{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T06:06:04Z","timestamp":1784268364690,"version":"3.55.0"},"reference-count":88,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100002386","name":"Cairo University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002386","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The rapid rise of multidrug-resistant\n                    <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                    (MDR\n                    <jats:italic>A. baumannii<\/jats:italic>\n                    ) poses a serious threat in healthcare settings, as these bacteria can cause infections that are untreatable with conventional antibiotics. This crisis has driven the search for alternative therapies, one of which is bacteriophages. In this study, we isolated a novel bacteriophage, vB_AbaM_EA1 (E7 for short), from wastewater and evaluated its potential activity against clinical MDR\n                    <jats:italic>A. baumannii<\/jats:italic>\n                    strains. Phage E7 successfully infects (27.5%) of the 40 clinical MDR\n                    <jats:italic>A. baumannii<\/jats:italic>\n                    isolates we tested. Laboratory characterization suggested that E7 is a highly efficient lytic phage, rapidly attaching to bacterial cells and producing 1000 new viral particles.\n                  <\/jats:p>\n                  <jats:p>A key finding was its potent activity against bacterial biofilms, a major source of persistent infections. Not only did Phage E7 effectively prevent the formation of new biofilms, but more importantly disrupted mature ones, which typically confer higher resistance to antibiotics.<\/jats:p>\n                  <jats:p>\n                    Genome sequencing confirmed that Phage E7 is a new member of the\n                    <jats:italic>Obolenskvirus<\/jats:italic>\n                    genus and that its genome lacks genes encoding bacterial toxins, antibiotic resistance, or lysogenic factors, indicating a mandatory safety profile for therapeutic use. Furthermore, E7 remained stable across a broad temperature range (-20 to 45\u00a0\u00b0C) and pH values (5\u20139) that it might encounter during storage and administration. In conclusion, Phage E7 is a stable, safe, and highly effective candidate for phage therapy against infections by MDR\n                    <jats:italic>A. baumannii<\/jats:italic>\n                    . Its ability to target both planktonic bacteria and biofilms makes it a promising candidate for future development into clinical applications.\n                  <\/jats:p>","DOI":"10.1186\/s12866-026-05262-7","type":"journal-article","created":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T03:25:48Z","timestamp":1784258748000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Isolation, characterization, and genomic analysis of a novel lytic bacteriophage with potent antibiofilm activity against multidrug-resistant Acinetobacter baumannii"],"prefix":"10.1186","volume":"26","author":[{"given":"Ethar","family":"M. Amin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramy K.","family":"Aziz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fathia E.","family":"Murad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marwa T.","family":"Elrakaiby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reham","family":"Samir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,17]]},"reference":[{"key":"5262_CR1","unstructured":"WHO. Global report on infection prevention and control 2024. Geneva: World Health Organization; 2024."},{"key":"5262_CR2","unstructured":"O\u2019Neill J. Tackling drug-resistant infections globally: final report and recommendations. London: HM Government; 2016."},{"issue":"12","key":"5262_CR3","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1016\/j.tibtech.2010.08.001","volume":"28","author":"M Kutateladze","year":"2010","unstructured":"Kutateladze M, Adamia R. Bacteriophages as potential new therapeutics to replace or supplement antibiotics. Trends Biotechnol. 2010;28(12):591\u20135.","journal-title":"Trends Biotechnol"},{"issue":"7","key":"5262_CR4","doi-asserted-by":"publisher","first-page":"1938","DOI":"10.1128\/JCM.36.7.1938-1941.1998","volume":"36","author":"A Jawad","year":"1998","unstructured":"Jawad A, Seifert H, Snelling AM, Heritage J, Hawkey PM. Survival of Acinetobacter baumannii on dry surfaces: comparison of outbreak and sporadic isolates. J Clin Microbiol. 