Nasopharyngeal Microbiome During Health and Illness in Early Life
Sunday, March 4, 2018
South Hall A2 (Convention Center)
Anna Lang, Kathryn E. Holt, Michael Inouye, Patrick G. Holt, Shu Mei Teo, Howard HF Tang, Louise M. Judd, Robert F. Lemanske, MD FAAAAI, Michael D. Evans, Daniel J. Jackson, MD FAAAAI, James E. Gern, MD FAAAAI

RATIONALE: There is increasing evidence that the airway microbiome influences the development of wheezing and childhood asthma. Here we characterize the composition of the human nasopharyngeal microbiome in the first two years of life during health and respiratory illness.

METHODS: Nasopharyngeal samples were collected from participants in Childhood Origins of ASThma, a prospective birth cohort study in Madison, Wisconsin, yielding 1616 samples from 259 children during periods of health (at 2, 4, 6, 9, 12, 18 and 24 months of age) and 1423 samples during respiratory illness from birth to 36 months. Samples were analyzed for bacterial microbiome composition using 16S rRNA gene deep sequencing, and for common respiratory viruses.

RESULTS: 91% of samples clustered into 11 microbiome profile groups (MPGs), each dominated by one of six genera: Haemophilus, Streptococcus, Moraxella, Staphylococcus, Corynebacterium and Alloiococcus. Periods of respiratory illness were significantly positively associated with MPGs dominated by Haemophilus (OR 3.9, p=8.4x10-16), Streptococcus (OR 3.8, p=8.9x10-18), or Moraxella (OR 2.1, p=3.4x10-12), and negatively associated with MPGs dominated by Staphylococcus (OR 0.22, p=2.5x10-4), Corynebacterium (OR 0.49, p=3.8x10-9) or Alloiococcus (OR 0.25, p=3.7x10-17). These effects remained when adjusting for presence of virus.

CONCLUSIONS: 11 MPG dominated early life nasopharyngeal microbiomes, and their frequencies differed between state of health and illness. These MPGs and associations with illness were remarkably similar to those observed in the Childhood Asthma Study (Perth, Australia), demonstrating prototypical, robust patterns of nasopharyngeal MPG composition during early childhood that are reproducibly associated with respiratory illnesses, independent of viral co-occurrence, in two distinct global hemispheres.