Next Generation Sequencing of Tracheal Aspirates in Children With Tracheostomy A Prospective Case‐Control Study

Background Tracheostomies are increasingly performed in children. The treatment of infections in tracheostomized patients is challenging because of the distinction between chronic colonization and acute infection. Next‐generation sequencing (NGS) is a promising alternative for identifying and quantifying pathogens in a short period. This study investigated the utility of NGS of tracheal aspirates from healthy and tracheostomized children (TC). Methods This monocentric prospective case‐control study recruited children with long‐term TC and compared the colonization of the lower airways with a control group of children who had undergone elective general surgery. Tracheal aspirates were analyzed using three methods: bacterial culture, polymerase chain reaction (PCR), and NGS. Results In total, 107 children were recruited for this study. Sixty‐two samples were excluded due to acute exacerbation, lack of tracheal secretion, or insufficient cfDNA concentration (< 0.3 ng/µl). Consequently, 45 samples (17 controls and 28 tracheotomized samples) were analyzed. Tracheal aspirates analyzed using NGS revealed a significantly higher prevalence of Pseudomonas aeruginosa ( p = 0.0001), Staphylococcus aureus ( p = 0.002), Stenotrophomonas maltophilia ( p = 0.004), and Moraxella catarrhalis ( p = 0.03) in TC. Through NGS, we were able to demonstrate that Pseudomonas aeruginosa was the dominant bacterium in 44% of the samples in which it was detected. Conclusions NGS can effectively identify a wide spectrum of DNA‐based pathogens (bacteria, viruses, and fungi) in the tracheal aspirates of children. Tracheostomized children were significantly more likely to be colonized by difficult‐to‐treat bacteria. Future research is required to evaluate the clinical benefits of NGS compared with standard microbiological procedures.