{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T19:52:14Z","timestamp":1790970734057,"version":"4.1.0"},"reference-count":57,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T00:00:00Z","timestamp":1765843200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CBMA \u201cContrato-Programa\u201d","award":["UIDB\/04050\/2020"],"award-info":[{"award-number":["UIDB\/04050\/2020"]}]},{"name":"ARNET \u201cContrato-Programa\u201d","award":["LA\/P\/0069\/2020"],"award-info":[{"award-number":["LA\/P\/0069\/2020"]}]},{"name":"national funds"},{"name":"ERDF-European Regional Development Fund"},{"name":"PhD fellowship","award":["2020.05005.BD"],"award-info":[{"award-number":["2020.05005.BD"]}]},{"name":"PhD fellowship","award":["2023.10837.CPCA.A1"],"award-info":[{"award-number":["2023.10837.CPCA.A1"]}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["2023.06638.CEECIND"],"award-info":[{"award-number":["2023.06638.CEECIND"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Klebsiella pneumoniae (Kp) is a leading cause of hospital-acquired infections representing a growing threat driven by emerging multidrug resistance (MDR) and hypervirulence. In this study, we aim to characterise the genomic and epidemiological landscape of Kp in a Portuguese regional hospital (Braga) lacking prior genomic data. We performed whole-genome sequencing of 115 Kp isolates collected from colonisation and infection cases. Phylogenetic, resistance, and virulence profiles were integrated with clinical and epidemiological data. Genomic analysis revealed high diversity, with 83.5% of isolates forming evolutionary clusters. Several novel sequence types (STs), as ST2623 and ST1562, were detected for the first time in Portugal to our knowledge. ST45, uncommonly associated with carbapenem resistance, emerged as dominant with multiple blaKPC-3-positive isolates. Results suggest active transmission of carbapenem resistance genes. One hypervirulent carbapenem-resistant ST13 warrants careful surveillance. Virulence-associated yersiniabactin was common (66.9%) but other hypervirulence loci were rare. Epidemiologically, MDR-Kp was associated with older hospitalised patients with prior antibiotic use and invasive procedures, while community-acquired infections were genetically diverse and affected younger patients with comorbidities. An unusually low number of respiratory infections was observed, likely reflecting strict COVID-19 mitigation measures. Although widespread dissemination of hypervirulent or MDR clones was not evident, the emergence of high-risk lineages and the detection of ongoing gene transmission episodes underscore the need for ongoing genomic surveillance. Immediate mitigation strategies could include reducing device use and hospital transfers, given the high prevalence of colonisation.<\/jats:p>","DOI":"10.3390\/biology14121795","type":"journal-article","created":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T15:41:12Z","timestamp":1765899672000},"page":"1795","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Hospital-Based Genomic Surveillance of Klebsiella pneumoniae: Trends in Resistance and Infection"],"prefix":"10.3390","volume":"14","author":[{"given":"Erica","family":"Olund-Matos","sequence":"first","affiliation":[{"name":"CBMA\u2014Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal"},{"name":"IB-S\u2014Institute of Science and Innovation for Bio-Sustainability, University of Minho, 4710-057 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2333-6127","authenticated-orcid":false,"given":"Ricardo","family":"Franco-Duarte","sequence":"additional","affiliation":[{"name":"CBMA\u2014Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal"},{"name":"IB-S\u2014Institute of Science and Innovation for Bio-Sustainability, University of Minho, 4710-057 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9","family":"Santa-Cruz","sequence":"additional","affiliation":[{"name":"ICVS\u2014Life and Health Sciences Research Institute, School of Medicine, University of Minho, 4710-057 Braga, Portugal"},{"name":"ICVS\/3B\u2019s\u2014PT Government Associated Laboratory, 4710-057 Braga, Portugal"},{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Nogueira","sequence":"additional","affiliation":[{"name":"CBMA\u2014Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal"},{"name":"IB-S\u2014Institute of Science and Innovation for Bio-Sustainability, University of Minho, 4710-057 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarida","family":"Correia-Neves","sequence":"additional","affiliation":[{"name":"ICVS\u2014Life and Health Sciences Research Institute, School of Medicine, University of Minho, 4710-057 Braga, Portugal"},{"name":"ICVS\/3B\u2019s\u2014PT Government Associated Laboratory, 4710-057 Braga, Portugal"},{"name":"Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 171 77 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5785-2418","authenticated-orcid":false,"given":"Diana","family":"Lopes","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5250-7706","authenticated-orcid":false,"given":"Rui Jorge","family":"Silva","sequence":"additional","affiliation":[{"name":"ICVS\u2014Life and Health Sciences Research Institute, School of Medicine, University of Minho, 4710-057 Braga, Portugal"},{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarida Ribeiro","family":"Ara\u00fajo","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In\u00eas Monteiro","family":"Ara\u00fajo","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Filipa","family":"Martins","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina Maia","family":"Nogueira","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberta","family":"Faustino","sequence":"additional","affiliation":[{"name":"2-CA-Braga\u2014Clinical Academic Centre, Hospital of Braga, 4710-243 Braga, Portugal"},{"name":"Clinical Pathology Service, Hospital of Braga, 4710-243 Braga, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8518-4130","authenticated-orcid":false,"given":"Pedro G.","family":"Cunha","sequence":"additional","affiliation":[{"name":"ICVS\u2014Life and Health Sciences Research Institute, School of Medicine, University of Minho, 4710-057 Braga, Portugal"},{"name":"ICVS\/3B\u2019s\u2014PT Government Associated Laboratory, 4710-057 Braga, Portugal"},{"name":"Clinical Academic Centre of Hospital Senhora da Oliveira, 4835-044 Guimar\u00e3es, Portugal"},{"name":"Medicine Department, Hospital Senhora da Oliveira, 4835-044 Guimar\u00e3es, Portugal"},{"name":"Centre for the Research and Treatment of Arterial Hypertension and Cardiovascular Risk, Internal Medicine Department, Hospital Senhora da Oliveira, 4835-044 Guimar\u00e3es, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2807-690X","authenticated-orcid":false,"given":"Pedro","family":"Soares","sequence":"additional","affiliation":[{"name":"CBMA\u2014Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal"},{"name":"IB-S\u2014Institute of Science and Innovation for Bio-Sustainability, University of Minho, 4710-057 Braga, 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