Open AccessComparative analysis of the sensitivity of metagenomic sequencing and PCR to detect a biowarfare simulant (Bacillus atrophaeus) in soil samples
Author(s) -
Delphine Plaire,
Simon Puaud,
MarieClaude MarsolierKergoat,
JeanMarc Elalouf
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0177112
Subject(s) - metagenomics , bacillus anthracis , dna extraction , biology , dna sequencing , dna , soil test , polymerase chain reaction , soil microbiology , soil water , microbiology and biotechnology , genetics , bacteria , gene , ecology
To evaluate the sensitivity of high-throughput DNA sequencing for monitoring biowarfare agents in the environment, we analysed soil samples inoculated with different amounts of Bacillus atrophaeus , a surrogate organism for Bacillus anthracis . The soil samples considered were a poorly carbonated soil of the silty sand class, and a highly carbonated soil of the silt class. Control soil samples and soil samples inoculated with 10, 10 3 , or 10 5 cfu were processed for DNA extraction. About 1% of the DNA extracts was analysed through the sequencing of more than 10 8 reads. Similar amounts of extracts were also studied for Bacillus atrophaeus DNA content by real-time PCR. We demonstrate that, for both soils, high-throughput sequencing is at least equally sensitive than real-time PCR to detect Bacillus atrophaeus DNA. We conclude that metagenomics allows the detection of less than 10 ppm of DNA from a biowarfare simulant in complex environmental samples.