{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T22:34:07Z","timestamp":1788820447798,"version":"build-2803163510"},"reference-count":101,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T00:00:00Z","timestamp":1763078400000},"content-version":"vor","delay-in-days":38,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Staphylococcus aureus is a pathogenic bacterium that is increasingly resistant to antibiotics. To identify genes that facilitate this resistance, we analyzed 1062 genomes from the NCBI Genome database. From these genomes, we compile a list of 229 antimicrobial resistance (AMR) genes from the CARD, ResFinder, MEGARes, and AR-ANNOT databases. We then constructed and analyzed their interaction network using multiple network analysis tools to identify critical central genes, designated as hub genes. Our findings revealed that\u00a0mecA, fosB, arlR, mepA, mgrA, and arlS held the highest significance in the interaction network, suggesting their roles as key genes in AMR. To further examine these genes, we performed functional enrichment and molecular function analyses to better understand the biological processes these genes impact. Additionally, our results indicate that these central genes are predominantly associated with antibiotic efflux and target replacement. These mechanisms confer resistance to disinfectants, fluoroquinolones, antiseptics, tetracyclines, and \u03b2-lactam penicillin. Identifying core genes associated with AMR and characterizing their biological functions provides crucial insight into the potential for developing new therapeutic strategies.<\/jats:p>","DOI":"10.1093\/nargab\/lqaf147","type":"journal-article","created":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T06:03:12Z","timestamp":1763100192000},"source":"Crossref","is-referenced-by-count":4,"title":["Network analysis of antimicrobial resistance in\n                    <i>Staphylococcus aureus<\/i>\n                    : characterization of hub genes and their functional implications"],"prefix":"10.1093","volume":"7","author":[{"given":"Md Imran","family":"Hasan","sequence":"first","affiliation":[{"name":"Texas A&M University-San Antonio, Texas, One University Way Department of Natural Sciences, , 78224 Texas ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davida S","family":"Smyth","sequence":"additional","affiliation":[{"name":"Texas A&M University-San Antonio, Texas, One University Way Department of Natural Sciences, , 78224 Texas ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3613-9517","authenticated-orcid":false,"given":"Ashley I","family":"Teufel","sequence":"additional","affiliation":[{"name":"Texas A&M University-San Antonio, Texas, One University Way Department of Natural Sciences, , 78224 Texas ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,11,14]]},"reference":[{"key":"2025111401030854700_B1","doi-asserted-by":"publisher","first-page":"11387","DOI":"10.3389\/bjbs.2023.11387","article-title":"Antimicrobial Resistance (AMR)","volume":"80","author":"Tang","year":"2023","journal-title":"Brit J Biom Sci"},{"key":"2025111401030854700_B2","doi-asserted-by":"publisher","first-page":"E3463","DOI":"10.1073\/pnas.1717295115","article-title":"Global increase and geographic convergence in antibiotic consumption between 2000 and 2015","volume":"115","author":"Klein","year":"2018","journal-title":"Proc Natl Acad Sci"},{"key":"2025111401030854700_B3","doi-asserted-by":"publisher","first-page":"74","DOI":"10.3126\/jmcjms.v11i2.58030","article-title":"Knowledge and beliefs about antimicrobial drug resistance and its implications in future prescribers","volume":"11","author":"Chaurasia","year":"2023","journal-title":"Janaki Medical College Journal of Medical Science"},{"key":"2025111401030854700_B4","article-title":"Others. Antimicrobial resistance: global report on surveillance","author":"World Health Organization","year":"2014"},{"key":"2025111401030854700_B5","article-title":"WHO bacterial priority pathogens list, 2024: bacterial pathogens of public health importance, to guide research, development and strategies to prevent and control antimicrobial resistance","author":"World Health Organization","year":"2024"},{"key":"2025111401030854700_B6","doi-asserted-by":"publisher","first-page":"46","DOI":"10.14202\/vetworld.2023.46-58","article-title":"A review of new emerging livestock-associated methicillin-resistant Staphylococcus aureus from pig farms","volume":"16","author":"Khairullah","year":"2023","journal-title":"Veterinary