{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T09:31:15Z","timestamp":1749115875216,"version":"3.37.3"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000060","name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["1-U01-AI124316","1-U01-AI124316","1-U01-AI124316","1-U01-AI124316","1-U01-AI124316"],"award-info":[{"award-number":["1-U01-AI124316","1-U01-AI124316","1-U01-AI124316","1-U01-AI124316","1-U01-AI124316"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases"},{"name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases"},{"name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases"},{"name":"U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p><jats:italic>Staphylococcus aureus<\/jats:italic> strains have been continuously evolving resistance to numerous classes of antibiotics including methicillin, vancomycin, daptomycin and linezolid, compounding the enormous healthcare and economic burden of the pathogen. Cation-adjusted Mueller-Hinton broth (CA-MHB) is the standard bacteriological media for measuring antibiotic susceptibility in the clinical lab, but the use of media that more closely mimic the physiological state of the patient, e.g. mammalian tissue culture media, can in certain circumstances reveal antibiotic activities that may be more predictive of effectiveness <jats:italic>in vivo<\/jats:italic>. In the current study, we use both types of media to explore antibiotic resistance phenomena in hospital-acquired USA100 lineage methicillin-resistant, vancomycin-intermediate <jats:italic>Staphylococcus aureus<\/jats:italic> (MRSA\/VISA) strain D712 <jats:italic>via<\/jats:italic> multidimensional high throughput analysis of growth rates, bacterial cytological profiling, RNA sequencing, and exo-metabolomics (HPLC and LC-MS). Here, we share data generated from these assays to shed light on the antibiotic resistance behavior of MRSA\/VISA D712 in both bacteriological and physiological media.<\/jats:p>","DOI":"10.1038\/s41597-019-0331-z","type":"journal-article","created":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T11:02:49Z","timestamp":1576580569000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media"],"prefix":"10.1038","volume":"6","author":[{"given":"Akanksha","family":"Rajput","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3732-2463","authenticated-orcid":false,"given":"Saugat","family":"Poudel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hannah","family":"Tsunemoto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Meehan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Szubin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Connor A.","family":"Olson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Lamsa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8813-5679","authenticated-orcid":false,"given":"Yara","family":"Seif","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Dillon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alison","family":"Vrbanac","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph","family":"Sugie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samira","family":"Dahesh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan M.","family":"Monk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3003-1030","authenticated-orcid":false,"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0975-9019","authenticated-orcid":false,"given":"Rob","family":"Knight","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3847-0422","authenticated-orcid":false,"given":"Victor","family":"Nizet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2357-6785","authenticated-orcid":false,"given":"Bernhard O.","family":"Palsson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam M.","family":"Feist","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joe","family":"Pogliano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,12,17]]},"reference":[{"key":"331_CR1","doi-asserted-by":"publisher","first-page":"e17936","DOI":"10.1371\/journal.pone.0017936","volume":"6","author":"S Monecke","year":"2011","unstructured":"Monecke, S. et al. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One 6, e17936 (2011).","journal-title":"PLoS One"},{"key":"331_CR2","first-page":"269","volume":"90","author":"WA McGuinness","year":"2017","unstructured":"McGuinness, W. A., Malachowa, N. & DeLeo, F. R. Vancomycin Resistance in Staphylococcus aureus. Yale J. Biol. Med. 90, 269\u2013281 (2017).","journal-title":"Yale J. Biol. Med."},{"key":"331_CR3","doi-asserted-by":"publisher","first-page":"5306","DOI":"10.1128\/AAC.02574-14","volume":"58","author":"M Roch","year":"2014","unstructured":"Roch, M. et al. Exposure of Staphylococcus aureus to subinhibitory concentrations of \u03b2-lactam antibiotics induces heterogeneous vancomycin-intermediate Staphylococcus aureus. Antimicrob. Agents Chemother. 58, 5306\u20135314 (2014).","journal-title":"Antimicrob. Agents Chemother."},{"key":"331_CR4","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s00109-013-1100-7","volume":"92","author":"G Sakoulas","year":"2014","unstructured":"Sakoulas, G. et al. Nafcillin enhances innate immune-mediated killing of methicillin-resistant Staphylococcus aureus. J. Mol. Med. 92, 139\u2013149 (2014).","journal-title":"J. Mol. Med."},{"key":"331_CR5","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/jac\/46.3.369","volume":"46","author":"LM Koeth","year":"2000","unstructured":"Koeth, L. M. et al. Comparison of cation-adjusted Mueller-Hinton broth with Iso-Sensitest broth for the NCCLS broth microdilution method. J. Antimicrob. Chemother. 46, 369\u2013376 (2000).","journal-title":"J. Antimicrob. Chemother."},{"key":"331_CR6","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1016\/j.ebiom.2015.05.021","volume":"2","author":"L Lin","year":"2015","unstructured":"Lin, L. et al. Azithromycin Synergizes with Cationic Antimicrobial Peptides to Exert Bactericidal and Therapeutic Activity Against Highly Multidrug-Resistant Gram-Negative Bacterial Pathogens. EBioMedicine 2, 690\u2013698 (2015).","journal-title":"EBioMedicine"},{"key":"331_CR7","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.ebiom.2017.05.026","volume":"20","author":"SC Ersoy","year":"2017","unstructured":"Ersoy, S. C. et al. Correcting a Fundamental Flaw in the Paradigm for Antimicrobial Susceptibility Testing. EBioMedicine 20, 173\u2013181 (2017).","journal-title":"EBioMedicine"},{"key":"331_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-019-0051-4","volume":"6","author":"S Poudel","year":"2019","unstructured":"Poudel, S. et al. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data 6, 43 (2019).","journal-title":"Sci Data"},{"key":"331_CR9","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa, F. et al. Scikit-learn: Machine Learning in Python. J. Mach. Learn. Res. 12, 2825\u20132830 (2011).","journal-title":"J. Mach. Learn. Res."},{"key":"331_CR10","doi-asserted-by":"publisher","first-page":"16169","DOI":"10.1073\/pnas.1311066110","volume":"110","author":"P Nonejuie","year":"2013","unstructured":"Nonejuie, P., Burkart, M., Pogliano, K. & Pogliano, J. Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules. Proc. Natl. Acad. Sci. USA 110, 16169\u201316174 (2013).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"331_CR11","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.ebiom.2016.01.020","volume":"4","author":"DT Quach","year":"2016","unstructured":"Quach, D. T., Sakoulas, G., Nizet, V., Pogliano, J. & Pogliano, K. Bacterial Cytological Profiling (BCP) as a Rapid and Accurate Antimicrobial Susceptibility Testing Method for Staphylococcus aureus. EBioMedicine 4, 95\u2013103 (2016).","journal-title":"EBioMedicine"},{"key":"331_CR12","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2006-7-10-r100","volume":"7","author":"AE Carpenter","year":"2006","unstructured":"Carpenter, A. E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).","journal-title":"Genome Biol."},{"key":"331_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2003\/548678","volume":"25","author":"K Rodenacker","year":"2003","unstructured":"Rodenacker, K. & Bengtsson, E. A feature set for cytometry on digitized microscopic images. Anal. Cell. Pathol. 25, 1\u201336 (2003).","journal-title":"Anal. Cell. Pathol."},{"key":"331_CR14","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1086\/514622","volume":"27","author":"JD Turnidge","year":"1998","unstructured":"Turnidge, J. D. The pharmacodynamics of beta-lactams. Clin. Infect. Dis. 27, 10\u201322 (1998).","journal-title":"Clin. Infect. Dis."},{"year":"2019","author":"JM Monk","key":"331_CR15","unstructured":"Monk, J. M. Staphylococcus aureus strain D712, whole genome shotgun sequencing project. GenBank, https:\/\/identifiers.org\/ncbi\/insdc:VFJD00000000.1 (2019)."},{"key":"331_CR16","unstructured":"Andrews, S. A quality control tool for high throughput sequence data. FastQC, http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/ (2010)."},{"key":"331_CR17","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"331_CR18","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","volume":"28","author":"JT Leek","year":"2012","unstructured":"Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882\u2013883 (2012).","journal-title":"Bioinformatics"},{"key":"331_CR19","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","volume":"8","author":"WE Johnson","year":"2007","unstructured":"Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118\u2013127 (2007).","journal-title":"Biostatistics"},{"year":"2019","author":"Palsson B","key":"331_CR20","unstructured":"Palsson, B. Staphylococcus aureus D712 LC\/MS, HPLC, BPC data. MassIVE, https:\/\/identifiers.org\/massive:MSV000084027 (2019)."},{"key":"331_CR21","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.8251049.v2","author":"A Rajput","year":"2019","unstructured":"Rajput, A. Growth Curve data (OD600). figshare, https:\/\/doi.org\/10.6084\/m9.figshare.8251049.v2 (2019)."},{"key":"331_CR22","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.8251340.v6","author":"A Rajput","year":"2019","unstructured":"Rajput, A. RNAseq pipeline. figshare, https:\/\/doi.org\/10.6084\/m9.figshare.8251340.v6 (2019)."},{"year":"2019","key":"331_CR23","unstructured":"NCBI Sequence Read Archive, http:\/\/identifiers.org\/ncbi\/insdc.sra:SRP188430 (2019)."},{"year":"2019","key":"331_CR24","unstructured":"Gene Expression Omnibus, https:\/\/identifiers.org\/GEO:GSE139141 (2019)."},{"key":"331_CR25","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.8251211.v1","author":"A Rajput","year":"2019","unstructured":"Rajput, A. RNAseq summary stats. figshare, https:\/\/doi.org\/10.6084\/m9.figshare.8251211.v1 (2019)."},{"key":"331_CR26","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.8251310.v1","author":"A Rajput","year":"2019","unstructured":"Rajput, A. Batch correction (RNAseq). figshare, https:\/\/doi.org\/10.6084\/m9.figshare.8251310.v1 (2019)."}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41597-019-0331-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-019-0331-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-019-0331-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T04:35:50Z","timestamp":1671251750000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41597-019-0331-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12,17]]},"references-count":26,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["331"],"URL":"https:\/\/doi.org\/10.1038\/s41597-019-0331-z","relation":{"references":[{"id-type":"uri","id":"https:\/\/identifiers.org\/ncbi\/insdc:VFJD00000000.1","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/identifiers.org\/massive:MSV000084027","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.8251049.v2","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.8251340.v6","asserted-by":"subject"},{"id-type":"uri","id":"http:\/\/identifiers.org\/ncbi\/insdc.sra:SRP188430","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/identifiers.org\/GEO:GSE139141","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.8251211.v1","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.8251310.v1","asserted-by":"subject"}]},"ISSN":["2052-4463"],"issn-type":[{"type":"electronic","value":"2052-4463"}],"subject":[],"published":{"date-parts":[[2019,12,17]]},"assertion":[{"value":"30 July 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 November 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 December 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"322"}}