{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T03:27:15Z","timestamp":1769743635996,"version":"3.49.0"},"reference-count":43,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p><jats:italic>Acinetobacter baumannii<\/jats:italic> is a Gram-negative opportunistic pathogen, responsible for nosocomial infections worldwide. In recent years, this microorganism has acquired resistance to various antibiotics, prompting the World Health Organization (WHO) to declare carbapenem-resistant <jats:italic>A. baumannii<\/jats:italic> (CRAB) a critical priority microorganism requiring urgent attention and the development of new therapeutic options. Here, we screened for prophages in 158 genomes of <jats:italic>A. baumannii<\/jats:italic>, comprising 139 complete genomes from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), and 19 newly sequenced clinical isolates. Additionally, we conducted phylogenetic analyses of prophages, highlighting their diversity and local clustering. The analyzed genomes harbored at least two prophage regions, resulting in the identification of a total of 950 prophage regions, of which 348 were considered complete prophages through software analysis and manual curation, while the remainder may represent prophage remnants. The complete prophages ranged from 28.6 to 103.9 kbp, with an average GC content of 39%. Based on genomic similarity, only 18 complete prophages were taxonomically classified to the genus <jats:italic>Vieuvirus<\/jats:italic>. Among all identified complete prophages, we identified 166 genes encoding for putative lysins, while prophage regions that were not considered complete could also harbor putative lysins. These findings highlight the abundance of prophage-encoded lysins in <jats:italic>A. baumannii<\/jats:italic> genomes, which are promising therapeutic agents for combating <jats:italic>A. baumannii<\/jats:italic> infections, particularly in the face of rising antibiotic resistance.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1532950","type":"journal-article","created":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T16:18:47Z","timestamp":1743524327000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Identifying phage Lysins through genomic analysis of prophages from Acinetobacter baumannii"],"prefix":"10.3389","volume":"16","author":[{"given":"Maria Leonor","family":"Raposo","sequence":"first","affiliation":[]},{"given":"Ana Carolina","family":"Pimentel","sequence":"additional","affiliation":[]},{"given":"Vera","family":"Manageiro","sequence":"additional","affiliation":[]},{"given":"Aida","family":"Duarte","sequence":"additional","affiliation":[]},{"given":"Manuela","family":"Cani\u00e7a","sequence":"additional","affiliation":[]},{"given":"Filipa F.","family":"Vale","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,4,1]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e126","DOI":"10.1093\/nar\/gks406","article-title":"PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies","volume":"40","author":"Akhter","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"284","DOI":"10.3390\/v11030284","article-title":"Broad bactericidal activity of the myoviridae bacteriophage Lysins LysAm24, LysECD7, and LysSi3 against gram-negative ESKAPE pathogens","volume":"11","author":"Antonova","year":"2019","journal-title":"Viruses"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1111\/2049-632X.12125","article-title":"Acinetobacter baumannii: evolution of a global pathogen","volume":"71","author":"Antunes","year":"2014","journal-title":"Pathog. 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J."},{"key":"ref30","first-page":"593","article-title":"taxmyPHAGE: automated taxonomy of dsDNA phage genomes at the genus and species level","author":"Millard","year":"2024"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2379","DOI":"10.1093\/bioinformatics\/btx157","article-title":"ViPTree: the viral proteomic tree server","volume":"33","author":"Nishimura","year":"2017","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"4558","DOI":"10.1128\/JVI.03277-12","article-title":"Molecular aspects and comparative genomics of bacteriophage Endolysins","volume":"87","author":"Oliveira","year":"2013","journal-title":"J. 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Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1080\/19490976.2024.2379440","article-title":"Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori genome project","volume":"16","author":"Vale","year":"2024","journal-title":"Gut Microbes"},{"key":"ref42","volume-title":"Prioritization of pathogens to guide discovery, research and development of new antibiotics for drug-resistant bacterial infections, including tuberculosis","year":"2017"},{"key":"ref43","volume-title":"WHO bacterial priority pathogens list, 2024: Bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance","year":"2024"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1532950\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T16:19:07Z","timestamp":1743524347000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1532950\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,1]]},"references-count":43,"alternative-id":["10.3389\/fmicb.2025.1532950"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1532950","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,1]]},"article-number":"1532950"}}