s pneumoniae serotypes  (ATCC)


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    ATCC s pneumoniae serotypes
    S Pneumoniae Serotypes, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    s pneumoniae  (ATCC)


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    ATCC s pneumoniae
    Enrichment of S. <t>pneumoniae</t> Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    S Pneumoniae, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s pneumoniae/product/ATCC
    Average 86 stars, based on 1 article reviews
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    s pneumoniae - by Bioz Stars, 2024-02
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    Images

    1) Product Images from "Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples"

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    Journal: bioRxiv

    doi: 10.1101/2024.02.11.579857

    Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL
    Figure Legend Snippet: Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Techniques Used: Selection

    Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Selection, Comparison

    Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.
    Figure Legend Snippet: Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Techniques Used:

    Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.
    Figure Legend Snippet: Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Techniques Used: Generated


    Figure Legend Snippet:

    Techniques Used:


    Figure Legend Snippet:

    Techniques Used:

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Comparison

    s pneumoniae 8140  (ATCC)


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    ATCC s pneumoniae 8140
    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA <t>(GPSC16,</t> serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    S Pneumoniae 8140, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s pneumoniae 8140/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    s pneumoniae 8140 - by Bioz Stars, 2024-02
    86/100 stars

    Images

    1) Product Images from "Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples"

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    Journal: bioRxiv

    doi: 10.1101/2024.02.11.579857

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    s pneumoniae r6  (ATCC)


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    ATCC s pneumoniae r6
    Enrichment of S. <t>pneumoniae</t> Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    S Pneumoniae R6, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s pneumoniae r6/product/ATCC
    Average 86 stars, based on 1 article reviews
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    s pneumoniae r6 - by Bioz Stars, 2024-02
    86/100 stars

    Images

    1) Product Images from "Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples"

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    Journal: bioRxiv

    doi: 10.1101/2024.02.11.579857

    Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL
    Figure Legend Snippet: Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Techniques Used: Selection

    Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Selection, Comparison

    Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.
    Figure Legend Snippet: Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Techniques Used:

    Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.
    Figure Legend Snippet: Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Techniques Used: Generated


    Figure Legend Snippet:

    Techniques Used:


    Figure Legend Snippet:

    Techniques Used:

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Comparison

    s pneumoniae malm6  (ATCC)


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    ATCC s pneumoniae malm6
    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA <t>(GPSC16,</t> serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    S Pneumoniae Malm6, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s pneumoniae malm6/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    s pneumoniae malm6 - by Bioz Stars, 2024-02
    86/100 stars

    Images

    1) Product Images from "Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples"

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    Journal: bioRxiv

    doi: 10.1101/2024.02.11.579857

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    s pneumoniae 110 58  (ATCC)


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    ATCC s pneumoniae 110 58
    S Pneumoniae 110 58, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    s pneumoniae 110 58 - by Bioz Stars, 2024-02
    86/100 stars

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    s pneumoniae atcc 706669  (ATCC)


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    ATCC s pneumoniae atcc 706669
    Enrichment of S. pneumoniae <t>Spn23F</t> in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the <t>23F</t> CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    S Pneumoniae Atcc 706669, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples"

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    Journal: bioRxiv

    doi: 10.1101/2024.02.11.579857

    Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    Spn23F whole genome enrichment assembly comparison. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors (black bars, > 50 bp) in each assembly. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .
    Figure Legend Snippet: Spn23F whole genome enrichment assembly comparison. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors (black bars, > 50 bp) in each assembly. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .

