{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T00:42:27Z","timestamp":1792284147006,"version":"4.4.0"},"reference-count":77,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Eur J Clin Microbiol Infect Dis"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Purpose<\/jats:title>\n                    <jats:p>\n                      Carbapenem-resistant\n                      <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                      (CRAB) represents a critical global health threat for which existing antibiotics are increasingly inadequate. This study aimed to establish a comprehensive genomic framework for the rational prioritization of virulent\n                      <jats:italic>Acinetobacter<\/jats:italic>\n                      bacteriophages as therapeutic candidates.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We performed large-scale comparative genomic analysis of 340 virulent\n                      <jats:italic>Acinetobacter<\/jats:italic>\n                      bacteriophages, integrating phylogenetic reconstruction, pangenome analysis, CRISPR spacer-based host interaction mapping, Anti-CRISPR protein identification, and systematic antimicrobial resistance (AMR) gene screening.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Genome sizes spanned a nearly 20-fold range, with a significant negative correlation between genome size and GC content (R\u00b2 = 0.139, \u03c1 = \u22120.630). Phylogenetic analysis revealed extensive divergence across multiple lineages with no dominant clade. Pangenome analysis identified 20,982 unique protein families, of which 76.2% were cloud genes, confirming a highly open genome architecture. CRISPR spacer matching yielded 1,480 high-confidence matches across 100 phage genomes, providing molecular evidence of broad historical infectivity. Anti-CRISPR profiling identified\n                      <jats:italic>Acinetobacter<\/jats:italic>\n                      phage XC1 as an exceptional therapeutic candidate harboring 55 predicted Anti-CRISPR proteins with canonical regulatory locus architecture. AMR screening identified 21 distinct AMR gene homologs (Loose RGI hits, 22.5 to 47.1% amino acid identity) distributed heterogeneously across the dataset, confirming abundant therapeutically clean candidates while flagging a subset warranting further scrutiny before therapeutic exclusion.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      These findings provide a multi-criteria genomic framework for rational phage candidate prioritization against multidrug-resistant\n                      <jats:italic>Acinetobacter<\/jats:italic>\n                      infections, with direct implications for evidence-based phage therapy development.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s10096-026-05580-8","type":"journal-article","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T07:03:30Z","timestamp":1783321410000},"page":"3117-3133","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic landscape of 340 virulent Acinetobacter bacteriophages reveals anti-CRISPR\u2013enriched candidates for therapeutic prioritization"],"prefix":"10.1007","volume":"45","author":[{"given":"S. M. Iqbal","family":"Mahamud","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md.","family":"Sahim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahjabin","family":"Sanam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jahin Fairuj","family":"Oishi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jarin","family":"Tabassum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nawshin Binte","family":"Shams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahfuja Maisha","family":"Ansary","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,6]]},"reference":[{"issue":"7","key":"5580_CR1","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1179\/2047773215Y.0000000030","volume":"109","author":"F Prestinaci","year":"2015","unstructured":"Prestinaci F, Pezzotti P, Pantosti A (2015) Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health 109(7):309\u2013318 doi:10.1179\/2047773215Y.0000000030 PubMed PMID: 26343252; PubMed Central PMCID: PMC4768623","journal-title":"Pathog Glob Health"},{"issue":"13","key":"5580_CR2","doi-asserted-by":"publisher","first-page":"1946","DOI":"10.3390\/healthcare11131946","volume":"11","author":"MA Salam","year":"2023","unstructured":"Salam MA, Al-Amin MY, Salam MT, Pawar JS, Akhter N, Rabaan AA et al (2023) Antimicrobial