{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T06:52:58Z","timestamp":1781679178215,"version":"3.54.5"},"reference-count":111,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"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. Cell. Infect. Microbiol."],"abstract":"<jats:p>\n                    Multidrug\u2212resistant (MDR) and extensively drug\u2212resistant (XDR)\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    strains remain a major threat in clinical settings, yet no contemporary genomic data are available from the Olomouc region, Czech Republic. We performed whole\u2212genome sequencing of 157 MDR isolates obtained from 133 patients hospitalized at two tertiary\u2212care hospitals in Olomouc between April 2020 and April 2024. The aim of this study was to delineate the clonal structure, resistance and virulence repertoires shaping the local epidemiology. Of the 157 isolates, 81 (51.6%) met XDR criteria, most commonly exhibiting susceptibility to colistin (37\/81, 45.7%). Four dominant high\u2212risk sequence types (STs) were identified: ST175 (n = 53), ST357 (n = 49), ST233 (n = 25), and ST235 (n = 11). ST357 comprised two phylogenetically and functionally distinct sublineages: a major cluster (43\/49) carrying\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>IMP\u22127<\/jats:sub>\n                    and\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>OXA\u22122<\/jats:sub>\n                    , and a smaller\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>VIM\u22122<\/jats:sub>\n                    \u2212positive cluster (5\/49) lacking\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>OXA\u22122<\/jats:sub>\n                    ,\n                    <jats:italic>oprD<\/jats:italic>\n                    ,\n                    <jats:italic>soxR<\/jats:italic>\n                    , and the\n                    <jats:italic>pvc<\/jats:italic>\n                    operon, correlating with an XDR phenotype and reduced biofilm\u2212associated virulence potential. All ST357 isolates carried the cytotoxic\n                    <jats:italic>exoU<\/jats:italic>\n                    gene. Both\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>IMP\u22127<\/jats:sub>\n                    and\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>VIM\u22122<\/jats:sub>\n                    were chromosomally encoded. ST175 isolates lacked acquired carbapenemase genes, except for a single\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>VIM\u22122<\/jats:sub>\n                    \u2212positive isolate. This lineage carried the highest number of virulence genes, dominated by adherence\u2212 and biofilm\u2212associated determinants together with the characteristic\n                    <jats:italic>exoS<\/jats:italic>\n                    <jats:sup>+<\/jats:sup>\n                    \/\n                    <jats:italic>exoT<\/jats:italic>\n                    <jats:sup>+<\/jats:sup>\n                    \/\n                    <jats:italic>exoY<\/jats:italic>\n                    <jats:sup>+<\/jats:sup>\n                    type III secretion system profile. All ST233 isolates carried\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>VIM\u22122<\/jats:sub>\n                    and exhibited an XDR phenotype, consistent with globally disseminated VIM\u22122 lineages. ST235 displayed the greatest diversity of carbapenemase genes, including\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>GES\u221214<\/jats:sub>\n                    (5\/11),\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>GES\u221229<\/jats:sub>\n                    (1\/11), and\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>VIM\u22121<\/jats:sub>\n                    (1\/11). This represented the first identification of a\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>VIM\u22121<\/jats:sub>\n                    \u2212positive ST235 isolate in Olomouc University Hospital, and, to our knowledge, the first documented occurrence of a VIM\u22121\u2212producing ST235 strain in the Czech Republic. All ST235 isolates were\n                    <jats:italic>exoU<\/jats:italic>\n                    \u2212positive. This study provides a recent whole\u2212genome analysis of MDR\/XDR\n                    <jats:italic>P. aeruginosa<\/jats:italic>\n                    in the Czech Republic, integrating resistome, virulome and molecular epidemiology. Our findings demonstrate that the local population is shaped by multiple high\u2212risk lineages with distinct resistance-virulence profiles, underscoring their clinical relevance and the necessity of genomic surveillance to guide therapy and prevent hospital transmission.