title: Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers.
abstract: OBJECTIVE
  Pneumococcal conjugate vaccines reduce the prevalence of vaccine serotypes carried in the nasopharynx. Because this could alter carriage of other potential pathogens, we assessed the nasopharyngeal microbiome of children who had been vaccinated with 10-valent pneumococcal non-typeable Haemophilus influenzae protein-D conjugate vaccine (PHiD-CV).
  
  
  METHODS
  Profiles of the nasopharyngeal microbiota of 60 children aged 12-59 months, who had been randomized to receive 2 doses of PHiD-CV (n=30) or Hepatitis A vaccine (n=30) 60 days apart, were constructed by 16S rRNA gene pyrosequencing of swab specimens collected before vaccination and 180 days after dose 1.
  
  
  RESULTS
  Prior to vaccination, Moraxella catarrhalis (median of 12.3% of sequences/subject), Streptococcus pneumoniae (4.4%) and Corynebacterium spp. (5.6%) were the most abundant nasopharyngeal bacterial species. Vaccination with PHiD-CV did not significantly alter the species composition, abundance, or prevalence of known pathogens. Distinct microbiomes were identified based on the abundances of Streptococcus, Moraxella, and Haemophilus species. These microbiomes shifted in composition over the study period and were independent of age, sex, school attendance, antibiotic exposure, and vaccination.
  
  
  CONCLUSIONS
  Vaccination of children with two doses of PHiD-CV did not significantly alter the nasopharyngeal microbiome. This suggests limited replacement carriage with pathogens other than non-vaccine strains of S. pneumoniae.
  
  
  BACKGROUND
  clinicaltrials.gov NCT01028326.
authors.affiliation: Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Leah M
authors.initials: LM
authors.lastname: Feazel
authors.affiliation: Dept. of Mathematical & Statistical Sciences, University of Colorado Denver, Aurora, CO, United States of America.
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Santorico
authors.affiliation: Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, CO, United States of America.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Robertson
authors.affiliation: KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya.
authors.forename: Mahfudh
authors.initials: M
authors.lastname: Bashraheil
authors.affiliation: KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya; Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; London School of Tropical Medicine and Hygiene, London, United Kingdom.
authors.forename: J Anthony G
authors.initials: JA
authors.lastname: Scott
authors.affiliation: Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, United States of America; University of Colorado Microbiome Research Consortium (MiRC), Aurora, CO, United States of America.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Frank
authors.affiliation: KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America.
authors.forename: Laura L
authors.initials: LL
authors.lastname: Hammitt
mesh_terms: D002675:Child, Preschool; D003352:Corynebacterium / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D006801:Humans; D007223:Infant; D007630:Kenya; D008297:Male; D064307:Microbiota / Q000235:genetics; D001936:Moraxella catarrhalis / Q000235:genetics / Q000302:isolation & purification; D009305:Nasopharynx / Q000382:microbiology*; D022242:Pneumococcal Vaccines / Q000276:immunology*; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D017422:Sequence Analysis, DNA; D013296:Streptococcus pneumoniae / Q000235:genetics / Q000302:isolation & purification; D014611:Vaccination; D018074:Vaccines, Conjugate / Q000276:immunology*
chemical_list: C547294:PHiD-CV vaccine; D022242:Pneumococcal Vaccines; D012336:RNA, Ribosomal, 16S; D018074:Vaccines, Conjugate