Identification of the antibacterial mechanism of cryptotanshinone on methicillin-resistant Staphylococcus aureus using bioinformatics analysis.

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This study aims to determine the antibacterial mechanisms of CT by integrating bioinformatics analysis and microbiology assay. The microarray data of GSE13203 was retrieved from the Gene Expression Omnibus (GEO) database to screen the differentially expressed genes (DEGs) of S. aureus strains that were treated with CT treatment. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to identify the potential target of CT. Data mining on the microarray dataset indicated that pyruvate kinase (PK) might be involved in the antimicrobial activities of CT. The minimum inhibition concentrations (MICs) of CT or vancomycin against the MRSA strain ATCC43300 and seven other clinical strains were determined using the broth dilution method. The effects of CT on the activity of PK were further measured. In vitro tests verified that CT inhibited the growth of an MRSA reference strain and seven other clinical strains. CT hampered the activity of the PK of ATCC43300 and five clinical MRSA strains. CT might hinder bacterial energy metabolism by inhibiting the activity of PK.", "claims": [{"id": "claim-method", "statement": "Then, gene expression differences between the CT treated samples and the control group were identified using the limma R package with the Empirical Bayes method29. The Benjamini–Hochberg false discovery rate (FDR) was used to correct for p-value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34741111", "locator": "sections[10] \"Raw data preprocessing and screening of DEGs\" paragraph 2", "quote": "Then, gene expression differences between the CT treated samples and the control group were identified using the limma R package with the Empirical Bayes method29. 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