Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a web-based resource

Abstract

Background: Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The previously developed tandem repeats database takes advantage of the release of genome sequence data for a growing number of bacteria to facilitate the identification of tandem repeats. The development of an assay then requires the evaluation of tandem repeat polymorphism on well-selected sets of isolates. In the case of major human pathogens, such as S. aureus, more than one strain is being sequenced, so that tandem repeats most likely to be polymorphic can now be selected in silico based on genome sequence comparison.

Results: In addition to the previously described general Tandem Repeats Database, we have developed a tool to automatically identify tandem repeats of a different length in the genome sequence of two (or more) closely related bacterial strains. Genome comparisons are pre-computed. The results of the comparisons are parsed in a database, which can be conveniently queried over the internet according to criteria of practical value, including repeat unit length, predicted size difference, etc. Comparisons are available for 16 bacterial species, and the orthopox viruses, including the variola virus and three of its close neighbors.

Conclusions: We are presenting an internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools accessible at http://minisatellites.u-psud.fr now comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial Genotyping Page" is a service for strain identification at the subspecies level.

Figure 1

The procedure to find polymorphic tandem repeats for use in strain typing. The steps leading from the release of a complete (or incomplete) genome sequence to the validation of new polymorphic markers are described. The purpose of the web-based tools developed is to facilitate the bioinformatics data-management steps.

Figure 2

Comparison of strains using different indexes. The four columns correspond to (from left to right): (1) mean %identity provided by BLAST when the match occurred on more than half the length of the 500 bp of submitted flanking sequence ; (2) proportion (%) of flanking sequences that matched on more than half their length between the two strains ; (3) proportion (%) of tandem repeats of a different size in the two strains ; and (4) plot of the positions of homologous tandem repeat loci in the two genomes which indirectly reflects large scale genome rearrangements. Species are listed according to the first index (mean %identity)

Figure 3

Example of a query in the Strain Comparison Page. On the top, the query page shows the 28 comparisons currently available (others will be added as new genome sequences are finished and released). Bottom, the result of a query performed for Mycobacterium tuberculosis strains H37Rv and CDC1551 is summarized.

Figure 4

Example of a query in the Strain Comparison Page for more than two strains. Top, the query page shows the 6 comparisons currently available (others will be added as new genome sequences are finished and released). Bottom, the result of a query performed for Escherichia coli strains O157:H7 Sakaï, O157:H7 EDL933, K12 and UPEC-CFT073 is summarized. In several loci, the size of the repeat is listed differently for the different strains, which is due to different detections by the Tandem Repeats Finder, usually as a result of internal variations within the tandem array. Total length is calculated from positions of matching flanking sequences in the different strains, and does not necessarily correspond to the length of the tandem repeat detected by TRF in the locus. "Number of alleles" refers to the number of predicted sizes differing by at least 5 bp among the strains compared.

Figure 5

Example of a query in the "Blast of PCR primers" page, providing the length of the PCR products in the strains/species where the primer pair matches, and links to the corresponding tandem repeats descriptions.

Figure 6

Proportion of predicted polymorphic (pink) and monomorphic (grey) tandem repeats according to different parameters (internal homogeneity of the repeat array (%matches) or total length). P-values obtained for the non-parametric Wilcoxon tests appear below each histogram.