AUTHOR=Tsai Ming-Hsin , Liu Yen-Yi , Soo Von-Wun 

TITLE=PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.01474

DOI=10.3389/fmicb.2017.01474

ISSN=1664-302X

ABSTRACT=<p>With the decline in the cost of whole-genome sequencing because of the introduction of next-generation sequencing (NGS) techniques, many public health and clinical laboratories have started to use bacterial whole genomes for epidemiological surveillance and clinical investigation. For epidemiological and clinical purposes in this “NGS era,” whole-genome-scale single nucleotide polymorphism (wgSNP) analysis for genotyping is considered suitable. In this paper, we present an online service, PathoBacTyper (<ext-link ext-link-type="uri" xlink:href="http://halst.nhri.org.tw/PathoBacTyper/" xmlns:xlink="http://www.w3.org/1999/xlink">http://halst.nhri.org.tw/PathoBacTyper/</ext-link>), for pathogenic bacteria identification and genotyping based on wgSNP analysis. More than 400 pathogenic bacteria can be identified and genotyped through this service. Four data sets containing 59 <italic>Salmonella</italic> Heidelberg isolates from three outbreaks with the same pulsed-field gel electrophoresis pattern, 34 <italic>Salmonella</italic> Typhimurium isolates from six outbreaks, 103 isolates of hospital-associated vancomycin-resistant <italic>Enterococcus faecium</italic> and 15 <italic>Legionella pneumophila</italic> isolates from clinical and environmental samples in Israel were used for demonstrating the operation and testing the performance of the PathoBacTyper service. The test results reveal the applicability of this service for epidemiological typing and clinical investigation.</p>