A General Map of Transcriptional Expression of Virulence, Metabolism, and Biofilm Formation Adaptive Changes of Staphylococcus aureus When Exposed to Different Antimicrobials.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35783396", "kind": "science-record", "revision": 5, "content_hash": "sha256:891c08d19cce3360414fcdcff501595a8bb8a99e9929915beeab435a3a11d387", "created_at": "2026-11-01T18:14:49Z", "updated_at": "2026-11-01T22:49:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A General Map of Transcriptional Expression of Virulence, Metabolism, and Biofilm Formation Adaptive Changes of Staphylococcus aureus When Exposed to Different Antimicrobials.", "doi": "10.3389/fmicb.2022.825041", "pmid": "35783396", "authors": ["Zun Ren", "Jinlong Yu", "Jiafei Du", "Yubo Zhang", "Musha Hamushan", "Feng Jiang", "Feiyang Zhang", "Boyong Wang", "Jin Tang", "Hao Shen", "Pei Han"], "journal": "Frontiers in microbiology", "year": 2022, "abstract": "Biofilm formation of Staphylococcus aureus is the major cause of implant-associated infections (IAIs). Antimicrobial treatment is one of the most effective therapeutic options for S. aureus infections. However, it can also lead to adaptive transcriptomic changes due to extreme selective pressure, which may increase the risk of antimicrobial resistance. To study the transcriptional changes in S. aureus upon exposure to antimicrobial agents, we obtained expression profiles of S. aureus treated with six antimicrobials (flucloxacillin, vancomycin, ciprofloxacin, clindamycin, erythromycin, and linezolid, n = 6 for each group). We also included an untreated control group (n = 8) downloaded from the Gene Expression Omnibus (GEO) database (GSE70043, GSE56100) for integrated bioinformatic analyses. We identified 82 (44 up, 38 down) and 53 (17 up, 36 down) differentially expressed genes (DEGs) in logarithmic and stationary phases, respectively. When exposed to different antimicrobial agents, we found that manganese import system genes and immune response gene sbi (immunoglobulin G-binding protein Sbi) were upregulated in S. aureus at all stages. During the logarithmic phase, we observed adaptive transcriptomic changes in S. aureus mainly in the stability of protein synthesis, adhesion, and biofilm formation. In the stationary phase, we observed a downregulation in genes related to amino biosynthesis, ATP synthesis, and DNA replication. We verified these results by qPCR. Importantly, these results could help our understanding of the molecular mechanisms underlying the proliferation and antimicrobial resistance of S. aureus.", "claims": [{"id": "claim-method", "statement": "Gene differential expression analysis was performed using the limma package (Ritchie et al., 2015). Genes with a corrected p < 0.05 and log2 fold change (FC) > 1 were considered to be DEGs. The integration of microarray data was performed by the “aggregateRanks” function (Kolde et al., 2012) following the Robust Rank Aggregation (RRA) procedure in R (Kolde et al., 2012).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35783396", "locator": "sections[4] \"Differentially Expressed Genes Analysis\" paragraph 2", "quote": "Gene differential expression analysis was performed using the limma package (Ritchie et al., 2015). Genes with a corrected p < 0.05 and log2 fold change (FC) > 1 were considered to be DEGs. The integration of microarray data was performed by the “aggregateRanks” function (Kolde et al., 2012) following the Robust Rank Aggregation (RRA) procedure in R (Kolde et al., 2012)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The microarray data (GSE70043 and GSE56100) are available on the GEO DataSets database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35783396", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The microarray data (GSE70043 and GSE56100) are available on the GEO DataSets database (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Robust Rank Aggregation of six public antimicrobial-treated microarray datasets identified 82 differentially expressed genes in the logarithmic phase and 53 in the stationary phase, with the findings verified by qPCR.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35783396", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 82 (44 up, 38 down) and 53 (17 up, 36 down) differentially expressed genes (DEGs) in logarithmic and stationary phases, respectively."}, {"asset": "source:pmid:35783396", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We verified these results by qPCR."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Robust Rank Aggregation of six public antimicrobial-treated microarray datasets identified 82 differentially expressed genes in the logarithmic phase and 53 in the stationary phase, with the findings verified by qPCR.", "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:35783396"], "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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We verified these results by qPCR. Importantly, these results could help our u", "upplementary Figure 2PCR verification of the qPCR primer product size and primer efficiency.Cl", "e. Supplementary Table 1Primer sequences for qPCR.Click here for additional data file."], "order_basis": "paper_text_order:1610", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Gene differential expression analysis was performed using the limma package (Ritchie et al., 2015). Genes with a corrected p < 0.05 and log2 fold change (FC) > 1 were considered to be DEGs. The integration of microarray data was performed by the “aggregateRanks” function (Kolde et al., 2012) following the Robust Rank Aggregation (RRA) procedure in R (Kolde et al., 2012)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}