{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T07:15:48Z","timestamp":1787814948002,"version":"build-2784847793"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2021,10,20]],"date-time":"2021-10-20T00:00:00Z","timestamp":1634688000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008296","name":"Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University","doi-asserted-by":"publisher","award":["Department Startup Funds"],"award-info":[{"award-number":["Department Startup Funds"]}],"id":[{"id":"10.13039\/100008296","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["1-U01-AI124316-01"],"award-info":[{"award-number":["1-U01-AI124316-01"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["1-U01-AI124316-01"],"award-info":[{"award-number":["1-U01-AI124316-01"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006710","name":"Wayne State University","doi-asserted-by":"publisher","award":["Research Scholars program"],"award-info":[{"award-number":["Research Scholars program"]}],"id":[{"id":"10.13039\/100006710","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Understating how antibiotic tolerance impacts subsequent resistance development in the clinical setting is important to identifying effective therapeutic interventions and prevention measures. This study describes a patient case of methicillin-resistant <jats:italic>Staphylococcus aureus<\/jats:italic> (MRSA) bacteremia which rapidly developed resistance to three primary MRSA therapies and identifies genetic and metabolic changes selected <jats:italic>in vivo<\/jats:italic> that are associated with rapid resistance evolution. Index blood cultures displayed susceptibility to all (non-beta-lactam) antibiotics with the exception of trimethoprim\/ sulfamethoxazole. One month after initial presentation, during the same encounter, blood cultures were again positive for MRSA, now displaying intermediate resistance to vancomycin and ceftaroline and resistance to daptomycin. Two weeks later, blood cultures were positive for a third time, still intermediate resistant to vancomycin and ceftaroline and resistant to daptomycin. Mutations in <jats:italic>mprF<\/jats:italic> and <jats:italic>vraT<\/jats:italic> were common to all multidrug resistant isolates whereas mutations in <jats:italic>tagH<\/jats:italic>, <jats:italic>agrB<\/jats:italic> and <jats:italic>saeR<\/jats:italic> and secondary <jats:italic>mprF<\/jats:italic> mutation emerged sequentially and transiently resulting in distinct <jats:italic>in vitro<\/jats:italic> phenotypes. The baseline mutation rate of the patient isolates was unremarkable ruling out the hypermutator phenotype as a contributor to the rapid emergence of resistance. However, the index isolate demonstrated pronounced tolerance to the antibiotic daptomycin, a phenotype that facilitates the subsequent development of resistance during antibiotic exposure. This study exemplifies the capacity of antibiotic-tolerant pathogens to rapidly develop both stable and transient genetic and phenotypic changes, over the course of a single patient encounter.<\/jats:p>","DOI":"10.1371\/journal.pone.0258592","type":"journal-article","created":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T03:46:17Z","timestamp":1634787977000},"page":"e0258592","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia"],"prefix":"10.1371","volume":"16","author":[{"given":"Christopher R.","family":"Miller","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan M.","family":"Monk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Szubin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5658-1973","authenticated-orcid":true,"given":"Andrew D.","family":"Berti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,10,20]]},"reference":[{"key":"pone.0258592.ref001","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/nrmicro.2016.34","article-title":"Distinguishing between resistance, tolerance and persistence to antibiotic treatment","volume":"14","author":"A Brauner","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"pone.0258592.ref002","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1126\/science.aba0150","article-title":"Tolerance to antibiotics affects response","volume":"367","author":"AD Berti","year":"2020","journal-title":"Science"},{"key":"pone.0258592.ref003","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1093\/jac\/dkw453","article-title":"Relationship between vancomycin tolerance and clinical outcomes in Staphylococcus aureus bacteraemia","volume":"72","author":"NS Britt","year":"2017","journal-title":"J Antimicrob Chemother"},{"key":"pone.0258592.ref004","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/s41564-018-0342-0","article-title":"The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification","volume":"4","author":"H Nicoloff","year":"2019","journal-title":"Nat Microbiol"},{"key":"pone.0258592.ref005","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1093\/infdis\/157.6.1150","article-title":"Penicillin resistance and defective lysis in clinical isolates of pneumococci: evidence for two kinds of antibiotic pressure operating in the clinical environment","volume":"157","author":"P