\n                  <\/jats:p>","DOI":"10.3389\/fcimb.2026.1843668","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T05:56:18Z","timestamp":1781675778000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["High\u2212risk lineages shape the resistome and virulome of multidrug\u2212resistant Pseudomonas aeruginosa"],"prefix":"10.3389","volume":"16","author":[{"given":"Kristyna","family":"Novakova","sequence":"first","affiliation":[{"name":"Department of Microbiology, University Hospital Olomouc","place":["Olomouc, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc","place":["Olomouc, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iva","family":"Sukkar","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine, Charles University","place":["Pilsen, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Palkovicova","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine, Charles University","place":["Pilsen, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katerina","family":"Fiserova","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Olomouc","place":["Olomouc, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc","place":["Olomouc, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iva","family":"Vagnerova","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Olomouc","place":["Olomouc, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc","place":["Olomouc, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vendula","family":"Pudova","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Olomouc","place":["Olomouc, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc","place":["Olomouc, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milan","family":"Kolar","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University Hospital Olomouc","place":["Olomouc, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc","place":["Olomouc, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,17]]},"reference":[{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10081533","article-title":"New variants of Pseudomonas aeruginosa high-risk clone ST233 associated with an outbreak in a Mexican paediatric hospital","volume":"10","author":"Aguilar-Rodea","year":"2022","journal-title":"Microorganisms"},{"key":"B34","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B80","doi-asserted-by":"publisher","first-page":"3998","DOI":"10.1128\/IAI.68.7.3998-4004.2000","article-title":"Acquisition of expression of the Pseudomonas aeruginosa ExoU cytotoxin leads to increased bacterial virulence in a murine model of acute pneumonia and systemic spread","volume":"68","author":"Allewelt","year":"2000","journal-title":"Infect. Immun."},{"key":"B1","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.3855\/jidc.18400","article-title":"Relationship between antimicrobial use and the highest number of multidrug-resistant-Pseudomonas aeruginosa: A 10-year study","volume":"18","author":"Almeida","year":"2024","journal-title":"J. Infection Developing Countries"},{"key":"B87","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2026.103159","article-title":"Molecular analysis of carbapenemase-producing Pseudomonas aeruginosa strains in a tertiary care hospital in Riyadh","volume":"19","author":"Alshammari","year":"2026","journal-title":"J. Infect. Public Health"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00495-24","article-title":"Outer membrane permeability of Pseudomonas aeruginosa through \u03b2-lactams: new evidence on the role of OprD and OpdP porins in antibiotic resistance","volume":"13","author":"Amisano","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"B107","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms12061116","article-title":"Genomic differences associated with resistance and virulence in Pseudomonas aeruginosa isolates from clinical and environmental sites","volume":"12","author":"Aroca Molina","year":"2024","journal-title":"Microorganisms"},{"key":"B32","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giz119","article-title":"PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria","volume":"8","author":"Bayliss","year":"2019","journal-title":"GigaScience"},{"key":"B95","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1186\/1471-2180-14-160","article-title":"The Pseudomonas aeruginosa RhlG and RhlAB genes are inversely regulated and RhlG is not required for rhamnolipid synthesis","volume":"14","author":"Bazire","year":"2014","journal-title":"BMC Microbiol."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.03242","article-title":"Persistence and microevolution of Pseudomonas aeruginosa in the cystic fibrosis lung: A single-patient longitudinal genomic study","volume":"10","author":"Bianconi","year":"2019","journal-title":"Front. Microbiol."},{"key":"B99","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.922976","article-title":"Genomic characterization of mutli-drug resistant Pseudomonas aeruginosa clinical isolates: evaluation and determination of ceftolozane\/tazobactam activity and resistance mechanisms","volume":"12","author":"Bitar","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B93","doi-asserted-by":"publisher","first-page":"7415","DOI":"10.1128\/AAC.01720-16","article-title":"Deciphering the resistome of the widespread Pseudomonas aeruginosa sequence type 175 international high-risk clone through whole-genome sequencing","volume":"60","author":"Cabot","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"B97","doi-asserted-by":"publisher","first-page":"7351","DOI":"10.1128\/JB.187.21.7351-7361.2005","article-title":"Rhamnolipids modulate swarming motility patterns of Pseudomonas aeruginosa","volume":"187","author":"Caiazza","year":"2005","journal-title":"J. Bacteriol."