(483) Describing the Oropharyngeal Microbiome in Pediatric Patients with Cystic Fibrosis Transmembrane Regulator Related Metabolic Syndrome.

Background: The future health of patients with CFTR Related Metabolic Syndrome (CRMS) is unclear due to lack of clinical characteristics and long-term data. We hypothesized that microbiome characteristics of CRMS patients might reveal similarities or differences compared with healthy controls and patients with cystic fibrosis (CF).

Methods: UCSF patients with a diagnosis of CRMS were enrolled. Concurrent with annual oropharyngeal (OP) swabs for microbiologic surveillance, a 2^nd OP swab was obtained for research purposes. Biospecimens underwent mechanical homogenization, RNA extraction, and metagenomic next generation sequencing (mNGS) library preparation followed by taxonomic alignment using the CZID pipeline. Taxonomic counts were used to assess microbiome composition and were compared to patient characteristics.

Results: Our study included 17 subjects with 1^st time OP specimens. The cohort had a median age of 3.79 years (5 weeks-13 years old), was 47% female (n=8), and 29% Hispanic (n=5). Racial composition was 41% white (n=7), 29% other (n=5), 18% unknown/not reported (n=3), and 12% Black or African American (n=2). Immunoreactive Trypsinogen on newborn screen (NBS) ranged from 67.48-174.21 ng/mL and sweat test results ranged from < 10-43 mmol/L. Weight for length and Body Mass Index (BMI) ranged from 4.03 to >99.99^th percentile. Pathogenic CFTR mutations were present in 88% (n=15) of subjects, with 59% (n=10) having the F508del mutation specifically. Using conventional respiratory culture optimized for CF pathogens, the majority of OP swabs demonstrated both normal respiratory flora (n=15, 88%) and methicillin sensitive Staphylococcus aureus (n=14, 82%), with additional results including K. variicola (n=1, 6%), S. marcescens (n=1, 6%), coliform (n=1, 6%), Group A Streptococcus (n=1, 6%), Yeast (n=1, 6%), beta-hemolytic streptococcus (n=1, 6%), Citrobacter koserii (n=1, 6%), H. parainfluenzae (n=1, 6%), and H. parahaemolyticus (n=1, 6%). Using mNGS, microbiome composition was strongly concordant with high biomass of normal oropharyngeal flora observed in healthy children, including Haemophilus, Streptococcus, Neisseria, and oral anaerobes. The overall level of microbiome alpha-diversity was high (median Simpson 0.77, Interquartile Range (IQR) 0.71-0.88, median Shannon 1.93, IQR 1.76-2.61) with relatively low percent dominance by the most abundance species in each sample (15.7%, IQR 13.0-21.1%). Most samples showed high biosimilarity in microbiome composition (median pair-wise Bray dissimilarity index 0.97, IQR 0.91-0.99). One sample showed moderate dysbiosis with Streptococcus pneumoniae dominance (51.6% of microbiome). The potentially virulent CF pathogens Staphylococcus, Pseudomonas, and Burkholderia occupied < 1% of each patient's oropharyngeal microbiome.

Conclusions: In this study of the oropharyngeal microbiome of 17 patients with CRMS, a high degree of microbial richness and diversity and a paucity of CF-typical pathogens was observed, consistent with maintenance of healthy OP microbiomes. Clinical CF-specific OP culture may overestimate the significance of OP Staphylococcus in patients without active respiratory disease. This may help guide routine care and management for patients with CRMS. Additional studies that follow longitudinal changes in CRMS microbiomes may be useful to predict conversion to a CF phenotype.

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