Resistance: A Growing Serious Threat for Global Public Health. Healthcare 11(13):1946. https:\/\/doi.org\/10.3390\/healthcare11131946 PubMed PMID: 37444780; PubMed Central PMCID: PMC10340576","journal-title":"Healthcare"},{"issue":"4","key":"5580_CR3","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics9040205","volume":"9","author":"R V\u00e1zquez-L\u00f3pez","year":"2020","unstructured":"V\u00e1zquez-L\u00f3pez R, Solano-G\u00e1lvez SG, Ju\u00e1rez Vignon-Whaley JJ, Abello Vaamonde JA, Padr\u00f3 Alonzo LA, Rivera Res\u00e9ndiz A et al (2020) Acinetobacter baumannii resistance: a real challenge for clinicians. Antibiotics (Basel, Switzerland) 9(4):205. https:\/\/doi.org\/10.3390\/antibiotics9040205","journal-title":"Antibiotics (Basel, Switzerland)"},{"issue":"12","key":"5580_CR4","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1016\/j.medine.2022.08.007","volume":"46","author":"R Reina","year":"2022","unstructured":"Reina R, Le\u00f3n-Moya C, Garnacho-Montero J (2022) Treatment of Acinetobacter baumannii severe infections. Med Intensiva Engl Ed 46(12):700\u201310. https:\/\/doi.org\/10.1016\/j.medine.2022.08.007","journal-title":"Med Intensiva Engl Ed"},{"issue":"1","key":"5580_CR5","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/s40265-024-02104-6","volume":"85","author":"A Iovleva","year":"2025","unstructured":"Iovleva A, Fowler VG, Doi Y (2025) Treatment Approaches for Carbapenem-Resistant Acinetobacter baumannii Infections. Drugs 85(1):21\u201340. https:\/\/doi.org\/10.1007\/s40265-024-02104-6","journal-title":"Drugs"},{"key":"5580_CR6","doi-asserted-by":"publisher","unstructured":"Dubey V, Reza N, Hope W (2025) Drug-resistant Acinetobacter baumannii: mortality, emerging treatments, and future pharmacological targets for a WHO priority pathogen. Munita JM, editor. Clin Microbiol Rev. ;38(3):e00279-24. https:\/\/doi.org\/10.1128\/cmr.00279-24","DOI":"10.1128\/cmr.00279-24"},{"key":"5580_CR7","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1016\/j.jgar.2024.03.020","volume":"37","author":"MG Wise","year":"2024","unstructured":"Wise MG, Karlowsky JA, Mohamed N, Hermsen ED, Kamat S, Townsend A et al (2024) Global trends in carbapenem- and difficult-to-treat-resistance among World Health Organization priority bacterial pathogens: ATLAS surveillance program 2018\u20132022. J Glob Antimicrob Resist 37:168\u2013175. https:\/\/doi.org\/10.1016\/j.jgar.2024.03.020","journal-title":"J Glob Antimicrob Resist"},{"issue":"1","key":"5580_CR8","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01110-18","volume":"63","author":"B Isler","year":"2019","unstructured":"Isler B, Doi Y, Bonomo RA, Paterson DL (2019) New treatment options against carbapenem-resistant Acinetobacter baumannii infections. Antimicrob Agents Chemother 63(1):e01110-18. https:\/\/doi.org\/10.1128\/AAC.01110-18","journal-title":"Antimicrob Agents Chemother"},{"key":"5580_CR9","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.006983","author":"N Karah","year":"2025","unstructured":"Karah N, Nemec A, Uhlin BE (2025) History of the taxonomy of Acinetobacter: the emergence of hospital-adapted species of global health concern. Int J Syst Evol Microbiol. https:\/\/doi.org\/10.1099\/ijsem.0.006983","journal-title":"Int J Syst Evol Microbiol"},{"issue":"7","key":"5580_CR10","doi-asserted-by":"publisher","first-page":"4172","DOI":"10.1128\/AAC.02992-14","volume":"58","author":"S Chusri","year":"2014","unstructured":"Chusri S, Chongsuvivatwong V, Rivera JI, Silpapojakul K, Singkhamanan K, McNeil E et al (2014) Clinical Outcomes of Hospital-Acquired Infection with Acinetobacter nosocomialis and Acinetobacter pittii. Antimicrob Agents Chemother 58(7):4172\u20134179. https:\/\/doi.org\/10.1128\/AAC.02992-14","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"5580_CR11","doi-asserted-by":"publisher","first-page":"e2937","DOI":"10.1097\/MD.0000000000002937","volume":"95","author":"Y Yang","year":"2016","unstructured":"Yang Y, Wang J, Fu Y, Ruan Z, Yu Y (2016) Acinetobacter seifertii Isolated from China: Genomic Sequence and Molecular Epidemiology Analyses. Med (Baltim) 95(9):e2937. https:\/\/doi.org\/10.1097\/MD.0000000000002937","journal-title":"Med (Baltim)"},{"issue":"04","key":"5580_CR12","doi-asserted-by":"publisher","first-page":"382","DOI":"10.24036\/eksakta\/vol25-iss04\/534","volume":"25","author":"AK Mardhiyah","year":"2024","unstructured":"Mardhiyah AK, Saharman YR, Sjatha F (2024) Mobile Genetic Elements Contributing to Carbapenem