411 - Use of Plasma Microbial Next Generation Sequencing in Pediatric Patients with Complicated Community Acquired Pneumonia

Publication Number: 2399.411

Emma J. Ward, University of Alabama School of Medicine, Birmingham, AL, United States; Maria S. Rueda Altez, University of Alabama at Birmingham, Birmingham, AL, United States; Meghan E. Hofto, University of Alabama at Birmingham, Birmingham, AL, United States

Background: Community-acquired pneumonia (CAP) is the most common reason for a healthcare encounter for children under age two, with 15% of cases being complicated by empyema, lung abscess or parapneumonic effusion. Molecular diagnostics such as plasma microbial next generation sequencing (mNGS) are a promising non-invasive tool for diagnosis and antimicrobial stewardship but have not been well studied.

Objective: The purpose of this study is to determine the clinical utility of mNGS testing in hospitalized pediatric patients with complicated CAP (cCAP).

Design/Methods: This is a retrospective medical record review of children aged 3 months to 19 years hospitalized with cCAP from January 2020 to June 2025. Underlying conditions predisposing to more severe respiratory infections were excluded. Administrative data including age, sex, race/ethnicity, and length of stay were collected. Record review was performed for symptoms, microbiologic testing, antibiotic use, and illness severity.

Results: A total of 295 cases of cCAP were identified. 70 (24%) patients had mNGS testing; 67 (23%) were positive. Patients with mNGS testing had a significantly longer hospital stay (median 7d vs 3d, p< 0.1), higher white blood cell count (17.1 vs 11.8), more anemia (49% vs 27%) and higher C-reactive protein levels (23.4 vs 11.5). They also had higher rates of effusions (90% vs 58%), chest tube placement (33% vs 11%), more days of symptoms pre-admission (7d vs 5d), more empiric broad spectrum antibiotic use (87% vs 56%), and longer duration of antibiotics (28d vs 10d). Patients with mNGS testing were less likely to have any positive culture. The most commonly identified pathogens by mNGS were Streptococcus pneumoniae (56%), Fusobacterium necrophorum (13%), and Haemophilus influenzae (9%). Most mNGS tests (50/70, 71%) resulted during the hospital stay. When the mNGS resulted prior to discharge, an antibiotic change was more likely (64% vs 15%). Of the 32 patients with an antibiotic change, 29 would have been covered by amoxicillin-clavulanate. Seven patients received unnecessary broad spectrum antibiotics, despite mNGS results for typical pathogens.

Conclusion(s): Plasma mNGS testing in pediatric patients with cCAP provided valuable microbiologic data with uncertain utility. While mNGS led to antibiotic changes in some cases, it primarily served to confirm pathogens already covered by standard therapies. These findings suggest that while mNGS may have a role in antimicrobial stewardship, its clinical impact in this context may be limited. Further research is needed to evaluate its broader use.

mNGS identified pathogens in cCAP patients


Analysis of antibiotic changes made after mNGS Results in cCAP Patients