{"doi":"10.1128/spectrum.02046-23","title":"A group B <i>Streptococcus</i> indexed transposon mutant library to accelerate genetic research on an important perinatal pathogen","abstract":"ABSTRACT Group B Streptococcus (GBS) is a major contributor to sepsis, meningitis, and pneumonia in newborns. Indexed bacterial mutant libraries accelerate pathogenesis research by allowing rapid screening of genes that contribute to disease. In this study, we created and characterized a large-scale GBS indexed library of Himar1 mini-transposon mutant strains grown as monocultures from a mixed transposon insertion library that we had previously used for transposon-genome junction sequencing. We used a high-throughput workflow to identify transposon insertion sites in chromosomal DNA purified from individual mutants. Following quality control steps and the removal of isogenic duplicate strains, we isolated 1,919 monocultures of unique transposon insertion mutants with even dispersion across the GBS genome. Our final library, stored in barcoded, traceable glycerol stocks, contains interruptions of 878 genes and 253 intergenic regions. We also validated select library mutants with confirmatory PCR and, when possible, specific phenotypic testing. While the library contains only sparse interruptions of essential or near-essential genes, the genes represented in the set span a wide range of predicted functional categories, including roles in metabolism, structure, and virulence. In conclusion, we developed and applied a high-throughput molecular analysis and bioinformatic pipeline to generate a GBS indexed library of unprecedented scale that we believe will be a useful genetic tool for fellow GBS researchers. IMPORTANCE Group B Streptococcus (GBS) is a significant global cause of serious infections, most of which affect pregnant women, newborns, and infants. Studying GBS genetic mutant strains is a valuable approach for learning more about how these infections are caused and is a key step toward developing more effective preventative and treatment strategies. In this resource report, we describe a newly created library of defined GBS genetic mutants, containing over 1,900 genetic variants, each with a unique disruption to its chromosome. An indexed library of this scale is unprecedented in the GBS field; it includes strains with mutations in hundreds of genes whose potential functions in human disease remain unknown. We have made this resource freely available to the broader research community through deposition in a publicly funded bacterial maintenance and distribution repository.","journal":"Microbiology Spectrum","year":2023,"id":379219,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":29.844511487584125,"corpus_rank":8690,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5833,"is_data_producer":true,"deposit_databanks":{"BioProject":["PRJNA1000625"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":428426,"name":"Gideon H. Hillebrand","orcid":"0000-0002-3391-4306","position":1,"is_corresponding":false},{"id":255654,"name":"Kathyayini P. Gopalakrishna","orcid":"0000-0001-6309-1841","position":2,"is_corresponding":false},{"id":1144057,"name":"Rebekah A. Rapp","orcid":null,"position":3,"is_corresponding":false},{"id":91697,"name":"Adam J. Ratner","orcid":"0000-0003-1761-794X","position":4,"is_corresponding":false},{"id":88887,"name":"Hervé Tettelin","orcid":"0000-0002-0615-3257","position":5,"is_corresponding":false},{"id":554650,"name":"Thomas A. Hooven","orcid":"0000-0003-1959-186X","position":6,"is_corresponding":false},{"id":490809,"name":"Venkata Hemanjani Bhavana","orcid":"0009-0008-0113-5325","position":0,"is_corresponding":true}],"reference_count":69,"raw_metadata":null,"created_at":"2026-07-19T01:16:52.622552Z","pmid":"37933989","pmcid":"PMC10714824","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":72.2222,"fair_a":56.25,"fair_i":40.0,"fair_r":25.0,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":72.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"PRJNA1000625","grounded":true,"rationale":"The paper provides a BioProject accession (PRJNA1000625) for the sequence reads, which is a persistent identifier scheme recognized in the rubric. [majority verdict 'yes' (4/5 passes agreed)]","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":"One complete mutant library for public access is stored at BEI Resources (beiresources.org).","grounded":true,"rationale":"BEI Resources is a named repository (managed by ATCC, listed in re3data).","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":0.5,"verdict":"partial","evidence":"One complete mutant library for public access is stored at BEI Resources (beiresources.org). 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'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 standard open license (e.g., CC0, CC BY) is named for the data; 'freely available' is not a license artefact.","gain":16.67,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. 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Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"fastq files","why":"The paper states that three fastq files were generated; FASTQ is an open, community-standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). 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