Néron Bertrand, Littner Eloi, Haudiquet Matthieu, Perrin Amandine, Cury Jean, Rocha Eduardo P C
Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris Cité, 75015 Paris, France.
Microbial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, France.
Microorganisms. 2022 Mar 24;10(4):700. doi: 10.3390/microorganisms10040700.
Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000 genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available on multiple public platforms.
整合子是灵活的基因交换平台，包含多个编码辅助基因的盒式结构，这些盒式结构的顺序由特定的整合酶打乱。嵌入移动遗传元件中的整合子通常含有多个抗生素抗性基因，它们在医院病原体中传播，导致了当前的抗生素抗性危机。然而，大多数整合子可能是静止的，编码的功能多样性要广泛得多。整合子查找器（IntegronFinder）是一种广泛用于在细菌基因组中识别新型整合子的软件，但该软件已经陈旧，缺乏处理非常大的草图基因组或宏基因组数据集的一些有用功能。在此，我们展示整合子查找器2.0版本。我们更新了代码，提高了其效率和可用性，使输出适应不完整的基因组数据，并添加了一些新功能。我们描述了这些变化，并通过分析20000多个全序列基因组中整合子的分布来说明该程序的相关性。我们还充分利用其新功能，分析了近4000个基因组中整合子和抗生素抗性基因的存在情况。我们的数据表明，[具体内容缺失]具有大量不同的整合子，并且在我们的质粒数据库中有最大的移动整合子。这些整合子的泛基因组总共包含165个不同的基因家族，其中大多数最大的家族与对多种抗生素的抗性有关。整合子查找器是一款免费的开源软件，可在多个公共平台上获取。
