Upper-airway organism detection profiles in children with respiratory tract infection assessed by targeted next-generation sequencing: a single-centre descriptive study in Changzhou, China, August 2022 to March 2024

Respiratory tract infection (RTI) is among the commonest reasons for children to seek medical care, and the spectrum of organisms detected in the airway may shift with epidemic-prevention policies and with the epidemic cycles of individual organisms. This study describes the profile of organisms detected in throat swabs from children presenting with RTI in Changzhou, China, between August 2022 and March 2024, a period that spans the abrupt relaxation of China’s COVID-19 prevention policies in December 2022. In this single-centre, retrospective, descriptive study, 2049 throat swab samples from pediatric respiratory tract infection patients of Changzhou Children’s Hospital from Aug 2022 to Mar 2024 were collected and detected by targeted next-generation sequencing technology that can simultaneously detect 107 organisms. Patients were stratified by age (< 1, 1 to < 3, 3 to < 7, 7 to < 13, and 13 to < 18 years) and by season (spring, March-May; summer, June-August; autumn, September-November; winter, December-February). Proportions are reported with 95% CIs; groups were compared using chi-square or Fisher’s exact tests followed by pairwise proportion tests with Bonferroni correction. Among 2049 RTI samples tested by targeted next-generation sequencing, the overall positivity rate was 98.00% (2008/2049). Haemophilus influenzae , Streptococcus pneumoniae and Mycoplasma pneumoniae were the most frequently identified organisms. Co-detection of two or more organisms occurred in 81.97% (1646/2008; 95% CI: 80.23%-83.59%) of samples with at least one organism detected. Age- and season-specific heterogeneity in the positivity rate was found. Notably, respiratory syncytial virus detection patterns changed during the study period. Rhinovirus and Streptococcus pneumoniae continued to be detected during strict prevention measures. Positivity rates of the most frequently detected organisms, except Mycoplasma pneumoniae , increased during the three months after relaxation. tNGS of throat swabs revealed frequent organism detection and co-detection, with marked age- and season-related variation, in children presenting with RTI during the post-pandemic transition. Not applicable.