World"},{"key":"2025111401030854700_B7","first-page":"526","article-title":"The epidemiology of Staphylococcus infections","volume-title":"Gram-Positive Pathogens","author":"Tenover","year":"2006"},{"key":"2025111401030854700_B8","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1016\/j.arcmed.2005.06.009","article-title":"Resistance to antibiotics: are we in the post-antibiotic era?","volume":"36","author":"Alanis","year":"2005","journal-title":"Archiv Med Res"},{"key":"2025111401030854700_B9","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1128\/AAC.44.6.1549-1555.2000","article-title":"A new class of genetic element, staphylococcal cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus","volume":"44","author":"Katayama","year":"2000","journal-title":"Antimicrob Agents Chem"},{"key":"2025111401030854700_B10","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1016\/j.tim.2017.05.011","article-title":"Transfer of antibiotic resistance in Staphylococcus aureus","volume":"25","author":"Haaber","year":"2017","journal-title":"Trends Microbiol"},{"key":"2025111401030854700_B11","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/s13059-017-1252-9","article-title":"Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice","volume":"18","author":"Harkins","year":"2017","journal-title":"Genome Biol"},{"key":"2025111401030854700_B12","doi-asserted-by":"publisher","first-page":"e01939","DOI":"10.1128\/AAC.01939-19","article-title":"Comprehensive genetic analysis of SCCmec elements from methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococci","volume":"64","author":"Iwase","year":"2020","journal-title":"Antimicrob Agents Chem"},{"key":"2025111401030854700_B13","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1080\/07853890701195262","article-title":"Efflux pumps as antimicrobial resistance mechanisms","volume":"39","author":"Poole","year":"2007","journal-title":"Ann Med"},{"key":"2025111401030854700_B14","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1128\/mr.51.1.88-134.1987","article-title":"Antimicrobial resistance of Staphylococcus aureus: genetic basis","volume":"51","author":"Lyon","year":"1987","journal-title":"Microbiol Rev"},{"key":"2025111401030854700_B15","doi-asserted-by":"publisher","first-page":"1429","DOI":"10.1046\/j.1365-2958.2003.03526.x","article-title":"Autoinduction and signal transduction in the regulation of staphylococcal virulence","volume":"48","author":"Novick","year":"2003","journal-title":"Mol Microbiol"},{"key":"2025111401030854700_B16","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/j.femsle.2004.11.016","article-title":"Quorum-sensing control in Staphylococci\u2014a target for antimicrobial drug therapy?","volume":"241","author":"Otto","year":"2004","journal-title":"FEMS Microbiol Lett"},{"key":"2025111401030854700_B17","doi-asserted-by":"publisher","first-page":"55","DOI":"10.3389\/fmicb.2018.00055","article-title":"Therapeutic targeting of the Staphylococcus aureus accessory gene regulator (agr) system","volume":"9","author":"Tan","year":"2018","journal-title":"Front Microbiol"},{"key":"2025111401030854700_B18","doi-asserted-by":"publisher","first-page":"4814","DOI":"10.1128\/JB.180.18.4814-4820.1998","article-title":"Deletion of the alternative sigma factor sigB in Staphylococcus aureus reveals its function as a global regulator of virulence genes","volume":"180","author":"Kullik","year":"1998","journal-title":"J Bacteriol"},{"key":"2025111401030854700_B19","doi-asserted-by":"publisher","first-page":"33","DOI":"10.3389\/fcimb.2012.00033","article-title":"Staphylococcal response to oxidative stress","volume":"2","author":"Gaupp","year":"2012","journal-title":"Front Cell Inf Microbiol"},{"key":"2025111401030854700_B20","doi-asserted-by":"publisher","first-page":"9175","DOI":"10.1074\/jbc.M808279200","article-title":"A close-up view of the VraSR two-component system: a mediator of antibiotic resistance in Staphylococcus aureus","volume":"284","author":"Belcheva","year":"2009","journal-title":"J Biol Chem"},{"key":"2025111401030854700_B21","doi-asserted-by":"publisher","first-page":"3334","DOI":"10.1038\/s41433-023-02539-3","article-title":"Single-cell transcriptomics of the ocular anterior segment: a comprehensive review","volume":"3:7","author":"Ahsanuddin","year":"2023","journal-title":"Eye (London, England)"},{"key":"2025111401030854700_B22","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/nature08454","article-title":"Molecular