Resistance in Acinetobacter baumannii: Current Insights. EKSAKTA Berk Ilm Bid MIPA 25(04):382\u2013398. https:\/\/doi.org\/10.24036\/eksakta\/vol25-iss04\/534","journal-title":"EKSAKTA Berk Ilm Bid MIPA"},{"issue":"3","key":"5580_CR13","doi-asserted-by":"publisher","first-page":"373","DOI":"10.3390\/pathogens10030373","volume":"10","author":"I Kyriakidis","year":"2021","unstructured":"Kyriakidis I, Vasileiou E, Pana ZD, Tragiannidis A (2021) Acinetobacter baumannii Antibiotic Resistance Mechanisms. Pathogens 10(3):373. https:\/\/doi.org\/10.3390\/pathogens10030373","journal-title":"Pathogens"},{"issue":"12","key":"5580_CR14","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23126582","volume":"23","author":"A Mart\u00ednez-Trejo","year":"2022","unstructured":"Mart\u00ednez-Trejo A, Ruiz-Ruiz JM, Gonzalez-Avila LU, Salda\u00f1a-Padilla A, Hern\u00e1ndez-Cortez C, Loyola-Cruz MA et al (2022) Evasion of antimicrobial activity in Acinetobacter baumannii by target site modifications: an effective resistance mechanism. Int J Mol Sci 23(12):6582. https:\/\/doi.org\/10.3390\/ijms23126582","journal-title":"Int J Mol Sci"},{"key":"5580_CR15","doi-asserted-by":"publisher","unstructured":"Sayid R, Van Den Hurk AWM, Rothschild-Rodriguez D, Herrema H, De Jonge PA, Nobrega FL (2024) Characteristics of phage-plasmids and their impact on microbial communities. Santini JM, editor. Essays Biochem. ;68(5):583\u201392. https:\/\/doi.org\/10.1042\/EBC20240014","DOI":"10.1042\/EBC20240014"},{"key":"5580_CR16","doi-asserted-by":"publisher","unstructured":"Pfeifer E, Bonnin RA, Rocha EPC (2022) Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion. Goldman GH, editor. mBio. ;13(5):e01851-22. https:\/\/doi.org\/10.1128\/mbio.01851-22","DOI":"10.1128\/mbio.01851-22"},{"issue":"5","key":"5580_CR17","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1038\/s41579-023-00993-0","volume":"22","author":"CR MacNair","year":"2024","unstructured":"MacNair CR, Rutherford ST, Tan MW (2024) Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 22(5):262\u2013275. https:\/\/doi.org\/10.1038\/s41579-023-00993-0","journal-title":"Nat Rev Microbiol"},{"key":"5580_CR18","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2025.102613","volume":"86","author":"LJ Getz","year":"2025","unstructured":"Getz LJ, Patel PH, Maxwell KL (2025) A solution to the postantibiotic era: phages as precision medicine. Curr Opin Microbiol 86:102613. https:\/\/doi.org\/10.1016\/j.mib.2025.102613","journal-title":"Curr Opin Microbiol"},{"key":"5580_CR19","doi-asserted-by":"publisher","unstructured":"Palaniappan R, Dayanithi G Therapeutic Efficacy of Bacteriophages. In: Bacteriophages in Therapeutics [Internet]. IntechOpen; 2021 [cited 2026 Mar 14]. Available from: https:\/\/www.intechopen.com\/chapters\/76569https:\/\/doi.org\/10.5772\/intechopen.97619","DOI":"10.5772\/intechopen.97619"},{"issue":"4","key":"5580_CR20","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1016\/j.tim.2018.10.008","volume":"27","author":"R Monteiro","year":"2019","unstructured":"Monteiro R, Pires DP, Costa AR, Azeredo J (2019) Phage therapy: going temperate? Trends Microbiol 27(4):368\u201378. https:\/\/doi.org\/10.1016\/j.tim.2018.10.008","journal-title":"Trends Microbiol"},{"issue":"10","key":"5580_CR21","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00954-17","volume":"61","author":"RT Schooley","year":"2017","unstructured":"Schooley RT, Biswas B, Gill JJ, Hernandez-Morales A, Lancaster J, Lessor L et al (2017) Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob Agents Chemother 61(10):e00954-17. https:\/\/doi.org\/10.1128\/AAC.00954-17","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"5580_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31455-5","volume":"13","author":"M Liu","year":"2022","unstructured":"Liu M, Hernandez-Morales A, Clark J, Le T, Biswas B, Bishop-Lilly KA et al (2022) Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy. Nat Commun 13(1):3776. https:\/\/doi.org\/10.1038\/s41467-022-31455-5","journal-title":"Nat Commun"},{"key":"5580_CR23","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1301089","volume":"14","author":"P He","year":"2024","unstructured":"He P, Cao F, Qu Q, Geng H, Yang X, Xu T et al (2024) Host range expansion of Acinetobacter phage vB_Ab4_Hep4 driven by a spontaneous tail tubular mutation. Front Cell Infect Microbiol 