{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:02:20Z","timestamp":1789981340994,"version":"4.0.1"},"reference-count":60,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009392","name":"Prince Sattam Bin Abdulaziz University","doi-asserted-by":"publisher","award":["PSAU\/2026\/R\/1448"],"award-info":[{"award-number":["PSAU\/2026\/R\/1448"]}],"id":[{"id":"10.13039\/100009392","id-type":"DOI","asserted-by":"publisher"}]},{"award":["PSAU\/2026\/R\/1448"],"award-info":[{"award-number":["PSAU\/2026\/R\/1448"]}],"id":[{"id":"https:\/\/ror.org\/04jt46d36","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Enterobacter cloacae (E. cloacae) is an important healthcare-associated pathogen with increasing antimicrobial resistance. Prophages and phage-inducible chromosomal islands (PICIs) are integral components of the E. cloacae genome, yet their contribution to resistance, virulence, and anti-phage defense remains poorly understood. To address this gap, we analyzed 35 complete E. cloacae genomes, identifying 139 intact prophages (10.8\u201385.7 kb) with an average GC content (~52%) close to that of the host (54\u201355%). Most prophages (86.6%) were assigned to the families Peduoviridae and Drexlerviridae within the class Caudoviricetes, and proteome-based clustering showed strong relatedness to phages infecting Enterobacteriaceae. The E. cloacae genomes harbored multiple antimicrobial resistance genes, notably fosA (97%), oqxA\/oqxB (89%) and blaCMH-3 (77%). However, on genomic-context verification none were genuinely prophage-encoded; they were instead located on the chromosome or plasmids. Virulence profiling revealed universal presence of ompA and high prevalence of csgG (94%), while the only confirmed prophage-encoded virulence determinants were the Shiga toxin genes stxA and stx1B. Additionally, 16 phage satellites were identified, containing conserved integration, replication, and packaging modules together with diverse accessory and anti-phage defense systems. Overall, prophages and phage satellites drive genome diversification in E. cloacae, with satellites notably serving as reservoirs of anti-phage defense, whereas resistance and virulence genes are located outside prophage and satellite regions.<\/jats:p>","DOI":"10.3390\/v18091045","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T08:03:47Z","timestamp":1789977827000},"page":"1045","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Genomics of the Enterobacter\u00a0cloacae Mobilome: Prophage Diversity and Anti-Phage Defense Systems in Phage Satellites"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9638-2458","authenticated-orcid":false,"given":"Alhassan","family":"Alrafaie","sequence":"first","affiliation":[{"name":"Department of Medical Laboratory, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-3663-2865","authenticated-orcid":false,"given":"Nasser","family":"Alqurainy","sequence":"additional","affiliation":[{"name":"Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia"},{"name":"Infectious Disease Research Department, King Abdullah International Medical Research Center, Riyadh 11426, Saudi Arabia"},{"name":"Ministry of National Guard-Health Affairs, Riyadh 11426, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s13568-024-01675-7","article-title":"Enterobacter cloacae from urinary tract infections: Frequency, protein analysis, and antimicrobial resistance","volume":"14","author":"Elbehiry","year":"2024","journal-title":"AMB Express"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e01380-21","DOI":"10.1128\/Spectrum.01380-21","article-title":"Genomic Investigation and Successful Containment of an Intermittent Common Source Outbreak of OXA-48-Producing Enterobacter cloacae Related to Hospital Shower Drains","volume":"9","author":"Nurjadi","year":"2021","journal-title":"Microbiol. Spectr."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Intra, J., Carcione, D., Sala, R.M., Siracusa, C., Brambilla, P., and Leoni, V. (2023). Antimicrobial Resistance Patterns of Enterobacter cloacae and Klebsiella aerogenes Strains Isolated from Clinical Specimens: A Twenty-Year Surveillance Study. Antibiotics, 12.","DOI":"10.3390\/antibiotics12040775"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"129","DOI":"10.2147\/IDR.S234678","article-title":"Carbapenem-Resistant Enterobacter cloacae Causing Nosocomial Infections in Southwestern China: Molecular Epidemiology, Risk Factors, and Predictors of Mortality","volume":"13","author":"Tian","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4670","DOI":"10.1038\/s41598-024-81595-5","article-title":"Genomic analysis of Enterobacter cloacae complex from Southern Thailand reveals insights into multidrug resistance genotypes and genetic