The Genomics of Streptococcus pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13
Identifieur interne : 000351 ( Main/Exploration ); précédent : 000350; suivant : 000352The Genomics of Streptococcus pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13
Auteurs : Carmen L. Sheppard [Royaume-Uni] ; Natalie Groves [Royaume-Uni] ; Nicholas Andrews [Royaume-Uni] ; David J. Litt [Royaume-Uni] ; Norman K. Fry [Royaume-Uni] ; Jo Southern [Royaume-Uni] ; Elizabeth Miller [Royaume-Uni]Source :
- Genes [ 2073-4425 ] ; 2019.
Descripteurs français
- KwdFr :
- Adolescent, Adulte, Caractéristiques familiales, Enfant, Enfant d'âge préscolaire, Génome bactérien, Humains, Infections à pneumocoques (), Infections à pneumocoques (microbiologie), Infections à pneumocoques (transmission), Infections à pneumocoques (épidémiologie), Phylogénie, Porteur sain (microbiologie), Porteur sain (épidémiologie), Programmes de vaccination (), Royaume-Uni, Streptococcus pneumoniae (génétique), Streptococcus pneumoniae (immunologie), Streptococcus pneumoniae (isolement et purification), Sérogroupe, Vaccin antipneumococcique conjugué heptavalent (usage thérapeutique), Vaccins antipneumococciques (usage thérapeutique).
- MESH :
- génétique : Streptococcus pneumoniae.
- immunologie : Streptococcus pneumoniae.
- isolement et purification : Streptococcus pneumoniae.
- microbiologie : Infections à pneumocoques, Porteur sain.
- usage thérapeutique : Infections à pneumocoques, Vaccin antipneumococcique conjugué heptavalent, Vaccins antipneumococciques.
- épidémiologie : Infections à pneumocoques, Porteur sain.
- Adolescent, Adulte, Caractéristiques familiales, Enfant, Enfant d'âge préscolaire, Génome bactérien, Humains, Infections à pneumocoques, Phylogénie, Programmes de vaccination, Royaume-Uni, Sérogroupe.
- Wicri :
- geographic : Royaume-Uni.
English descriptors
- KwdEn :
- Adolescent, Adult, Carrier State (epidemiology), Carrier State (microbiology), Child, Child, Preschool, Family Characteristics, Genome, Bacterial, Heptavalent Pneumococcal Conjugate Vaccine (therapeutic use), Humans, Immunization Programs (statistics & numerical data), Phylogeny, Pneumococcal Infections (epidemiology), Pneumococcal Infections (microbiology), Pneumococcal Infections (prevention & control), Pneumococcal Infections (transmission), Pneumococcal Vaccines (therapeutic use), Serogroup, Streptococcus pneumoniae (genetics), Streptococcus pneumoniae (immunology), Streptococcus pneumoniae (isolation & purification), United Kingdom.
- MESH :
- chemical , therapeutic use : Heptavalent Pneumococcal Conjugate Vaccine, Pneumococcal Vaccines.
- geographic : United Kingdom.
- epidemiology : Carrier State, Pneumococcal Infections.
- genetics : Streptococcus pneumoniae.
- immunology : Streptococcus pneumoniae.
- isolation & purification : Streptococcus pneumoniae.
- microbiology : Carrier State, Pneumococcal Infections.
- prevention & control : Pneumococcal Infections.
- statistics & numerical data : Immunization Programs.
- transmission : Pneumococcal Infections.
- Adolescent, Adult, Child, Child, Preschool, Family Characteristics, Genome, Bacterial, Humans, Phylogeny, Serogroup.
Abstract
We used whole genome sequencing (WGS) analysis to investigate the population structure of 877
Url:
DOI: 10.3390/genes10090687
PubMed: 31500179
PubMed Central: 6771020
Affiliations:
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Le document en format XML
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adolescent</term>
<term>Adult</term>
<term>Carrier State (epidemiology)</term>
<term>Carrier State (microbiology)</term>
<term>Child</term>
<term>Child, Preschool</term>
<term>Family Characteristics</term>
<term>Genome, Bacterial</term>
<term>Heptavalent Pneumococcal Conjugate Vaccine (therapeutic use)</term>
<term>Humans</term>
<term>Immunization Programs (statistics & numerical data)</term>
<term>Phylogeny</term>
<term>Pneumococcal Infections (epidemiology)</term>
<term>Pneumococcal Infections (microbiology)</term>
<term>Pneumococcal Infections (prevention & control)</term>
<term>Pneumococcal Infections (transmission)</term>
<term>Pneumococcal Vaccines (therapeutic use)</term>
<term>Serogroup</term>
<term>Streptococcus pneumoniae (genetics)</term>
<term>Streptococcus pneumoniae (immunology)</term>
<term>Streptococcus pneumoniae (isolation & purification)</term>
<term>United Kingdom</term>
</keywords>
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<term>Adulte</term>
<term>Caractéristiques familiales</term>
<term>Enfant</term>
<term>Enfant d'âge préscolaire</term>
<term>Génome bactérien</term>
<term>Humains</term>
<term>Infections à pneumocoques ()</term>
<term>Infections à pneumocoques (microbiologie)</term>
<term>Infections à pneumocoques (transmission)</term>
<term>Infections à pneumocoques (épidémiologie)</term>
<term>Phylogénie</term>
<term>Porteur sain (microbiologie)</term>
<term>Porteur sain (épidémiologie)</term>
<term>Programmes de vaccination ()</term>
<term>Royaume-Uni</term>
<term>Streptococcus pneumoniae (génétique)</term>
<term>Streptococcus pneumoniae (immunologie)</term>
<term>Streptococcus pneumoniae (isolement et purification)</term>
<term>Sérogroupe</term>
<term>Vaccin antipneumococcique conjugué heptavalent (usage thérapeutique)</term>
<term>Vaccins antipneumococciques (usage thérapeutique)</term>
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<term>Pneumococcal Vaccines</term>
</keywords>
<keywords scheme="MESH" type="geographic" xml:lang="en"><term>United Kingdom</term>
