{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T12:45:18Z","timestamp":1786193118113,"version":"build-2736575974"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T00:00:00Z","timestamp":1786147200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T00:00:00Z","timestamp":1786147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Ministry of Defence"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"abstract":"Abstract<\/jats:title>\n \n Pseudomonas aeruginosa<\/jats:italic>\n is a major cause of ventilator-associated pneumonia (VAP) and is increasingly associated with extensive antimicrobial resistance, limiting therapeutic options and contributing to poor clinical outcomes. The emergence of high-risk clones that combine multidrug resistance and virulence-associated traits represents a growing public health concern.\n <\/jats:p>\n \n In this study, 100 clinical\n P. aeruginosa<\/jats:italic>\n isolates recovered from VAP patients were screened using culture-based identification and antimicrobial susceptibility testing. Two isolates exhibiting the most extensive resistance profiles, consistent with pandrug-resistant (PDR) phenotypes, and associated with fatal clinical outcomes were selected for whole-genome sequencing using Oxford Nanopore technology.\n <\/jats:p>\n Comprehensive genomic analyses were performed to characterize antimicrobial resistance determinants, chromosomal resistance mutations, virulence-associated genes, mobile genetic elements, genomic islands, and phylogenomic relationships. Both isolates were assigned to sequence type ST308 and serogroup O11, a globally disseminated high-risk lineage. Core-genome phylogenomic analysis of 52 genomes identified 144,617 informative SNPs across 5,085 shared core genes and showed that the two Egyptian isolates differed by only 74 core-genome SNPs while clustering within the international ST308 lineage.<\/jats:p>\n \n The isolates harbored an extensive resistome including\n blaNDM-1<\/jats:italic>\n ,\n blaOXA-10<\/jats:italic>\n ,\n blaOXA-488<\/jats:italic>\n ,\n qnrVC1<\/jats:italic>\n ,\n rmtF<\/jats:italic>\n ,\n sul1<\/jats:italic>\n ,\n sul2<\/jats:italic>\n ,\n floR<\/jats:italic>\n , and\n msrE<\/jats:italic>\n . High-confidence chromosomal resistance mutations were detected in\n gyrA<\/jats:italic>\n (T83I),\n parC<\/jats:italic>\n (S87L),\n oprD<\/jats:italic>\n (Q402HfsTer99),\n nalC<\/jats:italic>\n ,\n nalD<\/jats:italic>\n , and\n pmrB<\/jats:italic>\n , supporting resistance to fluoroquinolones, carbapenems, and polymyxins. Two complete class 1 integrons and one In0 structure, all carrying the class 1 integrase IntI1, were identified, comprising integron-associated multidrug resistance modules containing\n qnrVC1<\/jats:italic>\n ,\n aadA11<\/jats:italic>\n ,\n aac(6\u2019)-II<\/jats:italic>\n ,\n dfrB5<\/jats:italic>\n ,\n sul1<\/jats:italic>\n ,\n qacE\u03941<\/jats:italic>\n ,\n rmtF<\/jats:italic>\n ,\n blaOXA-10<\/jats:italic>\n , and\n blaPAC-1<\/jats:italic>\n . In contrast,\n blaNDM-1<\/jats:italic>\n was located within a distinct ISVsa3-associated resistance island together with\n ble<\/jats:italic>\n and\n msrE<\/jats:italic>\n . Genomic island analysis further demonstrated the co-localization of key resistance determinants and the\n exoU<\/jats:italic>\n virulence factor within predicted genomic islands.\n <\/jats:p>\n \n Both isolates carried a highly conserved virulome, including\n exoU<\/jats:italic>\n ,\n exoT<\/jats:italic>\n , type VI secretion system components, iron-acquisition systems, and biofilm-associated genes. Collectively, these findings indicate the convergence of resistance islands, integron-associated multidrug resistance modules, chromosomal resistance mechanisms, and virulence-associated determinants within a globally disseminated ST308\/O11 high-risk clone associated with fatal VAP cases in Egypt.\n <\/jats:p>\n \n To our knowledge, this study provides the first comprehensive genomic characterization of ST308\/O11\n P. aeruginosa<\/jats:italic>\n exhibiting a pandrug-resistant phenotype based on the antimicrobial panel tested and associated with fatal ventilator-associated pneumonia in Egypt. Furthermore, by integrating cohort-level screening of 100 clinical isolates with comparative whole-genome analysis, this work provides additional insight into the genomic diversity of globally disseminated high-risk lineages through the accumulation of resistance and virulence determinants.\n <\/jats:p>","DOI":"10.1186\/s12866-026-05465-y","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T22:55:30Z","timestamp":1786143330000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomics of fatal ST308\/O11 Pseudomonas aeruginosa from Egypt characterizes conserved resistance architecture, integron-associated multidrug resistance modules, and blaNDM-1 resistance islands"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-5101-622X","authenticated-orcid":false,"given":"Ahmed A.","family":"Sanad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ghada A.","family":"El-Sherbeny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adel A.","family":"El-Morsi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed F.","family":"Gad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hossam I.","family":"Gebeer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed G.","family":"Seadawy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,8]]},"reference":[{"issue":"5","key":"5465_CR1","doi-asserted-by":"publisher","first-page":"888","DOI":"10.1007\/s00134-020-05980-0","volume":"46","author":"L Papazian","year":"2020","unstructured":"Papazian L, Klompas M, Luyt CE. 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All procedures involving human-derived samples were conducted in accordance with the ethical standards of the institutional research committee and the Declaration of Helsinki. Written informed consent was obtained from all participants prior to sample collection.","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":"705"}}