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  1. Article ; Online: A global genomic perspective on the multidrug-resistant

    Hawkins, Paulina A / Chochua, Sopio / Lo, Stephanie W / Belman, Sophie / Antonio, Martin / Kwambana-Adams, Brenda / von Gottberg, Anne / du Plessis, Mignon / Cornick, Jen / Beall, Bernard / Breiman, Robert F / Bentley, Stephen D / McGee, Lesley / The Global Pneumococcal Sequencing Consortium

    Microbial genomics

    2023  Volume 9, Issue 4

    Abstract: The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization ... ...

    Abstract The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization against
    MeSH term(s) Streptococcus pneumoniae ; Vaccines, Conjugate ; Phylogeny ; Penicillins/pharmacology ; Genomics
    Chemical Substances Vaccines, Conjugate ; Penicillins
    Language English
    Publishing date 2023-04-07
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000998
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.

    Epping, Lennard / van Tonder, Andries J / Gladstone, Rebecca A / The Global Pneumococcal Sequencing Consortium / Bentley, Stephen D / Page, Andrew J / Keane, Jacqueline A

    Microbial genomics

    2018  Volume 4, Issue 7

    Abstract: Streptococcus pneumoniae is responsible for 240 000-460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the ... ...

    Abstract Streptococcus pneumoniae is responsible for 240 000-460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98 % concordance using a k-mer-based method, can process 10 000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 15-21×. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 licence from: https://github.com/sanger-pathogens/seroba.
    MeSH term(s) Alleles ; Child, Preschool ; Databases, Genetic ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Pneumococcal Infections/microbiology ; Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; Serogroup ; Serotyping/methods ; Software ; Streptococcus mitis/genetics ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/genetics ; Streptococcus pneumoniae/isolation & purification ; Whole Genome Sequencing
    Language English
    Publishing date 2018-06-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000186
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: SeroBA

    Epping, Lennard / van Tonder, Andries J. / Gladstone, Rebecca A. / The Global Pneumococcal Sequencing Consortium / Bentley, Stephen D. / Page, Andrew J. / Keane, Jacqueline A.

    rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

    2018  

    Abstract: Streptococcus pneumoniae is responsible for 240 000–460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the ... ...

    Abstract Streptococcus pneumoniae is responsible for 240 000–460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98 % concordance using a k-mer-based method, can process 10 000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 15–21×. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 licence from: https://github.com/sanger-pathogens/seroba

    Peer Reviewed
    Keywords Streptococcus pneumoniae ; serotyping ; pneumococcal ; whole genome sequencing ; k-mer method ; 610 Medizin und Gesundheit ; ddc:610
    Language English
    Publishing date 2018-06-15
    Publisher Robert Koch-Institut
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  4. Article ; Online: A

    Ndlangisa, Kedibone M / du Plessis, Mignon / Lo, Stephanie / de Gouveia, Linda / Chaguza, Chrispin / Antonio, Martin / Kwambana-Adams, Brenda / Cornick, Jennifer / Everett, Dean B / Dagan, Ron / Hawkins, Paulina A / Beall, Bernard / Corso, Alejandra / Grassi Almeida, Samanta Cristine / Ochoa, Theresa J / Obaro, Stephen / Shakoor, Sadia / Donkor, Eric S / Gladstone, Rebecca A /
    Ho, Pak Leung / Paragi, Metka / Doiphode, Sanjay / Srifuengfung, Somporn / Ford, Rebecca / Moïsi, Jennifer / Saha, Samir K / Bigogo, Godfrey / Sigauque, Betuel / Eser, Özgen Köseoglu / Elmdaghri, Naima / Titov, Leonid / Turner, Paul / Kumar, K L Ravi / Kandasamy, Rama / Egorova, Ekaterina / Ip, Margaret / Breiman, Robert F / Klugman, Keith P / McGee, Lesley / Bentley, Stephen D / von Gottberg, Anne / The Global Pneumococcal Sequencing Consortium

    Microbial genomics

    2022  Volume 8, Issue 4

    Abstract: Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a ... ...

    Abstract Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005-2014 were characterized by whole-genome sequencing (WGS). Multi-locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005-2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre-PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non-vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.
    MeSH term(s) Humans ; Pneumococcal Infections/epidemiology ; Pneumococcal Infections/prevention & control ; Pneumococcal Vaccines ; Serogroup ; South Africa/epidemiology ; Streptococcus pneumoniae/genetics ; Vaccines, Conjugate
    Chemical Substances Pneumococcal Vaccines ; Vaccines, Conjugate
    Language English
    Publishing date 2022-05-22
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000746
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.

    Gladstone, Rebecca A / Lo, Stephanie W / Goater, Richard / Yeats, Corin / Taylor, Ben / Hadfield, James / Lees, John A / Croucher, Nicholas J / van Tonder, Andries J / Bentley, Leon J / Quah, Fu Xiang / Blaschke, Anne J / Pershing, Nicole L / Byington, Carrie L / Balaji, Veeraraghavan / Hryniewicz, Waleria / Sigauque, Betuel / Ravikumar, K L / Almeida, Samanta Cristine Grassi /
    Ochoa, Theresa J / Ho, Pak Leung / du Plessis, Mignon / Ndlangisa, Kedibone M / Cornick, Jennifer E / Kwambana-Adams, Brenda / Benisty, Rachel / Nzenze, Susan A / Madhi, Shabir A / Hawkins, Paulina A / Pollard, Andrew J / Everett, Dean B / Antonio, Martin / Dagan, Ron / Klugman, Keith P / von Gottberg, Anne / Metcalf, Benjamin J / Li, Yuan / Beall, Bernard W / McGee, Lesley / Breiman, Robert F / Aanensen, David M / Bentley, Stephen D / The Global Pneumococcal Sequencing Consortium

    Microbial genomics

    2020  Volume 6, Issue 5

    Abstract: Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase ... ...

    Abstract Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (
    MeSH term(s) DNA Transposable Elements ; Databases, Genetic ; Drug Resistance, Bacterial ; Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Phylogeography ; Poland ; Polysaccharides, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Serogroup ; South Africa ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/genetics ; Streptococcus pneumoniae/isolation & purification ; Utah
    Chemical Substances DNA Transposable Elements ; Polysaccharides, Bacterial
    Language English
    Publishing date 2020-04-29
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000357
    Database MEDical Literature Analysis and Retrieval System OnLINE

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