Evaluation of a stepwise approach using microbiota analysis, species-specific qPCRs and culture for the diagnosis of lower respiratory tract infections

In clinical practice, the diagnosis of lower respiratory tract infections (LRTIs) is based on culture. The aim of this study was to evaluate whether a stepwise approach using microbiota analysis, species-specific quantitative real-time (q)PCRs and culture has the potential to be a more accurate and efficient diagnostic approach than culture alone. Sixty-two sputa obtained in a routine clinical setting from patients with a suspected LRTI were included. All sputa were analysed by culture, microbiota analysis based on the 16S ribosomal RNA gene and multiple species-specific qPCRs. Microbiota and culture data were compared to investigate whether cut-off values for microbiota analysis could be determined. For microbiota analysis, a relative abundance of 25% was identified as the cut-off value for the detection of both genera Streptococcus and Haemophilus. Microbiota analysis combined with species-specific qPCRs resulted in a significant increase in the number of positive sputa (73% vs 58%; p = 0.003) as well as in the number of identified pathogens (51 vs 37; p = 0.049) compared to culture. A stepwise approach using microbiota analysis, species-specific qPCRs and culture has the potential to be used in clinical settings for the diagnosis of LRTIs in the near future.