Phylogenomics of NTHi during PCV13 Implementation

Between 2008/09 and 2012/13 the molecular epidemiology of non-typeable Haemophilus influenzae (NTHi) carriage in children <5 years of age was determined; a period that included pneumococcal conjugate vaccine (PCV) 13 introduction. Significantly increased carriage in post-PCV13 years was observed. NTHi were characterised into eleven discrete, temporally stable lineages, congruent with current knowledge regarding the clonality of NTHi such that the increase could not be linked to the expansion of a particular clone. However pre-PCV13, NTHi co-carried with vaccine serotype pneumococci. Moreover, lineage specific associations with S. pneumoniae were also observed in both periods.