{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:56:40Z","timestamp":1790751400019,"version":"4.1.0"},"reference-count":42,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"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. Microbiol."],"abstract":"<jats:p>\n                    The convergence of hypervirulence and carbapenem resistance in\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    represents a critical threat to global public health. However, the genomic mechanisms underlying this convergence, particularly the interplay between chromosomal background and mobile genetic elements, remain incompletely understood. Here, we integrated complete genome data from 102 clinical isolates from Qujing, China, with a global dataset of 4,262 genomes to construct a multi-layer population genomic framework. Using comparative genomics and sequence-similarity network analyses, we characterized the structural organization of the core genome and the population structures of plasmids and prophages. We show that the ST11 lineage serves as a central hub for the convergence of hypervirulence and carbapenem resistance. Plasmids are organized into discrete, functionally specialized communities, among which a dominant community is strongly enriched for hypervirulence and multidrug resistance determinants and preferentially associates with ST11. In contrast, the core genome exhibits a highly constrained structural organization, with most core genes embedded within conserved synteny modules, indicating strong evolutionary constraints on chromosomal architecture. Furthermore, prophages form structured yet more conserved communities that show non-random associations with plasmid types and selectively contribute to the dissemination of resistance genes. Notably, we identified a previously unreported plasmid harboring multiple copies of key virulence loci, underscoring the ongoing modular evolution of high-risk elements. Together, these findings reveal that the convergence of hypervirulence and resistance is driven by lineage-specific plasmid compatibility within a structurally constrained chromosomal background, and they establish a network-based framework for understanding the evolution of high-risk\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    lineages.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1932987","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:05:21Z","timestamp":1790748321000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["A central hub for convergence: multi-layer genomic networks reveal lineage-specific plasmid compatibility driving hypervirulence and carbapenem resistance in ST11 Klebsiella pneumoniae"],"prefix":"10.3389","volume":"17","author":[{"given":"Xuan","family":"Hai","sequence":"first","affiliation":[{"name":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-Ling","family":"Wang","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Chen","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Fei","family":"Lu","sequence":"additional","affiliation":[{"name":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiu-Ping","family":"Li","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong-Jian","family":"Li","sequence":"additional","affiliation":[{"name":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao-Fu","family":"Yue","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Mei","family":"Song","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling-Ling","family":"Yang","sequence":"additional","affiliation":[{"name":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Chen","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Center of Clinical Laboratory, Qujing Central Hospital, Qujing Affiliated Hospital of Kunming Medical University","place":["Qujing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Yang","family":"Zhi","sequence":"additional","affiliation":[{"name":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1609\/icwsm.v3i1.13937","article-title":"Gephi: an open source software for exploring and manipulating networks","volume":"3","author":"Bastian","year":"2009","journal-title":"ICWSM"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e2502752122","DOI":"10.1073\/pnas.2502752122","article-title":"Evolution of gene order in prokaryotes is driven primarily by gene gain and loss","volume":"122","author":"Brezner","year":"2025","journal-title":"Proc. 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Commun."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.jgar.2021.02.020","article-title":"A global perspective on the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae","volume":"25","author":"Lan","year":"2021","journal-title":"J Glob Antimicrob Resist"},{"key":"ref21","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":"ref22","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/s13073-024-01399-0","article-title":"KleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide","volume":"16","author":"Li","year":"2024","journal-title":"Genome Med."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"4","DOI":"10.3389\/fcimb.2018.00004","article-title":"Colonization, infection, and the accessory genome of Klebsiella pneumoniae","volume":"8","author":"Martin","year":"2018","journal-title":"Front. 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Rep."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1080\/21505594.2016.1222343","article-title":"The global epidemiology of carbapenemase-producing Enterobacteriaceae","volume":"8","author":"Van Duin","year":"2017","journal-title":"Virulence"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41467-023-44351-3","article-title":"Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64","volume":"15","author":"Wang","year":"2024","journal-title":"Nat. Commun."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: faster than PHASTER, better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"msag117","DOI":"10.1093\/molbev\/msag117","article-title":"IQ-TREE 3: phylogenomic inference software using complex evolutionary models","volume":"43","author":"Wong","year":"2026","journal-title":"Mol. Biol. Evol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1016\/j.tim.2016.09.007","article-title":"Klebsiella pneumoniae population genomics and antimicrobial-resistant clones","volume":"24","author":"Wyres","year":"2016","journal-title":"Trends Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","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":"ref40","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1038\/s42003-021-02148-4","article-title":"Clinical evolution of ST11 carbapenem resistant and hypervirulent Klebsiella pneumoniae","volume":"4","author":"Xie","year":"2021","journal-title":"Commun. Biol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"e0014322","DOI":"10.1128\/msphere.00143-22","article-title":"Sequence-based genomic analysis reveals transmission of antibiotic resistance and virulence among carbapenemase-producing Klebsiella pneumoniae strains","volume":"7","author":"Zhang","year":"2022","journal-title":"mSphere"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"D871","DOI":"10.1093\/nar\/gkae968","article-title":"VFDB 2025: an integrated resource for exploring anti-virulence compounds","volume":"53","author":"Zhou","year":"2025","journal-title":"Nucleic Acids Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1932987\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T06:05:23Z","timestamp":1790748323000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1932987\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":42,"alternative-id":["10.3389\/fmicb.2026.1932987"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1932987","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]},"article-number":"1932987"}}