Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data

PeerJ
Robert A Petit IiiTimothy D Read

Abstract

It is possible to detect bacterial species in shotgun metagenome datasets through the presence of only a few sequence reads. However, false positive results can arise, as was the case in the initial findings of a recent New York City subway metagenome project. False positives are especially likely when two closely related are present in the same sample. Bacillus anthracis, the etiologic agent of anthrax, is a high-consequence pathogen that shares >99% average nucleotide identity with Bacillus cereus group (BCerG) genomes. Our goal was to create an analysis tool that used k-mers to detect B. anthracis, incorporating information about the coverage of BCerG in the metagenome sample. Using public complete genome sequence datasets, we identified a set of 31-mer signatures that differentiated B. anthracis from other members of the B. cereus group (BCerG), and another set which differentiated BCerG genomes (including B. anthracis) from other Bacillus strains. We also created a set of 31-mers for detecting the lethal factor gene, the key genetic diagnostic of the presence of anthrax-causing bacteria. We created synthetic sequence datasets based on existing genomes to test the accuracy of a k-mer based detection model. We found 239,503 ...Continue Reading

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Citations

Feb 7, 2020·International Journal of Molecular Sciences·Valery V PanyukovOlga N Ozoline
Nov 15, 2018··S.S. KiselevV.V. Panyukov

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Datasets Mentioned

BETA
SRR1748708

Methods Mentioned

BETA
Illumina sequencing
whole genome shotgun sequencing
PCR

Software Mentioned

samtools
FASTX Toolkit
fastq
DB
Mashtree
ART
BWA
BEDTools
Kraken
Jellyfish

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