2628. Nasopharyngeal Microbiome in the First Weeks of Life Distinguishes Infants Who Subsequently Develop Lower Respiratory Tract Infections

Background Colonization of the nasopharynx (NP) is the initial event in the pathogenesis of lower respiratory tract infections (LRTI). Evidence is accumulating that the NP microbiome influences host immune responses and whether colonization progresses to disease or not. We hypothesized that infants who experience LRTI early in life display distinct NP microbiome characteristics prior to infection, and potentially as early as the newborn period. Methods As part of the “Southern Africa Mother Infant Pertussis Study” in Zambia, NP samples were prospectively collected approximately every 2 weeks beginning at birth, through 3 months of age, in conjunction with clinical data. Samples were also collected when an infant experienced respiratory symptoms. We identified infants from the cohort with LRTI and matched with asymptomatic controls. We performed 16S ribosomal DNA amplicon sequencing on DNA extracted from the NP samples using Illumina MiSeq, and analyzed the data using Qiime2 and PathoScope2. We described the NP microbiome characteristics of asymptomatic infants and infants with LRTI and their changes over time and compared between the two populations at each 2-week interval using the R package DESeq2. Results Ten infants who had LRTI during the study period were matched with 17 healthy asymptomatic controls, together contributing 183 samples with high-quality reads. In asymptomatic infants, Dolosigranulum, Haemophilus and Moraxella’s relative abundance increased over the first 3 months of life, while Corynebacterium and Staphylococcus relative abundance decreased in the NP microbiome (Figure 1). In contrast, infants who developed LRTI had increased abundance of Staphylococcus, Anaerobacillus, and Bacillus, and decreased relative abundance of Dolosigranulum and Moraxella compared with asymptomatic controls (Figure 2). These differences were already present at the time of first sample collection (age 1 week). Conclusion Infants who develop LRTI early in life demonstrate altered NP microbial composition as early as the first week of life. These differences could potentially lead to early identification of at-risk infants. If confirmed, interventions to prevent LRTI in infancy could be evaluated to reduce respiratory mortality and morbidity. Disclosures All authors: No reported disclosures.