14:1301089. https:\/\/doi.org\/10.3389\/fcimb.2024.1301089","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"5580_CR24","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/s12866-025-03790-2","volume":"25","author":"S Liu","year":"2025","unstructured":"Liu S, Lei T, Tan Y, Huang X, Zhao W, Zou H et al (2025) Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber\/spike proteins. BMC Microbiol 25(1):73. https:\/\/doi.org\/10.1186\/s12866-025-03790-2","journal-title":"BMC Microbiol"},{"key":"5580_CR25","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1462620","volume":"14","author":"MM Islam","year":"2024","unstructured":"Islam MM, Mahbub NU, Shin WS, Oh MH (2024) Phage-encoded depolymerases as a strategy for combating multidrug-resistant Acinetobacter baumannii. Front Cell Infect Microbiol 14:1462620. https:\/\/doi.org\/10.3389\/fcimb.2024.1462620","journal-title":"Front Cell Infect Microbiol"},{"issue":"10","key":"5580_CR26","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24109100","volume":"24","author":"OY Timoshina","year":"2023","unstructured":"Timoshina OY, Kasimova AA, Shneider MM, Matyuta IO, Nikolaeva AY, Evseev PV et al (2023) Friunavirus phage-encoded depolymerases specific to different capsular types of Acinetobacter baumannii. Int J Mol Sci 24(10):9100. https:\/\/doi.org\/10.3390\/ijms24109100","journal-title":"Int J Mol Sci"},{"issue":"9","key":"5580_CR27","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa389","volume":"7","author":"S Aslam","year":"2020","unstructured":"Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S et al (2020) Lessons learned from the first 10 consecutive cases of intravenous bacteriophage therapy to treat multidrug-resistant bacterial infections at a single center in the United States. Open Forum Infect Dis 7(9):ofaa389. https:\/\/doi.org\/10.1093\/ofid\/ofaa389","journal-title":"Open Forum Infect Dis"},{"key":"5580_CR28","doi-asserted-by":"publisher","first-page":"1716306","DOI":"10.3389\/fmed.2025.1716306","volume":"12","author":"J Lin","year":"2025","unstructured":"Lin J, Dai G, Zhang L, Xu P, Zhao P, Zhou Y et al (2025) Case Report: Bacteriophage-antibiotic therapy for extensively drug-resistant Acinetobacter baumannii in critically ill patient with respiratory infection. Front Med 12:1716306. https:\/\/doi.org\/10.3389\/fmed.2025.1716306","journal-title":"Front Med"},{"key":"5580_CR29","doi-asserted-by":"publisher","first-page":"1432703","DOI":"10.3389\/fmed.2024.1432703","volume":"11","author":"J Qu","year":"2024","unstructured":"Qu J, Zou J, Zhang J, Qu J, Lu H (2024) Phage therapy for extensively drug resistant Acinetobacter baumannii infection: case report and in vivo evaluation of the distribution of phage and the impact on gut microbiome. Front Med 11:1432703. https:\/\/doi.org\/10.3389\/fmed.2024.1432703","journal-title":"Front Med"},{"issue":"6","key":"5580_CR30","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 (2018) Phage Therapy Faces Evolutionary Challenges. Viruses 10(6):323. https:\/\/doi.org\/10.3390\/v10060323","journal-title":"Viruses"},{"key":"5580_CR31","doi-asserted-by":"publisher","unstructured":"Maxwell KL (2016) Phages Fight Back: Inactivation of the CRISPR-Cas Bacterial Immune System by Anti-CRISPR Proteins. Dutch RE, editor. PLOS Pathog. ;12(1):e1005282. https:\/\/doi.org\/10.1371\/journal.ppat.1005282","DOI":"10.1371\/journal.ppat.1005282"},{"issue":"1","key":"5580_CR32","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1146\/annurev-genet-120417-031321","volume":"52","author":"SY Stanley","year":"2018","unstructured":"Stanley SY, Maxwell KL (2018) Phage-Encoded Anti-CRISPR Defenses. Annu Rev Genet 52(1):445\u2013464. https:\/\/doi.org\/10.1146\/annurev-genet-120417-031321","journal-title":"Annu Rev Genet"},{"issue":"1","key":"5580_CR33","doi-asserted-by":"publisher","first-page":"3699","DOI":"10.1038\/s41467-024-48074-x","volume":"15","author":"Y Bhoobalan-Chitty","year":"2024","unstructured":"Bhoobalan-Chitty Y, Xu S, Martinez-Alvarez L, Karamycheva S, Makarova KS, Koonin EV et al (2024) Regulatory sequence-based discovery of anti-defense genes in archaeal viruses. Nat Commun 15(1):3699. https:\/\/doi.org\/10.1038\/s41467-024-48074-x","journal-title":"Nat Commun"},{"issue":"1","key":"5580_CR34","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1146\/annurev-micro-041222-024843","volume":"78","author":"SJ Hobbs","year":"2024","unstructured":"Hobbs SJ, Kranzusch PJ (2024) Nucleotide Immune Signaling in CBASS, Pycsar, Thoeris, and CRISPR Antiphage Defense. Annu Rev Microbiol 