Shigella is ranked as the second leading cause of diarrheal disease worldwide. Though infection occurs in people of all ages, most of the disease burden constitutes among the children less than 5 years in low and middle income countries. Recent increasing incidence of drug resistant strains make this as a priority pathogen under the antimicrobial resistance surveillance by WHO. Despite this, only limited genomic studies on drug resistant Shigella exists. Here we report the first complete genome of clinical S. flexneri serotype 2a and S. sonnei strains using a hybrid approach of both long-read MinION (Oxford Nanopore Technologies) and short-read Ion Torrent 400 bp sequencing platforms. The utilization of this novel approach in the present study helped to identify the complete plasmid sequence of pSS1653 with structural genetic information of AMR genes such as sulII, tetA, tetR, aph(6)-Id and aph(3'')-Ib. Identification of AMR genes in mobile elements in this human-restricted enteric pathogen is a potential threat for dissemination to other gut pathogens. The information on Shigella at genome level could help us to understand the genome dynamics of existing and emerging resistant clones.

中文翻译：

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对临床志贺氏菌菌株的完整基因组分析揭示了具有抗性决定因素的质粒 pSS1653：混合方法的胜利。

志贺氏菌被列为全球腹泻病的第二大原因。尽管感染发生在所有年龄段的人群中，但在中低收入国家，大部分疾病负担是在 5 岁以下儿童中。最近耐药菌株发生率的增加使其成为世界卫生组织抗菌素耐药性监测的重点病原体。尽管如此，针对耐药志贺氏菌的基因组研究仍然有限。在这里，我们使用长读长 MinION (Oxford Nanopore Technologies) 和短读长 Ion Torrent 400 bp 测序平台的混合方法，报告了临床福氏链球菌血清型 2a 和宋内链球菌菌株的第一个完整基因组。在本研究中利用这种新方法有助于鉴定 pSS1653 的完整质粒序列以及 AMR 基因的结构遗传信息，例如 sulII、tetA、tetR、aph(6)-Id 和 aph(3'')-Ib。在这种人类限制性肠道病原体的移动元件中鉴定 AMR 基因是传播到其他肠道病原体的潜在威胁。志贺氏菌基因组水平的信息可以帮助我们了解现有和新兴抗性克隆的基因组动态。