</keywords>
<keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Carrier State</term>
<term>Pneumococcal Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Streptococcus pneumoniae</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Streptococcus pneumoniae</term>
</keywords>
<keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Streptococcus pneumoniae</term>
</keywords>
<keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Streptococcus pneumoniae</term>
</keywords>
<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Streptococcus pneumoniae</term>
</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Streptococcus pneumoniae</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Infections à pneumocoques</term>
<term>Porteur sain</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Carrier State</term>
<term>Pneumococcal Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="prevention & control" xml:lang="en"><term>Pneumococcal Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Immunization Programs</term>
</keywords>
<keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Pneumococcal Infections</term>
</keywords>
<keywords scheme="MESH" qualifier="usage thérapeutique" xml:lang="fr"><term>Infections à pneumocoques</term>
<term>Vaccin antipneumococcique conjugué heptavalent</term>
<term>Vaccins antipneumococciques</term>
</keywords>
<keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à pneumocoques</term>
<term>Porteur sain</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Adolescent</term>
<term>Adult</term>
<term>Child</term>
<term>Child, Preschool</term>
<term>Family Characteristics</term>
<term>Genome, Bacterial</term>
<term>Humans</term>
<term>Phylogeny</term>
<term>Serogroup</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Adolescent</term>
<term>Adulte</term>
<term>Caractéristiques familiales</term>
<term>Enfant</term>
<term>Enfant d'âge préscolaire</term>
<term>Génome bactérien</term>
<term>Humains</term>
<term>Infections à pneumocoques</term>
<term>Phylogénie</term>
<term>Programmes de vaccination</term>
<term>Royaume-Uni</term>
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<front><div type="abstract" xml:lang="en"><p>We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 <italic>Streptococcus pneumoniae</italic>
isolates from five carriage studies from 2002 (<italic>N</italic>
= 346), 2010 (<italic>N</italic>
= 127), 2013 (<italic>N</italic>
= 153), 2016 (<italic>N</italic>
= 187) and 2018 (<italic>N</italic>
= 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.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Miller, E" uniqKey="Miller E">E. Miller</name>
</author>
<author><name sortKey="Andrews, N J" uniqKey="Andrews N">N.J. Andrews</name>
</author>
<author><name sortKey="Waight, P A" uniqKey="Waight P">P.A. Waight</name>
</author>
<author><name sortKey="Slack, M P" uniqKey="Slack M">M.P. Slack</name>
</author>
<author><name sortKey="George, R C" uniqKey="George R">R.C. George</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hussain, M" uniqKey="Hussain M">M. Hussain</name>
</author>
<author><name sortKey="Melegaro, A" uniqKey="Melegaro A">A. Melegaro</name>
</author>
<author><name sortKey="Pebody, R G" uniqKey="Pebody R">R.G. Pebody</name>
</author>
<author><name sortKey="George, R" uniqKey="George R">R. George</name>
</author>
<author><name sortKey="Edmunds, W J" uniqKey="Edmunds W">W.J. Edmunds</name>
</author>
<author><name sortKey="Talukdar, R" uniqKey="Talukdar R">R. Talukdar</name>
</author>
<author><name sortKey="Martin, S A" uniqKey="Martin S">S.A. Martin</name>
</author>
<author><name sortKey="Efstratiou, A" uniqKey="Efstratiou A">A. Efstratiou</name>
</author>
<author><name sortKey="Miller, E" uniqKey="Miller E">E. Miller</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Flasche, S" uniqKey="Flasche S">S. Flasche</name>
</author>
<author><name sortKey="Van Hoek, A J" uniqKey="Van Hoek A">A.J. van Hoek</name>
</author>
<author><name sortKey="Sheasby, E" uniqKey="Sheasby E">E. Sheasby</name>
</author>
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<author><name sortKey="Gupta, S" uniqKey="Gupta S">S. Gupta</name>
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<affiliations><list><country><li>Royaume-Uni</li>
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<tree><country name="Royaume-Uni"><noRegion><name sortKey="Sheppard, Carmen L" sort="Sheppard, Carmen L" uniqKey="Sheppard C" first="Carmen L." last="Sheppard">Carmen L. Sheppard</name>
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<name sortKey="Andrews, Nicholas" sort="Andrews, Nicholas" uniqKey="Andrews N" first="Nicholas" last="Andrews">Nicholas Andrews</name>
<name sortKey="Fry, Norman K" sort="Fry, Norman K" uniqKey="Fry N" first="Norman K." last="Fry">Norman K. Fry</name>
<name sortKey="Fry, Norman K" sort="Fry, Norman K" uniqKey="Fry N" first="Norman K." last="Fry">Norman K. Fry</name>
<name sortKey="Groves, Natalie" sort="Groves, Natalie" uniqKey="Groves N" first="Natalie" last="Groves">Natalie Groves</name>
<name sortKey="Litt, David J" sort="Litt, David J" uniqKey="Litt D" first="David J." last="Litt">David J. Litt</name>
<name sortKey="Miller, Elizabeth" sort="Miller, Elizabeth" uniqKey="Miller E" first="Elizabeth" last="Miller">Elizabeth Miller</name>
<name sortKey="Southern, Jo" sort="Southern, Jo" uniqKey="Southern J" first="Jo" last="Southern">Jo Southern</name>
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