78(1):255\u2013276. https:\/\/doi.org\/10.1146\/annurev-micro-041222-024843","journal-title":"Annu Rev Microbiol"},{"issue":"6299","key":"5580_CR35","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad5147","volume":"353","author":"P Mohanraju","year":"2024","unstructured":"Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, Van Der Oost J (2024) Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353(6299):aad5147. https:\/\/doi.org\/10.1126\/science.aad5147","journal-title":"Science"},{"key":"5580_CR36","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.909886","volume":"13","author":"G Yadav","year":"2022","unstructured":"Yadav G, Singh R (2022) In silico analysis reveals the co-existence of CRISPR-Cas type I-F1 and type I-F2 systems and its association with restricted phage invasion in Acinetobacter baumannii. Front Microbiol 13:909886. https:\/\/doi.org\/10.3389\/fmicb.2022.909886","journal-title":"Front Microbiol"},{"key":"5580_CR37","doi-asserted-by":"publisher","unstructured":"Scarrone M, Turner D, Dion M, Tremblay D, Moineau S (2025) In silico and in vitro comparative analysis of 79 Acinetobacter baumannii clinical isolates. Gonzalez V, editor. Microbiol Spectr. ;13(7):e02849-24. https:\/\/doi.org\/10.1128\/spectrum.02849-24","DOI":"10.1128\/spectrum.02849-24"},{"issue":"1","key":"5580_CR38","doi-asserted-by":"publisher","DOI":"10.3390\/v10010005","volume":"10","author":"D Turner","year":"2017","unstructured":"Turner D, Ackermann HW, Kropinski AM, Lavigne R, Sutton JM, Reynolds DM (2017) Comparative analysis of 37 Acinetobacter bacteriophages. Viruses 10(1):5. https:\/\/doi.org\/10.3390\/v10010005","journal-title":"Viruses"},{"issue":"2","key":"5580_CR39","doi-asserted-by":"publisher","DOI":"10.3390\/v14020181","volume":"14","author":"H Oliveira","year":"2022","unstructured":"Oliveira H, Domingues R, Evans B, Sutton JM, Adriaenssens EM, Turner D (2022) Genomic diversity of bacteriophages infecting the genus Acinetobacter. Viruses 14(2):181. https:\/\/doi.org\/10.3390\/v14020181","journal-title":"Viruses"},{"key":"5580_CR40","doi-asserted-by":"publisher","first-page":"1720092","DOI":"10.3389\/fmicb.2026.1720092","volume":"17","author":"SJL Pang","year":"2026","unstructured":"Pang SJL, Wee SK, Yap EPH (2026) Genomic landscape of complete Acinetobacter phages: clustering, core-shell genes, and synteny insights. Front Microbiol 17:1720092. https:\/\/doi.org\/10.3389\/fmicb.2026.1720092","journal-title":"Front Microbiol"},{"issue":"D1","key":"5580_CR41","doi-asserted-by":"publisher","first-page":"D56","DOI":"10.1093\/nar\/gkae1114","volume":"53","author":"EW Sayers","year":"2025","unstructured":"Sayers EW, Cavanaugh M, Frisse L, Pruitt KD, Schneider VA, Underwood BA et al (2025) GenBank 2025 update. Nucleic Acids Res 53(D1):D56\u201361. https:\/\/doi.org\/10.1093\/nar\/gkae1114 PubMed PMID: 39558184; PubMed Central PMCID: PMC11701615","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"5580_CR42","doi-asserted-by":"publisher","first-page":"66","DOI":"10.3390\/v8030066","volume":"8","author":"T Mihara","year":"2016","unstructured":"Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H et al (2016) Linking Virus Genomes with Host Taxonomy. Viruses 8(3):66. https:\/\/doi.org\/10.3390\/v8030066","journal-title":"Viruses"},{"key":"5580_CR43","doi-asserted-by":"publisher","unstructured":"Tynecki P, Guzi\u0144ski A, Kazimierczak J, Jadczuk M, Dastych J, Onisko A PhageAI - Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing [Internet]. bioRxiv; 2020 [cited 2026 Mar 14]. p. 2020.07.11.198606. Available from: https:\/\/www.biorxiv.org\/content\/https:\/\/doi.org\/10.1101\/2020.07.11.198606v1 doi:10.1101\/2020.07.11.198606","DOI":"10.1101\/2020.07.11.198606v1"},{"issue":"14","key":"5580_CR44","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153 PubMed PMID: 24642063","journal-title":"Bioinformatics"},{"issue":"W1","key":"5580_CR45","doi-asserted-by":"publisher","first-page":"W537","DOI":"10.1093\/nar\/gky","volume":"46","author":"E Afgan","year":"2018","unstructured":"Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M et al (2018) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46(W1):W537\u2013W544. https:\/\/doi.org\/10.1093\/nar\/gky379 PubMed PMID: 29790989; PubMed Central PMCID: PMC6030816","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"5580_CR46","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic I, Bork P (2024) Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 