    Techniques Used: Comparison, Generated

    Difference in normalised coverage per locus between NAS and control channels across the Spn23F genome when targeting whole genome (blue) or CBL (red). NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. The grey dashed line at 0 indicates equivalent coverage at a given locus between NAS and control channels; > 0 indicates NAS channels generated greater coverage, < 0 indicates control channels generated greater coverage. Data shown for 0.1 dilutions of Spn23F only. Grey column in each plot highlights 23F CBL locus. Rows show different species for the non-target which was mixed with Spn23F in each sample.
    Figure Legend Snippet: Difference in normalised coverage per locus between NAS and control channels across the Spn23F genome when targeting whole genome (blue) or CBL (red). NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. The grey dashed line at 0 indicates equivalent coverage at a given locus between NAS and control channels; > 0 indicates NAS channels generated greater coverage, < 0 indicates control channels generated greater coverage. Data shown for 0.1 dilutions of Spn23F only. Grey column in each plot highlights 23F CBL locus. Rows show different species for the non-target which was mixed with Spn23F in each sample.

    Techniques Used: Generated

    Spn23F CBL enrichment assembly comparison. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions (8 × 10 − 4 23F CBL proportion) with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors (black bars > 50 bp) in each assembly.
    Figure Legend Snippet: Spn23F CBL enrichment assembly comparison. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions (8 × 10 − 4 23F CBL proportion) with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors (black bars > 50 bp) in each assembly.

    Techniques Used: Comparison, Generated


    Figure Legend Snippet:

    Techniques Used:

    Absolute yield in megabases (Mb) of bases aligning to the whole genome of Spn23F (top) and 23F CBL (bottom) . Each data point represents the enrichment of the Spn23F whole genome or 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.
    Figure Legend Snippet: Absolute yield in megabases (Mb) of bases aligning to the whole genome of Spn23F (top) and 23F CBL (bottom) . Each data point represents the enrichment of the Spn23F whole genome or 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Techniques Used:

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Sequencing

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a partial CBL reference database. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Rows describe the non-target species in the mixture, columns describe the alignment method used. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a partial CBL reference database. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Rows describe the non-target species in the mixture, columns describe the alignment method used. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Comparison

    Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a partial CBL database using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.
    Figure Legend Snippet: Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a partial CBL database using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Techniques Used:

    Normalised coverage difference between NAS and control channels across 23F CBL using a partial CBL reference database using Minimap2 and GNASTy. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Columns describe the non-target species. Rows describe the proportion of target DNA present in the sample.
    Figure Legend Snippet: Normalised coverage difference between NAS and control channels across 23F CBL using a partial CBL reference database using Minimap2 and GNASTy. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Columns describe the non-target species. Rows describe the proportion of target DNA present in the sample.

    Techniques Used: Generated

    Serotype 23F prediction using reads aligning a to partial CBL reference database using Minimap2 and GNASTy. Y-axis describes the proportion of reference CBL k-mers matched by PneumoKITy , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). Columns describe the 23F CBL DNA proportion in the sample. Rows describe the non-target species mixed with Spn23F. Sub-serotypes (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.
    Figure Legend Snippet: Serotype 23F prediction using reads aligning a to partial CBL reference database using Minimap2 and GNASTy. Y-axis describes the proportion of reference CBL k-mers matched by PneumoKITy , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). Columns describe the 23F CBL DNA proportion in the sample. Rows describe the non-target species mixed with Spn23F. Sub-serotypes (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Techniques Used:

    Spn23F CBL assembly comparison across alignment methods using a partial CBL database during NAS using Minimap2 and GNASTy. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.
    Figure Legend Snippet: Spn23F CBL assembly comparison across alignment methods using a partial CBL database during NAS using Minimap2 and GNASTy. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Techniques Used: Comparison, Generated

    Spn23F CBL assembly comparison across alignment methods using a full CBL database during NAS. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.
    Figure Legend Snippet: Spn23F CBL assembly comparison across alignment methods using a full CBL database during NAS. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Techniques Used: Comparison, Generated

    Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL
    Figure Legend Snippet: Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Techniques Used: Selection

    Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Selection, Comparison

    Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a full CBL database for mock nasopharyngeal samples using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.
    Figure Legend Snippet: Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a full CBL database for mock nasopharyngeal samples using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Techniques Used:

    Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.
    Figure Legend Snippet: Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Techniques Used:

    Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.
    Figure Legend Snippet: Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Techniques Used: Generated


    Figure Legend Snippet:

    Techniques Used:

    Effect of minimum alignment identity on Spn23F whole genome enrichment. Boxplots represent distributions of enrichment values of Spn23F whole genome in all samples. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Effect of minimum alignment identity on Spn23F whole genome enrichment. Boxplots represent distributions of enrichment values of Spn23F whole genome in all samples. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used:

    Effect of minimum alignment identity on Spn23F whole genome enrichment across sample concentrations and contaminating species. Lines connect the same sample with different minimum alignment identity thresholds. Columns indicate the % Spn23F DNA in the sample, rows indicate the non-target type. Colours describe the species of the non-target species. No library was sequenced at 0.1% Spn23F DNA with a Streptococcus non-target species. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Effect of minimum alignment identity on Spn23F whole genome enrichment across sample concentrations and contaminating species. Lines connect the same sample with different minimum alignment identity thresholds. Columns indicate the % Spn23F DNA in the sample, rows indicate the non-target type. Colours describe the species of the non-target species. No library was sequenced at 0.1% Spn23F DNA with a Streptococcus non-target species. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used:

    Effect of size selection on read length distributions for Spn23F whole genome enrichment. Histograms for reads accepted ( top ) and rejected ( middle ) by NAS in adaptive channels, and all reads in control channels ( bottom ).
    Figure Legend Snippet: Effect of size selection on read length distributions for Spn23F whole genome enrichment. Histograms for reads accepted ( top ) and rejected ( middle ) by NAS in adaptive channels, and all reads in control channels ( bottom ).

    Techniques Used: Selection


    Figure Legend Snippet:

    Techniques Used:

    Enrichment comparison of Spn23F genome with and without size selection, which removed DNA fragments < 10 kb in length. Each data point represents the enrichment of Spn23F in a single barcoded library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred. Black points highlight distributions means. Distributions were compared using a paired Wilcoxon test.
    Figure Legend Snippet: Enrichment comparison of Spn23F genome with and without size selection, which removed DNA fragments < 10 kb in length. Each data point represents the enrichment of Spn23F in a single barcoded library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred. Black points highlight distributions means. Distributions were compared using a paired Wilcoxon test.

    Techniques Used: Comparison, Selection


    Figure Legend Snippet:

    Techniques Used:

    Normalised coverage across Spn23F genome for enrichment of 23F CBL for the Spn23F-only sample. Coverage was normalised by dividing the number of read bases aligned at each position in the Spn23F genome by the total number of bases generated for a sample by adaptive or control channels in gigabases (Gb). Columns describe library type; unselected or size-selected. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .
    Figure Legend Snippet: Normalised coverage across Spn23F genome for enrichment of 23F CBL for the Spn23F-only sample. Coverage was normalised by dividing the number of read bases aligned at each position in the Spn23F genome by the total number of bases generated for a sample by adaptive or control channels in gigabases (Gb). Columns describe library type; unselected or size-selected. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .

    Techniques Used: Generated

    Simulation read length comparison of graph pseudoalignment parameters and Minimap2. X-axis describes either the k size used in graph pseudoalignment or Minimap2 alignment. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL; TPs, reads that were correctly accepted, FPs, reads that were incorrectly accepted, TNs, reads that were correctly rejected, and FNs, reads that were incorrectly rejected.
    Figure Legend Snippet: Simulation read length comparison of graph pseudoalignment parameters and Minimap2. X-axis describes either the k size used in graph pseudoalignment or Minimap2 alignment. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL; TPs, reads that were correctly accepted, FPs, reads that were incorrectly accepted, TNs, reads that were correctly rejected, and FNs, reads that were incorrectly rejected.

