A comparison of different pre-lysis methods and extraction kits for recovery of Stretococcus agalacticae (Lancefield group B Streptococcus) DNA from whole blood

Sub-optimal recovery of bacterial DNA from whole blood samples can limit the sensitivity of molecular assays to detect pathogenic bacteria. We compared 3 different pre-lysis protocols (none, mechanical pre-lysis and achromopeptidasepre-lysis) and 5 commercially available DNA extraction platforms for direct detection of Group B Streptococcus (GBS) in spiked whole blood samples, without enrichment culture. DNA was extracted using the QIAamp Blood Mini kit (Qiagen), UCP Pathogen Mini kit (Qiagen), QuickGene DNA Whole Blood kit S (Fuji), Speed Xtract Nucleic Acid Kit 200 (Qiagen) and MagNA Pure Compact Nucleic Acid Isolation Kit I (Roche Diagnostics Corp). Mechanical pre-lysis increased yields of bacterial genomic DNA by 51.3 fold (95% confidence interval; 31.6–85.1, p < 0.001) and pre-lysis with achromopeptidase by 6.1 fold (95% CI; 4.2–8.9, p < 0.001), compared with no pre-lysis. Differences in yield dueto pre-lysis were 2–3 fold larger than differences in yield between extraction methods. Including a pre-lysis step can improve the limits of detection of GBS using PCR or other molecular methods without need for culture.

TRIPPy: Trailed Image Photometry in Python

Photometry of moving sources typically suffers from a reduced signal-to-noise ratio (S/N) or flux measurements biased to incorrect low values through the use of circular apertures. To address this issue, we present the software package, TRIPPy: TRailed Image Photometry in Python. TRIPPy introduces the pill aperture, which is the natural extension of the circular aperture appropriate for linearly trailed sources. The pill shape is a rectangle with two semicircular end-caps and is described by three parameters, the trail length and angle, and the radius. The TRIPPy software package also includes a new technique to generate accurate model point-spread functions (PSFs) and trailed PSFs (TSFs) from stationary background sources in sidereally tracked images. The TSF is merely the convolution of the model PSF, which consists of a moffat profile, and super-sampled lookup table. From the TSF, accurate pill aperture corrections can be estimated as a function of pill radius with an accuracy of 10 mmag for highly trailed sources. Analogous to the use of small circular apertures and associated aperture corrections, small radius pill apertures can be used to preserve S/Ns of low flux sources, with appropriate aperture correction applied to provide an accurate, unbiased flux measurement at all S/Ns.