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. 2025 May 8;25(1):675.
doi: 10.1186/s12879-025-11051-w.

Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory infection

Chunhong Li #  1 , Xinghong Zhang #  2 , Panyan Liu  1 , Manping Lu  2 , Lin Xiao  2 , Fengyu Ou  2 , Hailan Deng  2 , Wenjian Zhang  2 , Zhenfeng Deng  3 , Shengqiang Luo  4
Affiliations

Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory infection

Chunhong Li et al. BMC Infect Dis. .

Abstract

Background: Acute respiratory infections (ARIs) pose a significant global health burden, particularly affecting infants and young children with high morbidity and mortality rates. Targeted next-generation sequencing (tNGS) has emerged as a rapid and cost-effective diagnostic tool capable of identifying a broad range of respiratory tract infections.

Methods: Oropharyngeal swabs and sputum samples were collected from patients and subjected to tNGS and sputum culture, respectively, for diagnosing ARIs. A retrospective analysis was conducted on clinical data to explore the clinical diagnosis and therapeutic application of tNGS.

Results: This study included 336 pediatric patients with confirmed ARIs. tNGS detected 38 potential pathogens, comprising 25 species (15 bacteria and 10 viruses) and 13 viral subtypes. The overall microbial detection rate using tNGS was 100%. The leading bacterial pathogens identified were Streptococcus pneumoniae (36.0%), Stenotrophomonas maltophilia (30.4%), Streptococcus intermedius (29.5%), Moraxella catarrhalis (27.1%), and Hemophilus influenzae (20.2%). The predominant viral pathogens included human adenovirus (31.3%), human rhinovirus (26.5%), human parainfluenza virus (25.0%), cytomegalovirus (19.0%), and human bocavirus (11.0%). Among the 94 patients who underwent simultaneous sputum culture and Gram staining, tNGS exhibited a superior detection rate compared to sputum culture (100% vs. 53.2%). Among the 50 patients with concordant positive results for both tNGS and sputum culture, 80% (40/50) demonstrated full or partial agreement. Additionally, tNGS revealed age-specific heterogeneity in pathogen distribution across different age groups.

Conclusion: Traditional diagnostic methods often fall short of meeting the diagnostic demands of ARIs. This study underscores the potential of tNGS in oropharyngeal swabs for enhancing pathogen detection, thereby improving the diagnosis, treatment, and prevention of ARIs.

Importance: This study represents the first investigation utilizing oropharyngeal swabs for tNGS in diagnosing and treating ARIs. By analyzing surveillance data from a local hospital's patients with ARIs, we have identified the spectrum of bacterial and viral pathogens and explored demographic differences among patients. These findings underscore the potential of tNGS in ARI surveillance, diagnosis, pathogen detection, and prevention.

Keywords: Acute respiratory infections; Diagnosis; Pathogen spectrum; Pharyngeal swabs; Targeted next-generation sequencing.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: This study was approved by the Ethics Committee of Binyang Women and Children’s Hospital and was conducted in accordance with the Declaration of Helsinki. Written informed consent was obtained from all patients’ parents or their legal representatives. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests. Conflict of interest: The authors have no competing interests to declare. Clinical trial number: Not applicable.

Figures

Fig. 1
Fig. 1
Flow diagram of the study
Fig. 2
Fig. 2
Distribution of potential pathogens in the study cohort and heterogeneity of the pathogen spectrum among different age groups of children
Fig. 3
Fig. 3
Distribution of genotyped viruses in the study cohort
Fig. 4
Fig. 4
Distribution of potential pathogens in the study cohort of 94 patients and the respective contributions of tNGS and sputum culture for pathogen detection. tNGS, targeted next generation sequencing
See this image and copyright information in PMC

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