null,"position":11,"is_corresponding":false},{"id":563451,"name":"Clémence Martin","orcid":"0000-0003-4385-5888","position":12,"is_corresponding":false},{"id":563452,"name":"Pierre-Régis Burgel","orcid":"0000-0003-0903-9828","position":13,"is_corresponding":false},{"id":600989,"name":"Charles Haworth","orcid":"0000-0001-7126-2874","position":14,"is_corresponding":false},{"id":503205,"name":"R. Andrés Floto","orcid":"0000-0002-2188-5659","position":15,"is_corresponding":false},{"id":486164,"name":"D.G. Downey","orcid":"0000-0002-6471-549X","position":16,"is_corresponding":false},{"id":390095,"name":"Lieven Dupont","orcid":"0000-0003-3961-1522","position":17,"is_corresponding":false},{"id":786792,"name":"Andrew Jones","orcid":"0000-0003-3232-1055","position":18,"is_corresponding":false},{"id":490649,"name":"J.S. Elborn","orcid":"0000-0002-2323-442X","position":19,"is_corresponding":false},{"id":884221,"name":"Joseph A. Eustace","orcid":null,"position":20,"is_corresponding":false},{"id":277383,"name":"Marcus Mall","orcid":"0000-0002-4057-2199","position":21,"is_corresponding":false},{"id":435467,"name":"Michael M. Tunney","orcid":"0000-0002-7433-7074","position":22,"is_corresponding":false},{"id":1391762,"name":"Barry J. Plant","orcid":"0000-0002-4611-6768","position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":null,"created_at":"2026-07-19T02:49:44.558743Z","pmid":"40506211","pmcid":"PMC12332466","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":61.1111,"fair_a":62.5,"fair_i":0.0,"fair_r":20.8333,"fair_zscore":0.8629,"fair_rationale":{"fair_score":56.25,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"PRJEB86888","grounded":true,"rationale":"The paper gives a persistent identifier (BioProject accession PRJEB86888) for the MiSeq sequencing data.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"European Bioinformatics Institute European Nucleotide Archive","grounded":true,"rationale":"The paper names the European Bioinformatics Institute European Nucleotide Archive as the repository holding the MiSeq sequencing data.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All the individual participant data collected during the trial after deidentification, and associated documents (protocol and consent form) will be available for sharing 6 months post-publication pending successful application to the CFMATTERS Data Consortium Committee.","grounded":false,"rationale":"The data availability statement points to a request process (application to the Data Consortium Committee), not a repository record, placing it in Colavizza category 1. 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[majority verdict 'yes' (4/5 passes agreed)]","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"All the individual participant data collected during the trial after deidentification, and associated documents (protocol and consent form) will be available for sharing 6 months post-publication pending successful application to the CFMATTERS Data Consortium Committee.","grounded":false,"rationale":"The paper states when the data become available (6 months post-publication) but does not state how long they persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format token is named for the released data; 'MiSeq sequencing data' does not specify a format.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard (e.g., MIAME, MINSEQE) is named; the named instruments (CFRSD, CFQR) are measurement tools, not data standards. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier for an external resource (e.g., source dataset, reference genome) is provided. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":20.83,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence for the data is stated; the CC-BY-NC 4.0 licence applies to the article only.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Illumina MiSeq","grounded":true,"rationale":"The paper names the specific instrument (Illumina MiSeq) used to produce the sequencing data. 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for an external resource (e.g., source dataset, reference genome) is provided. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"All the individual participant data collected during the trial after deidentification, and associated documents (protocol and consent form) will be available for sharing 6 months post-publication pending successful application to the CFMATTERS Data Consortium Committee.","why":"The paper states when the data become available (6 months post-publication) but does not state how long they persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:55:20.596966Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}