BackgroundThe analysis of microbiome in respiratory samples is a topic of great interest in chronic respiratory diseases. The method used to prepare sputum samples for microbiome analysis is very heterogeneous. The selection of the most suitable methodology for DNA extraction is fundamental to have the most representative data. The objective of this study was to compare different conditions for DNA extraction from sputum in adult patients with bronchiectasis.MethodsFive sputum samples from bronchiectasis patients were collected at the Policlinico Hospital in Milan, Italy. Eighteen conditions for DNA extraction were compared, including two enzyme-based (Roche and Zymo) and one beads-based (Mobio) technique. These techniques were tested with/without Dithiothreitol (DTT) and with/without lysostaphin (0.18 and 0.36 mg/mL) step. DNA was quantified, tested using Real-time PCR for 16S rDNA and S. aureus and, then, microbiome was evaluated.ResultsAlthough 16S rDNA was similarly detected across all the different techniques, Roche kit gave the highest DNA yield. The lowest Ct values for Real-time PCR for S. aureus was identified when lysostaphin was added. Considering genera from microbiome, alpha diversity indices did not show any significant differences between techniques, while relative abundances were more similar in presence of DTT.ConclusionsNone of the conditions emerged to be superior to the others even if enzyme-based kits seem to be needed in order to have a higher extraction yield.Electronic supplementary materialThe online version of this article (10.1186/s40248-018-0166-z) contains supplementary material, which is available to authorized users.

Aims: To compare the contouring of organs at risk (OAR) between a clinical specialist radiation therapist (CSRT) and radiation oncologists (ROs) with different levels of expertise (senior-SRO, junior-JRO, fellow-FRO). Methods: On ten planning computed tomography (CT) image sets of patients undergoing breast radiotherapy (RT), the observers independently contoured the contralateral breast, heart, left anterior descending artery (LAD), oesophagus, kidney, liver, spinal cord, stomach and trachea. The CSRT was instructed by the JRO e SRO. The inter-observer variability of contoured volumes was measured using the Dice similarity coefficient (DSC) (threshold of ≥ 0.7 for good concordance) and the centre of mass distance (CMD). The analysis of variance (ANOVA) was performed and a p-value < 0.01 was considered statistically significant. Results: Good overlaps (DSC > 0.7) were obtained for all OARs, except for LAD (DSC = 0.34 ± 0.17, mean ± standard deviation) and oesophagus (DSC = 0.66 ± 0.06, mean ± SD). The mean CMD < 1 cm was achieved for all the OARs, but spinal cord (CMD = 1.22 cm). By pairing the observers, mean DSC > 0.7 and mean CMD < 1 cm were achieved in all cases. The best overlaps were seen for the pairs JRO-CSRT(DSC = 0.82; CMD = 0.49 cm) and SRO-JRO (DSC = 0.80; CMD = 0.51 cm). Conclusions: Overall, good concordance was found for all the observers. Despite the short training in contouring, CSRT obtained good concordance with his tutor (JRO). Great variability was seen in contouring the LAD, due to its difficult visualization and identification of CT scans without contrast.