1998;36(7):1938\u201341.","journal-title":"J Clin Microbiol"},{"issue":"3","key":"5262_CR5","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1128\/CMR.00058-07","volume":"21","author":"AY Peleg","year":"2008","unstructured":"Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev. 2008;21(3):538\u201382.","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"5262_CR6","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1111\/2049-632X.12125","volume":"71","author":"LC Antunes","year":"2014","unstructured":"Antunes LC, Visca P, Towner KJ. Acinetobacter baumannii: evolution of a global pathogen. Pathog Dis. 2014;71(3):292\u2013301.","journal-title":"Pathog Dis"},{"issue":"8","key":"5262_CR7","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1007\/s12275-016-6146-0","volume":"54","author":"Y Gong","year":"2016","unstructured":"Gong Y, Shen X, Huang G, Zhang C, Luo X, Yin S, et al. Epidemiology and resistance features of Acinetobacter baumannii isolates from the ward environment and patients in the burn ICU of a Chinese hospital. J Microbiol. 2016;54(8):551\u20138.","journal-title":"J Microbiol"},{"key":"5262_CR8","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.3389\/fmicb.2016.01717","volume":"7","author":"G Huang","year":"2016","unstructured":"Huang G, Yin S, Gong Y, Zhao X, Zou L, Jiang B, et al. Multilocus sequence typing analysis of carbapenem-resistant Acinetobacter baumannii in a Chinese burns institute. Front Microbiol. 2016;7:1717.","journal-title":"Front Microbiol"},{"issue":"4","key":"5262_CR9","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1586\/eri.13.21","volume":"11","author":"I Abbott","year":"2013","unstructured":"Abbott I, Cerqueira GM, Bhuiyan S, Peleg AY. Carbapenem resistance in Acinetobacter baumannii: laboratory challenges, mechanistic insights and therapeutic strategies. Expert Rev Anti-Infect Ther. 2013;11(4):395\u2013409.","journal-title":"Expert Rev Anti-Infect Ther"},{"issue":"1","key":"5262_CR10","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1086\/653120","volume":"51","author":"J Fishbain","year":"2010","unstructured":"Fishbain J, Peleg AY. Treatment of Acinetobacter infections. Clin Infect Dis. 2010;51(1):79\u201384.","journal-title":"Clin Infect Dis"},{"issue":"1","key":"5262_CR11","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.ijantimicag.2008.02.016","volume":"32","author":"M Dizbay","year":"2008","unstructured":"Dizbay M, Altuncekic A, Sezer BE, Ozdemir K, Arman D. Colistin and tigecycline susceptibility among multidrug-resistant Acinetobacter baumannii isolated from ventilator-associated pneumonia. Int J Antimicrob Agents. 2008;32(1):29\u201332.","journal-title":"Int J Antimicrob Agents"},{"issue":"12","key":"5262_CR12","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1038\/nrmicro1789","volume":"5","author":"L Dijkshoorn","year":"2007","unstructured":"Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol. 2007;5(12):939\u201351.","journal-title":"Nat Rev Microbiol"},{"key":"5262_CR13","doi-asserted-by":"publisher","first-page":"3711","DOI":"10.2147\/IDR.S332051","volume":"14","author":"A Gedefie","year":"2021","unstructured":"Gedefie A, Demsis W, Ashagrie M, Kassa Y, Tesfaye M, Tilahun M, et al. Acinetobacter baumannii biofilm formation and its role in disease pathogenesis: a review. Infect Drug Resist. 2021;14:3711\u20139.","journal-title":"Infect Drug Resist"},{"issue":"4","key":"5262_CR14","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.ijantimicag.2009.12.011","volume":"35","author":"N H\u00f8iby","year":"2010","unstructured":"H\u00f8iby N, Bjarnsholt T, Givskov M, Molin S, Ciofu O. Antibiotic resistance of bacterial biofilms. Int J Antimicrob Agents. 2010;35(4):322\u201332.","journal-title":"Int J Antimicrob Agents"},{"issue":"3","key":"5262_CR15","doi-asserted-by":"publisher","first-page":"291","DOI":"10.4103\/0974-777X.68538","volume":"2","author":"V Manchanda","year":"2010","unstructured":"Manchanda V, Sanchaita S, Singh N. Multidrug resistant acinetobacter. J Glob Infect Dis. 2010;2(3):291\u2013304.","journal-title":"J Glob Infect Dis"},{"issue":"1","key":"5262_CR16","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1042\/ETLS20170002","volume":"1","author":"DR Roach","year":"2017","unstructured":"Roach DR, Debarbieux L. Phage therapy: awakening a sleeping giant. Emerg Top Life Sci. 2017;1(1):93\u2013103.","journal-title":"Emerg Top Life Sci"},{"key":"5262_CR17","first-page":"26","volume":"3","author":"J-M