Abstract
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 (http://halst.nhri.org.tw/PathoBacTyper/), 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 Salmonella Heidelberg isolates from three outbreaks with the same pulsed-field gel electrophoresis pattern, 34 Salmonella Typhimurium isolates from six outbreaks, 103 isolates of hospital-associated vancomycin-resistant Enterococcus faecium and 15 Legionella pneumophila 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.
Highlights
The genomic DNA of organisms carries genetic information that is biologically functional
We demonstrated the operation of PathoBacTyper by identifying and genotyping four data sets, such as 59 Salmonella Heidelberg whole-genome sequencing (WGS) raw reads from three outbreaks previously sequenced by Bekal et al (2016), 34 Salmonella Typhimurium isolates (Leekitcharoenphon et al, 2014), 103 isolates of hospitalassociated vancomycin-resistant Enterococcus faecium (De Been et al, 2015) and 15 Legionella pneumophila isolates from clinical and environmental samples in Israel (Moran-Gilad et al, 2015)
In species identification, useruploaded WGS reads are distributed to a prebuilt reference data set comprising 478 pathogenic bacterial genomes; possible species can be identified according to the quantity of the mapped reads
Summary
The genomic DNA of organisms carries genetic information that is biologically functional. The NGS platform typically generates millions of short sequences, and the analysis of such a large number of short WGS sequences to generate the required information, such as the genotype and resistance to different strains, is a challenge. Because most researchers in clinical and public health laboratories lack expertise in bioinformatics, developing a simple and easy-to-use analytical platform for automating the analysis of WGS primitive sequence fragments and for performing genotypic comparison of different strains in the laboratory is necessary
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