diversity","volume":"15","author":"Yaikhan","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"354","DOI":"10.4161\/viru.24498","article-title":"Importance of prophages to evolution and virulence of bacterial pathogens","volume":"4","author":"Fortier","year":"2013","journal-title":"Virulence"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1111\/evo.14153","article-title":"Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments","volume":"75","author":"Wendling","year":"2021","journal-title":"Evolution"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1038\/s41396-023-01463-4","article-title":"Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes","volume":"17","author":"Huang","year":"2023","journal-title":"ISME J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"164708","DOI":"10.1016\/j.scitotenv.2023.164708","article-title":"Antibiotic resistance genes in bacteriophages from wastewater treatment plant and hospital wastewaters","volume":"892","author":"Pires","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Zhou, W., Zhou, H., Sun, Y., Gao, S., Zhang, Y., Cao, X., Zhang, Z., Shen, H., and Zhang, C. (2020). Characterization of clinical enterococci isolates, focusing on the vancomycin-resistant enterococci in a tertiary hospital in China: Based on the data from 2013 to 2018. BMC Infect. Dis., 20.","DOI":"10.1186\/s12879-020-05078-4"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Li, D., Liang, W., Hu, Q., Ren, J., Xue, F., Liu, Q., and Tang, F. (2022). The effect of a spontaneous induction prophage, phi458, on biofilm formation and virulence in avian pathogenic Escherichia coli. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1049341"},{"key":"ref_12","first-page":"000726","article-title":"Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps","volume":"7","author":"Nepal","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5359","DOI":"10.3390\/toxins7124889","article-title":"Prophage-Encoded Staphylococcal Enterotoxin A: Regulation of Production in Staphylococcus aureus Strains Representing Different Sea Regions","volume":"7","author":"Zeaki","year":"2015","journal-title":"Toxins"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e0045221","DOI":"10.1128\/mSphere.00452-21","article-title":"Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens","volume":"6","author":"Kondo","year":"2021","journal-title":"mSphere"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1038\/s41579-025-01156-z","article-title":"Genetics, ecology and evolution of phage satellites","volume":"23","author":"Seed","year":"2025","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1146\/annurev-virology-031413-085446","article-title":"The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites","volume":"2","author":"Christie","year":"2015","journal-title":"Annu. Rev. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1093\/nar\/gkad123","article-title":"Identification and characterization of thousands of bacteriophage satellites across bacteria","volume":"51","author":"Sousa","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Liu, W.Y., Wong, C.F., Chung, K.M.K., Jiang, J.W., and Leung, F.C.C. (2013). Comparative Genome Analysis of Enterobacter cloacae. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0074487"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Yu, X., Zhang, W., Zhao, Z., Ye, C., Zhou, S., Wu, S., Han, L., Han, Z., and Ye, H. (2019). Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance. BMC Genom., 20.","DOI":"10.1186\/s12864-019-6225-9"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"000565.v3","DOI":"10.1099\/acmi.0.000565.v3","article-title":"Draft genome sequence of Enterobacter cloacae ST473 harbouring blaCMH-3 isolated from a human patient diagnosed with recurrent bacteriuria in Nigeria","volume":"5","author":"David","year":"2023","journal-title":"Access Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Kananizadeh, P., Oshiro, S., Watanabe, S., Iwata, S., Kuwahara-Arai, K., Shimojima, M., Ogawa, M., Tada, T., and Kirikae, T. (2020). Emergence of carbapenem-resistant and colistin-susceptible Enterobacter cloacae complex co-harboring blaIMP-1 and mcr-9 in Japan. BMC Infect. Dis., 20.","DOI":"10.1186\/s12879-020-05021-7"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"001204","DOI":"10.1099\/mic.0.001204","article-title":"Genomic characterization of antimicrobial resistance in mcr-carrying ESBL-producing Escherichia coli from pigs and humans","volume":"168","author":"Pungpian","year":"2022","journal-title":"Microbiology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2007.00778.x","article-title":"A molecular Swiss army knife: OmpA structure, function and expression","volume":"273","author":"Smith","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1128\/mr.57.3.683-702.1993","article-title":"Mechanisms of genome propagation and helper exploitation by satellite phage P4","volume":"57","author":"Lindqvist","year":"1993","journal-title":"Microbiol. Rev."