Fr\u00e8re","year":"2016","unstructured":"Fr\u00e8re J-M, Rigali S. The alarming increase in antibiotic-resistant bacteria. Drug Target Rev. 2016;3:26\u201330.","journal-title":"Drug Target Rev"},{"issue":"1","key":"5262_CR18","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1111\/j.1574-6968.2012.02573.x","volume":"332","author":"AV Popova","year":"2012","unstructured":"Popova AV, Zhilenkov EL, Myakinina VP, Krasilnikova VM, Volozhantsev NV. Isolation and characterization of wide host range lytic bacteriophage AP22 infecting Acinetobacter baumannii. FEMS Microbiol Lett. 2012;332(1):40\u20136.","journal-title":"FEMS Microbiol Lett"},{"issue":"7","key":"5262_CR19","doi-asserted-by":"publisher","first-page":"e0181671","DOI":"10.1371\/journal.pone.0181671","volume":"12","author":"V Abat\u00e1ngelo","year":"2017","unstructured":"Abat\u00e1ngelo V, Peressutti Bacci N, Boncompain CA, Amadio AA, Carrasco S, Su\u00e1rez CA, et al. Broad-range lytic bacteriophages that kill Staphylococcus aureus local field strains. PLoS ONE. 2017;12(7):e0181671.","journal-title":"PLoS ONE"},{"issue":"213","key":"5262_CR20","first-page":"2161","volume":"5","author":"MN Mohammed-Ali","year":"2015","unstructured":"Mohammed-Ali MN, Jamalludeen NM. Isolation and characterization of bacteriophage against methicillin resistant Staphylococcus aureus. J Med Microbiol Diagn. 2015;5(213):2161\u201307031000213.","journal-title":"J Med Microbiol Diagn"},{"issue":"8","key":"5262_CR21","doi-asserted-by":"publisher","first-page":"e0160242","DOI":"10.1371\/journal.pone.0160242","volume":"11","author":"KM Verstappen","year":"2016","unstructured":"Verstappen KM, Tulinski P, Duim B, Fluit AC, Carney J, Van Nes A, et al. The effectiveness of bacteriophages against methicillin-resistant Staphylococcus aureus ST398 nasal colonization in pigs. PLoS ONE. 2016;11(8):e0160242.","journal-title":"PLoS ONE"},{"issue":"2","key":"5262_CR22","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.chom.2019.01.014","volume":"25","author":"KE Kortright","year":"2019","unstructured":"Kortright KE, Chan BK, Koff JL, Turner PE. Phage therapy: a renewed approach to combat antibiotic-resistant bacteria. Cell Host Microbe. 2019;25(2):219\u201332.","journal-title":"Cell Host Microbe"},{"issue":"1","key":"5262_CR23","doi-asserted-by":"publisher","first-page":"69","DOI":"10.2174\/138920110790725401","volume":"11","author":"E Kutter","year":"2010","unstructured":"Kutter E, De Vos D, Gvasalia G, Alavidze Z, Gogokhia L, Kuhl S, et al. Phage therapy in clinical practice: treatment of human infections. Curr Pharm Biotechnol. 2010;11(1):69\u201386.","journal-title":"Curr Pharm Biotechnol"},{"issue":"6","key":"5262_CR24","doi-asserted-by":"publisher","first-page":"323","DOI":"10.3390\/v10060323","volume":"10","author":"C Torres-Barcel\u00f3","year":"2018","unstructured":"Torres-Barcel\u00f3 C. Phage therapy faces evolutionary challenges. Viruses. 2018;10(6):323.","journal-title":"Viruses"},{"issue":"4","key":"5262_CR25","doi-asserted-by":"publisher","first-page":"178","DOI":"10.3390\/v10040178","volume":"10","author":"C Rohde","year":"2018","unstructured":"Rohde C, Resch G, Pirnay J-P, Blasdel BG, Debarbieux L, Gelman D, et al. Expert opinion on three phage therapy related topics: bacterial phage resistance, phage training and prophages in bacterial production strains. Viruses. 2018;10(4):178.","journal-title":"Viruses"},{"issue":"4","key":"5262_CR26","doi-asserted-by":"publisher","first-page":"205","DOI":"10.3390\/v10040205","volume":"10","author":"ZD Moye","year":"2018","unstructured":"Moye ZD, Woolston J, Sulakvelidze A. Bacteriophage applications for food production and processing. Viruses. 2018;10(4):205.","journal-title":"Viruses"},{"key":"5262_CR27","doi-asserted-by":"crossref","unstructured":"Schooley RT, Biswas B, Gill JJ, Hernandez-Morales A, Lancaster J, Lessor L et al. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii Infection. Antimicrob Agents Chemother. 2017;61(10):e00954-17.","DOI":"10.1128\/AAC.00954-17"},{"issue":"5","key":"5262_CR28","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1128\/JCM.03565-13","volume":"52","author":"S Pournaras","year":"2014","unstructured":"Pournaras S, Gogou V, Giannouli M, Dimitroulia E, Dafopoulou K, Tsakris A, et al. Single-locus-sequence-based typing of bla OXA-51-like genes for rapid assignment of Acinetobacter baumannii clinical isolates to international clonal lineages. J Clin Microbiol. 