Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China.
Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China.
J Glob Antimicrob Resist. 2023 Dec;35:268-270. doi: 10.1016/j.jgar.2023.10.009. Epub 2023 Oct 20.
Prevotella bivia is a species that commonly colonizes various human body sites, and it is associated with lots of human infections. However, until now, no complete genome sequence of this species has been published. Here, we assembled the first complete genome of P. bivia from a clinically derived strain PLW0727, to characterize its general genomic features, and to profile the capacity in encoding antibiotic resistance and virulence factors.
Whole-genome sequencing was performed using Illumina and Nanopore platforms. Hybrid assembly was conducted using flye v2.9.1 and Unicycler v0.4.9b. Assembly completeness was assessed using CheckM v1.0.12. Comprehensive genome annotation was performed using eggNOG-mapper v2.1.5 and PATRIC v3.6.10.
The complete genome of PLW0727 consists of two circular chromosomes, chr1 and chr2, exhibiting a completeness of 99.66%, a G+C content of 39.5%, and a total size of 2.43 Mb. Chr1 and chr2 have lengths of 1 272 652 bp and 1 155 021 bp, harbouring 1 132 CDSs and 1 055 CDSs, respectively. Completion of the genome significantly reduced the proportion of hypothetical CDS annotations compared with the draft genomes. A gene-encoding antibiotic resistance to beta-lactams (i.e., cfxA3) has been annotated in chr2. By providing the genome sequence, strain PLW0727 was identified as a human pathogen with a probability of 0.614 using the PathogenFinder. Furthermore, genes involved in virulence-related functions, including host cell adherence and capsule immune modulation were also annotated.
This study assembles the first complete genome for P. bivia, providing valuable genomic insights into its phylogeny, pathogenicity, and antibiotic resistance. These findings have important implications for the clinical management and prevention of P. bivia infections.
普氏拟杆菌是一种常见于人体各种部位的物种，与许多人类感染有关。然而，到目前为止，还没有发表过该物种的完整基因组序列。在这里，我们从临床分离株 PLW0727 中组装了第一个完整的 P. bivia 基因组，以表征其一般基因组特征，并分析其编码抗生素耐药性和毒力因子的能力。
使用 Illumina 和 Nanopore 平台进行全基因组测序。使用 flye v2.9.1 和 Unicycler v0.4.9b 进行混合组装。使用 CheckM v1.0.12 评估组装的完整性。使用 eggNOG-mapper v2.1.5 和 PATRIC v3.6.10 进行全面的基因组注释。
PLW0727 的完整基因组由两个圆形染色体 chr1 和 chr2 组成，其完整性为 99.66%，G+C 含量为 39.5%，总大小为 2.43 Mb。chr1 和 chr2 的长度分别为 1 272 652 bp 和 1 155 021 bp，分别包含 1 132 个 CDS 和 1 055 个 CDS。与草图基因组相比，基因组的完成显著降低了假设性 CDS 注释的比例。在 chr2 中注释了编码对抗生素β-内酰胺（即 cfxA3）的耐药性的基因。通过提供基因组序列，使用 PathogenFinder 鉴定 PLW0727 菌株为人病原体的概率为 0.614。此外，还注释了与毒力相关功能相关的基因，包括宿主细胞粘附和荚膜免疫调节。
本研究组装了第一个 P. bivia 的完整基因组，为其系统发育、致病性和抗生素耐药性提供了有价值的基因组见解。这些发现对 P. bivia 感染的临床管理和预防具有重要意义。