    Techniques Used: Comparison

    Comparison of graph pseudoalignment parameters and Minimap2 based on proportions of bases correctly assigned to positive and negative categories. Minimap2 results are indicated by the black dashed line on each facet. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL: TPs, reads that were correctly accepted; TNs, reads that were correctly rejected.
    Figure Legend Snippet: Comparison of graph pseudoalignment parameters and Minimap2 based on proportions of bases correctly assigned to positive and negative categories. Minimap2 results are indicated by the black dashed line on each facet. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL: TPs, reads that were correctly accepted; TNs, reads that were correctly rejected.

    Techniques Used: Comparison

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
    Figure Legend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Techniques Used: Comparison

    Absolute yield (in megabases) of bases aligning to the 23F CBL when aligning to a full CBL database. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.
    Figure Legend Snippet: Absolute yield (in megabases) of bases aligning to the 23F CBL when aligning to a full CBL database. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Techniques Used:

    Normalised coverage difference between NAS and control channels across 23F CBL using a full CBL reference database. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Rows describe the proportion of target DNA present in the sample.
    Figure Legend Snippet: Normalised coverage difference between NAS and control channels across 23F CBL using a full CBL reference database. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Rows describe the proportion of target DNA present in the sample.

    Techniques Used: Generated

    s pneumoniae tw01 0057  (ATCC)


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    ATCC s pneumoniae tw01 0057
    S Pneumoniae Tw01 0057, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    s pneumoniae k13 0810  (ATCC)


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    ATCC s pneumoniae k13 0810
    S Pneumoniae K13 0810, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    s pneumoniae  (ATCC)


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    ATCC s pneumoniae
    Sequences of primers used for singleplex and multiplex real-time EG-PCR assays
    S Pneumoniae, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes"

    Article Title: Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes

    Journal: BMC Infectious Diseases

    doi: 10.1186/s12879-024-09028-2

    Sequences of primers used for singleplex and multiplex real-time EG-PCR assays
    Figure Legend Snippet: Sequences of primers used for singleplex and multiplex real-time EG-PCR assays

    Techniques Used: Multiplex Assay, Sequencing, Amplification

    Tm values of primers used for singleplex and multiplex real-time PCR assays
    Figure Legend Snippet: Tm values of primers used for singleplex and multiplex real-time PCR assays

    Techniques Used: Multiplex Assay, Real-time Polymerase Chain Reaction, Intra Assay, Inter Assay

    The sensitivity of simultaneous detection of S. aureus , S. pneumoniae , E. coli ( A ) and A. baumannii , K. pneumoniae , P. aeruginosa ( B ) with concentrations ranging 10 6 to 12.8 CFU/mL. LOD of simultaneous detection of S. aureus , S. pneumoniae , E. coli was 1600 CFU/mL and the same for A. baumannii, K. pneumoniae, P. aeruginosa
    Figure Legend Snippet: The sensitivity of simultaneous detection of S. aureus , S. pneumoniae , E. coli ( A ) and A. baumannii , K. pneumoniae , P. aeruginosa ( B ) with concentrations ranging 10 6 to 12.8 CFU/mL. LOD of simultaneous detection of S. aureus , S. pneumoniae , E. coli was 1600 CFU/mL and the same for A. baumannii, K. pneumoniae, P. aeruginosa

    Techniques Used:

    Performance of EG-mPCR assays compared with the conventional culture method
    Figure Legend Snippet: Performance of EG-mPCR assays compared with the conventional culture method

    Techniques Used:

    Frequency of common AMR genes detected in microbiologically-confirmed target bacteria either phenotypically resistant to 3rd/4th cephalosporins, carbapenem, macrolide and oxacillin
    Figure Legend Snippet: Frequency of common AMR genes detected in microbiologically-confirmed target bacteria either phenotypically resistant to 3rd/4th cephalosporins, carbapenem, macrolide and oxacillin