},{"key":"B49","unstructured":"Flourish data visualization platform"},{"key":"B35","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using Plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B74","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1111\/j.1365-2958.2006.05269.x","article-title":"PtxR modulates the expression of QS-controlled virulence factors in the Pseudomonas aeruginosa strain PAO1","volume":"61","author":"Carty","year":"2006","journal-title":"Mol. Microbiol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.4274\/mjima.galenos.2024.24193.17","article-title":"Comparison of the infection characteristics and antimicrobial use among patients hospitalized in the intensive care unit during and after the COVID-19 pandemic periods","volume":"13","author":"\u00c7a\u015fkurlu","year":"2024","journal-title":"Mediterr. J. Infection Microbes Antimicrobials"},{"key":"B36","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B22","doi-asserted-by":"publisher","first-page":"2578","DOI":"10.1128\/JCM.00102-11","article-title":"Most multidrug-resistant Pseudomonas aeruginosa isolates from hospitals in Eastern France belong to a few clonal types","volume":"49","author":"Cholley","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s12864-026-12585-2","article-title":"Genome-wide co-occurrence patterns link mobile genetic elements, antimicrobial resistance and defence systems in Pseudomonas aeruginosa","volume":"27","author":"Choudhury","year":"2026","journal-title":"BMC Genomics"},{"key":"B75","doi-asserted-by":"publisher","first-page":"6927","DOI":"10.1128\/JB.00801-08","article-title":"Paerucumarin, a new metabolite produced by the Pvc gene cluster from Pseudomonas aeruginosa","volume":"190","author":"Clarke-Pearson","year":"2008","journal-title":"J. Bacteriol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1016\/j.cmi.2021.05.011","article-title":"Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence resistome analysis","volume":"27","author":"Cortes-Lara","year":"2021","journal-title":"Clin. Microbiol. Infection"},{"key":"B67","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1097\/QCO.0000000000000966","article-title":"MDR\/XDR\/PDR or DTR? Which definition best fits the resistance profile of Pseudomonas aeruginosa","volume":"36","author":"Cosentino","year":"2023","journal-title":"Curr. Opin. Infect. Dis."},{"key":"B43","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"JModelTest 2: More models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nat. Methods"},{"key":"B102","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2020.106196","article-title":"Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired \u03b2-lactamases: 2020 update","volume":"56","author":"del Barrio-Tofi\u00f1o","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1674635","article-title":"Genetic and virulence factors behind the success of high-risk Pseudomonas aeruginosa clones: Insights from comparative genomics and an experimental infection model","volume":"16","author":"de Sales","year":"2025","journal-title":"Front. Microbiol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"1371","DOI":"10.1128\/JB.02273-12","article-title":"Bacterial community morphogenesis is intimately linked to the intracellular redox state","volume":"195","author":"Dietrich","year":"2013","journal-title":"J. Bacteriol."},{"key":"B72","doi-asserted-by":"publisher","first-page":"1308","DOI":"10.1111\/j.1365-2958.2006.05306.x","article-title":"The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa","volume":"61","author":"Dietrich","year":"2006","journal-title":"Mol. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.765113","article-title":"Genomic characterization of carbapenem-non-susceptible Pseudomonas aeruginosa clinical isolates from Saudi Arabia revealed a global dissemination of GES-5-producing ST235 and VIM-2-producing ST233 sub-lineages","volume":"12","author":"Doumith","year":"2022","journal-title":"Front. Microbiol."},{"key":"B98","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms14010109","article-title":"Understanding Pseudomonas aeruginosa biofilms: quorum sensing, c-di-GMP signalling, and emerging antibiofilm approaches","volume":"14","author":"Elbehiry","year":"2026","journal-title":"Microorganisms"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1374466","article-title":"Antimicrobial resistance of Pseudomonas aeruginosa: Navigating clinical impacts, current resistance trends, and innovations in breaking therapies","volume":"15","author":"Elfadadny","year":"2024","journal-title":"Front. Microbiol."