2014;52(5):1653\u20137.","journal-title":"J Clin Microbiol"},{"issue":"8","key":"5262_CR29","doi-asserted-by":"publisher","first-page":"2974","DOI":"10.1128\/JCM.01021-06","volume":"44","author":"JF Turton","year":"2006","unstructured":"Turton JF, Woodford N, Glover J, Yarde S, Kaufmann ME, Pitt TL. Identification of Acinetobacter baumannii by detection of the bla OXA-51-like carbapenemase gene intrinsic to this species. J Clin Microbiol. 2006;44(8):2974\u20136.","journal-title":"J Clin Microbiol"},{"key":"5262_CR30","unstructured":"CLSI. Performance Standards for Antimicrobial Susceptibility Testing. 30th ed. CLSI supplement M100. Wayne, PA: Clinical and Laboratory Standards Institute; 2020."},{"issue":"1","key":"5262_CR31","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1128\/aem.46.1.165-170.1983","volume":"46","author":"PH Krumperman","year":"1983","unstructured":"Krumperman PH. Multiple antibiotic resistance indexing of Escherichia coli to identify high-risk sources of fecal contamination of foods. Appl Environ Microbiol. 1983;46(1):165\u201370.","journal-title":"Appl Environ Microbiol"},{"key":"5262_CR32","first-page":"69","volume-title":"Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions","author":"AM Kropinski","year":"2009","unstructured":"Kropinski AM, Mazzocco A, Waddell TE, Lingohr E, Johnson RP. Enumeration of bacteriophages by double agar overlay plaque assay. In: Clokie MRJ, Kropinski AM, editors. Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions. Totowa (NJ): Humana; 2009. p. 69\u201376."},{"key":"5262_CR33","first-page":"15","volume-title":"Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions","author":"R Van Twest","year":"2009","unstructured":"Van Twest R, Kropinski AM. Bacteriophage enrichment from water and soil. In: Clokie MRJ, Kropinski AM, editors. Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions. Totowa (NJ): Humana; 2009. p. 15\u201321."},{"key":"5262_CR34","first-page":"437","volume-title":"Bacteriophages: Biology and Applications","author":"K Carlson","year":"2005","unstructured":"Carlson K. Working with bacteriophages: common techniques and methodological approaches. In: Kutter E, Sulakvelidze A, editors. Bacteriophages: Biology and Applications. Boca Raton (FL): CRC; 2005. p. 437\u201394."},{"issue":"1","key":"5262_CR35","doi-asserted-by":"publisher","first-page":"35","DOI":"10.3390\/ph12010035","volume":"12","author":"P Hyman","year":"2019","unstructured":"Hyman P. Phages for phage therapy: isolation, characterization, and host range breadth. Pharmaceuticals. 2019;12(1):35.","journal-title":"Pharmaceuticals"},{"key":"5262_CR36","doi-asserted-by":"publisher","first-page":"1077995","DOI":"10.3389\/fcimb.2023.1077995","volume":"13","author":"BM Zaki","year":"2023","unstructured":"Zaki BM, Fahmy NA, Aziz RK, Samir R, El-Shibiny A. Characterization and comprehensive genome analysis of novel bacteriophage, vB_Kpn_ZCKp20p, with lytic and anti-biofilm potential against clinical multidrug-resistant Klebsiella pneumoniae. Front Cell Infect Microbiol. 2023;13:1077995.","journal-title":"Front Cell Infect Microbiol"},{"key":"5262_CR37","doi-asserted-by":"publisher","first-page":"e2261","DOI":"10.7717\/peerj.2261","volume":"4","author":"N Bonilla","year":"2016","unstructured":"Bonilla N, Rojas MI, Cruz GNF, Hung S-H, Rohwer F, Barr JJ. Phage on tap\u2013a quick and efficient protocol for the preparation of bacteriophage laboratory stocks. PeerJ. 2016;4:e2261.","journal-title":"PeerJ"},{"key":"5262_CR38","first-page":"141","volume-title":"Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions","author":"E Kutter","year":"2009","unstructured":"Kutter E. Phage host range and efficiency of plating. In: Clokie MRJ, Kropinski AM, editors. Bacteriophages: methods and protocols, Volume 1: Isolation, Characterization, and Interactions. Totowa (NJ): Humana; 2009. p. 141\u20139."},{"issue":"3","key":"5262_CR39","doi-asserted-by":"publisher","first-page":"e0118557","DOI":"10.1371\/journal.pone.0118557","volume":"10","author":"M Khan Mirzaei","year":"2015","unstructured":"Khan Mirzaei M, Nilsson AS. Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS ONE. 2015;10(3):e0118557.","journal-title":"PLoS ONE"},{"issue":"2","key":"5262_CR40","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1007\/s00705-022-05694-2","volume":"168","author":"D Turner","year":"2023","unstructured":"Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, et al. