Whole-Genome-Based Helicobacter pylori Geographic Surveillance: A Visualized and Expandable Webtool.
Whole-Genome-Based Helicobacter pylori Geographic Surveillance: A Visualized and Expandable Webtool.
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DOI：
10.3389/fmicb.2021.687259
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发表时间：
2021
影响因子：
5.2
通讯作者：
Tan H
中科院分区：
文献类型：
--
作者：
Jiang X;Xu Z;Zhang T;Li Y;Li W;Tan H
幽门螺杆菌表现出与临床结果相关的特定地理分布。尽管幽门螺杆菌在世界范围内的感染率很高，但幽门螺杆菌的遗传流行病学监测仍有待改进。本研究采用基于全基因组测序（WGS）的单核苷酸多态性（SNPs）分析方法，促进幽门螺杆菌基因组群体分析，促进微生物基因分型策略在全球范围内的推广。下载1211份公开的幽门螺杆菌基因组，构建幽门螺杆菌分型工具HpTT （H. pylori typing tool）。结合元数据，我们开发了两个级别的基因组分型，包括大陆尺度和嵌套在大陆尺度中的国家尺度。结果表明，亚洲是我们数据集中最大的分离源，而欧洲和大洋洲的分离源相对更广泛。更具体地说，瑞士和澳大利亚是其相应大陆广泛隔离的主要来源。为了整合所有的分类信息，使研究人员能够轻松快速地将他们的数据集与现有的全球数据库进行比较，开发了一个用户友好的网站（https://db.cngb.org/HPTT/），其中包含基因组分型工具和可视化工具。为了进一步证实网站的有效性，我们下载了10个新组装的基因组，并按照我们的预期精确地定位在分支上进行了测试。综上所述，幽门螺杆菌分型工具（HpTT）是一种新型的基因组流行病学工具，可以同时实现高分辨率的基因组分型分析和可视化，为幽门螺杆菌的遗传群体结构、进化分析和流行病学监测提供见解。
Helicobacter pylori exhibit specific geographic distributions that are related to clinical outcomes. Despite the high infection rate of H. pylori throughout the world, the genetic epidemiology surveillance of H. pylori still needs to be improved. This study used the single nucleotide polymorphisms (SNPs) profiling approach based on whole genome sequencing (WGS) to facilitate genomic population analyses of H. pylori and encourage the dissemination of microbial genotyping strategies worldwide. A total number of 1,211 public H. pylori genomes were downloaded and used to construct the typing tool, named HpTT (H. pylori Typing Tool). Combined with the metadata, we developed two levels of genomic typing, including a continent-scale and a country scale that nested in the continent scale. Results showed that Asia was the largest isolate source in our dataset, while isolates from Europe and Oceania were comparatively more widespread. More specifically, Switzerland and Australia are the main sources of widespread isolates in their corresponding continents. To integrate all the typing information and enable researchers to compare their dataset against the existing global database easily and rapidly, a user-friendly website (https://db.cngb.org/HPTT/) was developed with both genomic typing tools and visualization tools. To further confirm the validity of the website, ten newly assembled genomes were downloaded and tested precisely located on the branch as we expected. In summary, the H. pylori typing tool (HpTT) is a novel genomic epidemiological tool that can achieve high-resolution analysis of genomic typing and visualizing simultaneously, providing insights into the genetic population structure, evolution analysis, and epidemiological surveillance of H. pylori.
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影响因子：
1.9
作者：
Attila, Tan;Zeybel, Mujdat;Mungan, Zeynel
通讯作者：
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通讯作者：
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通讯作者：
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