摘要

       挪威是抗菌素耐药性 (AMR) 水平最低的国家之一。 AMR，通过位于转座子或接合质粒上的获得性基因，是给定细菌抵抗抗生素所需的基因水平传递。在这项工作中，对来自大肠杆菌和来自挪威患者的肺炎克雷伯菌分离株的全基因组序列和杂交组装数据进行了生物信息学分析。为了检测分离物中的推定质粒，使用了 SPAdes 中的质粒组装模式，然后使用 PlasmidFinder 和两个精选的质粒数据库（Brooks 和 PLSDB）对结果重叠群进行注释。此外，ResFinder 和综合抗生素耐药数据库 (CARD) 用于鉴定抗生素耐药基因 (ARG)。 IncFIB 质粒被检测为大肠杆菌和肺炎克雷伯菌分离物中最普遍的质粒。此外，诸如 aph(3″)-Ib、aph(6)-Id、sul1、sul2、tet(D) 和 qnrS1 等 ARG 被鉴定为挪威大肠杆菌和肺炎克雷伯菌中最丰富的质粒介导的 ARG分别隔离。使用混合组装，我们能够更自信地定位质粒并预测 ARG。总之，使用全基因组测序数据进行质粒鉴定和 ARG 检测在很大程度上取决于选择的数据库；因此，最好使用多种工具和/或混合组装来获得可靠的识别结果。

       Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results. 

https://www.mdpi.com/2076-2607/9/1/52