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Open AccessArticle

The Genomics of Streptococcus pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13

1
Vaccine Preventable Bacteria Section, Public Health England—National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK
2
Statistics, Modelling and Economics, Public Health England—National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK
3
Immunisation and Countermeasures, Public Health England—National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK
*
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 687; https://doi.org/10.3390/genes10090687
Received: 12 August 2019 / Revised: 20 August 2019 / Accepted: 27 August 2019 / Published: 6 September 2019
(This article belongs to the Special Issue Evolutionary Genetics of Streptococcus pneumoniae)
We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N = 346), 2010 (N = 127), 2013 (N = 153), 2016 (N = 187) and 2018 (N = 64) in UK households which covers the period pre-PCV7 to post-PCV13 implementation. The genomic lineages seen in the population were determined using multi-locus sequence typing (MLST) and PopPUNK (Population Partitioning Using Nucleotide K-mers) which was used for local and global comparisons. A Roary core genome alignment of all the carriage genomes was used to investigate phylogenetic relationships between the lineages. The results showed an influx of previously undetected sequence types after vaccination associated with non-vaccine serotypes. A small number of lineages persisted throughout, associated with both non-vaccine and vaccine types (such as ST199), or that could be an example of serotype switching from vaccine to non-vaccine types (ST177). Serotype 3 persisted throughout the study years, represented by ST180 and Global Pneumococcal Sequencing Cluster (GPSC) 12; the local PopPUNK analysis and core genome maximum likelihood phylogeny separated them into two clades, one of which is only seen in later study years. The genomic data showed that serotype replacement in the carriage studies was mostly due to a change in genotype as well as serotype, but that some important genetic lineages, previously associated with vaccine types, persisted. View Full-Text
Keywords: Streptococcus pneumoniae; population; genomics; carriage; epidemiology Streptococcus pneumoniae; population; genomics; carriage; epidemiology
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Sheppard, C.L.; Groves, N.; Andrews, N.; Litt, D.J.; Fry, N.K.; Southern, J.; Miller, E. The Genomics of Streptococcus pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13. Genes 2019, 10, 687.

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