52(W1):W78-82. https:\/\/doi.org\/10.1093\/nar\/gkae268","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"5580_CR47","doi-asserted-by":"publisher","first-page":"W246","DOI":"10.1093\/nar\/gky425","volume":"46","author":"D Couvin","year":"2018","unstructured":"Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, N\u00e9ron B et al (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 46(W1):W246-51. https:\/\/doi.org\/10.1093\/nar\/gky425","journal-title":"Nucleic Acids Res"},{"key":"5580_CR48","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. https:\/\/doi.org\/10.1186\/1471-2105-10-421 PubMed PMID: 20003500; PubMed Central PMCID: PMC2803857","journal-title":"BMC Bioinformatics"},{"key":"5580_CR49","doi-asserted-by":"publisher","unstructured":"Yin Y, Yang B, Entwistle S (2019) Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches. Claesson MJ, editor. mSystems. ;4(5):e00455-19. https:\/\/doi.org\/10.1128\/mSystems.00455-19","DOI":"10.1128\/mSystems.00455-19"},{"issue":"D1","key":"5580_CR50","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2022","unstructured":"Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA et al (2022) CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 51(D1):D690\u2013D699. https:\/\/doi.org\/10.1093\/nar\/gkac920 PubMed PMID: 36263822; PubMed Central PMCID: PMC9825576","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"5580_CR51","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10040700","volume":"10","author":"B N\u00e9ron","year":"2022","unstructured":"N\u00e9ron B, Littner E, Haudiquet M, Perrin A, Cury J, Rocha E (2022) IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella. Microorganisms 10(4):700. https:\/\/doi.org\/10.3390\/microorganisms10040700","journal-title":"Microorganisms"},{"key":"5580_CR52","doi-asserted-by":"publisher","unstructured":"Scarrone M, Turner D, Wittmann J, Rohde C, Labrie SJ, Tremblay DM et al (2025) JJ <>Dennehy editor. Complete genome of five Acinetobacter baumannii phages. Microbiol Resour Announc 14 8 e00463\u2013e00425 https:\/\/doi.org\/10.1128\/mra.00463-25","DOI":"10.1128\/mra.00463-25"},{"issue":"5","key":"5580_CR53","doi-asserted-by":"publisher","first-page":"335","DOI":"10.3390\/cimb47050335","volume":"47","author":"C Wang","year":"2025","unstructured":"Wang C, Zhao S, Jiang H, Shi H, Li J, Zhao C et al (2025) Biological Characteristics and Genomic Analysis of Acinetobacter nosocomialis Lytic Phage XC1. Curr Issues Mol Biol 47(5):335. https:\/\/doi.org\/10.3390\/cimb47050335","journal-title":"Curr Issues Mol Biol"},{"issue":"6","key":"5580_CR54","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1007\/s00284-023-03295-z","volume":"80","author":"Y Li","year":"2023","unstructured":"Li Y, Xiao S, Huang G (2023) Acinetobacter baumannii Bacteriophage: Progress in Isolation, Genome Sequencing, Preclinical Research, and Clinical Application. Curr Microbiol 80(6):199. https:\/\/doi.org\/10.1007\/s00284-023-03295-z","journal-title":"Curr Microbiol"},{"key":"5580_CR55","doi-asserted-by":"publisher","unstructured":"Pope WH, Jacobs-Sera D, Russell DA, Rubin DHF, Kajee A, Msibi ZNP et al (2014) Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the Mycobacterium Neighborhood. Katze MG, editor. mBio. ;5(6):e02145-14. https:\/\/doi.org\/10.1128\/mBio.02145-14","DOI":"10.1128\/mBio.02145-14"},{"issue":"1","key":"5580_CR56","doi-asserted-by":"publisher","first-page":"189","DOI":"10.3390\/ddc2010012","volume":"2","author":"X Xia","year":"2023","unstructured":"Xia X (2023) Optimizing Protein Production in Therapeutic Phages against a Bacterial Pathogen, Mycobacterium abscessus. Drugs Drug Candidates 2(1):189\u2013209. https:\/\/doi.org\/10.3390\/ddc2010012","journal-title":"Drugs Drug Candidates"},{"issue":"4","key":"5580_CR57","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/S0923-2508(03)00068-8","volume":"154","author":"RW Hendrix","year":"2003","unstructured":"Hendrix RW, Hatfull GF, Smith MCM (2003) Bacteriophages with tails: chasing their origins and evolution. Res Microbiol 154(4):253\u2013257. https:\/\/doi.org\/10.1016\/S0923-2508(03)00068-8","journal-title":"Res Microbiol"},{"issue":"1","key":"5580_CR58","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/s42003-025-07459-4","volume":"8","author":"W Yi","year":"2025","unstructured":"Yi W, Zhu N, Peng Z, Chu X, Sun H, Song L et al (2025) In silico characterization of defense system hotspots in Acinetobacter spp. Commun Biol 8(1):39. https:\/\/doi.org\/10.1038\/s42003-025-07459-4","journal-title":"Commun