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch Virol. 2023;168(2):74.","journal-title":"Arch Virol"},{"key":"5262_CR41","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1007\/978-1-60327-164-6_15","volume":"501","author":"AM Kropinski","year":"2009","unstructured":"Kropinski AM. Measurement of the rate of attachment of bacteriophage to cells. Methods Mol Biol. 2009;501:151\u20135.","journal-title":"Methods Mol Biol"},{"issue":"1","key":"5262_CR42","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1186\/s12866-025-03854-3","volume":"25","author":"J Su","year":"2025","unstructured":"Su J, Tan Y, Liu S, Zou H, Huang X, Chen S, et al. Characterization of a novel lytic phage vB_AbaM_AB4P2 encoding depolymerase and its application in eliminating biofilms formed by Acinetobacter baumannii. BMC Microbiol. 2025;25(1):123.","journal-title":"BMC Microbiol"},{"issue":"1","key":"5262_CR43","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12941-022-00492-9","volume":"21","author":"B Sisakhtpour","year":"2022","unstructured":"Sisakhtpour B, Mirzaei A, Karbasizadeh V, Hosseini N, Shabani M, Moghim S. The characteristic and potential therapeutic effect of isolated multidrug-resistant Acinetobacter baumannii lytic phage. Ann Clin Microbiol Antimicrob. 2022;21(1):1.","journal-title":"Ann Clin Microbiol Antimicrob"},{"issue":"1","key":"5262_CR44","doi-asserted-by":"publisher","first-page":"B11","DOI":"10.1002\/9780471729259.mc01b01s22","volume":"22","author":"JH Merritt","year":"2011","unstructured":"Merritt JH, Kadouri DE, O\u2019Toole GA. Growing and analyzing static biofilms. Curr Protoc Microbiol. 2011;22(1):B11\u20138.","journal-title":"Curr Protoc Microbiol"},{"issue":"3","key":"5262_CR45","doi-asserted-by":"publisher","first-page":"e01923","DOI":"10.1128\/aac.01923-21","volume":"66","author":"L Blasco","year":"2022","unstructured":"Blasco L, Bleriot I, Gonz\u00e1lez de Aledo M, Fern\u00e1ndez-Garc\u00eda L, Pacios O, Oliveira H, et al. Development of an anti-Acinetobacter baumannii biofilm phage cocktail: genomic adaptation to the host. Antimicrob Agents Chemother. 2022;66(3):e01923\u201321.","journal-title":"Antimicrob Agents Chemother"},{"key":"5262_CR46","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.mib.2017.09.004","volume":"39","author":"DP Pires","year":"2017","unstructured":"Pires DP, Melo L, Vilas Boas D, Sillankorva S, Azeredo J. Phage therapy as an alternative or complementary strategy to prevent and control biofilm-related infections. Curr Opin Microbiol. 2017;39:48\u201356.","journal-title":"Curr Opin Microbiol"},{"key":"5262_CR47","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","volume":"9","author":"RK Aziz","year":"2008","unstructured":"Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.","journal-title":"BMC Genomics"},{"issue":"1","key":"5262_CR48","doi-asserted-by":"publisher","first-page":"8365","DOI":"10.1038\/srep08365","volume":"5","author":"T Brettin","year":"2015","unstructured":"Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5(1):8365.","journal-title":"Sci Rep"},{"key":"5262_CR49","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-9173-0_1","volume":"1962","author":"PP Chan","year":"2019","unstructured":"Chan PP, Lowe TM. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol. 2019;1962:1\u201314.","journal-title":"Methods Mol Biol"},{"issue":"D1","key":"5262_CR50","doi-asserted-by":"publisher","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","volume":"51","author":"RD Olson","year":"2023","unstructured":"Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, et al. Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 2023;51(D1):D678\u201389.","journal-title":"Nucleic Acids Res"},{"key":"5262_CR51","doi-asserted-by":"crossref","unstructured":"Wattam AR, Bowers N, Brettin T, Conrad N, Cucinell C, Davis JJ, et al. Comparative genomic analysis of bacterial data in BV-BRC: an example exploring antimicrobial resistance. In: Setubal JC, Almeida NF, Wattam AR, editors. Comparative genomic: methods and protocols. New York (NY): Springer; 2024. p. 547-71.","DOI":"10.1007\/978-1-0716-3838-5_18"},{"issue":"6","key":"5262_CR52","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1093\/bioinformatics\/btx713","volume":"34","author":"Y Tanizawa","year":"2018","unstructured":"Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018;34(6):1037\u20139.","journal-title":"Bioinformatics"},{"issue":"1","key":"5262_CR53","doi-asserted-by":"publisher","first-page":"btac776","DOI":"10.1093\/bioinformatics\/btac776","volume":"39","author":"G Bouras","year":"2023","unstructured":"Bouras G, Nepal R, Houtak G, Psaltis AJ, Wormald P-J, Vreugde S. