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Published on: November 28, 2016
Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory
Chunhong Li1, Xinghong Zhang2, Panyan Liu1
1Infection Diagnosis Center, Guangxi KingMed Diagnostics, Nanning, People's Republic of China.
Insights
Targeted next-generation sequencing (tNGS) of oropharyngeal swabs offers a comprehensive diagnostic approach for acute respiratory infections (ARIs) in children. This method significantly improves pathogen detection compared to traditional techniques, aiding in better treatment and prevention strategies.
Area of Science:
- Pediatric Infectious Diseases
- Microbiology
- Genomics
Background:
- Acute respiratory infections (ARIs) represent a major global health challenge, particularly for infants and young children, associated with high rates of illness and death.
- Targeted next-generation sequencing (tNGS) is an emerging, rapid, and cost-effective diagnostic tool for identifying a wide array of respiratory pathogens.
Purpose of the Study:
- This study is the first to use oropharyngeal swabs with tNGS for diagnosing and treating ARIs in pediatric patients.
- To identify the spectrum of bacterial and viral pathogens causing ARIs and analyze demographic variations.
- To evaluate the clinical utility of tNGS in ARI diagnosis and treatment.
Main Methods:
- Oropharyngeal swabs and sputum samples were collected from 336 pediatric patients diagnosed with ARIs.
- Samples were analyzed using tNGS and, in parallel, sputum culture for pathogen identification.
- Retrospective analysis of clinical data was performed to assess the diagnostic and therapeutic applications of tNGS.
Main Results:
- tNGS identified 38 potential pathogens (15 bacteria, 10 viruses, 13 viral subtypes) with a 100% detection rate.
- Leading pathogens included Streptococcus pneumoniae, Stenotrophomonas maltophilia, and human adenovirus.
- tNGS demonstrated a significantly higher detection rate (100%) compared to sputum culture (53.2%) and revealed age-specific pathogen distribution.
Conclusions:
- tNGS using oropharyngeal swabs significantly enhances pathogen detection for ARIs compared to conventional methods.
- The findings support the potential of tNGS for improved diagnosis, targeted treatment, and effective prevention of ARIs.
- tNGS offers a valuable tool for ARI surveillance and clinical management.
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.