networks as sensors and drivers of common human diseases","volume":"461","author":"Schadt","year":"2009","journal-title":"Nature"},{"key":"2025111401030854700_B23","doi-asserted-by":"publisher","first-page":"146995","DOI":"10.1016\/j.gene.2022.146995","article-title":"Emergence of sulphonamide resistance in azithromycin-resistant pediatric strains of Salmonella typhi and Paratyphi A: a genomics insight","volume":"851","author":"Kumar","year":"2023","journal-title":"Gene"},{"key":"2025111401030854700_B24","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/s41579-023-00933-y","article-title":"Antibiotic perturbations to the gut microbiome","volume":"21","author":"Fishbein","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"2025111401030854700_B25","article-title":"Investigating Sandhoff Disease in Saskatchewan","author":"Fitterer","year":"2013"},{"key":"2025111401030854700_B26","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.ymthe.2022.09.017","article-title":"Preclinical studies in Krabbe disease: a model for the investigation of novel combination therapies for lysosomal storage diseases","volume":"31","author":"Heller","year":"2023","journal-title":"Mol Ther"},{"key":"2025111401030854700_B27","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.pbiomolbio.2023.02.002","article-title":"Latent tuberculosis and computational biology: a less-talked affair","volume":"178","author":"Sarmah","year":"2023","journal-title":"Prog Biophys Mol Biol"},{"key":"2025111401030854700_B28","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1038\/s41576-023-00649-y","article-title":"Genomic surveillance for antimicrobial resistance\u2014a one health perspective","volume":"25","author":"Djordjevic","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2025111401030854700_B29","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1021\/pr100918u","article-title":"Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus","volume":"10","author":"Cherkasov","year":"2011","journal-title":"J Proteome Res"},{"key":"2025111401030854700_B30","doi-asserted-by":"publisher","first-page":"10796","DOI":"10.1038\/s41598-018-29120-3","article-title":"Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus","volume":"8","author":"Kim","year":"2018","journal-title":"Sci Rep"},{"key":"2025111401030854700_B31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12866-021-02392-y","article-title":"Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis","volume":"21","author":"Li","year":"2021","journal-title":"BMC Microbiol"},{"key":"2025111401030854700_B32","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.gene.2015.08.068","article-title":"Gene network analysis reveals the association of important functional partners involved in antibiotic resistance: a report on an important pathogenic bacterium Staphylococcus aureus","volume":"575","author":"Anitha","year":"2016","journal-title":"Gene"},{"key":"2025111401030854700_B33","doi-asserted-by":"publisher","first-page":"4148","DOI":"10.1016\/j.csbj.2024.11.011","article-title":"Machine learning and network analysis with focus on the biofilm in Staphylococcus aureus","volume":"23","author":"Zhang","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"key":"2025111401030854700_B34","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1186\/s12866-024-03692-9","article-title":"Advancements in MRSA treatment: the role of berberine in enhancing antibiotic therapy","volume":"24","author":"Zhou","year":"2024","journal-title":"BMC Microbiol"},{"key":"2025111401030854700_B35","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.ejps.2017.06.003","article-title":"Identification of histone deacetylase (HDAC) as a drug target against MRSA via interolog method of protein-protein interaction prediction","volume":"106","author":"Uddin","year":"2017","journal-title":"Eur J Pharm Sci"},{"key":"2025111401030854700_B36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-021-04342-x","article-title":"Centrality of drug targets in protein networks","volume":"22","author":"Viacava\u00a0Follis","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2025111401030854700_B37","first-page":"D517","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025111401030854700_B38","doi-asserted-by":"publisher","first-page":"000748","DOI":"10.1099\/mgen.0.000748","article-title":"ResFinder\u2013an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes","volume":"8","author":"Florensa","year":"2022","journal-title":"Microbial