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oa Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae

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  • Authors: David Cleary1​,2​ ,  Vanessa Devine3​ ,  Denise Morris1​ ,  Karen Osman1​ ,  Rebecca Gladstone4​ ,  Stephen Bentley4​ ,  Saul Faust1​,5​ , Stuart Clarke1​,2​,6​,*
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    • 1​ 1​Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK 2​ 2​NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK 3​ 3​Northern Ireland Centre for Stratified Medicine and Clinical Translational Research Innovation Centre, Londonderry, UK 4​ 4​Pathogen Genomics, Wellcome Trust Sanger Institute, UK 5​ 5​NIHR Southampton Clinical Research Facility, University Hospital Southampton Foundation NHS Trust, Southampton, UK 6​ 6​Global Health Research Institute, University of Southampton, Southampton, UK
  • *Correspondence: Stuart Clarke [email protected]
  • First Published Online: 06 August 2018, Microbial Genomics , 2018 4, doi: 10.1099/mgen.0.000209
  • Subject: Research Article - Microbial Evolution and Epidemiology - Population Genomics
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  • The implementation of pneumococcal conjugate vaccines (PCVs) has led to a decline in vaccine-type disease. However, there is evidence that the epidemiology of non-typeable Haemophilus influenzae (NTHi) carriage and disease can be altered as a consequence of PCV introduction. We explored the epidemiological shifts in NTHi carriage using whole genome sequencing over a 5-year period that included PCV13 replacement of PCV7 in the UK’s National Immunization Programme in 2010. Between 2008/09 and 2012/13 (October to March), nasopharyngeal swabs were taken from children <5 years of age. Significantly increased carriage post-PCV13 was observed and lineage-specific associations with Streptococcus pneumoniae were seen before but not after PCV13 introduction. NTHi were characterized into 11 discrete, temporally stable lineages, congruent with current knowledge regarding the clonality of NTHi. The increased carriage could not be linked to the expansion of a particular clone and different co-carriage dynamics were seen before PCV13 implementation when NTHi co-carried with vaccine serotype pneumococci. In summary, PCV13 introduction has been shown to have an indirect effect on NTHi epidemiology and there exists both negative and positive, distinct associations between pneumococci and NTHi. This should be considered when evaluating the impacts of pneumococcal vaccine design and policy.

  • All supporting data, code and protocols have been provided within the article or through supplementary data files. One supplementary table, one supplementary figure and one supplementary data file are available with the online version of this article.

© 2018 The Authors | Published by the Microbiology Society

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