The PneuCarriage Project : A multi-centre comparative study to identify the best serotyping methods for examining pneumococcal carriage in vaccine evaluation studies
- Satzke, Catherine, Dunne, Eileen, Porter, Barbara, Klugman, Keith, Mulholland, Kim, PneuCarriage project group, Greenhill, Andrew
- Authors: Satzke, Catherine , Dunne, Eileen , Porter, Barbara , Klugman, Keith , Mulholland, Kim , PneuCarriage project group , Greenhill, Andrew
- Date: 2015
- Type: Text , Journal article
- Relation: PLoS Medicine Vol. 12, no. 11 (2015), p. 1-30
- Full Text:
- Reviewed:
- Description: Background: The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. Methods and Findings: Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. Conclusions: Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high. © 2015 Satzke et al. *For a complete list of authors, please see acknowledgments in the published article.
- Authors: Satzke, Catherine , Dunne, Eileen , Porter, Barbara , Klugman, Keith , Mulholland, Kim , PneuCarriage project group , Greenhill, Andrew
- Date: 2015
- Type: Text , Journal article
- Relation: PLoS Medicine Vol. 12, no. 11 (2015), p. 1-30
- Full Text:
- Reviewed:
- Description: Background: The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. Methods and Findings: Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. Conclusions: Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high. © 2015 Satzke et al. *For a complete list of authors, please see acknowledgments in the published article.
Multilocus sequence typing of Streptococcus pneumoniae by use of mass spectrometry
- Dunne, Eileen, Ong, Engkok, Moser, Ralf, Siba, Peter, Phuanukoonnon, Suparat, Greenhill, Andrew, Robins-Browne, Roy, Mulholland, Edward, Satzke, Catherine
- Authors: Dunne, Eileen , Ong, Engkok , Moser, Ralf , Siba, Peter , Phuanukoonnon, Suparat , Greenhill, Andrew , Robins-Browne, Roy , Mulholland, Edward , Satzke, Catherine
- Date: 2011
- Type: Text , Journal article
- Relation: Journal of Clinical Microbiology Vol. 49, no. 11 (2011), p. 3756-3760
- Full Text: false
- Reviewed:
- Description: Multilocus sequence typing (MLST) is an important tool for the global surveillance of bacterial pathogens that is performed by comparing the sequences of designated housekeeping genes. We developed and tested a novel mass spectrometry-based method for MLST of Streptococcus pneumoniae. PCR amplicons were subjected to in vitro transcription and base-specific cleavage, followed by analysis of the resultant fragments by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Comparison of the cleavage fragment peak patterns to a reference sequence set permitted automated identification of alleles. Validation experiments using 29 isolates of S. pneumoniae revealed that the results of MALDI-TOF MS MLST matched those obtained by traditional sequence-based MLST for 99% of alleles and that the MALDITOF MS method accurately identified two single-nucleotide variations. The MADLI-TOF MS method was then used for MLST analysis of 43 S. pneumoniae isolates from Papua New Guinean children. The majority of the isolates present in this population were not clonal and contained seven new alleles and 30 previously unreported sequence types.
- «
- ‹
- 1
- ›
- »