},{"key":"B29","unstructured":"Breakpoint tables for interpretation of MICs and zone diameters version 14.0 2024"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004651","article-title":"Coexistence and within-host evolution of diversified lineages of hypermutable Pseudomonas aeruginosa in long-term cystic fibrosis infections","volume":"10","author":"Feliziani","year":"2014","journal-title":"PloS Genet."},{"key":"B89","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.3390\/antibiotics14111162","article-title":"Cefiderocol resistance in Pseudomonas aeruginosa ST175: a case report with genomic analysis","volume":"14","author":"Fern\u00e1ndez","year":"2025","journal-title":"Antibiotics"},{"key":"B113","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1128\/CMR.00043-12","article-title":"Adaptive and mutational resistance: Role of porins and efflux pumps in drug resistance","volume":"25","author":"Fern\u00e1ndez","year":"2012","journal-title":"Clin. Microbiol. Rev."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/msystems.01007-20","article-title":"Phenotypic and genomic comparison of the two most common ExoU-positive Pseudomonas aeruginosa clones, PA14 and ST235","volume":"5","author":"Fischer","year":"2020","journal-title":"mSystems"},{"key":"B103","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2024.e41540","article-title":"High-risk Pseudomonas aeruginosa clones harbouring \u03b2-lactamases: 2024 update","volume":"11","author":"Flores-Vega","year":"2025","journal-title":"Heliyon"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2023.106788","article-title":"Insight into phylogenomic bias of BlaVIM-2 or BlaNDM-1 dissemination amongst carbapenem-resistant Pseudomonas aeruginosa","volume":"61","author":"Fortunato","year":"2023","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B81","doi-asserted-by":"publisher","first-page":"11","DOI":"10.3390\/microorganisms7120707","article-title":"Pseudomonas aeruginosa toxin ExoU as a therapeutic target in the treatment of bacterial infections","volume":"7","author":"Foulkes","year":"2019","journal-title":"Microorganisms"},{"key":"B82","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1042\/BCJ20200780","article-title":"A pipeline to evaluate inhibitors of the Pseudomonas aeruginosa exotoxin U","volume":"478","author":"Foulkes","year":"2021","journal-title":"Biochem. J."},{"key":"B104","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1093\/jac\/dkx453","article-title":"Italian nationwide survey on Pseudomonas aeruginosa from invasive infections: Activity of ceftolozane\/tazobactam and comparators, and molecular epidemiology of carbapenemase producers","volume":"73","author":"Giani","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"B59","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","article-title":"Clinker & Clustermap.Js: automatic generation of gene cluster comparison figures","volume":"37","author":"Gilchrist","year":"2021","journal-title":"Bioinformatics"},{"key":"B105","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1089\/mdr.2013.0085","article-title":"Characterization of carbapenem nonsusceptible Pseudomonas aeruginosa in Denmark: A nationwide, prospective study","volume":"20","author":"Hansen","year":"2014","journal-title":"Microb. Drug Resist."},{"key":"B84","doi-asserted-by":"publisher","first-page":"2492","DOI":"10.1038\/ismej.2017.103","article-title":"Optimised chronic infection models demonstrate that siderophore \u201ccheating\u201d in Pseudomonas aeruginosa is context specific","volume":"11","author":"Harrison","year":"2017","journal-title":"ISME J."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00031-19","article-title":"Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections","volume":"32","author":"Horcajada","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"B68","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1128\/JCM.00684-10","article-title":"Regional spread of Pseudomonas aeruginosa ST357 producing IMP-7 metallo-\u03b2-lactamase in Central Europe","volume":"49","author":"Hrab\u00e1k","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"B30","year":"2017"},{"key":"B39","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.Org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B66","doi-asserted-by":"publisher","first-page":"1803","DOI":"10.1093\/cid\/ciy378","article-title":"Difficult-to-treat resistance in gram-negative bacteremia at 173 US hospitals: retrospective cohort analysis of prevalence, predictors, and outcome of resistance to all first-line agents","volume":"67","author":"Kadri","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics14040353","article-title":"Carbapenem-resistant Pseudomonas aeruginosa\u2019s resistome: Pan-genomic plasticity, the impact of transposable elements and jumping genes","volume":"14","author":"Karampatakis","year":"2025","journal-title":"Antibiotics"},{"key":"B110","doi-asserted-by":"publisher","first-page":"e01199-19","DOI":"10.1128\/AAC","article-title":"Interaction of ArmZ with the DNA-binding domain of MexZ induces expression of MexXY multidrug efflux pump genes and antimicrobial resistance in Pseudomonas aeruginosa","volume":"63","author":"Kawalek","year":"2019"},{"key":"B37","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3390\/ph16091230","article-title":"Age of antibiotic resistance in MDR\/XDR clinical pathogen of Pseudomonas aeruginosa","volume":"16","author":"Kothari","year":"2023","journal-title":"Pharmaceuticals"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"20740","DOI":"10.1038\/s41598-021-00178-w","article-title":"Comparative evaluation of nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis","volume":"11","author":"Lee","year":"2021","journal-title":"Sci. Rep."