P-680. Etiologic investigation by targeted next-generation sequencing for community-acquired pneumonia of unknown etiology in children

TL;DR

This study uses targeted next-generation sequencing to identify pathogens in children with pneumonia cases where no cause was previously found.

Contribution

The study introduces broad-panel targeted next-generation sequencing to detect previously undetected pathogens in pediatric community-acquired pneumonia of unknown etiology.

Findings

tNGS identified additional pathogens in 70.8% of CAP-UKN cases in children.

Streptococcus pneumoniae and Haemophilus influenzae were frequently detected in pediatric CAP-UKN cases.

Human betaherpesvirus was the most common viral pathogen detected in CAP-UKN cases.

Abstract

Despite advancements in diagnostics, many pediatric community-acquired pneumonia (CAP) cases lack identified pathogens. We aimed to characterize CAP of unknown etiology (CAP-UKN) in children by applying broad-panel targeted next-generation sequencing (tNGS).Fig. 1.Epidemiology of CAP with no pathogens detected in Korean children based on weekly discharge monitoringFig. 2.Age group distribution and CAP pathogen detection in children

Epidemiology of CAP with no pathogens detected in Korean children based on weekly discharge monitoring

Age group distribution and CAP pathogen detection in children

From September 2023 to November 2024, a prospective surveillance study was conducted across 26 hospitals in Korea. CAP-UKN was defined as cases with no detected pathogens or detection of only human rhinovirus (HRV), human bocavirus (HBoV), human coronavirus (HCoV), or common colonizers. Residual respiratory specimens were analyzed using 16S rRNA/internal transcribed spacer (ITS) sequencing and tNGS.Fig. 3.Comparative heat map of clinical characteristics based on etiologic pathogens identifiedTable 1.Viral and bacterial pathogens detected by mNGS in patients with CAP of unknown etiology

Comparative heat map of clinical characteristics based on etiologic pathogens identified

Viral and bacterial pathogens detected by mNGS in patients with CAP of unknown etiology

Among 605 pediatric CAP cases, 178 (29.4%) were classified as CAP-UKN, including 77 (12.7%) with no pathogen detected (CAP-NPD). CAP-NPD was more common in children aged 5–10 years (46.8%) and showed clinical features similar to Mycoplasma pneumoniae pneumonia, whereas HRV/HBoV/HCoV-positive cases were more frequent in children aged 1–4 years (57.4%) and resembled viral pneumonia. tNGS identified additional pathogens in 70.8% of CAP-UKN specimens (109/154 in children). Streptococcus pneumoniae was detected in 45.5%, Haemophilus influenzae in 29.9%, and Neisseria meningitidis in 26.0% of pediatric cases. Human betaherpesvirus was the most common viral pathogen (5.2%), followed by cytomegalovirus (4.5%) and SARS-CoV-2 (3.9%). By 16S/ITS sequencing, additional bacteria and/or fungi were detected in 23.8% of children and 56.7% of adults. Most were commensal flora such as H. influenzae, Moraxella catarrhalis, and Viridans streptococci. Compared to pediatric patients, adults showed higher detection rates of pyogenic bacteria (36.0% vs. 11.7%) and herpesviruses (61.3% vs. 36.4%) and experienced more severe outcomes, including ICU admissions (29.3% vs. 5.3%) and invasive ventilation (22.6% vs. 4.0%).

Pediatric CAP-UKN may involve undetected atypical pathogens or overlooked respiratory viruses, including herpesviruses. Broad-panel tNGS enhances pathogen detection, offering important insights into the complex and previously unrecognized etiologies of pediatric CAP.

All Authors: No reported disclosures

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