University of Oxford, Department of Biology, Oxford, United Kingdom.
Harvard Medical School, Department of Biomedical Informatics, Boston, Massachusetts, USA.
mBio. 2023 Apr 25;14(2):e0253722. doi: 10.1128/mbio.02537-22. Epub 2023 Feb 22.
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. Under stress, the integron can generate combinatorial variation in resistance cassette expression by cassette reshuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here, we test this hypothesis by selecting for increased-piperacillin-resistance populations of Pseudomonas aeruginosa with a mobile integron containing a difficult-to-mobilize β-lactamase cassette to minimize the potential for adaptive cassette reshuffling. We found that integron activity can decrease the overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations albeit at the cost of a reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes. Tackling the public health challenge created by antibiotic resistance requires understanding the mechanisms driving its evolution. Mobile integrons are widespread genetic platforms heavily involved in the spread of antibiotic resistance. Through the action of the integrase enzyme, integrons allow bacteria to capture, excise, and shuffle antibiotic resistance gene cassettes. This integrase enzyme is characterized by its ability to recognize a wide range of recombination sites, which allows it to easily capture diverse resistance cassettes but which may also lead to off-target reactions with the rest of the genome. Using experimental evolution, we tested the off-target impact of integron activity. We found that integrons increased the fitness of the surviving bacteria through extensive genomic rearrangements of the plasmids carrying the integrons, reducing their ability to spread horizontally. These results show that integrons not only accelerate resistance evolution but also can generate extensive structural variation, driving bacterial evolution beyond antibiotic resistance.
整合子是一种移动遗传元件，在抗生素耐药性的传播中发挥了重要作用。在压力下，整合子可以通过盒式重组产生耐药盒表达的组合变化，从而加速耐药性的进化。然而，整合子整合酶位点识别模体的灵活性暗示了整合酶对基因组其余部分可能存在潜在的非靶标效应，这可能具有重要的进化后果。在这里，我们通过选择具有移动整合子的铜绿假单胞菌增加哌拉西林耐药性种群来测试这一假设，该整合子包含一个难以移动的β-内酰胺酶盒，以最大限度地减少适应性盒式重组的可能性。我们发现，整合子的活性可以降低整体存活率，但也可以提高存活种群的适应性。整合子介导的非靶标反转通过破坏在缺乏功能整合酶的对照群体中发生突变的昂贵的接合基因，加速了质粒的适应。含有整合子介导反转的质粒与携带突变的质粒相比，成本较低，稳定性较高，尽管代价是接合能力降低。这些发现强调了整合子在驱动细菌进化方面创造结构变异的潜力，它们提供了一个有趣的例子，说明抗生素压力如何导致接合基因的丧失。 应对抗生素耐药性带来的公共卫生挑战需要了解驱动其进化的机制。移动整合子是广泛参与抗生素耐药性传播的遗传平台。通过整合酶酶的作用，整合子允许细菌捕获、切除和混合抗生素耐药基因盒。这种整合酶酶的特点是能够识别广泛的重组位点，这使其能够轻松捕获不同的耐药盒，但也可能导致与基因组其余部分的非靶标反应。通过实验进化，我们测试了整合子活性的非靶标影响。我们发现，整合子通过整合子携带质粒的广泛基因组重排增加了存活细菌的适应性，降低了它们水平传播的能力。这些结果表明，整合子不仅加速了耐药性的进化，而且还可以产生广泛的结构变异，推动细菌进化超越抗生素耐药性。
