mStrain: strain-level identification of Yersinia pestis using metagenomic data
Xiuwei Qian1,2, Yarong Wu2, Xiujuan Zuo1,2
1School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
Motivation:
High-resolution target pathogen detection using metagenomic sequencing data represents a major challenge due to the low concentration of target pathogens in samples. We introduced mStrain, a novel Yesinia pestis strain/lineage-level identification tool that utilizes metagenomic data. mStrain successfully identified Y. pestis at the strain/lineage level by extracting sufficient information regarding single-nucleotide polymorphisms (SNPs), which can therefore be an effective tool for identification and source tracking of Y. pestis based on metagenomic data during a plague outbreak.
Definition:
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Strain-Level Identification:
Assigning the reads in the metagenomic sequencing data to an exactly known or most closely representative Y. pestis strain.
Lineage-Level Identification:
Assigning the reads in the metagenomic sequencing data to a specific lineage on the phylogenetic tree.
Canosnps:
The unique and typical SNPs present in all representative strains.
Ancestor/Derived State:
An SNP is defined as the ancestor state when consistent with the allele of Yersinia pseudotuberculosis strain IP32953; otherwise, the SNP is defined as the derived state.
Availability And Implementation:
The code for running mStrain, the test dataset, and instructions for running the code can be found at the following GitHub repository: https://github.com/xwqian1123/mStrain.
Insights
mStrain accurately identifies *Yersinia pestis* at the strain and lineage levels using metagenomic data. This tool aids in plague outbreak surveillance and source tracking by analyzing single-nucleotide polymorphisms (SNPs).
Area of Science:
- Genomics
- Bioinformatics
- Epidemiology
Background:
- Metagenomic sequencing is crucial for pathogen detection, but low pathogen concentration poses challenges.
- Accurate strain-level identification of pathogens like *Yersinia pestis* is vital for outbreak response.
Purpose of the Study:
- To introduce mStrain, a novel tool for high-resolution *Yersinia pestis* strain and lineage identification from metagenomic data.
- To demonstrate mStrain's capability in extracting single-nucleotide polymorphism (SNP) information for precise pathogen characterization.
Main Methods:
- mStrain utilizes metagenomic sequencing data to identify *Yersinia pestis* strains and lineages.
- The tool analyzes single-nucleotide polymorphisms (SNPs) to differentiate between strains and lineages.
- The study defines SNPs based on ancestral and derived states relative to *Yersinia pseudotuberculosis* IP32953.
Main Results:
- mStrain successfully identified *Y. pestis* at the strain and lineage levels.
- The tool effectively extracted sufficient SNP information from metagenomic data for accurate identification.
- mStrain demonstrated potential for effective identification and source tracking during plague outbreaks.
Conclusions:
- mStrain is an effective tool for *Yersinia pestis* strain/lineage identification using metagenomic data.
- The tool can aid in real-time surveillance and source tracking during plague outbreaks.
- Availability of mStrain's code and data facilitates its application and further development.
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