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Multiple-locus variable number tandem repeat analysis for Streptococcus pneumoniae: comparison with PFGE and MLST.

Elberse KE, Nunes S, Sá-Leão R, van der Heide HG, Schouls LM - PLoS ONE (2011)

Bottom Line: Furthermore, the Wallace of MLVA to clonal complex of MLST was even higher: 99.5%.For some isolates belonging to a single MLST clonal complex although displaying different serotypes, MLVA was more discriminatory, generating groups according to serotype or serogroup.In the companion paper published simultaneously in this issue we applied the MLVA to assess the pneumococcal population structure of isolates causing invasive disease in The Netherlands before the introduction of the 7-valent conjugate vaccine.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Infectious Diseases and Perinatal Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands. Karin.Elberse@rivm.nl

ABSTRACT
In the era of pneumococcal conjugate vaccines, surveillance of pneumococcal disease and carriage remains of utmost importance as important changes may occur in the population. To monitor these alterations reliable genotyping methods are required for large-scale applications. We introduced a high throughput multiple-locus variable number tandem repeat analysis (MLVA) and compared this method with pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The MLVA described here is based on 8 BOX loci that are amplified in two multiplex PCRs. The labeled PCR products are sized on an automated DNA sequencer to accurately determine the number of tandem repeats. The composite of the number of repeats of the BOX loci makes up a numerical profile that is used for identification and clustering. In this study, MLVA was performed on 263 carriage isolates that were previously characterized by MLST and PFGE. MLVA, MLST and PFGE (cut-off of 80%) yielded 164, 120, and 87 types, respectively. The three typing methods had Simpson's diversity indices of 98.5% or higher. Congruence between MLST and MLVA was high. The Wallace of MLVA to MLST was 0.874, meaning that if two strains had the same MLVA type they had an 88% chance of having the same MLST type. Furthermore, the Wallace of MLVA to clonal complex of MLST was even higher: 99.5%. For some isolates belonging to a single MLST clonal complex although displaying different serotypes, MLVA was more discriminatory, generating groups according to serotype or serogroup. Overall, MLVA is a promising genotyping method that is easy to perform and a relatively cheap alternative to PFGE and MLST. In the companion paper published simultaneously in this issue we applied the MLVA to assess the pneumococcal population structure of isolates causing invasive disease in The Netherlands before the introduction of the 7-valent conjugate vaccine.

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High congruence between MLVA and MLST.Minimum spanning tree of the results obtained by MLST (A) and MLVA (B) for the 263 isolates of the test collection. Each circle indicates a genotype. The size of the circle is proportional to the number of isolates with the same type. Lines linking two types denote a single locus difference between those types. In Figure 1A the MLST complexes are indicated by halos. Seven MLST complexes are discussed in the manuscript and these are colored and named according to the nomenclature of S. pneumoniae MLST database (www.mlst.net, last accessed on October 20, 2010). The white nodes represent the isolates within this test collection that are not discussed. The same colors were applied to the minimum spanning tree based on MLVA in Figure 1B. This minimum spanning tree is based on the entire MLVA database (last accessed on October 20, 2010), and only the branches are made visible. The MLVA types of the 263 isolates used in this study were depicted as circles. The halos indicate the MLVA complexes.
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pone-0019668-g001: High congruence between MLVA and MLST.Minimum spanning tree of the results obtained by MLST (A) and MLVA (B) for the 263 isolates of the test collection. Each circle indicates a genotype. The size of the circle is proportional to the number of isolates with the same type. Lines linking two types denote a single locus difference between those types. In Figure 1A the MLST complexes are indicated by halos. Seven MLST complexes are discussed in the manuscript and these are colored and named according to the nomenclature of S. pneumoniae MLST database (www.mlst.net, last accessed on October 20, 2010). The white nodes represent the isolates within this test collection that are not discussed. The same colors were applied to the minimum spanning tree based on MLVA in Figure 1B. This minimum spanning tree is based on the entire MLVA database (last accessed on October 20, 2010), and only the branches are made visible. The MLVA types of the 263 isolates used in this study were depicted as circles. The halos indicate the MLVA complexes.

Mentions: Although there was considerable concordance between MLST and MLVA, some of the isolates that were grouped by MLST could be further distinguished by MLVA. In Figure 1A a minimum spanning tree is depicted based on the MLST results for the 263 isolates of the test collection. Fifty-six clonal complexes (CC), and 13 singletons were detected and the 7 largest CCs were chosen for further comparisons and are highlighted in color. To visualize the relationship between MLST and MLVA, the same color legend was applied to the minimum spanning tree based on MLVA (Fig. 1B). To create this minimum spanning tree, the entries in the entire MLVA database (n = 2973) were used. Subsequently, a subnetwork was generated displaying the branches and complexes of the complete tree but only the nodes representing the isolates used in this study.