Moreillon","year":"1988","journal-title":"J Infect Dis"},{"key":"pone.0258592.ref006","doi-asserted-by":"crossref","first-page":"14734","DOI":"10.1073\/pnas.1906169116","article-title":"Epistasis between antibiotic tolerance, persistence, and resistance mutations","volume":"116","author":"I Levin-Reisman","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0258592.ref007","doi-asserted-by":"crossref","first-page":"e03482","DOI":"10.1128\/mBio.03482-20","article-title":"Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections","volume":"12","author":"I Santi","year":"2021","journal-title":"mBio"},{"key":"pone.0258592.ref008","doi-asserted-by":"crossref","first-page":"577564","DOI":"10.3389\/fmicb.2020.577564","article-title":"Combating Antibiotic Tolerance Through Activating Bacterial Metabolism","volume":"11","author":"Y Liu","year":"2020","journal-title":"Front Microbiol"},{"key":"pone.0258592.ref009","doi-asserted-by":"crossref","first-page":"e02095","DOI":"10.1128\/mBio.02095-19","article-title":"Antibiotics: Combatting Tolerance To Stop Resistance","volume":"10","author":"EM Windels","year":"2019","journal-title":"mBio"},{"key":"pone.0258592.ref010","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1126\/science.aay3041","article-title":"Effect of tolerance on the evolution of antibiotic resistance under drug combinations","volume":"367","author":"J Liu","year":"2020","journal-title":"Science"},{"key":"pone.0258592.ref011","doi-asserted-by":"crossref","first-page":"3540","DOI":"10.1128\/AAC.46.11.3540-3548.2002","article-title":"An elevated mutation frequency favors development of vancomycin resistance in Staphylococcus aureus","volume":"46","author":"F Schaaff","year":"2002","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref012","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1086\/378810","article-title":"Hypermutation as a factor contributing to the acquisition of antimicrobial resistance","volume":"37","author":"J. Bl\u00e1zquez","year":"2003","journal-title":"Clin Infect Dis Off Publ Infect Dis Soc Am"},{"key":"pone.0258592.ref013","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/jac\/47.5.647","article-title":"Mutation frequencies for resistance to fusidic acid and rifampicin in Staphylococcus aureus","volume":"47","author":"AJ O\u2019Neill","year":"2001","journal-title":"J Antimicrob Chemother"},{"key":"pone.0258592.ref014","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1086\/374937","article-title":"High rate of macrolide resistance in Staphylococcus aureus strains from patients with cystic fibrosis reveals high proportions of hypermutable strains","volume":"187","author":"A-L Prunier","year":"2003","journal-title":"J Infect Dis"},{"key":"pone.0258592.ref015","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01542-18","article-title":"Daptomycin Resistance and Tolerance Due to Loss of Function in Staphylococcus aureus dsp1 and asp23","volume":"63","author":"EM Barros","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref016","article-title":"Distinct Effectiveness of Oritavancin against Tolerance-Induced Staphylococcus aureus","volume":"9","author":"AD Berti","year":"2020","journal-title":"Antibiot Basel Switz."},{"key":"pone.0258592.ref017","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1084\/jem.193.9.1067","article-title":"Staphylococcus aureus resistance to human defensins and evasion of neutrophil killing via the novel virulence factor MprF is based on modification of membrane lipids with l-lysine","volume":"193","author":"A Peschel","year":"2001","journal-title":"J Exp Med"},{"key":"pone.0258592.ref018","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.ijmm.2019.05.010","article-title":"MprF-mediated daptomycin resistance","volume":"309","author":"CM Ernst","year":"2019","journal-title":"Int J Med Microbiol IJMM"},{"key":"pone.0258592.ref019","first-page":"153","article-title":"Phenotypic and genotypic correlates of daptomycin-resistant methicillin-susceptible Staphylococcus aureus clinical isolates","volume":"55","author":"K-M Kang","year":"2017","journal-title":"J Microbiol Seoul Korea"},{"key":"pone.0258592.ref020","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1128\/AAC.01651-12","article-title":"VraT\/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus","volume":"57","author":"S Boyle-Vavra","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref021","doi-asserted-by":"crossref","first-page":"3424","DOI":"10.1128\/AAC.00356-06","article-title":"Role of VraSR in antibiotic resistance and antibiotic-induced stress response in Staphylococcus aureus","volume":"50","author":"S Gardete","year":"2006","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref022","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1128\/AAC.00432-10","article-title":"VraSR two-component regulatory system contributes to mprF-mediated decreased susceptibility to daptomycin in in vivo-selected clinical strains of methicillin-resistant Staphylococcus aureus","volume":"56","author":"S Mehta","year":"2012","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref023","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.1093\/jac\/dkaa221","article-title":"Detection of