The application value of metagenomic next-generation sequencing in children with invasive pneumococcal disease

BACKGROUND: A retrospective analysis was conducted to explore the sensitivity and specificity of metagenomic next-generation sequencing (mNGS) in blood, cerebrospinal fluid, and pleural effusion samples in children with invasive pneumococcal disease (IPD), and the impact of detection timing on prognosis and cost. METHODS: Children with IPD admitted to Hebei Children’s Hospital from 1 January 2017 to 1 March 2021 were allocated to 1 of 3 groups according to the clinical symptoms and lesions (Group 1: bacteremia; Group 2: meningitis; Group 3: pleurisy). Taking Alere BinaxNow(®) Streptococcus pneumoniae (S. pneumoniae) antigen detection and blood culture as the gold standard, receiver operating characteristic (ROC) was used to establish the diagnostic value of mNGS. RESULTS: A total of 96 cases were enrolled in the study, comprising Group 1 (n=65), Group 2 (n=17), and Group 3 (n=14). The positive rate of mNGS test was 62.5% (n=60), and the total coincidence rate was 75.0%. Delayed mNGS was found to have no significant effect on the 30-day survival rate; however, the species-specific read number (SSRN) of S. pneumoniae detected by mNGS in the early stage of the disease was higher, and it could significantly reduce the hospitalization days and costs (P<0.05). CONCLUSIONS: The sensitivity and specificity of mNGS are high in the identification of S. pneumoniae in blood, cerebrospinal fluid, and pleural effusion samples, and the SSRN of S. pneumoniae is related to the interval from onset to sample collection. Early mNGS detection has no significant effect on the 30-day survival rate among children with IPD, but it can reduce hospitalization costs and duration.