Temporal GWAS identifies a widely distributed putative adhesin contributing to pathogen success in Shigella spp
Temporal GWAS identifies a widely distributed putative adhesin contributing to pathogen success in Shigella spp
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DOI：
10.1101/2022.08.23.504947
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发表时间：
2022-08
期刊：
影响因子：
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通讯作者：
R. Bennett;P. M. De Silva;Rebecca J. Bengtsson;M. Horsburgh;T. R. Blower;K. Baker
中科院分区：
文献类型：
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作者：
R. Bennett;P. M. De Silva;Rebecca J. Bengtsson;M. Horsburgh;T. R. Blower;K. Baker
志贺氏菌属细菌是全球腹泻疾病负担的主要原因，每年导致全球超过 200,000 人死亡，其中福氏志贺氏菌是主要致病菌种。志贺氏菌耐药性（AMR）的增加和缺乏许可的疫苗导致世界卫生组织将志贺氏菌视为开发新抗菌药物的优先微生物。了解是什么推动了这种病原体的长期存在和成功，对于志贺氏菌病的持续管理至关重要，并且与其他肠道细菌相关。为了确定过去 100 年来志贺氏菌进化的关键遗传驱动因素，我们使用一种称为时间全基因组关联研究 (tGWAS) 的新方法，分析了历史默里菌种（n=45，1917-1954 年间分离）和相对现代的菌种（n=262，1950-2011 年间分离）中的弗氏志贺菌。我们确定了 48 个基因内的 SNP (n=94)、COG (n=359) 和显着 kmers 与时间显着正相关。其中包括 T3SS 编码基因、参与细胞内竞争的蛋白质、获得性抗菌素耐药性基因、插入序列和未知功能的基因（28%，调查的命中数为 49/172）。在未知的蛋白质中，我们鉴定了一种新的质粒携带的假定粘附素，名为 Stv。基因组流行病学分析表明，Stv 与 S. flexneri 多个系统群的克隆扩张有关，其获得早于谱系 III S. sonnei 的多药耐药性获得和全球传播。 Stv 及其近亲广泛分布于其他肠杆菌科和细菌中，表明其重要性可能超出志贺氏菌范围。这项工作强调了在历史分离株收集中使用 tGWAS 的有效性，以识别随着时间的推移病原体成功的新贡献者。这种方法很容易转化为其他病原体，我们在志贺氏菌中的应用确定了 Stv，一种假定的粘附素和潜在的药物靶点，广泛分布于 AMR 优先组肠杆菌科细菌中。作者摘要 志贺氏菌病是全世界腹泻病的主要原因，是多种肠杆菌科细菌中的代表，世卫组织已宣布志贺氏菌病为迫切需要新抗菌药物的优先病原体。大多数志贺氏菌病是由福氏志贺氏菌和宋内志贺氏菌引起的。在这项研究中，我们整理了跨越 94 年的弗氏链球菌分离株，涵盖抗生素时代之前和之后，以实施一种新型生物信息学技术——时间 GWAS (tGWAS)，以确定该时期病原体成功的关键因素。除了恢复 AMR 和毒力基因外，我们还鉴定了一种新型的、可移动的假定粘附素，本文命名为 Stv，它似乎有助于多个志贺氏菌属物种的克隆扩张，并且存在于更广泛的肠杆菌科细菌中。我们的结果表明，Stv 在控制志贺氏菌和其他感染方面的潜在重要性，以及 tGWAS 方法在识别支持 AMR 病原体随时间进化和扩张的生物驱动因素方面的有效性。
Bacteria of the genus Shigella are a major contributor to the global diarrhoeal disease burden causing >200,000 deaths per annum globally where S. flexneri is the major pathogenic species. Increasing antimicrobial resistance (AMR) in Shigella and the lack of a licenced vaccine has led WHO to recognise Shigella as a priority organism for the development of new antimicrobials. Understanding what drives the long-term persistence and success of this pathogen is critical for ongoing shigellosis management and is relevant for other enteric bacteria. To identify key genetic drivers of Shigella evolution over the past 100 years, we analysed S. flexneri from the historical Murray collection (n=45, isolated between 1917-1954) alongside a comparatively modern collection (n=262, isolated between 1950-2011) using a novel approach called temporal genome-wide association study (tGWAS). We identified SNPs (n=94), COGs (n=359) and significant kmers within 48 genes significantly positively associated with time. These included T3SS encoding genes, proteins involved in intracellular competition, acquired antimicrobial resistance genes, insertion sequences, and genes of unknown function (28%, 49/172 of those hits investigated). Among the unknown proteins we identified a novel plasmid borne putative adhesin, named Stv. Genomic epidemiological analyses reveal that Stv was associated with clonal expansions of multiple phylogroups of S. flexneri and its acquisition predates multidrug resistance acquisition and the global dissemination of Lineage III S. sonnei. Stv, and close relatives, are widely distributed in other Enterobactericeae and bacteria, indicating that its importance likely extends beyond shigellae. This work highlights the effectiveness of using tGWAS on historical isolate collections for identifying novel contributors to pathogen success over time. This approach is readily translatable to other pathogens and our application in Shigella identified Stv, a putative adhesin and potential drug target that is widely distributed across the AMR priority group Enterobacteriaceae. Author Summary Shigellosis is a leading cause of diarrhoeal disease worldwide and is represented among the multiple Enterobacteriaceae which WHO have declared as priority pathogens for which new antimicrobials are urgently needed. The majority of shigellosis is caused by the species Shigella flexneri and Shigella sonnei. In this study we collated S. flexneri isolates that spanned a 94-year period, encompassing the pre- and post-antibiotic era to implement a novel bioinformatic technique, temporal GWAS (tGWAS), to identify key factors of pathogen success during this time period. Alongside recovering AMR and virulence genes, we also identified a novel, mobilisable putative adhesin, named Stv herein, which appeared to contribute to clonal expansions across multiple Shigella species and is present across the broader Enterobacteriaceae. Our results indicate the potential importance of Stv in controlling Shigella and other infections, and the validity of a tGWAS approach for identifying biological drivers underpinning the evolution and expansion of AMR pathogens over time.