heterogeneous vancomycin intermediate resistance in MRSA isolates from Latin America","volume":"75","author":"BE Castro","year":"2020","journal-title":"J Antimicrob Chemother"},{"key":"pone.0258592.ref024","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/jac\/dkp394","article-title":"Genetic changes associated with glycopeptide resistance in Staphylococcus aureus: predominance of amino acid substitutions in YvqF\/VraSR","volume":"65","author":"Y Kato","year":"2010","journal-title":"J Antimicrob Chemother"},{"key":"pone.0258592.ref025","first-page":"62","article-title":"Exposure of Staphylococcus aureus to Targocil Blocks Translocation of the Major Autolysin Atl across the Membrane, Resulting in a Significant Decrease in Autolysis","author":"KB Tiwari","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref026","doi-asserted-by":"crossref","first-page":"4183","DOI":"10.1128\/JB.00197-06","article-title":"Lesions in teichoic acid biosynthesis in Staphylococcus aureus lead to a lethal gain of function in the otherwise dispensable pathway","volume":"188","author":"MA D\u2019Elia","year":"2006","journal-title":"J Bacteriol"},{"key":"pone.0258592.ref027","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1128\/JCM.41.1.5-14.2003","article-title":"Cell wall thickening is a common feature of vancomycin resistance in Staphylococcus aureus","volume":"41","author":"L Cui","year":"2003","journal-title":"J Clin Microbiol"},{"key":"pone.0258592.ref028","doi-asserted-by":"crossref","first-page":"3922","DOI":"10.1128\/AAC.01226-10","article-title":"Correlation of daptomycin resistance in a clinical Staphylococcus aureus strain with increased cell wall teichoic acid production and D-alanylation","volume":"55","author":"U Bertsche","year":"2011","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref029","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1128\/CMR.00042-09","article-title":"Reduced vancomycin susceptibility in Staphylococcus aureus, including vancomycin-intermediate and heterogeneous vancomycin-intermediate strains: resistance mechanisms, laboratory detection, and clinical implications","volume":"23","author":"BP Howden","year":"2010","journal-title":"Clin Microbiol Rev"},{"key":"pone.0258592.ref030","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1099\/mic.0.000317","article-title":"Dissecting the regulation of bile-induced biofilm formation in Staphylococcus aureus","volume":"162","author":"D Ulluwishewa","year":"2016","journal-title":"Microbiol Read Engl"},{"key":"pone.0258592.ref031","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.chembiol.2012.11.013","article-title":"Discovery of wall teichoic acid inhibitors as potential anti-MRSA \u03b2-lactam combination agents","volume":"20","author":"H Wang","year":"2013","journal-title":"Chem Biol"},{"key":"pone.0258592.ref032","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00890-20","article-title":"Prolonged Exposure to \u03b2-Lactam Antibiotics Reestablishes Susceptibility of Daptomycin-Nonsusceptible Staphylococcus aureus to Daptomycin","volume":"64","author":"RE Jenson","year":"2020","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref033","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1089\/mdr.2017.0156","article-title":"Impact of Multiple Single-Nucleotide Polymorphisms Within mprF on Daptomycin Resistance in Staphylococcus aureus","volume":"24","author":"S-J Yang","year":"2018","journal-title":"Microb Drug Resist Larchmt N"},{"key":"pone.0258592.ref034","doi-asserted-by":"crossref","first-page":"4930","DOI":"10.1128\/AAC.00970-15","article-title":"Frequency and Distribution of Single-Nucleotide Polymorphisms within mprF in Methicillin-Resistant Staphylococcus aureus Clinical Isolates and Their Role in Cross-Resistance to Daptomycin and Host Defense Antimicrobial Peptides","volume":"59","author":"AS Bayer","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref035","doi-asserted-by":"crossref","first-page":"2303","DOI":"10.3389\/fmicb.2017.02303","article-title":"Daptomycin Resistance in Clinical MRSA Strains Is Associated with a High Biological Fitness Cost","volume":"8","author":"M Roch","year":"2017","journal-title":"Front Microbiol."},{"key":"pone.0258592.ref036","doi-asserted-by":"crossref","first-page":"1492","DOI":"10.1128\/AAC.46.5.1492-1502.2002","article-title":"Accessory gene regulator (agr) locus in geographically diverse Staphylococcus aureus isolates with reduced susceptibility to vancomycin","volume":"46","author":"G Sakoulas","year":"2002","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref037","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/1471-2180-13-93","article-title":"Impact of agr dysfunction on virulence profiles and infections associated with a novel methicillin-resistant Staphylococcus aureus (MRSA) variant of the lineage ST1-SCCmec IV","volume":"13","author":"FA Ferreira","year":"2013","journal-title":"BMC Microbiol"},{"key":"pone.0258592.ref038","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1146\/annurev.genet.42.110807.091640","article-title":"Quorum sensing in staphylococci","volume":"42","author":"RP Novick","year":"2008","journal-title":"Annu Rev