    Techniques Used: Bacteria

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    ATCC s pneumoniae serotypes
    S Pneumoniae Serotypes, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC s pneumoniae
    Enrichment of S. <t>pneumoniae</t> Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae 8140
    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA <t>(GPSC16,</t> serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae r6
    Enrichment of S. <t>pneumoniae</t> Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae malm6
    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA <t>(GPSC16,</t> serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae 110 58
    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA <t>(GPSC16,</t> serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae atcc 706669
    Enrichment of S. pneumoniae <t>Spn23F</t> in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the <t>23F</t> CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae tw01 0057
    Enrichment of S. pneumoniae <t>Spn23F</t> in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the <t>23F</t> CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    ATCC s pneumoniae k13 0810
    Enrichment of S. pneumoniae <t>Spn23F</t> in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the <t>23F</t> CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.
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    Image Search Results


    Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques: Sequencing

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques: Sequencing

    Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques: Selection

    Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques: Selection, Comparison

    Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques:

    Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques: Generated

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet:

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques:

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: To test this hypothesis, we generated mock communities containing mixtures of genomic DNA from S. pneumoniae , the serotype 23F pneumococcal isolate ATCC 700669 , referred to as ‘Spn23F’, with that of closely and distantly related non-target species.

    Techniques: Comparison

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Sequencing

    Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Sequencing

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Sequencing

    Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Selection

    Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Selection, Comparison

    Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Generated

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet:

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Sequencing

    Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment of S. pneumoniae Spn23F in samples containing closely and distantly related non-target species. ( a ) Representation of evolutionary relatedness of non-target species and the target, S. pneumoniae Spn23F. ( b ) Experimental setup of target DNA dilution series with non-target DNA. ( c ) Representation of two enrichment experiments, either targeting the whole Spn23F genome (blue) or the 23F CBL sequence present on the Spn23F chromosome. ( d ) Enrichment results of Spn23F whole genome or 23F CBL at different concentrations of target DNA. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting target DNA diluted at different concentrations with non-target DNA. Columns describe the non-target species within each mixture. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Sequencing

    Spn23F whole genome enrichment assembly comparison. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors (black bars, > 50 bp) in each assembly. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F whole genome enrichment assembly comparison. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors (black bars, > 50 bp) in each assembly. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison, Generated

    Difference in normalised coverage per locus between NAS and control channels across the Spn23F genome when targeting whole genome (blue) or CBL (red). NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. The grey dashed line at 0 indicates equivalent coverage at a given locus between NAS and control channels; > 0 indicates NAS channels generated greater coverage, < 0 indicates control channels generated greater coverage. Data shown for 0.1 dilutions of Spn23F only. Grey column in each plot highlights 23F CBL locus. Rows show different species for the non-target which was mixed with Spn23F in each sample.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Difference in normalised coverage per locus between NAS and control channels across the Spn23F genome when targeting whole genome (blue) or CBL (red). NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. The grey dashed line at 0 indicates equivalent coverage at a given locus between NAS and control channels; > 0 indicates NAS channels generated greater coverage, < 0 indicates control channels generated greater coverage. Data shown for 0.1 dilutions of Spn23F only. Grey column in each plot highlights 23F CBL locus. Rows show different species for the non-target which was mixed with Spn23F in each sample.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Generated

    Spn23F CBL enrichment assembly comparison. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions (8 × 10 − 4 23F CBL proportion) with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors (black bars > 50 bp) in each assembly.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F CBL enrichment assembly comparison. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions (8 × 10 − 4 23F CBL proportion) with each non-target organism. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors (black bars > 50 bp) in each assembly.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison, Generated

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet:

