Introduction: qPCR can be useful for the detection and absolute quantification of target genes, whilst 16S rRNA MiSeq sequencing (NGS) provides data on the relative abundance of taxa within a community. Here we compare total, P. aeruginosa (PA) and H. influenzae (HI) bacterial density with ecological metrics obtained by NGS.

 Methods: Sputum samples (n=219) collected in the iBEST study at Days 1, 8 and Day 29 from patients receiving tobramycin inhalation powder (TIP; n=54) and placebo (n=19) were analysed by qPCR and NGS. The relationship between ecological metrics and total bacterial (16S rRNA), PA (oprL and ecfX) and HI (hpD and smpB) density was compared.

Results: There was a significant reduction in total bacterial density between Day 1 and 29 in the TIP group (p< 0.001), with no difference in the placebo group (p=0.980). A significant decrease in PA density with TIP treatment was also apparent for both qPCR targets (oprL: p<0.001; ecfX: p<0.001), with no difference for the placebo group (p=0.740 and p=0.970, respectively). There was a significant negative correlation between Shannon-Wiener diversity and oprL and ecfX gene copy number (r=-0.427; p<0.001 and r=0.406; p<0.001), with a positive association between dominance and PA copy number (r=0.440; p<0.001 and r=0.430; p<0.001, respectively). No decrease in density or association with ecological markers was apparent in either treatment arm (p>0.05) for HI.

 Conclusion: Higher density of pathogens, such as PA, was associated with lower community diversity and higher dominance, highlighting that qPCR may be a useful end-point in clinical studies.

Supported by EU/EFPIA IMI iABC grant n° 115721