Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
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Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences

Filetype[PDF-1.38 MB]


  • English
    • Details Supporting Files Datasets Related Documents You May Also Like

    Details:

    • Alternative Title:
      BMC Genomics
    • Personal Author:
    • Corporate Authors:
      on behalf of the Active Bacterial Core surveillance team
    • Description:
      Background

      Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type). This study evaluates the prediction performance for previously uncharacterized (new) PBP types and the probability of encountering new PBP types, both of which impact the overall prediction accuracy.

      Results

      The MM and RF methods were used to predict MICs of 4309 previously reported pneumococcal isolates in 2 datasets and the results were compared to the known broth microdilution MICs to 6 β-lactams. Based on a method that specifically evaluated predictions for new PBP types, the RF results were more accurate than MM results for new PBP types and showed percent essential agreement (MICs agree within ±1 dilution) >97%, percent category agreement (interpretive results agree) >93%, major discrepancy (sensitive isolate predicted as resistant) rate < 1.2%, and very major discrepancy (resistant isolate predicted as sensitive) rate < 1.4% for all 6 β-lactams. The identification of new PBP types over time was well approximated by a diminishingly increasing curve (Pearson’s r = 0.99) and minimally impacted overall MIC prediction performance.

      Conclusions

      MIC prediction using the RF method could be an accurate alternative of phenotypic susceptibility testing even in the presence of previously uncharacterized PBP types.

      Electronic supplementary material

      The online version of this article (doi:10.1186/s12864-017-4017-7) contains supplementary material, which is available to authorized users.

    • Subjects:
    • Source:
      BMC Genomics. 18.
    • Pubmed ID:
      28810827
    • Pubmed Central ID:
      PMC5558719
    • Document Type:
      Journal Article
    • Collection(s):
    • Main Document Checksum:
    • Download URL:
    • File Type:

    Datasets

      • Additional file 5: Table S4. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Transpeptidase domain (TPD) amino acid residuals of the 3 penicillin-binding proteins (PBPs) for Dataset1 isolates. (CSV 6391Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 4: Table S3. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Transpeptidase domain (TPD) amino acid residuals of the 3 penicillin-binding proteins (PBPs) for Dataset1 isolates. (CSV 9068Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 6: Table S5. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Results of tuning RF model parameter mtry, number of variables randomly sampled as candidates at each split. (CSV 430 bytes)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 8: Table S7. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        The positive predictive value (PPV) and negative predictive value (NPV) for β-Lactam resistance. (CSV 569 bytes)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 4: Table S3. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Transpeptidase domain (TPD) amino acid residuals of the 3 penicillin-binding proteins (PBPs) for Dataset1 isolates. (CSV 9068Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 5: Table S4. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Transpeptidase domain (TPD) amino acid residuals of the 3 penicillin-binding proteins (PBPs) for Dataset1 isolates. (CSV 6391Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 2: Table S2. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        List 1781 Dataset2 isolates. (CSV 260Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 6: Table S5. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Results of tuning RF model parameter mtry, number of variables randomly sampled as candidates at each split. (CSV 430 bytes)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 7: Table S6. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Results of a 10-fold cross-validation of the RF model. (CSV 1009 bytes)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 1: Table S1. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        List of 2528 Dataset1 isolates. (CSV 254Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 2: Table S2. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        List 1781 Dataset2 isolates. (CSV 260Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 1: Table S1. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        List of 2528 Dataset1 isolates. (CSV 254Â kb)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 7: Table S6. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        Results of a 10-fold cross-validation of the RF model. (CSV 1009 bytes)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]
        Additional file 8: Table S7. of Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
        Dataset Icon
        Cite
        Filetype[HTM]
        Personal Author:
        Beall, Bernard W. ;
        Chochua, Sopio
        ...
        2017 | NCIRD
        08/16/2017
        Description:
        The positive predictive value (PPV) and negative predictive value (NPV) for β-Lactam resistance. (CSV 569 bytes)
        File Type:
        Filetype[HTM]
        File Type:
        Filetype[HTM]

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