},{"key":"B44","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (ITOL) v6: Recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B60","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1128\/CMR.00040-09","article-title":"Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms","volume":"22","author":"Lister","year":"2009","journal-title":"Clin. Microbiol. Rev."},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232415779","article-title":"Role of efflux pumps on antimicrobial resistance in Pseudomonas aeruginosa","volume":"23","author":"Lorusso","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"B56","doi-asserted-by":"publisher","first-page":"D265","DOI":"10.1093\/nar\/gkz991","article-title":"CDD\/SPARCLE: the conserved domain database in 2020","volume":"48","author":"Lu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2020.00003","article-title":"Combining standard molecular typing and whole genome sequencing to investigate Pseudomonas aeruginosa epidemiology in intensive care units","volume":"8","author":"Magalh\u00e3es","year":"2020","journal-title":"Front. Public Health"},{"key":"B64","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infection"},{"key":"B45","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/ng.3148","article-title":"Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis","volume":"47","author":"Marvig","year":"2015","journal-title":"Nat. Genet."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1347521","article-title":"Extensively drug-resistant Pseudomonas aeruginosa: Clinical features and treatment with ceftazidime\/avibactam and ceftolozane\/tazobactam in a tertiary care university hospital centre in Portugal \u2013 A cross-sectional and retrospective observational study","volume":"15","author":"Mendes Pedro","year":"2024","journal-title":"Front. Microbiol."},{"key":"B88","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.jgar.2023.11.014","article-title":"Unveiling a high-risk epidemic clone (ST 357) of \u2018difficult to treat extensively drug-resistant\u2019 (DT-XDR) Pseudomonas aeruginosa from a burn patient in Bangladesh: a resilient beast revealing coexistence of four classes of beta lactamases","volume":"36","author":"Mondol","year":"2024","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"B106","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2012.00408","article-title":"MexXY multidrug efflux system of Pseudomonas aeruginosa","volume":"3","author":"Morita","year":"2012","journal-title":"Front. Microbiol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/s41597-024-03571-y","article-title":"Exploring and retrieving sequence and metadata for species across the tree of life with NCBI datasets","volume":"11","author":"O\u2019Leary","year":"2024","journal-title":"Sci. Data"},{"key":"B20","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.drup.2015.08.002","article-title":"The increasing threat of Pseudomonas aeruginosa high-risk clones","author":"Oliver","year":"2015","journal-title":"Drug Resistance Updates"},{"key":"B8","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.gendis.2019.04.001","article-title":"Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit; a critical review","volume":"6","author":"Pachori","year":"2019","journal-title":"Genes Dis."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/AAC.01811-17","article-title":"Molecular characterization of carbapenemase-producing Pseudomonas aeruginosa of Czech origin and evidence for clonal spread of extensively resistant sequence type 357 expressing IMP-7 metallo-\u03b2-lactamase","volume":"61","author":"Papagiannitsis","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"B109","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8121884","article-title":"Unravelling the features of success of VIM-producing ST111 and ST235 Pseudomonas aeruginosa in a Greek hospital","volume":"8","author":"Papagiannitsis","year":"2020","journal-title":"Microorganisms"},{"key":"B61","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1111\/j.1574-6976.2009.00175.x","article-title":"Gene cassettes and cassette arrays in mobile resistance integrons","volume":"33","author":"Partridge","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"B91","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1093\/jac\/dkz030","article-title":"High incidence of MDR and XDR Pseudomonas aeruginosa isolates obtained from