van Belkum Alex, Soriaga Leah B, LaFave Matthew C, Akella Srividya, Veyrieras Jean-Baptiste, Barbu E Magda, Shortridge Dee, Blanc Bernadette, Hannum Gregory, Zambardi Gilles, Miller Kristofer, Enright Mark C, Mugnier Nathalie, Brami Daniel, Schicklin Stéphane, Felderman Martina, Schwartz Ariel S, Richardson Toby H, Peterson Todd C, Hubby Bolyn, Cady Kyle C
bioMérieux, Marcy l'Etoile, France.
Synthetic Genomics, Inc., La Jolla, California, USA.
mBio. 2015 Nov 24;6(6):e01796-15. doi: 10.1128/mBio.01796-15.
Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.
P. aeruginosa is both an antibiotic-refractory pathogen and an important model system for type I CRISPR-Cas bacterial immune systems. By combining the genome sequences of 672 newly and previously sequenced genomes, we were able to provide a global view of the phylogenetic distribution, conservation, and potential targets of these systems. This analysis identified a new and putatively mobile P. aeruginosa CRISPR-Cas subtype, characterized the diverse distribution of known CRISPR-inhibiting genes, and provided a potential new use for CRISPR spacer libraries in accessory genome analysis. Our data demonstrated the importance of CRISPR-Cas systems in modulating the accessory genomes of globally distributed strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields. Understanding why certain genotypes of P. aeruginosa are clinically prevalent and adept at horizontally acquiring virulence and antibiotic resistance elements is of major clinical and economic importance.
铜绿假单胞菌是一种具有大基因组和广泛基因型多样性的抗生素难治性病原体。从历史上看，铜绿假单胞菌一直是理解基于I型成簇规律间隔短回文重复序列（CRISPR）和CRISPR相关蛋白（CRISPR-Cas）的细菌免疫系统功能的分子机制的主要模型系统。然而，关于这些CRISPR-Cas系统在塑造铜绿假单胞菌辅助基因组和抗生素抗性元件中的系统发育分布和潜在作用的信息知之甚少。我们使用计算方法来识别和表征672个基因组中的CRISPR-Cas系统，在此过程中，我们鉴定出一种先前未报道的、推测具有移动性的I-C型铜绿假单胞菌CRISPR-Cas系统。此外，含有未受抑制的I-F型和I-E型CRISPR-Cas系统的基因组平均比没有CRISPR-Cas系统的基因组小约300 kb。计算机分析表明，辅助基因组（n = 22,036个基因）包含了大多数已鉴定的CRISPR-Cas靶点。我们还组装了一个全球间隔序列文库，有助于在下一代测序（NGS）数据中识别难以表征的移动遗传元件，并对大多数铜绿假单胞菌菌株进行CRISPR分型。总之，我们的分析表明，CRISPR-Cas系统在塑造全球分布的铜绿假单胞菌分离株的辅助基因组中发挥着重要作用。
铜绿假单胞菌既是一种抗生素难治性病原体，也是I型CRISPR-Cas细菌免疫系统的重要模型系统。通过结合672个新测序和先前测序的基因组序列，我们能够提供这些系统的系统发育分布、保守性和潜在靶点的全局视图。该分析鉴定出一种新的、推测具有移动性的铜绿假单胞菌CRISPR-Cas亚型，表征了已知CRISPR抑制基因的不同分布，并为CRISPR间隔序列文库在辅助基因组分析中的潜在新用途提供了依据。我们的数据证明了CRISPR-Cas系统在调节全球分布菌株的辅助基因组中的重要性，同时也为多个领域的后续基因组和实验研究提供了大量数据。了解为什么某些基因型的铜绿假单胞菌在临床上普遍存在且善于水平获取毒力和抗生素抗性元件具有重大的临床和经济意义。