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics. 2023;39(1):btac776.","journal-title":"Bioinformatics"},{"issue":"11","key":"5262_CR54","doi-asserted-by":"publisher","first-page":"e1008214","DOI":"10.1371\/journal.pcbi.1008214","volume":"16","author":"J Ramsey","year":"2020","unstructured":"Ramsey J, Rasche H, Maughmer C, Criscione A, Mijalis E, Liu M, et al. Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PLOS Comput Biol. 2020;16(11):e1008214.","journal-title":"PLOS Comput Biol"},{"issue":"15","key":"5262_CR55","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","volume":"430","author":"L Zimmermann","year":"2018","unstructured":"Zimmermann L, Stephens A, Nam S-Z, Rau D, K\u00fcbler J, Lozajic M, et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol. 2018;430(15):2237\u201343.","journal-title":"J Mol Biol"},{"key":"5262_CR56","unstructured":"Grant J, Enns E, Marinier E, Saha-Mandal A, Chen C, Graham M. Proksee: a web server for assembling, annotating and visualizing bacterial genomes. 2022. Available from: https:\/\/proksee.ca\/."},{"key":"5262_CR57","doi-asserted-by":"publisher","first-page":"e11396","DOI":"10.7717\/peerj.11396","volume":"9","author":"AJ Hockenberry","year":"2021","unstructured":"Hockenberry AJ, Wilke CO. BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains. PeerJ. 2021;9:e11396.","journal-title":"PeerJ"},{"issue":"2","key":"5262_CR58","doi-asserted-by":"publisher","first-page":"342","DOI":"10.3390\/v14020342","volume":"14","author":"K Yukgehnaish","year":"2022","unstructured":"Yukgehnaish K, Rajandas H, Parimannan S, Manickam R, Marimuthu K, Petersen B, et al. PhageLeads: rapid assessment of phage therapeutic suitability using an ensemble machine learning approach. Viruses. 2022;14(2):342.","journal-title":"Viruses"},{"key":"5262_CR59","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28\u201336.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"issue":"D1","key":"5262_CR60","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2023","unstructured":"Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res. 2023;51(D1):D690\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"5262_CR61","doi-asserted-by":"publisher","first-page":"D756","DOI":"10.1093\/nar\/gkad979","volume":"52","author":"RH Wang","year":"2024","unstructured":"Wang RH, Yang S, Liu Z, Zhang Y, Wang X, Xu Z, et al. PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations. Nucleic Acids Res. 2024;52(D1):D756\u201361.","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"5262_CR62","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","volume":"51","author":"DS Wishart","year":"2023","unstructured":"Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 2023;51(W1):W443\u201350.","journal-title":"Nucleic Acids Res"},{"key":"5262_CR63","unstructured":"Bouras G. phold: Phage Annotation using Protein Structures. GitHub. Available from: https:\/\/github.com\/gbouras13\/phold."},{"issue":"16","key":"5262_CR64","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","volume":"37","author":"CL Gilchrist","year":"2021","unstructured":"Gilchrist CL, Chooi Y-H. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics. 2021;37(16):2473\u20135.","journal-title":"Bioinformatics"},{"key":"5262_CR65","doi-asserted-by":"crossref","unstructured":"Garneau JR, Depardieu F, Fortier LC, Bikard D, Monot M. PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci. Rep. 2017;7(1):8292.","DOI":"10.1038\/s41598-017-07910-5"},{"key":"5262_CR66","doi-asserted-by":"crossref","unstructured":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. BioRxiv 2022;2022.04.08.487609.","DOI":"10.1101\/2022.04.08.487609"},{"key":"5262_CR67","unstructured":"Duarte JAG. PhageDPO: phage depolymerase finder. [Master\u2019s thesis]. Braga,Universidade do Minho (Portugal); 2021."},{"issue":"2","key":"5262_CR68","doi-asserted-by":"publisher","first-page":"e00359","DOI":"10.1128\/mSphere.00359-16","volume":"2","author":"Y Nishimura","year":"2017","unstructured":"Nishimura Y, Watai H, Honda T, Mihara T, Omae K, Roux S, et al. Environmental viral genomes shed new light on virus-host interactions in the ocean. mSphere. 