Genom"},{"key":"2025111401030854700_B39","doi-asserted-by":"publisher","first-page":"D561","DOI":"10.1093\/nar\/gkz1010","article-title":"MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data","volume":"48","author":"Doster","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025111401030854700_B40","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob Agents Chem"},{"key":"2025111401030854700_B41","doi-asserted-by":"publisher","first-page":"D492","DOI":"10.1093\/nar\/gkp858","article-title":"The NCBI biosystems database","volume":"38","author":"Geer","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2025111401030854700_B42","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob Agents Chem"},{"key":"2025111401030854700_B43","doi-asserted-by":"publisher","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025111401030854700_B44","article-title":"GitHub-tseemann\/abricate: mass screening of contigs for antimicrobial and virulence genes","author":"Seemann","year":"2020","journal-title":"GitHub"},{"key":"2025111401030854700_B45","doi-asserted-by":"publisher","first-page":"15189","DOI":"10.1038\/s41598-023-42154-6","article-title":"Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae","volume":"13","author":"Vieira","year":"2023","journal-title":"Sci Rep"},{"key":"2025111401030854700_B46","doi-asserted-by":"publisher","first-page":"e00261","DOI":"10.1128\/spectrum.00261-22","article-title":"Detection of a novel metallo-\u03b2-lactamase, CAM-2, in a metagenome-assembled genome from China","volume":"10","author":"Xiang","year":"2022","journal-title":"Microbiol Spect"},{"key":"2025111401030854700_B47","doi-asserted-by":"publisher","first-page":"e1219","DOI":"10.1002\/mbo3.1219","article-title":"Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment","volume":"10","author":"Antelo","year":"2021","journal-title":"MicrobiologyOpen"},{"key":"2025111401030854700_B48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-15-293","article-title":"jvenn: an interactive Venn diagram viewer","volume":"15","author":"Bardou","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2025111401030854700_B49","doi-asserted-by":"publisher","first-page":"2348","DOI":"10.7150\/ijbs.57810","article-title":"Capivasertib restricts SARS-CoV-2 cellular entry: a potential clinical application for COVID-19","volume":"17","author":"Sun","year":"2021","journal-title":"Int J Biol Sci"},{"key":"2025111401030854700_B50","doi-asserted-by":"publisher","first-page":"5216","DOI":"10.1080\/21655979.2022.2037374","article-title":"Hepatoprotective mechanism of Silybum marianum on nonalcoholic fatty liver disease based on network pharmacology and experimental verification","volume":"13","author":"Jiang","year":"2022","journal-title":"Bioengineered"},{"key":"2025111401030854700_B51","doi-asserted-by":"publisher","first-page":"D808","DOI":"10.1093\/nar\/gks1094","article-title":"STRING v9. 1: protein\u2013protein interaction networks, with increased coverage and integration","volume":"41","author":"Franceschini","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025111401030854700_B52","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2025111401030854700_B53","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1038\/nature02555","article-title":"Evidence for dynamically organized modularity in the yeast protein\u2013protein interaction network","volume":"430","author":"Han","year":"2004","journal-title":"Nature"},{"key":"2025111401030854700_B54","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1752-0509-8-S4-S11","article-title":"cytoHubba: identifying hub objects and sub-networks from complex interactome","volume":"8","author":"Chin","year":"2014","journal-title":"BMC Syst Biol"},{"key":"2025111401030854700_B55","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1038\/s41598-020-79235-9","article-title":"Identifying of biomarkers associated with gastric cancer based on 11 topological analysis methods of CytoHubba","volume":"11","author":"Ma","year":"2021","journal-title":"Sci Rep"},{"key":"2025111401030854700_B56","first-page":"1","article-title":"The igraph software","volume":"1695","author":"Csardi","year":"2006","journal-title":"Complex syst"},{"key":"2025111401030854700_B57","doi-asserted-by":"publisher","first-page":"105737","DOI":"10.1016\/j.micpath.2022.105737","article-title":"Functional insights of antibiotic resistance mechanism in Helicobacter pylori: Driven by gene interaction