Abstract
Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit) were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum) and one solid (Underarm deodorant), the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar), and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method.
Highlights
The Polymerase Chain Reaction (PCR) is commonly used to detect pathogens from various sample types [1,2]
As such samples are suspected of containing pathogens, initial processing of samples is often required to be conducted under Biological Safety Level 3 (BSL3) conditions or higher
All the methods produced extracts that resulted in positive PCR results when taken from the 10% Bg/powder sample types
Summary
The Polymerase Chain Reaction (PCR) is commonly used to detect pathogens from various sample types [1,2]. Prior to performing PCR, DNA must be extracted efficiently from samples. In order to be used confidently, DNA extraction techniques must process different sample types (i.e. dry powders, liquids, solids, swabs) of potentially unknown composition. Talcum powder has been reported to be a common sample received by the US Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory [3]. As such samples are suspected of containing pathogens, initial processing of samples is often required to be conducted under Biological Safety Level 3 (BSL3) conditions or higher. BSL3 laboratory facilities are known to place ergonomic restrictions on operatives and general molecular biology practice [4], and it is important that any DNA extraction method is as easy to use with a low as possible logistic and operative burden
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