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

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).

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.

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.

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.