2017;2(2):e00359\u201316.","journal-title":"mSphere"},{"issue":"1","key":"5262_CR69","first-page":"5","volume":"6","author":"A Millard","year":"2025","unstructured":"Millard A, Denise R, Lestido M, Nicholas MT, Webster D, Turner D, et al. taxmyPHAGE: automated taxonomy of dsDNA phage genomes at the genus and species level. Phage. 2025;6(1):5\u201311.","journal-title":"Phage"},{"issue":"11","key":"5262_CR70","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.3390\/v12111268","volume":"12","author":"C Moraru","year":"2020","unstructured":"Moraru C, Varsani A, Kropinski AM. VIRIDIC\u2014A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses. 2020;12(11):1268.","journal-title":"Viruses"},{"issue":"4","key":"5262_CR71","first-page":"194","volume":"2","author":"G Rangel-Pineros","year":"2021","unstructured":"Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sir\u00e9n K, Reyes A, et al. From trees to clouds: PhageClouds for fast comparison of\u223c 640,000 phage genomic sequences and host-centric visualization using genomic network graphs. Phage. 2021;2(4):194\u2013203.","journal-title":"Phage"},{"issue":"10325","key":"5262_CR72","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","volume":"399","author":"CJ Murray","year":"2022","unstructured":"Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Aguilar GR, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629\u201355.","journal-title":"Lancet"},{"key":"5262_CR73","doi-asserted-by":"publisher","first-page":"1282413","DOI":"10.3389\/fpubh.2023.1282413","volume":"11","author":"Y Zhang","year":"2023","unstructured":"Zhang Y, Xu G, Miao F, Huang W, Wang H, Wang X. Insights into the epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Acinetobacter baumannii infections in critically ill children. Front Public Health. 2023;11:1282413.","journal-title":"Front Public Health"},{"issue":"1","key":"5262_CR74","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.cell.2022.11.017","volume":"186","author":"SA Strathdee","year":"2023","unstructured":"Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell. 2023;186(1):17\u201331.","journal-title":"Cell"},{"issue":"4","key":"5262_CR75","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1099\/jmm.0.000229","volume":"65","author":"R Davis","year":"2016","unstructured":"Davis R, Brown PD. Multiple antibiotic resistance index, fitness and virulence potential in respiratory Pseudomonas aeruginosa from Jamaica. J Med Microbiol. 2016;65(4):261\u201371.","journal-title":"J Med Microbiol"},{"issue":"1","key":"5262_CR76","doi-asserted-by":"publisher","first-page":"31","DOI":"10.4161\/bact.1.1.14942","volume":"1","author":"MR Clokie","year":"2011","unstructured":"Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. Bacteriophage. 2011;1(1):31\u201345.","journal-title":"Bacteriophage"},{"issue":"1","key":"5262_CR77","doi-asserted-by":"publisher","first-page":"28","DOI":"10.2174\/138920110790725410","volume":"11","author":"ST Abedon","year":"2010","unstructured":"Abedon ST, Thomas-Abedon C. Phage therapy pharmacology. Curr Pharm Biotechnol. 2010;11(1):28\u201347.","journal-title":"Curr Pharm Biotechnol"},{"issue":"3","key":"5262_CR78","doi-asserted-by":"publisher","first-page":"e1220348","DOI":"10.1080\/21597081.2016.1220348","volume":"6","author":"ST Abedon","year":"2016","unstructured":"Abedon ST. Phage therapy dosing: The problem(s) with multiplicity of infection (MOI). Bacteriophage. 2016;6(3):e1220348.","journal-title":"Bacteriophage"},{"issue":"5","key":"5262_CR79","doi-asserted-by":"publisher","first-page":"373","DOI":"10.4103\/1735-5362.213982","volume":"12","author":"H Ghajavand","year":"2017","unstructured":"Ghajavand H, Esfahani BN, Havaei A, Fazeli H, Jafari R, Moghim S. Isolation of bacteriophages against multidrug resistant Acinetobacter baumannii. Res Pharm Sci. 2017;12(5):373\u201380.","journal-title":"Res Pharm Sci"},{"issue":"1","key":"5262_CR80","doi-asserted-by":"publisher","first-page":"2481178","DOI":"10.1080\/19490976.2025.2481178","volume":"17","author":"E Kurilovich","year":"2025","unstructured":"Kurilovich E, Geva-Zatorsky N. Effects of bacteriophages on gut microbiome functionality. Gut Microbes. 2025;17(1):2481178.","journal-title":"Gut Microbes"},{"issue":"3","key":"5262_CR81","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/s40259-013-0081-y","volume":"28","author":"J Yan","year":"2014","unstructured":"Yan J, Mao J, Xie J. Bacteriophage polysaccharide depolymerases and biomedical applications. BioDrugs. 