Horizontal gene transfer mediated by integrative and conjugative elements (ICE) is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The rate of ICE-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. In this paper, we report a big data analysis of ICE and associated cargo genes across over 200,000 bacterial genomes representing 1,345 genera. Our results reveal that half of bacterial genomes contain one or more known ICE features ("ICE genomes") and that the associated genetic cargo may play an important role in the spread of AMR genes within and between bacterial genera. We identify 43 AMR genes that appear only in ICEgenomes and never in non-ICE genomes. A further set of 95 AMR genes are found >5x more often in ICE versus non-ICEgenomes. In contrast, only 29 AMR genes are observed more frequently (at least 5:1) in non-ICE genomes compared toICE genomes. Analysis of NCBI antibiotic susceptibility assay data reveals that ICE genomes are also over-represented amongst phenotypically resistant isolates, suggesting that ICE processes are critical for both genotypic and phenotypic AMR. These results, as well as the underlying big data resource, are important foundational tools for understanding bacterial evolution, particularly in relation to important bacterial phenotypes such as AMR.

中文翻译：

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数百个细菌属内和跨细菌属的整合和共轭元件（ICE）和相关的货运基因

由整合和结合元件（ICE）介导的水平基因转移被认为是细菌的重要进化机制。它使生物能够快速进化出新的表型特性，包括抗菌素耐药性（AMR）和毒力。ICE介导的货物基因交换的速率尚未在细菌类群之内和之间得到全面研究。在本文中，我们报告了代表1345个属的200,000多个细菌基因组中ICE和相关货物基因的大数据分析。我们的结果表明，一半细菌基因组包含一个或多个已知的ICE特征（“ ICE基因组”），并且相关的遗传物质可能在细菌属内和之间的AMR基因传播中起重要作用。我们确定了43个AMR基因，它们仅出现在ICE基因组中，而从未出现在非ICE基因组中。与非ICE基因组相比，在ICE中发现的另一组95个AMR基因的频率高出5倍。相反，与ICE基因组相比，在非ICE基因组中仅观察到29个AMR基因的频率更高（至少5：1）。对NCBI抗生素敏感性分析数据的分析表明，在表型抗性分离株中ICE基因组也被过度代表，这表明ICE过程对于基因型和表型AMR都是至关重要的。这些结果以及潜在的大数据资源，是理解细菌进化的重要基础工具，尤其是与重要细菌表型（例如AMR）相关的工具。对NCBI抗生素敏感性分析数据的分析表明，在表型抗性分离株中ICE基因组也被过度代表，这表明ICE过程对于基因型和表型AMR都是至关重要的。这些结果以及潜在的大数据资源，是理解细菌进化的重要基础工具，尤其是与重要细菌表型（例如AMR）相关的工具。对NCBI抗生素敏感性分析数据的分析表明，在表型抗性分离株中ICE基因组也被过度代表，这表明ICE过程对于基因型和表型AMR都是至关重要的。这些结果以及潜在的大数据资源，是理解细菌进化的重要基础工具，尤其是与重要细菌表型（例如AMR）相关的工具。