Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America reveal close similarities.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34168208", "kind": "science-record", "revision": 5, "content_hash": "sha256:dbf360c258367b9fe88a7e0ee110c66acffccc6458c08728aded673b0ef0a975", "created_at": "2026-11-01T15:41:39Z", "updated_at": "2026-11-01T18:55:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America reveal close similarities.", "doi": "10.1038/s41598-021-92684-0", "pmid": "34168208", "authors": ["Dvison de Melo Pacífico", "Cecília Leite Costa", "Hercules Moura", "John R Barr", "Guilherme Augusto Maia", "Vilmar Benetti Filho", "Renato Simões Moreira", "Glauber Wagner", "Regina Maria Cavalcanti Pilotto Domingues", "Carlos Quesada-Gómez", "Eliane de Oliveira Ferreira", "Gerly Anne de Castro Brito"], "journal": "Scientific reports", "year": 2021, "abstract": "Clostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), isolated in Brazil, and NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica. C. difficile isolates were cultured and extracellular proteins were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Genomic analysis revealed that these isolates shared most of the gene composition. Only 83 and 290 NAP1/027 genes were considered singletons in ICC-45 and NAP1/027, respectively. Exoproteome analysis revealed 197 proteins, of which 192 were similar in both strains. Only five proteins were exclusive to the ICC-45 strain. These proteins were involved with catalytic and binding functions and indirectly interacted with proteins related to pathogenicity. Most proteins, including TcdA, TcdB, flagellin subunit, and cell surface protein, were overrepresented in the ICC-45 strain; 14 proteins, including mature S-layer protein, were present in higher proportions in LIBA5756. Data are available via ProteomeXchange with identifier PXD026218. These data show close similarity between the genome and proteins in the supernatant of two strains with hypervirulent features isolated in Latin America and underscore the importance of epidemiological surveillance of the transmission and emergence of new strains.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD026218.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34168208", "locator": "sections[14] \"Exoproteins identification and characterization\" paragraph 4", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD026218."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34168208"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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partner repository with the dataset identifier PXD026218.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD026218.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34168208:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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["Ribulose-phosphate 3-epimerase", "gi|126700194", "rpe1", "24"]], "row_count": 6, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[4]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34168208:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34f16d5937f6457b56493ce05040adfd824a7a0d2bfe39050fb63c642bf3c974", "bytes": 2530, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#Tab2", "version": null, "note": "Relative amount of proteins secreted by Clostridioides difficile strains ICC-45 and NAP1/027 (LIBA5756).", "structure": {"pmcid": "PMC8225638", "section_index": 4, "section_title": "Analysis of proteins identified in culture supernatants of C. difficile strains", "row_count": 33, "column_count": 6}, "table": {"label": "Table 2", "caption": "Relative amount of proteins secreted by Clostridioides 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Genomic analysis revealed that these isolat", "from stress. In agreement with our study, a proteomic analysis of C. difficile 630 strain showed a"], "order_basis": "paper_text_order:603", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["(iscR; a DNA ligand), 4) ribulose phosphate (rpe1; implicated in carbohydrate metabolism), and", "teracts with ribulose-phosphate 3-epimerase (Rpe1), which then interacts with nitroreductase ("], "order_basis": "paper_text_order:2307", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["atants of these two strains9. However, using western blotting, Costa et al.9 showed that ICC-45 releases l"], "order_basis": "paper_text_order:8249", "id": "assay:3"}]}