Biol"},{"issue":"5","key":"5580_CR59","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1007\/s00203-026-04785-x","volume":"208","author":"R Ibrahim","year":"2026","unstructured":"Ibrahim R, Aranjani JM (2026) Bacterial defense mechanisms against bacteriophages: an evolutionary arms race. Arch Microbiol 208(5):229. https:\/\/doi.org\/10.1007\/s00203-026-04785-x","journal-title":"Arch Microbiol"},{"issue":"11","key":"5580_CR60","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics14111134","volume":"14","author":"Y Wang","year":"2025","unstructured":"Wang Y, Li L, Liang Y, Xu K, Ye Y, He M (2025) Phage therapy for Acinetobacter baumannii infections: a review on advances in classification, applications, and translational roadblocks. Antibiotics Basel 14(11):1134. https:\/\/doi.org\/10.3390\/antibiotics14111134","journal-title":"Antibiotics Basel"},{"issue":"10","key":"5580_CR61","doi-asserted-by":"publisher","first-page":"5806","DOI":"10.1128\/AAC.02877-15","volume":"60","author":"JM Regeimbal","year":"2016","unstructured":"Regeimbal JM, Jacobs AC, Corey BW, Henry MS, Thompson MG, Pavlicek RL et al (2016) Personalized Therapeutic Cocktail of Wild Environmental Phages Rescues Mice from Acinetobacter baumannii Wound Infections. Antimicrob Agents Chemother 60(10):5806\u20135816. https:\/\/doi.org\/10.1128\/AAC.02877-15","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"5580_CR62","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18236-8","volume":"11","author":"CM Bellas","year":"2020","unstructured":"Bellas CM, Schroeder DC, Edwards A, Barker G, Anesio AM (2020) Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems. Nat Commun 11(1):4403. https:\/\/doi.org\/10.1038\/s41467-020-18236-8","journal-title":"Nat Commun"},{"issue":"1","key":"5580_CR63","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.14408","volume":"17","author":"M Tokuda","year":"2024","unstructured":"Tokuda M, Shintani M (2024) Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 17(1):e14408. https:\/\/doi.org\/10.1111\/1751-7915.14408","journal-title":"Microb Biotechnol"},{"issue":"6","key":"5580_CR64","doi-asserted-by":"publisher","first-page":"3127","DOI":"10.1093\/nar\/gkab133","volume":"49","author":"MB Dion","year":"2021","unstructured":"Dion MB, Plante PL, Zufferey E, Shah SA, Corbeil J, Moineau S (2021) Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter. Nucleic Acids Res 49(6):3127\u20133138. https:\/\/doi.org\/10.1093\/nar\/gkab133","journal-title":"Nucleic Acids Res"},{"key":"5580_CR65","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1148579","volume":"14","author":"S Aggarwal","year":"2023","unstructured":"Aggarwal S, Dhall A, Patiyal S, Choudhury S, Arora A, Raghava GPS (2023) An ensemble method for prediction of phage-based therapy against bacterial infections. Front Microbiol 14:1148579. https:\/\/doi.org\/10.3389\/fmicb.2023.1148579","journal-title":"Front Microbiol"},{"issue":"7","key":"5580_CR66","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2023.168036","volume":"435","author":"KS Makarova","year":"2023","unstructured":"Makarova KS, Wolf YI, Koonin EV (2023) In silico approaches for prediction of anti-CRISPR proteins. J Mol Biol 435(7):168036. https:\/\/doi.org\/10.1016\/j.jmb.2023.168036","journal-title":"J Mol Biol"},{"issue":"14","key":"5580_CR67","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2024.e34692","volume":"10","author":"H Kadkhoda","year":"2024","unstructured":"Kadkhoda H, Gholizadeh P, Samadi Kafil H, Ghotaslou R, Pirzadeh T, Ahangarzadeh Rezaee M et al (2024) Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance. Heliyon 10(14):e34692. https:\/\/doi.org\/10.1016\/j.heliyon.2024.e34692","journal-title":"Heliyon"},{"issue":"2","key":"5580_CR68","doi-asserted-by":"publisher","first-page":"205","DOI":"10.3390\/pathogens10020205","volume":"10","author":"M Tyumentseva","year":"2021","unstructured":"Tyumentseva M, Mikhaylova Y, Prelovskaya A, Tyumentsev A, Petrova L, Fomina V et al (2021) Genomic and Phenotypic Analysis of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates Carrying Different Types of CRISPR\/Cas Systems. Pathogens 10(2):205. https:\/\/doi.org\/10.3390\/pathogens10020205","journal-title":"Pathogens"},{"issue":"7987","key":"5580_CR69","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1038\/s41586-023-06612-5","volume":"623","author":"S Camara-Wilpert","year":"2023","unstructured":"Camara-Wilpert S, Mayo-Mu\u00f1oz D, Russel J, Fagerlund RD, Madsen JS, Fineran PC et