{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T10:49:22Z","timestamp":1770461362836,"version":"3.49.0"},"reference-count":34,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,1,12]],"date-time":"2022-01-12T00:00:00Z","timestamp":1641945600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","doi-asserted-by":"publisher","award":["UIDP\/04378\/2020, UIDP\/04378\/2020, LA\/P\/0140\/2020, DL57\/2016\/CP1346\/CT0032"],"award-info":[{"award-number":["UIDP\/04378\/2020, UIDP\/04378\/2020, LA\/P\/0140\/2020, DL57\/2016\/CP1346\/CT0032"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>The changing epidemiology of carbapenem-resistant Klebsiella pneumoniae in Southern European countries is challenging for infection control, and it is critical to identify and track new genetic entities (genes, carbapenemases, clones) quickly and with high precision. We aimed to characterize the strain responsible for the first recognized outbreak by an NDM-1-producing K. pneumoniae in Portugal, and to elucidate its diffusion in an international context. NDM-1-producing multidrug-resistant K. pneumoniae isolates from hospitalized patients (2018\u20132019) were characterized using FTIR spectroscopy, molecular typing, whole-genome sequencing, and comparative genomics with available K. pneumoniae ST11 KL105 genomes. FT-IR spectroscopy allowed the rapid (ca. 4 h after incubation) identification of the outbreak strains as ST11 KL105, supporting outbreak control. Epidemiological information supports a community source but without linkage to endemic regions of NDM-1 producers. Whole-genome comparison with previous DHA-1-producing ST11 KL105 strains revealed the presence of different plasmid types and antibiotic resistance traits, suggesting the entry of a new strain. In fact, this ST11 KL105 clade has successfully disseminated in Europe with variable beta-lactamases, but essentially as ESBL or DHA-1 producers. We expand the distribution map of NDM-1-producing K. pneumoniae in Europe, at the expense of a successfully established ST11 KL105 K. pneumoniae clade circulating with variable plasmid backgrounds and beta-lactamases. Our work further supports the use of FT-IR as an asset to support quick infection control.<\/jats:p>","DOI":"10.3390\/antibiotics11010092","type":"journal-article","created":{"date-parts":[[2022,1,12]],"date-time":"2022-01-12T09:10:36Z","timestamp":1641978636000},"page":"92","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["NDM-1 Introduction in Portugal through a ST11 KL105 Klebsiella pneumoniae Widespread in Europe"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1171-0326","authenticated-orcid":false,"given":"\u00c2ngela","family":"Novais","sequence":"first","affiliation":[{"name":"UCIBIO, Laborat\u00f3rio de Microbiologia, Departamento de Ci\u00eancias Biol\u00f3gicas, Faculdade de Farm\u00e1cia, Universidade do Porto, 4050-313 Porto, Portugal"},{"name":"Associate Laboratory i4HB\u2014Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"}]},{"given":"Rita Veiga","family":"Ferraz","sequence":"additional","affiliation":[{"name":"Centro Hospitalar do T\u00e2mega e Sousa, 4564-007 Penafiel, Portugal"}]},{"given":"Mariana","family":"Viana","sequence":"additional","affiliation":[{"name":"Centro Hospitalar do T\u00e2mega e Sousa, 4564-007 Penafiel, Portugal"}]},{"given":"Paula Martins","family":"da Costa","sequence":"additional","affiliation":[{"name":"Centro Hospitalar do T\u00e2mega e Sousa, 4564-007 Penafiel, Portugal"},{"name":"Department of Clinical Chemistry, Centro Hospitalar Universit\u00e1rio do Porto, 4099-001 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5810-8215","authenticated-orcid":false,"given":"Lu\u00edsa","family":"Peixe","sequence":"additional","affiliation":[{"name":"UCIBIO, Laborat\u00f3rio de Microbiologia, Departamento de Ci\u00eancias Biol\u00f3gicas, Faculdade de Farm\u00e1cia, Universidade do Porto, 4050-313 Porto, Portugal"},{"name":"Associate Laboratory i4HB\u2014Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/s41579-019-0315-1","article-title":"Population genomics of Klebsiella pneumoniae","volume":"18","author":"Wyres","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1038\/s41564-019-0492-8","article-title":"Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread","volume":"4","author":"David","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_3","first-page":"895","article-title":"Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods","volume":"13","author":"Lee","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Guerra, A.M., Lira, A., Lameir\u00e3o, A., Selaru, A., Abreu, G., Lopes, P., Mota, M., Novais, \u00c2., and Peixe, L. (2020). Multiplicity of carbapenemase-producers three years after a KPC-3-producing Klebsiella pneumoniae ST147-K64 hospital outbreak. Antibiotics, 13.","DOI":"10.3390\/antibiotics9110806"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.3201\/eid2606.191517","article-title":"Emergence of New Non-Clonal Group 258 High-Risk Clones among Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Isolates, France","volume":"26","author":"Bonnin","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3039","DOI":"10.1093\/jac\/dky284","article-title":"Characterization of carbapenemase-producing Enterobacteriaceae from colonized patients in a university hospital in Madrid, Spain, during the R-GNOSIS project depicts increased clonal diversity over time with maintenance of high-risk clones","volume":"73","author":"Bonten","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bonura, C., Giuffr\u00e8, M., Aleo, A., Fasciana, T., Di Bernardo, F., Stampone, T., Giammanco, A., The MDR-GN Working Group, Palma, D.M., and Mammina, C. (2015). An Update of the Evolving Epidemic of blaKPC Carrying Klebsiella pneumoniae in Sicily, Italy, 2014: Emergence of Multiple Non-ST258 Clones. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0132936"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e01355-14","DOI":"10.1128\/mBio.01355-14","article-title":"Epidemic Klebsiella pneumoniae ST258 is a hybrid strain","volume":"5","author":"Chen","year":"2014","journal-title":"mBio"},{"key":"ref_9","first-page":"e000149","article-title":"Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China","volume":"4","author":"Dong","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1093\/jac\/dky492","article-title":"Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307","volume":"74","author":"Wyres","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.ebiom.2017.04.032","article-title":"Nationwide surveillance of clinical carbapenem-resistant Enterobacteriaceae (CRE) strains in China","volume":"19","author":"Zhang","year":"2017","journal-title":"EBioMedicine"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"289","DOI":"10.3201\/eid2602.190594","article-title":"Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China","volume":"26","author":"Zhou","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e00386-19","DOI":"10.1128\/mSystems.00386-19","article-title":"A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool","volume":"5","author":"Rodrigues","year":"2020","journal-title":"mSystems"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2471","DOI":"10.1007\/s10096-020-03956-y","article-title":"Fourier transform infrared (FT-IR) spectroscopy typing: A real-time analysis of an outbreak by carbapenem-resistant Klebsiella pneumoniae","volume":"39","author":"Silva","year":"2020","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_15","unstructured":"Dire\u00e7\u00e3o-Geral da Sau\u0301de (2019, November 05). Infe\u00e7o\u0303es e Resist\u00eancias aos Antimicrobianos: Relat\u00f3rio Anual do Programa Priorit\u00e1rio 2018. Available online: https:\/\/www.dgs.pt\/portal-da-estatistica-da-saude\/diretorio-de-informacao\/diretorio-de-informacao\/por-serie-1003038-pdf.aspx?v=%3d%3dDwAAAB%2bLCAAAAAAABAArySzItzVUy81MsTU1MDAFAHzFEfkPAAAA."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1016\/j.ijmm.2014.08.003","article-title":"Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: A successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFIIK)","volume":"304","author":"Rodrigues","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.3389\/fmicb.2016.01000","article-title":"KPC-3-Producing Klebsiella pneumoniae in Portugal Linked to Previously Circulating Non-CG258 Lineages and Uncommon Genetic Platforms (Tn4401d-IncFIA and Tn4401d-IncN)","volume":"7","author":"Rodrigues","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.3201\/eid2509.190656","article-title":"Epidemiology of Carbapenemase-Producing Klebsiella pneumoniae in a Hospital, Portugal","volume":"25","author":"Pereira","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_19","first-page":"000349","article-title":"Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital","volume":"7","author":"Modesto","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.jgar.2020.04.007","article-title":"Epidemiology of carbapenemase-producing Klebsiella pneumoniae in northern Portugal: Predominance of KPC-2 and OXA-48","volume":"22","author":"Lopes","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/jac\/dkz542","article-title":"Occurrence of NDM-1-producing Morganella morganii and Proteus mirabilis in a single patient in Portugal: Probable in vivo transfer by conjugation","volume":"75","author":"Goncalves","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e01077-15","DOI":"10.1128\/genomeA.01077-15","article-title":"Draft Genome Sequence of the First NDM-1-Producing Providencia stuartii Strain Isolated in Portugal","volume":"3","author":"Manageiro","year":"2015","journal-title":"Genome Announc."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1586\/14787210.2014.856756","article-title":"The spread and acquisition of NDM-1: A multifactorial problem","volume":"12","author":"Wailan","year":"2014","journal-title":"Expert. Rev. Anti. Infect. Ther."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.1093\/jac\/dkz176","article-title":"Emergence of NDM-1-producing Klebsiella pneumoniae in Greece: Evidence of a widespread clonal outbreak","volume":"74","author":"Politi","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.ijantimicag.2019.03.013","article-title":"Dynamics of clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings over time","volume":"53","author":"Ribeiro","year":"2019","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3156","DOI":"10.1093\/jac\/dkaa339","article-title":"Genomic background of the Klebsiella pneumoniae NDM-1 outbreak in Poland, 2012-18","volume":"75","author":"Izdebski","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_27","first-page":"e000263","article-title":"Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains","volume":"5","author":"Wang","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Bowers, J.R., Kitchel, B., Driebe, E.M., MacCannell, D.R., Roe, C., Lemmer, D., de Man, T., Rasheed, J.K., Engelthaler, D.M., and Keim, P. (2015). Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0133727"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s10096-018-3431-3","article-title":"Fourier transform infrared spectroscopy: Unlocking fundamentals and prospects for bacterial strain typing","volume":"38","author":"Novais","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1080\/14756366.2017.1344235","article-title":"Beta-lactamase database (BLDB)\u2014structure and function","volume":"32","author":"Naas","year":"2017","journal-title":"J. Enzyme Inhib. Med. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"4281","DOI":"10.1128\/JCM.01634-13","article-title":"Blue-carba, an easy biochemical test for detection of diverse carbapenemase producers directly from bacterial cultures","volume":"51","author":"Pires","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1093\/jac\/dkt065","article-title":"Validation of carbapebemase and extended-spectrum \u03b2-lactamase multiplex endpoint PCR assays according to ISO 15189","volume":"68","author":"Bogaerts","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4073","DOI":"10.1128\/JCM.01924-13","article-title":"wzi gene sequencing, a rapid method to determine the capsular type of Klebsiella strains","volume":"51","author":"Brisse","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref_34","first-page":"e000224","article-title":"mlplasmids: A user-friendly tool to predict plasmid- and chromosome-derived sequences for single species","volume":"4","author":"Rogers","year":"2018","journal-title":"Microb. Genom."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/1\/92\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:27:22Z","timestamp":1760362042000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/1\/92"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,12]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1]]}},"alternative-id":["antibiotics11010092"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics11010092","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,12]]}}}