network and centrality-based nodes essentiality analysis","volume":"171","author":"Gollapalli","year":"2022","journal-title":"Microb Pathogenesis"},{"key":"2025111401030854700_B58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-021-04459-z","article-title":"PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains","volume":"22","author":"Her","year":"2021","journal-title":"BMC bioinformatics"},{"key":"2025111401030854700_B59","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"2025111401030854700_B60","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"2025111401030854700_B61","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","article-title":"phytools: an R package for phylogenetic comparative biology (and other things)","author":"Revell","year":"2012","journal-title":"Methods Ecol Evol"},{"key":"2025111401030854700_B62","doi-asserted-by":"publisher","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","article-title":"ShinyGO: a graphical gene-set enrichment tool for animals and plants","volume":"36","author":"Ge","year":"2020","journal-title":"Bioinformatics"},{"key":"2025111401030854700_B63","doi-asserted-by":"publisher","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The Gene Ontology knowledgebase in 2023","volume":"224","author":"Aleksander","year":"2023","journal-title":"Genetics"},{"key":"2025111401030854700_B64","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1093\/nar\/gkg034","article-title":"STRING: a database of predicted functional associations between proteins","volume":"31","author":"Mering","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2025111401030854700_B65","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1038\/s41467-019-08746-5","article-title":"Scale-free networks are rare","volume":"10","author":"Broido","year":"2019","journal-title":"Nat Commun"},{"key":"2025111401030854700_B66","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/j.compbiolchem.2004.07.001","article-title":"Scale-free networks versus evolutionary drift","volume":"28","author":"Przytycka","year":"2004","journal-title":"Comput Biol Chem"},{"key":"2025111401030854700_B67","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.cotox.2020.03.004","article-title":"Antibiotics-induced oxidative stress","volume":"20","author":"Guillouzo","year":"2020","journal-title":"Curr Opin Toxicol"},{"key":"2025111401030854700_B68","unstructured":"Teufel A, Smyth D. GoPopPie: an R Package for hybrid Piechart-Lollipop plots for gene ontology enrichment visualization. Zenodo. 2025. 10.5281\/zenodo.15936975."},{"key":"2025111401030854700_B69","doi-asserted-by":"publisher","first-page":"e1000605","DOI":"10.1371\/journal.pcbi.1000605","article-title":"Annotation error in public databases: misannotation of molecular function in enzyme superfamilies","volume":"5","author":"Schnoes","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2025111401030854700_B70","doi-asserted-by":"publisher","first-page":"e1009935","DOI":"10.1371\/journal.pcbi.1009935","article-title":"Urgent need for consistent standards in functional enrichment analysis","volume":"18","author":"Wijesooriya","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2025111401030854700_B71","doi-asserted-by":"publisher","first-page":"4383","DOI":"10.1093\/bioinformatics\/btaa548","article-title":"Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons","volume":"36","author":"Wei","year":"2020","journal-title":"Bioinformatics"},{"key":"2025111401030854700_B72","doi-asserted-by":"publisher","first-page":"3283","DOI":"10.1128\/AAC.00220-13","article-title":"The Staphylococcus aureus thiol\/oxidative stress global regulator Spx controls trfA, a gene implicated in cell wall antibiotic resistance","volume":"57","author":"Jousselin","year":"2013","journal-title":"Antimicrob Agents Chem"},{"key":"2025111401030854700_B73","doi-asserted-by":"publisher","first-page":"e03117","DOI":"10.1128\/spectrum.03117-22","article-title":"Pan-genome analysis of Staphylococcus aureus reveals key factors influencing genomic plasticity","volume":"10","author":"Liu","year":"2022","journal-title":"Microbiol Spect"},{"key":"2025111401030854700_B74","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1128\/MMBR.66.4.671-701.2002","article-title":"Regulation of bacterial drug export systems","volume":"66","author":"Grkovic","year":"2002","journal-title":"Microbiol Mol Biol Rev"},{"key":"2025111401030854700_B75","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s12866-023-02785-1","article-title":"Genomic