Genet"},{"key":"pone.0258592.ref039","doi-asserted-by":"crossref","first-page":"34736","DOI":"10.1074\/jbc.M205367200","article-title":"Transmembrane topology of AgrB, the protein involved in the post-translational modification of AgrD in Staphylococcus aureus","volume":"277","author":"L Zhang","year":"2002","journal-title":"J Biol Chem"},{"key":"pone.0258592.ref040","doi-asserted-by":"crossref","first-page":"16695","DOI":"10.1074\/jbc.M411372200","article-title":"Identification of the putative staphylococcal AgrB catalytic residues involving the proteolytic cleavage of AgrD to generate autoinducing peptide","volume":"280","author":"R Qiu","year":"2005","journal-title":"J Biol Chem"},{"key":"pone.0258592.ref041","doi-asserted-by":"crossref","first-page":"4534","DOI":"10.1128\/IAI.00679-07","article-title":"A nonsense mutation in agrA accounts for the defect in agr expression and the avirulence of Staphylococcus aureus 8325\u20134 traP::kan","volume":"75","author":"RP Adhikari","year":"2007","journal-title":"Infect Immun"},{"key":"pone.0258592.ref042","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1128\/JB.06771-11","article-title":"Organizational requirements of the SaeR binding sites for a functional P1 promoter of the sae operon in Staphylococcus aureus","volume":"194","author":"H Cho","year":"2012","journal-title":"J Bacteriol"},{"key":"pone.0258592.ref043","doi-asserted-by":"crossref","first-page":"204","DOI":"10.3389\/fcimb.2017.00204","article-title":"The SaeRS Two-Component System Controls Survival of Staphylococcus aureus in Human Blood through Regulation of Coagulase","volume":"7","author":"H Guo","year":"2017","journal-title":"Front Cell Infect Microbiol"},{"key":"pone.0258592.ref044","doi-asserted-by":"crossref","first-page":"ofaa302","DOI":"10.1093\/ofid\/ofaa302","article-title":"Antibiotics and Innate Immunity: A Cooperative Effort Toward the Successful Treatment of Infections","volume":"7","author":"A Berti","year":"2020","journal-title":"Open Forum Infect Dis"},{"key":"pone.0258592.ref045","doi-asserted-by":"crossref","first-page":"561","DOI":"10.3389\/fmicb.2020.00561","article-title":"The Accessory Gene saeP of the SaeR\/S Two-Component Gene Regulatory System Impacts Staphylococcus aureus Virulence During Neutrophil Interaction","volume":"11","author":"MM Collins","year":"2020","journal-title":"Front Microbiol"},{"key":"pone.0258592.ref046","article-title":"The SaeRS Two-Component System of Staphylococcus aureus","volume":"7","author":"Q Liu","year":"2016","journal-title":"Genes"},{"key":"pone.0258592.ref047","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1126\/science.aaj2191","article-title":"Antibiotic tolerance facilitates the evolution of resistance","volume":"355","author":"I Levin-Reisman","year":"2017","journal-title":"Science"},{"key":"pone.0258592.ref048","doi-asserted-by":"crossref","first-page":"6983","DOI":"10.1128\/AAC.01303-15","article-title":"Stepwise decrease in daptomycin susceptibility in clinical Staphylococcus aureus isolates associated with an initial mutation in rpoB and a compensatory inactivation of the clpX gene","volume":"59","author":"KT B\u00e6k","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0258592.ref049","volume-title":"Performance standards for antimicrobial susceptibility testing. CLSI document M100-ED29","author":"Clinical and Laboratory Standards Institute","year":"2019"},{"key":"pone.0258592.ref050","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1093\/jac\/dkp319","article-title":"Occurrence of vancomycin-tolerant and heterogeneous vancomycin-intermediate strains (hVISA) among Staphylococcus aureus causing bloodstream infections in nine USA hospitals","volume":"64","author":"HS Sader","year":"2009","journal-title":"J Antimicrob Chemother"},{"key":"pone.0258592.ref051","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1006\/meth.1999.0901","article-title":"Determining mutation rates in bacterial populations","volume":"20","author":"WA Rosche","year":"2000","journal-title":"Methods San Diego Calif"},{"key":"pone.0258592.ref052","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.mimet.2007.11.010","article-title":"Comparison of multiple methods for quantification of microbial biofilms grown in microtiter plates","volume":"72","author":"E Peeters","year":"2008","journal-title":"J Microbiol Methods"},{"key":"pone.0258592.ref053","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.ijantimicag.2011.06.010","article-title":"Mechanisms of in-vitro-selected daptomycin-non-susceptibility in Staphylococcus aureus","volume":"38","author":"D Patel","year":"2011","journal-title":"Int J Antimicrob Agents"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0258592","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T03:47:03Z","timestamp":1634788023000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0258592"}},"subtitle":[],"editor":[{"given":"Herminia","family":"de Lencastre","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,10,20]]},"references-count":53,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2021,10,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0258592","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,20]]}}}