{"doi":"10.1099/mgen.0.001162","title":"Genomic characterization of Bordetella pertussis in South Africa, 2015–2019","abstract":"Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes ( ptxP , ptxA , ptxB , prn and fimH ) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3 . The dominant genotype was ptxP 3 -ptxA 1 -ptxB2-prn 2 -fimH 2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.","journal":"Microbial Genomics","year":2023,"id":381342,"datarank":0.3635631977560667,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.12214751089095162,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.12214751089095162,"corpus_percentile":50.94762899357933,"corpus_rank":6342,"citation_count":4,"citer_count":4,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6448,"is_data_producer":true,"deposit_databanks":{"BioProject":["PRJNA929342"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":680425,"name":"Mignon du Plessis","orcid":"0000-0001-9186-0679","position":1,"is_corresponding":false},{"id":1146889,"name":"Michael R. Weigand","orcid":"0000-0002-7278-0160","position":2,"is_corresponding":false},{"id":1147295,"name":"Yanhui Peng","orcid":null,"position":3,"is_corresponding":false},{"id":1147296,"name":"Dineo Mogale","orcid":null,"position":4,"is_corresponding":false},{"id":680424,"name":"Linda de Gouveia","orcid":"0000-0002-1418-8468","position":5,"is_corresponding":false},{"id":242125,"name":"Marta C. Nunes","orcid":"0000-0003-3788-878X","position":6,"is_corresponding":false},{"id":227043,"name":"Shabir A. Madhi","orcid":"0000-0002-7629-0636","position":7,"is_corresponding":false},{"id":5182,"name":"Heather J. Zar","orcid":"0000-0002-9046-759X","position":8,"is_corresponding":false},{"id":407349,"name":"Gary Reubenson","orcid":"0000-0003-2541-4165","position":9,"is_corresponding":false},{"id":239824,"name":"Arshad Ismail","orcid":"0000-0003-4672-5915","position":10,"is_corresponding":false},{"id":422017,"name":"M. Lucia Tondella","orcid":"0000-0002-4759-2985","position":11,"is_corresponding":false},{"id":227049,"name":"Cheryl Cohen","orcid":"0000-0003-0376-2302","position":12,"is_corresponding":false},{"id":227093,"name":"Sibongile Walaza","orcid":"0000-0001-7588-2480","position":13,"is_corresponding":false},{"id":227091,"name":"Anne von Gottberg","orcid":"0000-0002-0243-7455","position":14,"is_corresponding":false},{"id":629773,"name":"Nicole Wolter","orcid":"0000-0002-9526-0133","position":15,"is_corresponding":false},{"id":1092223,"name":"Fahima Moosa","orcid":"0000-0003-0281-3649","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":null,"created_at":"2026-07-19T01:17:08.831117Z","pmid":"38117675","pmcid":"PMC10763497","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":83.3333,"fair_a":62.5,"fair_i":0.0,"fair_r":41.6667,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"PRJNA929342","grounded":true,"rationale":"The dataset is identified by the BioProject accession PRJNA929342, which is a persistent identifier scheme.","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":"The genome sequences for 32 South Africa B. pertussis isolates are available on NCBI, organized under BioProject accession number PRJNA929342.","grounded":true,"rationale":"NCBI is a named data repository that issues accessions and commits to retention. 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[majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The genome sequences for 32 South Africa B. pertussis isolates are available on NCBI, organized under BioProject accession number PRJNA929342.","grounded":true,"rationale":"The dataset identifier appears only in the body text (data availability statement), not in the reference list.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The genome sequences for 32 South Africa B. pertussis isolates are available on NCBI, organized under BioProject accession number PRJNA929342.","grounded":true,"rationale":"The text gives a route to the data with no stated precondition; the data are available on NCBI.","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The genome sequences for 32 South Africa B. pertussis isolates are available on NCBI, organized under BioProject accession number PRJNA929342.","grounded":true,"rationale":"The paper describes the action of availability on NCBI but does not label the access level with an explicit term such as 'open access' or 'publicly available'.","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No gatekeeper is named for the data; the data are deposited in a public repository without any access restrictions.","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":null,"grounded":false,"rationale":"No sentence in the paper addresses when the data become available or how long they persist. [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":"The paper does not name any file format for the released data.","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, MIxS) is named; only a manuscript reporting guideline is absent. [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":"The reference genome used was B. pertussis E476 (vaccine strain: Tohama I – accession number: CP010964).","grounded":false,"rationale":"The paper includes an identifier (CP010964) for a reference genome that is not its own dataset. [downgraded to 'no' — no verifiable quote from the paper]","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":41.67,"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 named; the article's CC-BY licence does not cover the data.","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":"Genomic libraries for Illumina sequencing were prepared (paired-end libraries, 2×300 bp) using the Nextera XT DNA v3 MiSeq sequencing kit.","grounded":true,"rationale":"The paper names specific instruments and kits used to produce the data. 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[majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"Neither a version token nor a date is provided to pin the data snapshot.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"All supporting data, code and protocols have been provided within the article or through supplementary data files.","grounded":true,"rationale":"The code is stated to be in the supplementary material, which is not an authoritative versioned repository. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"This work was supported by the National Institute for Communicable Diseases of the National Health Laboratory Service, the US Centers for Disease Control and Prevention (cooperative agreement number 5U51IP000155) and Sanofi Pasteur (cooperative agreement number PER00059). This work was supported, in part, by a Fogarty International Center Global Infectious Disease research training grant, National Institutes of Health, to the University of Pittsburgh and National Institute for Communicable Diseases (D43TW011255).","grounded":true,"rationale":"The paper includes award/grant numbers for funders.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No licence for the data is named; the article's CC-BY licence does not cover the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"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. 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Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The genome sequences for 32 South Africa B. pertussis isolates are available on NCBI, organized under BioProject accession number PRJNA929342.","why":"The dataset identifier appears only in the body text (data availability statement), not in the reference list.","gain":4.17,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"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. 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In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard (e.g., MIAME, MINSEQE, MIxS) is named; only a manuscript reporting guideline is absent. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. 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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":"The reference genome used was B. pertussis E476 (vaccine strain: Tohama I – accession number: CP010964).","why":"The paper includes an identifier (CP010964) for a reference genome that is not its own dataset. [downgraded to 'no' — no verifiable quote from the paper]","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":null,"why":"No sentence in the paper addresses when the data become available or how long they persist. [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.","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. 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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":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:05:35.564550Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}