and phenotypic profiling of Staphylococcus aureus isolates from bovine mastitis for antibiotic resistance and intestinal infectivity","volume":"23","author":"Majumder","year":"2023","journal-title":"BMC Microbiol"},{"key":"2025111401030854700_B76","doi-asserted-by":"publisher","first-page":"1378","DOI":"10.3390\/antibiotics11101378","article-title":"Molecular basis of non-$\\beta$-lactam antibiotics resistance in Staphylococcus aureus","volume":"11","author":"Lade","year":"2022","journal-title":"Antibiotics"},{"key":"2025111401030854700_B77","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1002\/iub.1289","article-title":"Penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus","volume":"66","author":"Fishovitz","year":"2014","journal-title":"IUBMB Life"},{"key":"2025111401030854700_B78","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.drup.2016.04.003","article-title":"Multidrug efflux pumps of Gram-positive bacteria","volume":"27","author":"Schindler","year":"2016","journal-title":"Drug Resistance Updates"},{"key":"2025111401030854700_B79","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1016\/j.diagmicrobio.2012.08.001","article-title":"Molecular epidemiology of methicillin-resistant Staphylococcus aureus in a Spanish hospital over a 4-year period: clonal replacement, decreased antimicrobial resistance, and identification of community-acquired and livestock-associated clones","volume":"74","author":"Menegotto","year":"2012","journal-title":"Diagn Micr Infec Dis"},{"key":"2025111401030854700_B80","doi-asserted-by":"publisher","first-page":"e1007800","DOI":"10.1371\/journal.ppat.1007800","article-title":"Staphylococcus aureus adhesion in endovascular infections is controlled by the ArlRS\u2013MgrA signaling cascade","volume":"15","author":"Kwiecinski","year":"2019","journal-title":"PLoS Pathogens"},{"key":"2025111401030854700_B81","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.ijbiomac.2021.08.199","article-title":"Focused review on dual inhibition of quorum sensing and efflux pumps: a potential way to combat multi drug resistant Staphylococcus aureus infections","volume":"190","author":"Kaur","year":"2021","journal-title":"Int J Biol Macromol"},{"key":"2025111401030854700_B82","doi-asserted-by":"publisher","first-page":"5967","DOI":"10.1016\/j.biomaterials.2012.05.031","article-title":"Biofilm formation in Staphylococcus implant infections. A review of molecular mechanisms and implications for biofilm-resistant materials","volume":"33","author":"Arciola","year":"2012","journal-title":"Biomaterials"},{"key":"2025111401030854700_B83","doi-asserted-by":"publisher","first-page":"16907","DOI":"10.1038\/s41598-020-73796-5","article-title":"Identification and characterization of mutations responsible for the $\\beta$-lactam resistance in oxacillin-susceptible mecA-positive Staphylococcus aureus","volume":"10","author":"Boonsiri","year":"2020","journal-title":"Sci Rep"},{"key":"2025111401030854700_B84","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.mimet.2011.04.012","article-title":"A novel flow cytometry-based assay for the quantification of Staphylococcus aureus adhesion to and invasion of eukaryotic cells","volume":"86","author":"Trouillet","year":"2011","journal-title":"J Microbiol Methods"},{"key":"2025111401030854700_B85","doi-asserted-by":"publisher","first-page":"e98216","DOI":"10.1172\/jci.insight.98216","article-title":"Targeting fundamental pathways to disrupt Staphylococcus aureus survival: clinical implications of recent discoveries","volume":"3","author":"Thomsen","year":"2018","journal-title":"JCI insight"},{"key":"2025111401030854700_B86","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.jprot.2013.10.027","article-title":"Proteome studies of bacterial antibiotic resistance mechanisms","volume":"97","author":"Vranakis","year":"2014","journal-title":"J Proteomics"},{"key":"2025111401030854700_B87","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1128\/CMR.00117-14","article-title":"The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria","volume":"28","author":"Li","year":"2015","journal-title":"Clin Microbiol Rev"},{"key":"2025111401030854700_B88","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1073\/pnas.96.3.887","article-title":"The minimal gene set member msrA, encoding peptide methionine sulfoxide reductase, is a virulence determinant of the plant pathogen Erwinia