{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T04:43:19Z","timestamp":1786509799518,"version":"build-2736575974"},"reference-count":50,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2025,2,18]],"date-time":"2025-02-18T00:00:00Z","timestamp":1739836800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,2,18]],"date-time":"2025-02-18T00:00:00Z","timestamp":1739836800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","award":["01KI2018"],"award-info":[{"award-number":["01KI2018"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2025,2,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              The surveillance of mobile genetic elements facilitating the spread of antimicrobial resistance genes has been challenging. Here, we tracked both clonal and plasmid transmission in colistin- and carbapenem-resistant\n              <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n              using short- and long-read sequencing technologies. We observed three clonal transmissions, all containing Incompatibility group (Inc) L plasmids and New Delhi metallo-beta-lactamase\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              , although not co-located on the same plasmid. One IncL-\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              plasmid had been transferred between sequence type (ST) 392 and ST15, and the promiscuous IncL-\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>OXA-48<\/jats:sub>\n              plasmid was likely shared between a singleton and a clonal transmission of ST392. Plasmids within clonal outbreaks and between clusters and STs had 0\u20132 single nucleotide polymorphism (SNP) differences, showing high stability upon transfer to same or different STs. The simplest explanation, without a comprehensive analysis with long-read sequencing, would be the spread of a single common IncL-\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              plasmid. However, here, we report\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              in five different plasmids, emphasizing the need to investigate plasmid-mediated transmission for effective containment of outbreaks.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                Antimicrobial resistance occupies a central stage in global public health emergencies. Recently, efforts to track the genetic elements that facilitate the spread of resistance genes in plasmids outbreaks, utilizing short-read sequencing technologies, have been described. However, incomplete plasmid reconstruction from short-read sequencing data hinders full knowledge about plasmid structure, which makes the exploration very challenging. In this study, we used both short- and long-read sequencing in clinical\n                <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                from University Hospital Centre Zagreb, Croatia, which was resistant to both last-resort antibiotics colistin and carbapenem. Our results show complex transmission networks and sharing of plasmids, emphasizing multiple transmissions of plasmids harboring carbapenem and\/or colistin resistance genes between and within\n                <jats:italic>K. pneumoniae<\/jats:italic>\n                clones. Only full-length sequencing plus a novel way of determining plasmid clusters resulted in the complete picture, showing how future active monitoring of plasmids as a vital tool for infection prevention and control could be implemented.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/msystems.01128-24","type":"journal-article","created":{"date-parts":[[2025,1,10]],"date-time":"2025-01-10T14:00:35Z","timestamp":1736517635000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":16,"title":["Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant\n            <i>Klebsiella pneumoniae<\/i>"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4234-7649","authenticated-orcid":true,"given":"Ifeoluwa","family":"Akintayo","sequence":"first","affiliation":[{"name":"Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg","place":["Freiburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marko","family":"Siroglavic","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Infection Prevention and Control, University Hospital Centre Zagreb","place":["Zagreb, Croatia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daria","family":"Frolova","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory\u2013European Bioinformatics Institute","place":["Hinxton, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mabel Budia","family":"Silva","sequence":"additional","affiliation":[{"name":"Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg","place":["Freiburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hajo","family":"Grundmann","sequence":"additional","affiliation":[{"name":"Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg","place":["Freiburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zamin","family":"Iqbal","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory\u2013European Bioinformatics Institute","place":["Hinxton, United Kingdom"]},{"name":"Milner Centre for Evolution, University of Bath","place":["Bath, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Budimir","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Infection Prevention and Control, University Hospital Centre Zagreb","place":["Zagreb, Croatia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1672-5789","authenticated-orcid":true,"given":"Sandra","family":"Reuter","sequence":"additional","affiliation":[{"name":"Institute for Infection Prevention and Control, Faculty of Medicine, University of Freiburg","place":["Freiburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","unstructured":"WHO. 2015. 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