patients with ventilator-associated pneumonia in Greece, Italy and Spain as part of the MagicBullet clinical trial","volume":"74","author":"P\u00e9rez","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"B90","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2020.106026","article-title":"Carbapenemase-producing Pseudomonas aeruginosa in Spain: interregional dissemination of the high-risk clones ST175 and ST244 carrying BlaVIM-2, BlaVIM-1, BlaIMP-8, BlaVIM-20 and BlaKPC-2","volume":"56","author":"P\u00e9rez-V\u00e1zquez","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B78","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nchembio764","article-title":"Rethinking \u201csecondary\u201d metabolism: physiological roles for phenazine antibiotics","volume":"2","author":"Price-Whelan","year":"2006","journal-title":"Nat. Chem. Biol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1186\/s13756-025-01599-2","article-title":"Protracted outbreaks of VIM-producing Pseudomonas aeruginosa in a surgical intensive care unit in France, January 2018 to June 2024","volume":"14","author":"Querin","year":"2025","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"B76","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/j.resmic.2010.01.003","article-title":"Phenazines affect biofilm formation by Pseudomonas aeruginosa in similar ways at various scales","volume":"161","author":"Ramos","year":"2010","journal-title":"Res. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1007\/s10096-019-03780-z","article-title":"Pathogenic characteristics of Pseudomonas aeruginosa bacteraemia isolates in a high-endemicity setting for ST175 and ST235 high-risk clones","volume":"39","author":"Recio","year":"2020","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B96","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.04146-23","article-title":"Mutation of Pseudomonas aeruginosa LasI\/RhlI diminishes its cytotoxicity, oxidative stress, inflammation, and apoptosis on THP-1 macrophages","volume":"12","author":"Ren","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02060-21","article-title":"TnCentral: a prokaryotic transposable element database and web portal for transposon analysis","volume":"12","author":"Ross","year":"2021","journal-title":"mBio"},{"key":"B86","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-024-09722-1","article-title":"Tracing the origin of NDM-1-producing and extensively drug-resistant Pseudomonas aeruginosa ST357 in the Netherlands","volume":"24","author":"Rossel","year":"2024","journal-title":"BMC Infect. Dis."},{"key":"B23","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1093\/jac\/dkw471","article-title":"Genomic islands 1 and 2 carry multiple antibiotic resistance genes in Pseudomonas aeruginosa ST235, ST253, ST111 and ST175 and are globally dispersed","volume":"72","author":"Roy Chowdhury","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"B79","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1111\/j.1365-2958.2004.04194.x","article-title":"ExoU is a potent intracellular phospholipase","volume":"53","author":"Sato","year":"2004","journal-title":"Mol. Microbiol."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1099\/MGEN.0.000685","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"B41","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1007\/s15010-024-02313-x","article-title":"Impact of multidrug resistance on the virulence and fitness of Pseudomonas aeruginosa: A microbiological and clinical perspective","volume":"52","author":"Sendra","year":"2024","journal-title":"Infection"},{"key":"B55","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B83","doi-asserted-by":"publisher","first-page":"8487","DOI":"10.1073\/pnas.0602138103","article-title":"Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients","volume":"103","author":"Smith","year":"2006","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B40","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"B47","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1093\/molbev\/msy242","article-title":"Beyond the SNP threshold: Identifying outbreak clusters using inferred transmissions","volume":"36","author":"Stimson","year":"2019","journal-title":"Mol. Biol. Evol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"719","DOI":"10.3390\/pathogens13090719","article-title":"Genomic insights into Vietnamese extended-spectrum \u03b2-lactamase-9-producing extensively drug-resistant Pseudomonas aeruginosa isolates belonging to the high-risk clone ST357 obtained from Bulgarian intensive care unit patients","volume":"13","author":"Strateva","year":"2024","journal-title":"Pathogens"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2025.2503430","article-title":"Pathogenicity and virulence of Pseudomonas aeruginosa: Recent advances and under-investigated topics","volume":"16","author":"Swain","year":"2025","journal-title":"Virulence"},{"key":"B100","doi-asserted-by":"publisher","DOI":"10.1128\/mra.00886-18","article-title":"Complete genome sequence of Pseudomonas aeruginosa K34-7, a carbapenem-resistant isolate of the high-risk sequence type 233","volume":"7","author":"Taiaroa","year":"2018","journal-title":"Microbiol. Resour. Announc."