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Absolute yield in megabases (Mb) of bases aligning to the whole genome of Spn23F (top) and 23F CBL (bottom) . Each data point represents the enrichment of the Spn23F whole genome or 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Absolute yield in megabases (Mb) of bases aligning to the whole genome of Spn23F (top) and 23F CBL (bottom) . Each data point represents the enrichment of the Spn23F whole genome or 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: CBL enrichment in mixtures of multiple pneumococci. a ) Experimental setup. Spn23F DNA (GPSC16, serotype 23F, red) was mixed in 50:50 proportions with other S. pneumoniae isolates with different serotypes (given by colour) and genotypes (given by Global Pneumococcal Sequence Cluster, GPSC). b ) Enrichment of multiple CBL in mixtures. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each CBL per library. X-axis and colour describes the serotype combination of the S. pneumoniae isolate mixed with Spn23F, columns describe the GPSC. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Sequencing

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a partial CBL reference database. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Rows describe the non-target species in the mixture, columns describe the alignment method used. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a partial CBL reference database. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Rows describe the non-target species in the mixture, columns describe the alignment method used. To plot on a log scale, all enrichment values had 0.01 added to them. Horizontal dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison

    Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a partial CBL database using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a partial CBL database using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Normalised coverage difference between NAS and control channels across 23F CBL using a partial CBL reference database using Minimap2 and GNASTy. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Columns describe the non-target species. Rows describe the proportion of target DNA present in the sample.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Normalised coverage difference between NAS and control channels across 23F CBL using a partial CBL reference database using Minimap2 and GNASTy. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Columns describe the non-target species. Rows describe the proportion of target DNA present in the sample.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Generated

    Serotype 23F prediction using reads aligning a to partial CBL reference database using Minimap2 and GNASTy. Y-axis describes the proportion of reference CBL k-mers matched by PneumoKITy , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). Columns describe the 23F CBL DNA proportion in the sample. Rows describe the non-target species mixed with Spn23F. Sub-serotypes (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Serotype 23F prediction using reads aligning a to partial CBL reference database using Minimap2 and GNASTy. Y-axis describes the proportion of reference CBL k-mers matched by PneumoKITy , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). Columns describe the 23F CBL DNA proportion in the sample. Rows describe the non-target species mixed with Spn23F. Sub-serotypes (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Spn23F CBL assembly comparison across alignment methods using a partial CBL database during NAS using Minimap2 and GNASTy. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F CBL assembly comparison across alignment methods using a partial CBL database during NAS using Minimap2 and GNASTy. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison, Generated

    Spn23F CBL assembly comparison across alignment methods using a full CBL database during NAS. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F CBL assembly comparison across alignment methods using a full CBL database during NAS. Each panel describes a Spn23F assembly generated from 0.1 Spn23F dilutions with S. mitis . For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison, Generated

    Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Tapestation images for unselected and size-selected samples. Mixed cultures from nasopharyngeal samples are denoted ‘Sample X’. DNA extractions from single isolate cultures, Spn23F and S. pneumoniae R6, were included as positive controls. Y-axis denotes normalised flourescent units (fU). X-axis denotes DNA fragment size (bp). Starting DNA concentrations for size selection: Sample 1: 100 ng/µL, Sample 3: 40 ng/µL, Spn23F: 100 ng/µL, S. pneumoniae R6: 100 ng/µL

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Selection

    Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment of 23F CBL across samples containing mixed cultures from nasopharyngeal swabs. All nasopharyngeal samples (denoted ‘Sample X’) were run without size selection, with control samples containing Spn23F mixed with S. pneumoniae R6 (denoted ‘Pneumo R6’) without size selection at 0.1 and 0.5 proportions (8 × 10 − 4 and 4 × 10 − 3 23F CBL DNA proportions respectively) run alongside. Equivalent control samples from a run with size selection are plotted for comparison. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points are observed enrichment values for each library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Selection, Comparison

    Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a full CBL database for mock nasopharyngeal samples using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Absolute yield in megabases (Mb) of bases aligning to the 23F CBL when aligning to a full CBL database for mock nasopharyngeal samples using Minimap2 and GNASTy. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Serotype 23F prediction from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy for enrichment. Y-axis describes the proportion of reference CBL k-mers matched by Pneumokity , with each data point describing an individual CBL. The lower limit of matching k-mers used by PneumoKITy (70%) to identify as CBL as present is marked by the grey dotted line. Predictions for the 23F CBL are highlighted in red. Shapes described the channel type (adaptive or control). X-axis describes the 23F CBL DNA proportion in the sample. Columns describe the nasopharyngeal mixed culture (denoted as ‘Sample X’) or S. pneumoniae R6 sample mixed with Spn23F. Subtypes based on wzy variation (e.g. 6A-I, 6A-II etc.) were removed from data to avoid redundancy.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Spn23F CBL assembly from mock nasopharyngeal microbiomes using graph pseudoalignment in GNASTy ( S = 75%) aligning to a full CBL database during NAS. Each panel describes a 23F CBL assembly generated from 0.1 Spn23F spike into mixed cultures (for ‘Sample X’) or 0.1 and 0.5 Spn23F spikes into S. pneumoniae R6. For each panel, the top plot shows the read coverage (solid), defined as the absolute number of bases aligning to a locus, and number of small errors ( ≤ 50 bp, dashed), whilst the bottom plot shows the aligned contigs (colours) and large errors ( > 50 bp) in each assembly.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Generated

    Effect of minimum alignment identity on Spn23F whole genome enrichment. Boxplots represent distributions of enrichment values of Spn23F whole genome in all samples. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Effect of minimum alignment identity on Spn23F whole genome enrichment. Boxplots represent distributions of enrichment values of Spn23F whole genome in all samples. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Effect of minimum alignment identity on Spn23F whole genome enrichment across sample concentrations and contaminating species. Lines connect the same sample with different minimum alignment identity thresholds. Columns indicate the % Spn23F DNA in the sample, rows indicate the non-target type. Colours describe the species of the non-target species. No library was sequenced at 0.1% Spn23F DNA with a Streptococcus non-target species. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Effect of minimum alignment identity on Spn23F whole genome enrichment across sample concentrations and contaminating species. Lines connect the same sample with different minimum alignment identity thresholds. Columns indicate the % Spn23F DNA in the sample, rows indicate the non-target type. Colours describe the species of the non-target species. No library was sequenced at 0.1% Spn23F DNA with a Streptococcus non-target species. Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Effect of size selection on read length distributions for Spn23F whole genome enrichment. Histograms for reads accepted ( top ) and rejected ( middle ) by NAS in adaptive channels, and all reads in control channels ( bottom ).

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Effect of size selection on read length distributions for Spn23F whole genome enrichment. Histograms for reads accepted ( top ) and rejected ( middle ) by NAS in adaptive channels, and all reads in control channels ( bottom ).

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Selection

    Enrichment comparison of Spn23F genome with and without size selection, which removed DNA fragments < 10 kb in length. Each data point represents the enrichment of Spn23F in a single barcoded library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred. Black points highlight distributions means. Distributions were compared using a paired Wilcoxon test.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment comparison of Spn23F genome with and without size selection, which removed DNA fragments < 10 kb in length. Each data point represents the enrichment of Spn23F in a single barcoded library. Dashed line describes enrichment = 1 i.e. no enrichment has occurred. Black points highlight distributions means. Distributions were compared using a paired Wilcoxon test.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison, Selection

    Normalised coverage across Spn23F genome for enrichment of 23F CBL for the Spn23F-only sample. Coverage was normalised by dividing the number of read bases aligned at each position in the Spn23F genome by the total number of bases generated for a sample by adaptive or control channels in gigabases (Gb). Columns describe library type; unselected or size-selected. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Normalised coverage across Spn23F genome for enrichment of 23F CBL for the Spn23F-only sample. Coverage was normalised by dividing the number of read bases aligned at each position in the Spn23F genome by the total number of bases generated for a sample by adaptive or control channels in gigabases (Gb). Columns describe library type; unselected or size-selected. Loci of interest are annotated by grey bars; CBL, as well as ICE Sp 23FST81 and ψ MM1 prophage which are missing in Spn23F .

