MersV1, PubMed, Curation, bibRecord, 000426

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

Identifieur interne : 000426 ( PubMed/Curation ); précédent : 000425; suivant : 000427

The 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.

RBID : pubmed:31500179

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 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.

DOI: 10.3390/genes10090687
PubMed: 31500179

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<term>Phylogeny</term>
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<front><div type="abstract" xml:lang="en">We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 <i>Streptococcus pneumoniae</i>
 isolates from five carriage studies from 2002 (<i>N</i>
 = 346), 2010 (<i>N</i>
 = 127), 2013 (<i>N</i>
 = 153), 2016 (<i>N</i>
 = 187) and 2018 (<i>N</i>
 = 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.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31500179</PMID>
<DateCompleted><Year>2020</Year>
<Month>01</Month>
<Day>16</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>01</Month>
<Day>16</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2073-4425</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>10</Volume>
<Issue>9</Issue>
<PubDate><Year>2019</Year>
<Month>09</Month>
<Day>06</Day>
</PubDate>
</JournalIssue>
<Title>Genes</Title>
<ISOAbbreviation>Genes (Basel)</ISOAbbreviation>
</Journal>
<ArticleTitle>The Genomics of <i>Streptococcus Pneumoniae</i>
 Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13.</ArticleTitle>
<ELocationID EIdType="pii" ValidYN="Y">E687</ELocationID>
<ELocationID EIdType="doi" ValidYN="Y">10.3390/genes10090687</ELocationID>
<Abstract><AbstractText>We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 <i>Streptococcus pneumoniae</i>
 isolates from five carriage studies from 2002 (<i>N</i>
 = 346), 2010 (<i>N</i>
 = 127), 2013 (<i>N</i>
 = 153), 2016 (<i>N</i>
 = 187) and 2018 (<i>N</i>
 = 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.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sheppard</LastName>
<ForeName>Carmen L</ForeName>
<Initials>CL</Initials>
<AffiliationInfo><Affiliation>Vaccine Preventable Bacteria Section, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK. carmen.sheppard@phe.gov.uk.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Groves</LastName>
<ForeName>Natalie</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Vaccine Preventable Bacteria Section, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Andrews</LastName>
<ForeName>Nicholas</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Statistics, Modelling and Economics, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Litt</LastName>
<ForeName>David J</ForeName>
<Initials>DJ</Initials>
<AffiliationInfo><Affiliation>Vaccine Preventable Bacteria Section, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Fry</LastName>
<ForeName>Norman K</ForeName>
<Initials>NK</Initials>
<AffiliationInfo><Affiliation>Vaccine Preventable Bacteria Section, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Immunisation and Countermeasures, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Southern</LastName>
<ForeName>Jo</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Immunisation and Countermeasures, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Miller</LastName>
<ForeName>Elizabeth</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>Immunisation and Countermeasures, Public Health England-National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>039/0031</GrantID>
<Acronym>DH_</Acronym>
<Agency>Department of Health</Agency>
<Country>United Kingdom</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2019</Year>
<Month>09</Month>
<Day>06</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>Switzerland</Country>
<MedlineTA>Genes (Basel)</MedlineTA>
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The Genomics of Streptococcus Pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13.

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

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