{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:32:19Z","timestamp":1789605139623,"version":"build-2803163510"},"reference-count":40,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T00:00:00Z","timestamp":1739404800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health\/National Institute of Allergy and Infectious Diseases","award":["R01AI139244"],"award-info":[{"award-number":["R01AI139244"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections present a significant clinical therapeutic challenge. Prophages are increasingly recognized as important genetic factors influencing the pathogenicity of S. aureus, yet their role in antibiotic persistence in MRSA remains underexplored. Our previous work demonstrated that prophage \u03d5SA169 promotes vancomycin (VAN) persistence in an experimental model of endocarditis caused by MRSA strains with a clonal complex (CC) 45 genetic background. However, it is unknown whether this persistence-promoting effect of \u03d5SA169 extends to other clinically relevant MRSA lineages. This study aims to elucidate the role of \u03d5SA169 in influencing VAN persistence across diverse MRSA genetic backgrounds. Methods: A pilot analysis of clinical data suggested that patients infected by MRSA containing \u03d5SA169-like prophage appear to have worse clinical outcomes. Thus, we lysogenized representative clinical resolving bacteremia (RB) MRSA strains with \u03d5SA169 and evaluated phenotypes closely associated with VAN persistence, including VAN susceptibility, biofilm formation, and the efficacy of VAN treatment in an experimental infective endocarditis (IE) model. Each \u03d5SA169 lysogenic strain was compared to its isogenic MRSA parental counterpart. Results: \u03d5SA169 lysogeny significantly promotes biofilm formation and enhances survival to VAN exposure under human-mimicking conditions for RB strains from CC5 and CC30. \u03d5SA169 lysogeny significantly reduces VAN effectiveness in the IE model due to RB lysogen from CC5 despite no detectable impact on VAN MICs. Conclusions: These results indicate that \u03d5SA169 promotes VAN persistence across clonal backgrounds, likely through biofilm formation and VAN tolerance. Targeting prophage could provide new strategies to combat persistent MRSA infections.<\/jats:p>","DOI":"10.3390\/antibiotics14020191","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T04:03:35Z","timestamp":1739419415000},"page":"191","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Prophage \u03d5SA169 Enhances Vancomycin Persistence in Methicillin-Resistant Staphylococcus aureus (MRSA)"],"prefix":"10.3390","volume":"14","author":[{"given":"Yi","family":"Li","sequence":"first","affiliation":[{"name":"The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5658-1973","authenticated-orcid":false,"given":"Andrew D.","family":"Berti","sequence":"additional","affiliation":[{"name":"Department of Pharmacy Practice, Wayne State University College of Pharmacy and Health Sciences, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wessam","family":"Abdelhady","sequence":"additional","affiliation":[{"name":"The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan Q.","family":"Xiong","sequence":"additional","affiliation":[{"name":"The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA"},{"name":"David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3316","DOI":"10.3390\/v4123316","article-title":"The Staphylococci phages family: An overview","volume":"4","author":"Deghorain","year":"2012","journal-title":"Viruses"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3462","DOI":"10.1128\/JB.01804-08","article-title":"Diversity of prophages in dominant Staphylococcus aureus clonal lineages","volume":"191","author":"Goerke","year":"2009","journal-title":"J. Bacteriol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/j.meegid.2013.04.022","article-title":"Phages of Staphylococcus aureus and their impact on host evolution","volume":"21","author":"Xia","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1007\/s00018-010-0389-4","article-title":"Mobile genetic elements of Staphylococcus aureus","volume":"67","author":"Malachowa","year":"2010","journal-title":"Cell Mol. Life Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1111\/j.1365-2958.2006.05441.x","article-title":"Prophages of Staphylococcus aureus Newman and their contribution to virulence","volume":"62","author":"Bae","year":"2006","journal-title":"Mol. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"100194","DOI":"10.1016\/j.xgen.2022.100194","article-title":"Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation","volume":"2","author":"Chaguza","year":"2022","journal-title":"Cell Genom."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1038\/ni1235","article-title":"Immune evasion by a staphylococcal complement inhibitor that acts on C3 convertases","volume":"6","author":"Rooijakkers","year":"2005","journal-title":"Nat. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1128\/JB.188.4.1310-1315.2006","article-title":"The innate immune modulators staphylococcal complement inhibitor and chemotaxis inhibitory protein of Staphylococcus aureus are located on beta-hemolysin-converting bacteriophages","volume":"188","author":"Rooijakkers","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5587","DOI":"10.1073\/pnas.0912403107","article-title":"Polymorphonuclear leukocytes mediate Staphylococcus aureus Panton-Valentine leukocidin-induced lung inflammation and injury","volume":"107","author":"Diep","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"McCarthy, A.J., Witney, A.A., and Lindsay, J.A. (2012). Staphylococcus aureus temperate bacteriophage: Carriage and horizontal gene transfer is lineage associated. Front. Cell Infect. Microbiol., 2.","DOI":"10.3389\/fcimb.2012.00006"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Ingmer, H., Gerlach, D., and Wolz, C. (2019). Temperate phages of Staphylococcus aureus. Microbiol. Spectr., 7.","DOI":"10.1128\/microbiolspec.GPP3-0058-2018"},{"key":"ref_12","doi-asserted-by":"crossref","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":"ref_13","doi-asserted-by":"crossref","unstructured":"Hernandez, D., Seidl, K., Corvaglia, A.R., Bayer, A.S., Xiong, Y.Q., and Francois, P. (2014). Genome sequences of sequence type 45 (ST45) persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia strain 300-169 and ST45 resolving MRSA bacteremia strain 301-188. Genome Announc., 2.","DOI":"10.1128\/genomeA.00174-14"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1086\/423145","article-title":"Persistent bacteremia due to methicillin-resistant Staphylococcus aureus infection is associated with agr dysfunction and low-level in vitro resistance to thrombin-induced platelet microbicidal protein","volume":"190","author":"Fowler","year":"2004","journal-title":"J. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Li, L., Wang, G., Li, Y., Francois, P., Bayer, A.S., Chen, L., Seidl, K., Cheung, A., and Xiong, Y.Q. (2020). Impact of the novel prophage varphiSA169 on persistent methicillin-resistant Staphylococcus aureus endovascular infection. mSystems, 5.","DOI":"10.1128\/msystems.00178-20"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5631","DOI":"10.1128\/AAC.05251-11","article-title":"Relationship of agr expression and function with virulence and vancomycin treatment outcomes in experimental endocarditis due to methicillin-resistant Staphylococcus aureus","volume":"55","author":"Seidl","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1093\/jac\/dku547","article-title":"Early agr activation correlates with vancomycin treatment failure in multi-clonotype MRSA endovascular infections","volume":"70","author":"Abdelhady","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_18","first-page":"205","article-title":"Improved understanding of factors driving methicillin-resistant Staphylococcus aureus epidemic waves","volume":"5","author":"Chatterjee","year":"2013","journal-title":"Clin. Epidemiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.1038\/ismej.2016.79","article-title":"Prophages mediate defense against phage infection through diverse mechanisms","volume":"10","author":"Qian","year":"2016","journal-title":"ISME J."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5578","DOI":"10.1128\/JB.00418-06","article-title":"Sau1: A novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages","volume":"188","author":"Waldron","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1002\/cmdc.202000677","article-title":"Therapeutic strategies to counteract antibiotic resistance in MRSA biofilm-associated infections","volume":"16","author":"Cascioferro","year":"2021","journal-title":"ChemMedChem"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Yee, R., Yuan, Y., Tarff, A., Brayton, C., Gour, N., Feng, J., and Zhang, Y. (2022). Eradication of Staphylococcus aureus biofilm infection by persister drug combination. Antibiotics, 11.","DOI":"10.3390\/antibiotics11101278"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1056\/NEJMoa053783","article-title":"Daptomycin versus standard therapy for bacteremia and endocarditis caused by Staphylococcus aureus","volume":"355","author":"Fowler","year":"2006","journal-title":"N. Engl. J. Med."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Baek, K.T., Frees, D., Renzoni, A., Barras, C., Rodriguez, N., Manzano, C., and Kelley, W.L. (2013). Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0077122"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/0042-6822(67)90105-5","article-title":"Properties of a cryptic high-frequency transducing phage in Staphylococcus aureus","volume":"33","author":"Novick","year":"1967","journal-title":"Virology"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1093\/infdis\/jiu007","article-title":"Impact of vancomycin on sarA-mediated biofilm formation: Role in persistent endovascular infections due to methicillin-resistant Staphylococcus aureus","volume":"209","author":"Abdelhady","year":"2014","journal-title":"J. Infect. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Challagundla, L., Reyes, J., Rafiqullah, I., Sordelli, D.O., Echaniz-Aviles, G., Velazquez-Meza, M.E., Castillo-Ramirez, S., Fittipaldi, N., Feldgarden, M., and Chapman, S.B. (2018). Phylogenomic classification and the evolution of clonal complex 5 methicillin-resistant Staphylococcus aureus in the western hemisphere. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01901"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Jiang, J.H., Cameron, D.R., Nethercott, C., Aires-de-Sousa, M., and Peleg, A.Y. (2023). Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin. Microbiol. Rev., 36.","DOI":"10.1128\/cmr.00148-22"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.jgar.2016.04.004","article-title":"Genomic insights into the emergence and spread of international clones of healthcare-, community- and livestock-associated meticillin-resistant Staphylococcus aureus: Blurring of the traditional definitions","volume":"6","author":"Bal","year":"2016","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1973","DOI":"10.3201\/eid2111.150452","article-title":"USA300 methicillin-resistant Staphylococcus aureus, United States, 2000\u20132013","volume":"21","author":"Carrel","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1086\/675283","article-title":"Continued emergence of USA300 methicillin-resistant Staphylococcus aureus in the United States: Results from a nationwide surveillance study","volume":"35","author":"Diekema","year":"2014","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1099\/mic.0.032466-0","article-title":"Transcription of the phage-encoded Panton-Valentine leukocidin of Staphylococcus aureus is dependent on the phage life-cycle and on the host background","volume":"155","author":"Wirtz","year":"2009","journal-title":"Microbiology"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"6694","DOI":"10.1128\/AEM.01789-14","article-title":"Combined use of bacteriophage K and a novel bacteriophage to reduce Staphylococcus aureus biofilm formation","volume":"80","author":"Alves","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1007\/7651_2014_185","article-title":"Bacteriophage transduction in Staphylococcus aureus: Broth-based method","volume":"1373","author":"Krausz","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Guerrero-Bustamante, C.A., and Hatfull, G.F. (2024). Bacteriophage tRNA-dependent lysogeny: Requirement of phage-encoded tRNA genes for establishment of lysogeny. mBio, 15.","DOI":"10.1128\/mbio.03260-23"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1099\/mic.0.000120","article-title":"Mycobacteriophage-repressor-mediated immunity as a selectable genetic marker: Adephagia and BPs repressor selection","volume":"161","author":"Petrova","year":"2015","journal-title":"Microbiology"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e2106005119","DOI":"10.1073\/pnas.2106005119","article-title":"Protection of bacteriophage-sensitive Escherichia coli by lysogens","volume":"119","author":"Brown","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Ersoy, S.C., Rose, W.E., Patel, R., Proctor, R.A., Chambers, H.F., Harrison, E.M., Pak, Y., and Bayer, A.S. (2021). A combined phenotypic-genotypic predictive algorithm for in vitro detection of bicarbonate: Beta-lactam sensitization among methicillin-resistant Staphylococcus aureus (MRSA). Antibiotics, 10.","DOI":"10.3390\/antibiotics10091089"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Atshan, S.S., Shamsudin, M.N., Lung, L.T., Sekawi, Z., Ghaznavi-Rad, E., and Pei, C.P. (2012). Comparative characterisation of genotypically different clones of MRSA in the production of biofilms. J. Biomed. Biotechnol., 2012.","DOI":"10.1155\/2012\/417247"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1093\/infdis\/jiy340","article-title":"Role of purine biosynthesis in persistent methicillin-resistant Staphylococcus aureus infection","volume":"218","author":"Li","year":"2018","journal-title":"J. Infect. Dis."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/2\/191\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:32:41Z","timestamp":1760027561000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/2\/191"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,13]]},"references-count":40,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2]]}},"alternative-id":["antibiotics14020191"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics14020191","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,13]]}}}