Xu Zhen, Shi Lulu, Meng Tao, Luo Mei, Zhu Jiaming, Wang Mingyu, Shen Wenlong
Department of Anorectal Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China.
State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.
Front Microbiol. 2024 Oct 15;15:1452795. doi: 10.3389/fmicb.2024.1452795. eCollection 2024.
Plasmids, the most important and versatile bacterial extrachromosomal DNA Molecules, has have been a center central topic for bacterial genetics and biology. However, the inability of short-read high-throughput sequencing methods to reliably assemble plasmids makes it difficult to investigate the diversity of plasmid structures and functions.
In this work, we used the long-read Nanopore sequencing method to address this issue, by producing high quality whole genome sequences of 33 bacterial strains from 11 perianal abscess-suffering patients.
Successful high quality assemblies were generated with this method, including 20 perfect assemblies out of 33 genomes. A total of 47 plasmids were identified from the bacterial strains, including 12 unique, newly identified, high quality circular plasmids. These plasmids were further subject to structural analysis, leading to the finding of significant diversification from previously known plasmids, suggesting the diversity of plasmid structure and function. Particularly, two -harboring conjugative plasmids were found from and , which were not previously reported. This works shows the feasibility of using long-read sequencing to identify plasmids, and the high diversity of plasmid structure and function that awaits further surveillance.
质粒是最重要且用途广泛的细菌染色体外DNA分子，一直是细菌遗传学和生物学的核心主题。然而，短读长高通量测序方法无法可靠地组装质粒，这使得研究质粒结构和功能的多样性变得困难。
在这项工作中，我们使用长读长纳米孔测序方法来解决这个问题，通过对11名肛周脓肿患者的33株细菌菌株进行高质量全基因组测序。
用这种方法成功生成了高质量的组装结果，33个基因组中有20个完美组装。从这些细菌菌株中总共鉴定出47个质粒，包括12个独特的、新鉴定的高质量环状质粒。对这些质粒进一步进行结构分析，发现其与先前已知的质粒有显著差异，表明质粒结构和功能具有多样性。特别是，从[具体菌株1]和[具体菌株2]中发现了两个携带接合性质粒，但此前未报道过。这项工作展示了使用长读长测序鉴定质粒的可行性，以及有待进一步监测的质粒结构和功能的高度多样性。
