Targeted sequencing maps pediatric airway organisms during China’s policy transition

Targeted next-generation sequencing of throat swabs detected at least one organism in 98.00% of 2,049 samples from children with respiratory tract infection treated at Changzhou Children’s Hospital in China between August 2022 and March 2024. The most frequently identified organisms were Haemophilus influenzae, Streptococcus pneumoniae and Mycoplasma pneumoniae. Among the 2,008 samples in which at least one organism was detected, 1,646, or 81.97%, contained two or more organisms; the reported 95% confidence interval was 80.23% to 83.59%. The study characterized the organisms found in children’s upper airways during a period that included the abrupt relaxation of China’s COVID-19 prevention policies in December 2022, but it did not establish that a detected organism caused the illness.

The investigators conducted a retrospective, single-centre descriptive study using a targeted next-generation sequencing assay that could simultaneously test for 107 organisms. The samples came from pediatric respiratory tract infection patients at Changzhou Children’s Hospital. Investigators stratified the study population into five age groups: under 1 year, 1 to under 3 years, 3 to under 7 years, 7 to under 13 years and 13 to under 18 years. They also divided observations into spring, defined as March through May; summer, June through August; autumn, September through November; and winter, December through February. Positive proportions were reported with 95% confidence intervals, while group comparisons used chi-square or Fisher’s exact tests followed by pairwise proportion tests with a Bonferroni correction. This observational design described detection profiles rather than evaluating whether a particular organism or combination of organisms caused symptoms, disease severity or any clinical outcome.

Of the 2,049 samples tested, 2,008 were positive and 41 were negative. Overall positivity and the organism-detection profiles varied across the age and season strata. These differences show that the organisms detected in throat swabs were not distributed uniformly among the pediatric age groups or across the calendar year. However, the study’s single-centre and retrospective design limits how broadly the results can be generalized to children receiving care at other hospitals or in other regions. The analysis also concerns organism detection rather than the proportion of positive results representing active infection, and the supplied findings do not show whether organisms detected in the upper airway were responsible for the patients’ respiratory symptoms.

Viral patterns were among the notable observations. Respiratory syncytial virus detection patterns changed during the study period, while rhinovirus and Streptococcus pneumoniae continued to be detected during strict prevention measures. During the three months after the December 2022 relaxation of those measures, positivity rates increased for all of the most frequently detected organisms except Mycoplasma pneumoniae. These were temporal associations within the study sample rather than evidence that policy changes directly produced the shifts in detection. The investigators noted that the spectrum of organisms in the airway may vary with epidemic-prevention policies and the epidemic cycles of individual organisms, but the descriptive data do not separate the effects of those factors. No intervention or clinical outcome comparison was conducted, and the findings therefore do not establish the clinical benefit of targeted sequencing or support conclusions about treatment effectiveness. Overall, the study documents frequent organism detection, extensive co-detection and age- and season-related variation in pediatric respiratory tract infection during China’s transition away from strict pandemic prevention policies.

Subject of Research: Upper-airway organism detection in children with respiratory tract infection

Article Title: 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

Article References: Mo, J., Yang, X., Li, J., Ni, T., Zhang, S., Yi, Y., & Zhang, W. (2026). 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. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14330-2

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14330-2

Keywords: pediatric respiratory infection, targeted next-generation sequencing, throat swabs, pathogen co-detection, respiratory syncytial virus, rhinovirus, Haemophilus influenzae, Streptococcus pneumoniae, Mycoplasma pneumoniae, Changzhou, Upper-airway, organism