Multiple-locus variable number tandem repeat analysis for Streptococcus pneumoniae: comparison with PFGE and MLST.

Elberse KE, Nunes S, Sá-Leão R, van der Heide HG, Schouls LM - PLoS ONE (2011)

High congruence between MLVA and MLST.Minimum spanning tree of the results obtained by MLST (A) and MLVA (B) for the 263 isolates of the test collection. Each circle indicates a genotype. The size of the circle is proportional to the number of isolates with the same type. Lines linking two types denote a single locus difference between those types. In Figure 1A the MLST complexes are indicated by halos. Seven MLST complexes are discussed in the manuscript and these are colored and named according to the nomenclature of S. pneumoniae MLST database (www.mlst.net, last accessed on October 20, 2010). The white nodes represent the isolates within this test collection that are not discussed. The same colors were applied to the minimum spanning tree based on MLVA in Figure 1B. This minimum spanning tree is based on the entire MLVA database (last accessed on October 20, 2010), and only the branches are made visible. The MLVA types of the 263 isolates used in this study were depicted as circles. The halos indicate the MLVA complexes.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3102655&req=5

pone-0019668-g001: High congruence between MLVA and MLST.Minimum spanning tree of the results obtained by MLST (A) and MLVA (B) for the 263 isolates of the test collection. Each circle indicates a genotype. The size of the circle is proportional to the number of isolates with the same type. Lines linking two types denote a single locus difference between those types. In Figure 1A the MLST complexes are indicated by halos. Seven MLST complexes are discussed in the manuscript and these are colored and named according to the nomenclature of S. pneumoniae MLST database (www.mlst.net, last accessed on October 20, 2010). The white nodes represent the isolates within this test collection that are not discussed. The same colors were applied to the minimum spanning tree based on MLVA in Figure 1B. This minimum spanning tree is based on the entire MLVA database (last accessed on October 20, 2010), and only the branches are made visible. The MLVA types of the 263 isolates used in this study were depicted as circles. The halos indicate the MLVA complexes.
Mentions: Although there was considerable concordance between MLST and MLVA, some of the isolates that were grouped by MLST could be further distinguished by MLVA. In Figure 1A a minimum spanning tree is depicted based on the MLST results for the 263 isolates of the test collection. Fifty-six clonal complexes (CC), and 13 singletons were detected and the 7 largest CCs were chosen for further comparisons and are highlighted in color. To visualize the relationship between MLST and MLVA, the same color legend was applied to the minimum spanning tree based on MLVA (Fig. 1B). To create this minimum spanning tree, the entries in the entire MLVA database (n = 2973) were used. Subsequently, a subnetwork was generated displaying the branches and complexes of the complete tree but only the nodes representing the isolates used in this study.

Bottom Line: Furthermore, the Wallace of MLVA to clonal complex of MLST was even higher: 99.5%.For some isolates belonging to a single MLST clonal complex although displaying different serotypes, MLVA was more discriminatory, generating groups according to serotype or serogroup.In the companion paper published simultaneously in this issue we applied the MLVA to assess the pneumococcal population structure of isolates causing invasive disease in The Netherlands before the introduction of the 7-valent conjugate vaccine.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Infectious Diseases and Perinatal Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands. Karin.Elberse@rivm.nl

ABSTRACT
In the era of pneumococcal conjugate vaccines, surveillance of pneumococcal disease and carriage remains of utmost importance as important changes may occur in the population. To monitor these alterations reliable genotyping methods are required for large-scale applications. We introduced a high throughput multiple-locus variable number tandem repeat analysis (MLVA) and compared this method with pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The MLVA described here is based on 8 BOX loci that are amplified in two multiplex PCRs. The labeled PCR products are sized on an automated DNA sequencer to accurately determine the number of tandem repeats. The composite of the number of repeats of the BOX loci makes up a numerical profile that is used for identification and clustering. In this study, MLVA was performed on 263 carriage isolates that were previously characterized by MLST and PFGE. MLVA, MLST and PFGE (cut-off of 80%) yielded 164, 120, and 87 types, respectively. The three typing methods had Simpson's diversity indices of 98.5% or higher. Congruence between MLST and MLVA was high. The Wallace of MLVA to MLST was 0.874, meaning that if two strains had the same MLVA type they had an 88% chance of having the same MLST type. Furthermore, the Wallace of MLVA to clonal complex of MLST was even higher: 99.5%. For some isolates belonging to a single MLST clonal complex although displaying different serotypes, MLVA was more discriminatory, generating groups according to serotype or serogroup. Overall, MLVA is a promising genotyping method that is easy to perform and a relatively cheap alternative to PFGE and MLST. In the companion paper published simultaneously in this issue we applied the MLVA to assess the pneumococcal population structure of isolates causing invasive disease in The Netherlands before the introduction of the 7-valent conjugate vaccine.

Show MeSH
Related in: MedlinePlus