AUTHOR=Jiang Xiaosen , Xu Zheng , Zhang Tongda , Li Yuan , Li Wei , Tan Hongdong 

TITLE=Whole-Genome-Based Helicobacter pylori Geographic Surveillance: A Visualized and Expandable Webtool

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.687259

DOI=10.3389/fmicb.2021.687259

ISSN=1664-302X

ABSTRACT=<p><italic>Helicobacter pylori</italic> exhibit specific geographic distributions that are related to clinical outcomes. Despite the high infection rate of <italic>H. pylori</italic> throughout the world, the genetic epidemiology surveillance of <italic>H. pylori</italic> 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 <italic>H. pylori</italic> and encourage the dissemination of microbial genotyping strategies worldwide. A total number of 1,211 public <italic>H. pylori</italic> genomes were downloaded and used to construct the typing tool, named <italic>Hp</italic>TT (<italic>H. pylori</italic> 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 (<ext-link ext-link-type="uri" xlink:href="https://db.cngb.org/HPTT/" xmlns:xlink="http://www.w3.org/1999/xlink">https://db.cngb.org/HPTT/</ext-link>) 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 <italic>H. pylori</italic> typing tool (<italic>Hp</italic>TT) 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 <italic>H. pylori</italic>.</p>