{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T18:27:49Z","timestamp":1793039269302,"version":"4.5.0"},"reference-count":88,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T00:00:00Z","timestamp":1772409600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"COCIBA Research Budget","award":["17357"],"award-info":[{"award-number":["17357"]}]},{"name":"Universidad San Francisco de Quito (USFQ) Collaboration Grant","award":["17577"],"award-info":[{"award-number":["17577"]}]},{"name":"Universidad San Francisco de Quito (USFQ) Collaboration Grant","award":["17579"],"award-info":[{"award-number":["17579"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives: Hospital outbreaks of Pseudomonas aeruginosa are difficult to control due to the pathogen\u2019s extensive repertoire, including its ability to form biofilms, adapt and persist in diverse environments, and develop multidrug resistance, all of which contribute to prolonged outbreaks. This study integrates the phenotypic, proteomic, and genomic characterization of a nosocomial outbreak comprising 38 clinical isolates and one environmental isolate recovered from the intensive care unit (ICU) of Hospital IESS Quito Sur. Methods: Clinical data were collected, antimicrobial susceptibility was assessed by minimum inhibitory concentration (MIC), carbapenemase genes were detected by multiple PCR and immunochromatographic assays, and the biofilm formation index (BFI) was determined. In addition, matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used for species identification and clustering based on spectral similarity. Twelve representative isolates underwent whole genome sequencing (WGS) to characterize the resistome and virulome and to compare phylogenetic relationships with proteomic clustering defined by MALDI Biotyper Compass Explorer software. Results: All isolates were identified as P. aeruginosa, and phenotypic antimicrobial susceptibility classified most isolates as multidrug resistant, including 32 CRPA strains. The blaVIM gene was detected in 22 isolates, while BFI analysis showed that all isolates formed moderate to strong biofilms. Genomic analysis revealed that most isolates belonged to ST111 and ST253, and both conserved and heterogeneous resistome and virulome profiles, with a broad distribution of determinants related to biofilm formation, stress tolerance, and persistence. Comparison between MALDI-TOF MS and WGS showed predominant concordance in clustering, mainly within subclusters but disagreement at the cluster level. Conclusions: The detection of carbapenemases, biofilm-forming ability, and virulence determinants associated with prolonged persistence highlights the need for integrated molecular tools, such as MALDI-TOF MS with MALDI Biotyper Compass Explorer software, to support epidemiological surveillance and to inform strategies aimed at mitigating prolonged hospital outbreaks caused by P. aeruginosa.<\/jats:p>","DOI":"10.3390\/antibiotics15030257","type":"journal-article","created":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T14:06:56Z","timestamp":1772460416000},"page":"257","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated Phenotypic, Proteomic (MALDI-TOF MS), and Genomic (WGS) Investigation of a Prolonged Hospital Outbreak of Pseudomonas aeruginosa with High Biofilm-Forming Capacity"],"prefix":"10.3390","volume":"15","author":[{"given":"Sandra Pamela","family":"Cangui-Panchi","sequence":"first","affiliation":[{"name":"Laboratorio de Bacteriolog\u00eda, Instituto de Microbiolog\u00eda, Colegio de Ciencias Biol\u00f3gicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danny Santiago","family":"Cangui-Panchi","sequence":"additional","affiliation":[{"name":"Asociaci\u00f3n Cient\u00edfica de Estudiantes de Medicina, Unidad Acad\u00e9mica de Salud y Bienestar, Universidad Cat\u00f3lica de Cuenca, Cuenca 010101, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ver\u00f3nica E.","family":"Palacios","sequence":"additional","affiliation":[{"name":"Hospital del Instituto Ecuatoriano de Seguridad Social (IESS) Quito-Sur, Quito 170111, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erika","family":"Becerra","sequence":"additional","affiliation":[{"name":"Hospital del Instituto Ecuatoriano de Seguridad Social (IESS) Quito-Sur, Quito 170111, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana L.","family":"Santamar\u00eda","sequence":"additional","affiliation":[{"name":"Hospital del Instituto Ecuatoriano de Seguridad Social (IESS) Quito-Sur, Quito 170111, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Hospital del Instituto Ecuatoriano de Seguridad Social (IESS) Quito-Sur, Quito 170111, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5215-164X","authenticated-orcid":false,"given":"Jorge","family":"Reyes-Chac\u00f3n","sequence":"additional","affiliation":[{"name":"Hospital del Instituto Ecuatoriano de Seguridad Social (IESS) Quito-Sur, Quito 170111, Ecuador"},{"name":"Facultad de Ciencias Qu\u00edmicas, Universidad Central del Ecuador, Quito 170521, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5089-8723","authenticated-orcid":false,"given":"Ant\u00f3nio","family":"Machado","sequence":"additional","affiliation":[{"name":"Laboratorio de Bacteriolog\u00eda, Instituto de Microbiolog\u00eda, Colegio de Ciencias Biol\u00f3gicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias e Tecnologia, Universidade dos A\u00e7ores (UAc), R. M\u00e3e de Deus 13A, 9500-321 Ponta Delgada, Portugal"},{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, BIOPOLIS Programa em Gen\u00f3mica, Biodiversidade e Planeamento, Universidade dos A\u00e7ores, Rua da M\u00e3e de Deus, 9500-321 Ponta Delgada, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8024-3509","authenticated-orcid":false,"given":"Daniel","family":"Garzon-Chavez","sequence":"additional","affiliation":[{"name":"Colegio de Ciencias de la Salud, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,2]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2024). 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