Division of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy.
Division of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy; University of Bologna, Italy.
J Glob Antimicrob Resist. 2023 Jun;33:152-154. doi: 10.1016/j.jgar.2023.02.015. Epub 2023 Mar 5.
Herein, we sequenced and assembled the genome of a Shigella sonnei isolate carrying several small plasmids using a hybrid approach that combined Oxford Nanopore Technologies and Illumina platforms.
Whole-genome sequencing was conducted using the Illumina iSeq 100 and Oxford Nanopore MinION systems, and the resulting reads were used for hybrid genome assembly via Unicycler. Coding sequences were annotated using RASTtk, while genes involved in antimicrobial resistance and virulence were identified using AMRFinderPlus. Plasmid nucleotide sequences were aligned to the NCBI non-redundant database using BLAST, and replicons were identified using PlasmidFinder.
The genome consisted of 1 chromosome (4 801 657 bp), 3 major plasmids (212 849 bp, 86 884 bp, and 83 425 bp, respectively) and 12 small cryptic plasmids (ranging from 8390 bp to 1822 bp). BLAST analysis revealed that all plasmids were highly similar to previously deposited sequences. Genome annotation predicted 5522 coding regions, including 19 antimicrobial resistance genes and 17 virulence genes. Four of the antimicrobial resistance genes were located in small plasmids, and four of the virulence genes were located in a large virulence plasmid.
The presence of antimicrobial resistance genes in small cryptic plasmids may represent an overlooked mechanism for the propagation of these genes among bacterial populations. Our work provides new data on these elements that may inform the development of new strategies to control the spread of extended spectrum β-lactamase-producing bacterial strains.
本研究采用结合牛津纳米孔技术和 Illumina 平台的混合方法，对携带多个小质粒的宋内志贺菌分离株进行了基因组测序和组装。
使用 Illumina iSeq 100 和 Oxford Nanopore MinION 系统进行全基因组测序，然后使用 Unicycler 对生成的读数进行混合基因组组装。使用 RASTtk 对编码序列进行注释，使用 AMRFinderPlus 识别与抗菌药物抗性和毒力相关的基因。使用 BLAST 将质粒核苷酸序列与 NCBI 非冗余数据库进行比对，并使用 PlasmidFinder 识别复制子。
基因组由 1 条染色体（4801657 bp）、3 个主要质粒（分别为 212849 bp、86884 bp 和 83425 bp）和 12 个小型隐秘质粒（范围为 8390 bp 至 1822 bp）组成。BLAST 分析表明，所有质粒与先前已提交的序列高度相似。基因组注释预测了 5522 个编码区，包括 19 个抗菌药物抗性基因和 17 个毒力基因。4 个抗菌药物抗性基因位于小型质粒中，4 个毒力基因位于一个大型毒力质粒中。
小型隐秘质粒中抗菌药物抗性基因的存在可能代表了这些基因在细菌群体中传播的一个被忽视的机制。我们的工作为这些元素提供了新的数据，可能为制定控制产扩展谱β-内酰胺酶细菌菌株传播的新策略提供信息。