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12866-024-03306-4","article-title":"Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings","volume":"24","author":"Talat","year":"2024","journal-title":"BMC Microbiol."},{"key":"B65","doi-asserted-by":"publisher","first-page":"ciae403","DOI":"10.1093\/cid\/ciae403","article-title":"Infectious Diseases Society of America 2024 guidance on the treatment of antimicrobial-resistant gram-negative infections","author":"Tamma","year":"2024","journal-title":"Clin. Infect. Dis"},{"key":"B62","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1128\/AAC.00783-09","article-title":"Dispersal of carbapenemase BlaVIM-1 gene associated with different Tn402 variants, mercury transposons, and conjugative plasmids in Enterobacteriaceae and Pseudomonas aeruginosa","volume":"54","author":"Tato","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"B17","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1016\/j.cmi.2017.06.018","article-title":"Global emergence of the widespread Pseudomonas aeruginosa ST235 clone","volume":"24","author":"Treepong","year":"2018","journal-title":"Clin. Microbiol. Infection"},{"key":"B2","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1016\/j.cmi.2024.12.005","article-title":"Trends in antimicrobial consumption: Long-term impact of the COVID-19 pandemic","volume":"31","author":"Tsuzuki","year":"2025","journal-title":"Clin. Microbiol. Infection"},{"key":"B85","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02122-20","article-title":"Epidemic territorial spread of IncP-2-type VIM-2 carbapenemase-encoding megaplasmids in nosocomial Pseudomonas aeruginosa populations","volume":"65","author":"Urbanowicz","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"B94","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1111\/j.1600-0463.2009.02466.x","article-title":"Inactivation of the RhlA gene in Pseudomonas aeruginosa prevents rhamnolipid production, disabling the protection against polymorphonuclear leukocytes","volume":"117","author":"Van Gennip","year":"2009","journal-title":"APMIS"},{"key":"B51","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1101\/gr.214270.116","article-title":"Fast and accurate de novo genome assembly from long uncorrected reads","volume":"27","author":"Vaser","year":"2017","journal-title":"Genome Res."},{"key":"B92","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.3201\/eid1808.111234","article-title":"VIM-2-producing multidrug-resistant Pseudomonas aeruginosa ST175 clone, Spain","volume":"18","author":"Viedma","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PloS One"},{"key":"B70","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1186\/s12866-025-03935-3","article-title":"Loss of OprD function is sufficient for carbapenem-resistance-only but insufficient for multidrug resistance in Pseudomonas aeruginosa","volume":"25","author":"Wang","year":"2025","journal-title":"BMC Microbiol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"000132","DOI":"10.1099\/mgen.0.000132","article-title":"Completing bacterial genome assemblies with multiplex MinION sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microb. Genom."},{"key":"B3","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.jhin.2024.01.003","article-title":"COVID-19 and antibiotic consumption in the intensive care units of the Polish tertiary hospital","volume":"145","author":"W\u00f3jkowska-Mach","year":"2024","journal-title":"J. Hosp. Infection"},{"key":"B101","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s12879-015-0861-8","article-title":"Dissemination of VIM-2 producing Pseudomonas aeruginosa ST233 at tertiary care hospitals in Egypt","volume":"15","author":"Zafer","year":"2015","journal-title":"BMC Infect. Dis."},{"key":"B33","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1619626","article-title":"A comprehensive review of the pathogenic mechanisms of Pseudomonas aeruginosa: Synergistic effects of virulence factors, quorum sensing, and biofilm formation","volume":"16","author":"Zhang","year":"2025","journal-title":"Front. Microbiol."},{"key":"B108","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1117017","article-title":"Whole-genome sequencing reveals high-risk clones of Pseudomonas aeruginosa in Guangdong, China","volume":"14","author":"Zhao","year":"2023","journal-title":"Front. Microbiol."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1843668\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T05:56:22Z","timestamp":1781675782000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1843668\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,17]]},"references-count":111,"alternative-id":["10.3389\/fcimb.2026.1843668"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2026.1843668","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,17]]},"article-number":"1843668"}}