al (2023) Bacteriophages suppress CRISPR\u2013Cas immunity using RNA-based anti-CRISPRs. Nature 623(7987):601\u20137. https:\/\/doi.org\/10.1038\/s41586-023-06612-5","journal-title":"Nature"},{"issue":"2","key":"5580_CR70","doi-asserted-by":"publisher","DOI":"10.1002\/btm2.10381","volume":"8","author":"K Khambhati","year":"2023","unstructured":"Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I et al (2023) Phage engineering and phage-assisted <sc>CRISPR\u2010Cas<\/sc> delivery to combat multidrug\u2010resistant pathogens. Bioeng Transl Med 8(2):e10381. https:\/\/doi.org\/10.1002\/btm2.10381","journal-title":"Bioeng Transl Med"},{"issue":"4","key":"5580_CR71","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1248\/jhs.56.442","volume":"56","author":"H Yan","year":"2010","unstructured":"Yan H, Li L, Zong M, Alam MJ, Shinoda S, Shi L (2010) Occurrence and Characteristics of Class 1 and 2 Integrons in Clinical Bacterial Isolates from Patients in South China. J Health Sci 56(4):442\u2013450. https:\/\/doi.org\/10.1248\/jhs.56.442","journal-title":"J Health Sci"},{"issue":"1","key":"5580_CR72","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/s44259-025-00117-z","volume":"3","author":"BWM Cook","year":"2025","unstructured":"Cook BWM, Hynes AP (2025) Re-evaluating what makes a phage unsuitable for therapy. Npj Antimicrob Resist 3(1):45. https:\/\/doi.org\/10.1038\/s44259-025-00117-z","journal-title":"Npj Antimicrob Resist"},{"issue":"1","key":"5580_CR73","doi-asserted-by":"publisher","first-page":"55","DOI":"10.3390\/antibiotics15010055","volume":"15","author":"N Abdraimova","year":"2026","unstructured":"Abdraimova N, Shitikov E, Kornienko M (2026) The Role of Genomics in Advancing and Standardising Bacteriophage Therapy. Antibiotics 15(1):55. https:\/\/doi.org\/10.3390\/antibiotics15010055","journal-title":"Antibiotics"},{"key":"5580_CR74","doi-asserted-by":"publisher","unstructured":"Zhang Y, Kitazumi A, Liao YT, De Los Reyes BG, Wu VCH (2023) Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Denes TG, editor. Microbiol Spectr. ;11(5):e00226-23. https:\/\/doi.org\/10.1128\/spectrum.00226-23","DOI":"10.1128\/spectrum.00226-23"},{"issue":"2","key":"5580_CR75","doi-asserted-by":"publisher","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 (2022) PhageLeads: rapid assessment of phage therapeutic suitability using an ensemble machine learning approach. Viruses 14(2):342. https:\/\/doi.org\/10.3390\/v14020342","journal-title":"Viruses"},{"issue":"3","key":"5580_CR76","doi-asserted-by":"publisher","first-page":"648","DOI":"10.5455\/jabet.2023.d156","volume":"6","author":"I Jabeen","year":"2023","unstructured":"Jabeen I, Mahamud S, Islam S, Lamisa A, Anjum A, Oishy S et al (2023) Genomic identification and characterization of prophages associated with Citrobacter freundii strains. J Adv Biotechnol Exp Ther 6(3):648. https:\/\/doi.org\/10.5455\/jabet.2023.d156","journal-title":"J Adv Biotechnol Exp Ther"},{"issue":"4","key":"5580_CR77","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1007\/s00284-025-04110-7","volume":"82","author":"SMI Mahamud","year":"2025","unstructured":"Mahamud SMI, Oishy SH, Roy S, Pal K, Rubaiyat RN, Ansary MM (2025) Comparative Genomic Analysis of 66 Bacteriophages Infecting Morganella morganii Strains. Curr Microbiol 82(4):137. https:\/\/doi.org\/10.1007\/s00284-025-04110-7","journal-title":"Curr Microbiol"}],"container-title":["European Journal of Clinical Microbiology &amp; Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10096-026-05580-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10096-026-05580-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10096-026-05580-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T00:02:39Z","timestamp":1792281759000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10096-026-05580-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,6]]},"references-count":77,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["5580"],"URL":"https:\/\/doi.org\/10.1007\/s10096-026-05580-8","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-9225929\/v1","asserted-by":"object"}]},"ISSN":["0934-9723","1435-4373"],"issn-type":[{"value":"0934-9723","type":"print"},{"value":"1435-4373","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,6]]},"assertion":[{"value":"25 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 July 2026","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","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}]}}