Molecular and genomic surveillance systems for bacterial pathogens currently rely on tracking clonally evolving lineages. By contrast, plasmids are usually excluded or analyzed with low-resolution techniques, despite being the primary vectors of antibiotic resistance genes across many key pathogens. Here, we used a combination of long- and short-read sequence data of Klebsiella pneumoniae isolates (n = 1,717) from a European survey to perform an integrated, continent-wide study of chromosomal and plasmid diversity. This revealed three contrasting modes of dissemination used by carbapenemase genes, which confer resistance to last-line carbapenems. First, bla_OXA-48-like genes have spread primarily via the single epidemic pOXA-48–like plasmid, which emerged recently in clinical settings and spread rapidly to numerous lineages. Second, bla_VIM and bla_NDM genes have spread via transient associations of many diverse plasmids with numerous lineages. Third, bla_KPC genes have transmitted predominantly by stable association with one successful clonal lineage (ST258/512) yet have been mobilized among diverse plasmids within this lineage. We show that these plasmids, which include pKpQIL-like and IncX3 plasmids, have a long association (and are coevolving) with the lineage, although frequent recombination and rearrangement events between them have led to a complex array of mosaic plasmids carrying bla_KPC. Taken altogether, these results reveal the diverse trajectories of antibiotic resistance genes in clinical settings, summarized as using one plasmid/multiple lineages, multiple plasmids/multiple lineages, and multiple plasmids/one lineage. Our study provides a framework for the much needed incorporation of plasmid data into genomic surveillance systems, an essential step toward a more comprehensive understanding of resistance spread.

细菌病原体的分子和基因组监测系统目前依赖于跟踪克隆进化谱系。相比之下，质粒通常被排除在外或使用低分辨率技术进行分析，尽管它是许多关键病原体中抗生素抗性基因的主要载体。在这里，我们使用来自欧洲调查的肺炎克雷伯菌分离株 ( n = 1,717)的长读长和短读长序列数据的组合，对染色体和质粒多样性进行综合的、全大陆的研究。这揭示了碳青霉烯酶基因使用的三种截然不同的传播模式，这些基因赋予了对最后一线碳青霉烯类的抗性。一、bla _OXA-48-like基因主要通过单一流行性 pOXA-48 样质粒传播，该质粒最近出现在临床环境中并迅速传播到众多谱系。其次，bla _VIM和bla _NDM基因通过许多具有众多谱系的不同质粒的瞬时关联传播。三、bla _KPC基因主要通过与一个成功的克隆谱系 (ST258/512) 的稳定关联而传播，但已在该谱系内的不同质粒中动员起来。我们表明，这些质粒，包括 pKpQIL 样质粒和 IncX3 质粒，与谱系有长期关联（并且正在共同进化），尽管它们之间频繁的重组和重排事件导致了一系列复杂的镶嵌质粒携带bla _KPC. 总而言之，这些结果揭示了临床环境中抗生素抗性基因的不同轨迹，总结为使用一个质粒/多个谱系、多个质粒/多个谱系和多个质粒/一个谱系。我们的研究为急需将质粒数据纳入基因组监测系统提供了一个框架，这是朝着更全面地了解耐药性传播迈出的重要一步。