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.virol.2004.01.016","article-title":"Bacteriophage P4 Vis protein is needed for prophage excision","volume":"322","author":"Spoldi","year":"2004","journal-title":"Virology"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Dokland, T. (2019). Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements. Viruses, 11.","DOI":"10.3390\/v11111003"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1038\/s41396-018-0156-3","article-title":"Phage-inducible chromosomal islands are ubiquitous within the bacterial universe","volume":"12","author":"Abdulrahman","year":"2018","journal-title":"ISME J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4502","DOI":"10.1128\/jvi.71.6.4502-4508.1997","article-title":"Derepression of prophage P2 by satellite phage P4: Cloning of the P4 epsilon gene and identification of its product","volume":"71","author":"Liu","year":"1997","journal-title":"J. Virol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1038\/s41564-022-01219-4","article-title":"A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome","volume":"7","author":"Vassallo","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"eads0768","DOI":"10.1126\/science.ads0768","article-title":"Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems","volume":"388","author":"Darracq","year":"2025","journal-title":"Science"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1038\/s41564-022-01162-4","article-title":"Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria","volume":"7","author":"Hsueh","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/s41564-022-01158-0","article-title":"Bacteria deplete deoxynucleotides to defend against bacteriophage infection","volume":"7","author":"Tal","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1016\/j.cell.2023.04.015","article-title":"Bacterial NLR-related proteins protect against phage","volume":"186","author":"Kibby","year":"2023","journal-title":"Cell"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Alsaadi, A., Imam, M., Alghamdi, A.A., Aljedani, S.S., Alsari, A., Aljami, H., and Bosaeed, M. (2025). Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1563781"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Fong, K., Lu, Y.T., Brenner, T., Falardeau, J., and Wang, S. (2022). Prophage Diversity Across Salmonella and Verotoxin-Producing Escherichia coli in Agricultural Niches of British Columbia, Canada. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.853703"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Yao, Y., Chen, Q., and Zhou, H. (2023). Virulence Factors and Pathogenicity Mechanisms of Acinetobacter baumannii in Respiratory Infectious Diseases. Antibiotics, 12.","DOI":"10.3390\/antibiotics12121749"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Zrelovs, N., Dislers, A., and Kazaks, A. (2020). Motley Crew: Overview of the Currently Available Phage Diversity. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.579452"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e0121120","DOI":"10.1128\/mSystems.01211-20","article-title":"Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems","volume":"6","author":"Pei","year":"2021","journal-title":"mSystems"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Aworh, M.K., Lawal, O.U., Egyir, B., and Hendriksen, R.S. (2025). In silico genomic insights into bacteriophages infecting ESBL-producing Escherichia coli from human, animal, and environmental sources. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-03913-9"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Olsen, N.S., Forero-Junco, L., Kot, W., and Hansen, L.H. (2020). Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment. Viruses, 12.","DOI":"10.3390\/v12090986"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e0285123","DOI":"10.1128\/mbio.02851-23","article-title":"Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus","volume":"15","author":"Foxall","year":"2024","journal-title":"mBio"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Braga, L.P.P., Soucy, S.M., Amgarten, D.E., da Silva, A.M., and Setubal, J.C. (2018). Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. Front. Ecol. Evol., 6.","DOI":"10.3389\/fevo.2018.00006"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"20200475","DOI":"10.1098\/rstb.2020.0475","article-title":"To Catch a Hijacker: Abundance, Evolution and Genetic Diversity of P4-like Bacterio-phage Satellites","volume":"377","author":"Rocha","year":"2022","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"O\u2019Hara, B.J., Barth, Z.K., McKitterick, A.C., and Seed, K.D. (2017). A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome. PLoS Genet., 13.","DOI":"10.1371\/journal.pgen.1006838"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.chom.2022.12.001","article-title":"A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature","volume":"31","author":"Alqurainy","year":"2023","journal-title":"Cell Host Microbe"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"6636","DOI":"10.1016\/j.cell.2025.08.019","article-title":"Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization","volume":"188","author":"He","year":"2025","journal-title":"Cell"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Abdallah, R., Yimagou, E.K., Hadjadj, L., Mediannikov, O., Ibrahim, A., Davoust, B., Barciela, A., Hernandez-Aguilar, R.A., Diatta, G., and Sokhna, C. (2022). Population Diversity of Antibiotic Resistant Enterobacterales in Samples From Wildlife Origin in Senegal: Identification of a Multidrug Resistance Transposon Carrying blaCTX\u2013M\u201315 in Escherichia coli. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.838392"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2514092","DOI":"10.1080\/21505594.2025.2514092","article-title":"Enterobacterales use capsules, transporters, mobile genetic elements, and other evolutionary adaptations to survive antibiotics exposure in the absence of resistance genes","volume":"16","author":"Mmatli","year":"2025","journal-title":"Virulence"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"20231088","DOI":"10.1098\/rspb.2023.1088","article-title":"Prophages and plasmids can display opposite trends in the types of accessory genes they carry","volume":"290","author":"Takeuchi","year":"2023","journal-title":"Proc. R. Soc. B Biol. Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"8034","DOI":"10.1128\/JB.00900-07","article-title":"Biofilm Formation-Gene Expression Relay System in Escherichia coli: Modulation of \u03c3S-Dependent Gene Expression by the CsgD Regulatory Protein via \u03c3S Protein Stabilization","volume":"189","author":"Gualdi","year":"2007","journal-title":"J. Bacteriol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"11075","DOI":"10.1021\/ja0522027","article-title":"In Vitro Characterization of Salmochelin and Enterobactin Trilactone Hydrolases IroD, IroE, and Fes","volume":"127","author":"Lin","year":"2005","journal-title":"J. Am. Chem. Soc."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1099\/mic.0.000003","article-title":"Shiga toxins and stx phages: Highly diverse entities","volume":"161","author":"Lucchesi","year":"2015","journal-title":"Microbiology"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1016\/j.chom.2022.02.018","article-title":"Phages and their satellites encode hotspots of antiviral systems","volume":"30","author":"Rousset","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.mib.2020.06.002","article-title":"Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation","volume":"56","author":"Marina","year":"2020","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3248","DOI":"10.1016\/j.cell.2022.07.014","article-title":"Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors","volume":"185","author":"Ojiogu","year":"2022","journal-title":"Cell"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1128\/JB.187.2.458-472.2005","article-title":"The LEE1 Promoters from both Enteropathogenic and Enterohemorrhagic Escherichia coli Can Be Activated by PerC-Like Proteins from Either Organism","volume":"187","author":"Porter","year":"2005","journal-title":"J. Bacteriol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"20220313","DOI":"10.1042\/BSR20220313","article-title":"FinO\/ProQ-Family Proteins: An Evolutionary Perspective","volume":"43","author":"Liao","year":"2023","journal-title":"Biosci. Rep."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.bbamcr.2004.02.013","article-title":"Type IV secretion: The Agrobacterium VirB\/D4 and related conjugation systems","volume":"1694","author":"Christie","year":"2004","journal-title":"Biochim. Biophys. Acta (BBA)-Mol. Cell Res."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1093\/molbev\/msm014","article-title":"Causes of Insertion Sequences Abundance in Prokaryotic Genomes","volume":"24","author":"Touchon","year":"2007","journal-title":"Mol. Biol. Evol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/9\/1045\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T08:09:23Z","timestamp":1789978163000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/9\/1045"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,20]]},"references-count":60,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["v18091045"],"URL":"https:\/\/doi.org\/10.3390\/v18091045","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,20]]}}}