chrysanthemi","volume":"96","author":"Hassouni","year":"1999","journal-title":"Proc Natl Acad Sci"},{"key":"2025111401030854700_B89","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.3390\/antibiotics12071225","article-title":"Epidemiology of antimicrobial resistance genes in Staphyloccocus aureus isolates from a public database in a one health perspective\u2014sample characteristics and isolates\u2019 sources","volume":"12","author":"Zaghen","year":"2023","journal-title":"Antibiotics"},{"key":"2025111401030854700_B90","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1007\/s13205-020-02387-y","article-title":"Characterization of methicillin-resistant Staphylococcus aureus through genomics approach","volume":"10","author":"Naorem","year":"2020","journal-title":"3 Biotech"},{"key":"2025111401030854700_B91","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1002\/med.21591","article-title":"Efflux pump inhibitors of clinically relevant multidrug resistant bacteria","volume":"39","author":"Lamut","year":"2019","journal-title":"Med Res Rev"},{"key":"2025111401030854700_B92","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1111\/mmi.14404","article-title":"The Staphylococcus aureus ArlRS two-component system regulates virulence factor expression through MgrA","volume":"113","author":"Crosby","year":"2020","journal-title":"Mol Microbiol"},{"key":"2025111401030854700_B93","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1128\/JB.188.5.1899-1910.2006","article-title":"Transcription profiling of the mgrA regulon in Staphylococcus aureus","volume":"188","author":"Luong","year":"2006","journal-title":"J Bacteriol"},{"key":"2025111401030854700_B94","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1093\/jac\/dkad126","article-title":"Up-regulation of resident chromosomal fosB gene expression: a novel mechanism of acquired fosfomycin resistance in MRSA","volume":"78","author":"Aiezza","year":"2023","journal-title":"J Antimicrob Chemother"},{"key":"2025111401030854700_B95","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1128\/AAC.50.4.1276-1281.2006","article-title":"MepR, a repressor of the Staphylococcus aureus MATE family multidrug efflux pump MepA, is a substrate-responsive regulatory protein","volume":"50","author":"Kaatz","year":"2006","journal-title":"Antimicrob Agents Chem"},{"key":"2025111401030854700_B96","doi-asserted-by":"publisher","first-page":"14036","DOI":"10.1073\/pnas.1509251112","article-title":"RNAIII of the Staphylococcus aureus agr system activates global regulator MgrA by stabilizing mRNA","volume":"112","author":"Gupta","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"2025111401030854700_B97","doi-asserted-by":"publisher","first-page":"3345","DOI":"10.1007\/s11030-025-11125-6","article-title":"Machine learning and cheminformatics-based identification of lichen-derived compounds targeting mutant PBP4R200L in Staphylococcus aureus","volume":"29","author":"Mathpal","year":"2025","journal-title":"Mol Divers"},{"key":"2025111401030854700_B98","doi-asserted-by":"publisher","first-page":"7751","DOI":"10.1002\/jcb.28049","article-title":"FtsA as a cidal target for Staphylococcus aureus: molecular docking and dynamics studies","volume":"120","author":"Ragunathan","year":"2019","journal-title":"J Cell Biochem"},{"key":"2025111401030854700_B99","article-title":"Antimicrobial Resistance Threats Update 2022 [Government Report]","author":"Centers for Disease Control and Prevention","year":"2024"},{"key":"2025111401030854700_B100","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat Commun"},{"key":"2025111401030854700_B101","doi-asserted-by":"publisher","first-page":"bav001","DOI":"10.1093\/database\/bav001","article-title":"EcoliNet: a database of cofunctional gene network for Escherichia coli","volume":"2015","author":"Kim","year":"2015","journal-title":"Database"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/7\/4\/lqaf147\/65287099\/lqaf147.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/7\/4\/lqaf147\/65287099\/lqaf147.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T06:03:17Z","timestamp":1763100197000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqaf147\/8322739"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,7]]},"references-count":101,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,10,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqaf147","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,12]]},"published":{"date-parts":[[2025,10,7]]},"article-number":"lqaf147"}}