2014;28(3):265\u201374.","journal-title":"BioDrugs"},{"issue":"2","key":"5262_CR82","doi-asserted-by":"publisher","first-page":"e0172303","DOI":"10.1371\/journal.pone.0172303","volume":"12","author":"D Turner","year":"2017","unstructured":"Turner D, Wand ME, Briers Y, Lavigne R, Sutton JM, Reynolds DM. Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki. PLoS ONE. 2017;12(2):e0172303.","journal-title":"PLoS ONE"},{"key":"5262_CR83","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.3389\/fmicb.2016.01590","volume":"7","author":"I Kusradze","year":"2016","unstructured":"Kusradze I, Karumidze N, Rigvava S, Dvalidze T, Katsitadze M, Amiranashvili I, et al. Characterization and testing the efficiency of Acinetobacter baumannii phage vB-GEC_Ab-M-G7 as an antibacterial agent. Front Microbiol. 2016;7:1590.","journal-title":"Front Microbiol"},{"issue":"1","key":"5262_CR84","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/jac\/dkx368","volume":"73","author":"K Kengkla","year":"2018","unstructured":"Kengkla K, Kongpakwattana K, Saokaew S, Apisarnthanarak A, Chaiyakunapruk N. Comparative efficacy and safety of treatment options for MDR and XDR Acinetobacter baumannii infections: a systematic review and network meta-analysis. J Antimicrob Chemother. 2018;73(1):22\u201332.","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"5262_CR85","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1186\/s12879-019-4272-0","volume":"19","author":"H Zeighami","year":"2019","unstructured":"Zeighami H, Valadkhani F, Shapouri R, Samadi E, Haghi F. Virulence characteristics of multidrug resistant biofilm forming Acinetobacter baumannii isolated from intensive care unit patients. BMC Infect Dis. 2019;19(1):629.","journal-title":"BMC Infect Dis"},{"key":"5262_CR86","doi-asserted-by":"publisher","first-page":"825828","DOI":"10.3389\/fmicb.2022.825828","volume":"13","author":"C Chang","year":"2022","unstructured":"Chang C, Yu X, Guo W, Guo C, Guo X, Li Q, et al. Bacteriophage-mediated control of biofilm: a promising new dawn for the future. Front Microbiol. 2022;13:825828.","journal-title":"Front Microbiol"},{"issue":"12","key":"5262_CR87","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/s41579-018-0070-8","volume":"16","author":"FL Nobrega","year":"2018","unstructured":"Nobrega FL, Vlot M, de Jonge PA, Dreesens LL, Beaumont HJ, Lavigne R, et al. Targeting mechanisms of tailed bacteriophages. Nat Rev Microbiol. 2018;16(12):760\u201373.","journal-title":"Nat Rev Microbiol"},{"issue":"3","key":"5262_CR88","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1128\/MMBR.00011-16","volume":"80","author":"S van Houte","year":"2016","unstructured":"van Houte S, Buckling A, Westra ER. Evolutionary ecology of prokaryotic immune mechanisms. Microbiol Mol Biol Rev. 2016;80(3):745\u201363.","journal-title":"Microbiol Mol Biol Rev"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-026-05262-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05262-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05262-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T05:26:23Z","timestamp":1784265983000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12866-026-05262-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,17]]},"references-count":88,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["5262"],"URL":"https:\/\/doi.org\/10.1186\/s12866-026-05262-7","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,17]]},"assertion":[{"value":"3 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable. This study did not involve human participants, human data, or animal subjects.Bacterial isolates used in this study were subsampled from anonymized isolates of pathogenic bacterial, biobanked at Kasr El-Aini Hospital, Cairo University, Cairo, Egypt. The research protocol for the experimental work involving these isolates (Protocol Serial Number: MI 2800) was reviewed and approved by the Research Ethics Committee for Experimental and Clinical Studies at the Faculty of Pharmacy, Cairo University, Cairo, Egypt on 26 October 2020.In accordance with the national regulations under which this committee operates, the need for consent to participate was deemed unnecessary. We have no access to any patient-identifying information. The research focuses solely on the microbiological and genomic characterization of the isolates and their phages, not on any patient-related data or outcomes. The study was conducted in compliance with the principles of the Declaration of Helsinki.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"648"}}