Clinical diagnostic value of throat swabs in pediatric acute lower respiratory tract infections using targeted next-generation sequencing

Abstract

Background: To evaluate the clinical utility of targeted next-generation sequencing (tNGS) for pathogen detection of pediatric acute lower respiratory tract infections (ALRTIs), with a particular focus on the use of throat swab samples. Methods: In this diagnostic accuracy study involving 132 children, throat swabs and bronchoalveolar lavage fluid (BALF) samples were collected and analyzed by tNGS, and the results were compared with those obtained from conventional diagnostic methods. The impact of prior antibiotic use on the detection rate of tNGS was evaluated, the consistency between throat swabs and BALF was assessed, and the economic cost and invasiveness of the sampling methods were examined. Results: This study enrolled 132 children, of whom 79 (60%) were boys and 53 (40%) were girls. Ninety-two (70%) of the patients had fever, and 128 (97%) had a cough. The detection rates of bacteria, viruses, and atypical pathogens in BALF samples by tNGS were 89.5% (n = 68), 98.2% (n = 108), and 77.8% (n = 63), respectively. Compared to traditional detection methods, tNGS showed significantly higher detection rates for bacteria and viruses (P < 0.001), but there was no statistically significant difference in the detection of atypical pathogens (P = 0.59). The use of antibiotics had no significant effect on bacterial detection by tNGS (P = 0.237). Using BALF-tNGS as the “gold standard,” the sensitivities of tNGS of throat swabs for detecting bacteria, viruses, and atypical pathogens were 95.83%, 88.16%, and 92.06%, respectively, with specificities of 55.95%, 83.93%, and 100%. In the analysis of economic costs and invasiveness, the cost of throat swab sampling was significantly lower than that of BALF sampling, and the associated pain score and complication rate were significantly lower (P < 0.05). Conclusions: tNGS with throat swabs offers higher sensitivity and specificity than traditional methods for diagnosing pediatric ALRTIs. As such, it offers a less invasive, more cost-effective alternative to BALF sampling.