title: The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development.
abstract: The nasopharynx (NP) is a reservoir for microbes associated with acute respiratory infections (ARIs). Lung inflammation resulting from ARIs during infancy is linked to asthma development. We examined the NP microbiome during the critical first year of life in a prospective cohort of 234 children, capturing both the viral and bacterial communities and documenting all incidents of ARIs. Most infants were initially colonized with Staphylococcus or Corynebacterium before stable colonization with Alloiococcus or Moraxella. Transient incursions of Streptococcus, Moraxella, or Haemophilus marked virus-associated ARIs. Our data identify the NP microbiome as a determinant for infection spread to the lower airways, severity of accompanying inflammatory symptoms, and risk for future asthma development. Early asymptomatic colonization with Streptococcus was a strong asthma predictor, and antibiotic usage disrupted asymptomatic colonization patterns. In the absence of effective anti-viral therapies, targeting pathogenic bacteria within the NP microbiome could represent a prophylactic approach to asthma.
authors: Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
authors: Shu Mei
authors: SM
authors: Teo
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Danny
authors: D
authors: Mok
authors: Melbourne Translational Genomics Platform, Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia.
authors: Kym
authors: K
authors: Pham
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Merci
authors: M
authors: Kusel
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Michael
authors: M
authors: Serralha
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Niamh
authors: N
authors: Troy
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Barbara J
authors: BJ
authors: Holt
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Belinda J
authors: BJ
authors: Hales
authors: Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, VIC 3010, Australia.
authors: Michael L
authors: ML
authors: Walker
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia.
authors: Elysia
authors: E
authors: Hollams
authors: Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
authors: Yury A
authors: YA
authors: Bochkov
authors: Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
authors: Kristine
authors: K
authors: Grindle
authors: Airway Disease Infection Section and MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, National Heart and Lung Institute, Imperial College London, Norfolk Place, London W2 1PG, UK.
authors: Sebastian L
authors: SL
authors: Johnston
authors: Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
authors: James E
authors: JE
authors: Gern
authors: Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, QLD 4059, Australia.
authors: Peter D
authors: PD
authors: Sly
authors: Telethon Kids Institute, The University of Western Australia, West Perth, WA 6008, Australia; Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, QLD 4059, Australia.
authors: Patrick G
authors: PG
authors: Holt
authors: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: kholt@unimelb.edu.au.
authors: Kathryn E
authors: KE
authors: Holt
authors: Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: minouye@unimelb.edu.au.
authors: Michael
authors: M
authors: Inouye
mesh_terms: D001249:Asthma / Q000453:epidemiology*; D006801:Humans; D007223:Infant; D008137:Longitudinal Studies; D064307:Microbiota; D009305:Nasopharynx / Q000382:microbiology* / Q000821:virology*; D012141:Respiratory Tract Infections / Q000382:microbiology / Q000473:pathology* / Q000821:virology; D018570:Risk Assessment