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Generated

    Simulation read length comparison of graph pseudoalignment parameters and Minimap2. X-axis describes either the k size used in graph pseudoalignment or Minimap2 alignment. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL; TPs, reads that were correctly accepted, FPs, reads that were incorrectly accepted, TNs, reads that were correctly rejected, and FNs, reads that were incorrectly rejected.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Simulation read length comparison of graph pseudoalignment parameters and Minimap2. X-axis describes either the k size used in graph pseudoalignment or Minimap2 alignment. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL; TPs, reads that were correctly accepted, FPs, reads that were incorrectly accepted, TNs, reads that were correctly rejected, and FNs, reads that were incorrectly rejected.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison

    Comparison of graph pseudoalignment parameters and Minimap2 based on proportions of bases correctly assigned to positive and negative categories. Minimap2 results are indicated by the black dashed line on each facet. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL: TPs, reads that were correctly accepted; TNs, reads that were correctly rejected.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Comparison of graph pseudoalignment parameters and Minimap2 based on proportions of bases correctly assigned to positive and negative categories. Minimap2 results are indicated by the black dashed line on each facet. Columns describe pseudoalignment parameters (mash: minimum S , cutoff: minimum read length). Rows describe categories of reads based on accept/reject decision and post-alignment to 23F CBL: TPs, reads that were correctly accepted; TNs, reads that were correctly rejected.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison

    Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Enrichment comparison of 23F CBL at different concentrations of target between Minimap2 and graph pseudoalignment in GNASTy when aligning to a full CBL reference database using V14 chemistry. Bar ranges are inter-quartile range of enrichment from 100 bootstrap samples of reads. Data points connected by lines are observed enrichment values for each library, with solid lines connecting the same genome diluted at different concentrations. Columns describe the type of non-target species (Non- Streptococcus = E. coli , Streptococcus = S. mitis and S. pneumoniae = S. pneumoniae R6). Dashed line describes enrichment = 1 i.e. no enrichment has occurred.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Comparison

    Absolute yield (in megabases) of bases aligning to the 23F CBL when aligning to a full CBL database. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Absolute yield (in megabases) of bases aligning to the 23F CBL when aligning to a full CBL database. Each data point represents the enrichment of the 23F CBL found within each library. Distributions from control and NAS channels were compared using a paired Wilcoxon test.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques:

    Normalised coverage difference between NAS and control channels across 23F CBL using a full CBL reference database. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Rows describe the proportion of target DNA present in the sample.

    Journal: bioRxiv

    Article Title: Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

    doi: 10.1101/2024.02.11.579857

    Figure Lengend Snippet: Normalised coverage difference between NAS and control channels across 23F CBL using a full CBL reference database. NAS-control coverage difference per gigabase (Gb) calculated by normalising the read coverage for each locus by the amount of data generated (in Gb) for each respective sample and channel, and then negating the normalised coverage for control channels from NAS channels for each locus. Rows describe the proportion of target DNA present in the sample.

    Article Snippet: All isolate bacterial strains used in this work included: E. coli DH5- α , Moraxella catarrhalis 0193-3, Haemophilus influenzae 0456-2, S. mitis SK142, Streptococcus oralis SK23, S. pneumoniae ATCC 706669 (referred to as ‘Spn23F’, GPSC16, serotype 23F), S. pneumoniae R6 (GPSC622, unencapsulated), S. pneumoniae 110.58 (GPSC81, unencapsulated), S. pneumoniae MalM6 (GPSC16, serotype 19F), S. pneumoniae 8140 (GPSC16, serotype 19A), S. pneumoniae Tw01-0057 (GPSC1, serotype 19F), S. pneumoniae K13-0810 (GPSC23, serotype 6B), and S. pneumoniae 99-4038 (GPSC3, serotype 3).

    Techniques: Generated