A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis

Abstract

BackgroundSome pathogenic bacteria are genetically very homogeneous, making strain discrimination difficult. In the last few years, tandem repeats have been increasingly recognized as markers of choice for genotyping a number of pathogens. The rapid evolution of these structures appears to contribute to the phenotypic flexibility of pathogens. The availability of whole-genome sequences has opened the way to the systematic evaluation of tandem repeats diversity and application to epidemiological studies.ResultsThis report presents a database () of tandem repeats from publicly available bacterial genomes which facilitates the identification and selection of tandem repeats. We illustrate the use of this database by the characterization of minisatellites from two important human pathogens, Yersinia pestis and Bacillus anthracis. In order to avoid simple sequence contingency loci which may be of limited value as epidemiological markers, and to provide genotyping tools amenable to ordinary agarose gel electrophoresis, only tandem repeats with repeat units at least 9 bp long were evaluated. Yersinia pestis contains 64 such minisatellites in which the unit is repeated at least 7 times. An additional collection of 12 loci with at least 6 units, and a high internal conservation were also evaluated. Forty-nine are polymorphic among five Yersinia strains (twenty-five among three Y. pestis strains). Bacillus anthracis contains 30 comparable structures in which the unit is repeated at least 10 times. Half of these tandem repeats show polymorphism among the strains tested.ConclusionsAnalysis of the currently available bacterial genome sequences classifies Bacillus anthracis and Yersinia pestis as having an average (approximately 30 per Mb) density of tandem repeat arrays longer than 100 bp when compared to the other bacterial genomes analysed to date. In both cases, testing a fraction of these sequences for polymorphism was sufficient to quickly develop a set of more than fifteen informative markers, some of which show a very high degree of polymorphism. In one instance, the polymorphism information content index reaches 0.82 with allele length covering a wide size range (600-1950 bp), and nine alleles resolved in the small number of independent Bacillus anthracis strains typed here.

Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation

“…All the repeat units at the different loci contained point mutations, and small insertions and deletions; this phenomenon was first described in the minisatellite in the human insulin gene, and has since been shown to be the case in all VNTR loci described, both eukaryotic and prokaryotic (Mazars et al, 2001;Owerbach & Aagaard, 1984). Like the VNTRs described in other bacterial genomes, and unlike those in eukaryotes, the repeat units in S. aureus are not G+C rich (Le Fleche et al, 2001). …”

Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

“…Typing of repetitive DNA markers, such as SSRs, is invaluable in genotyping organisms with limited genetic diversity (1,23). However, inherent problems in sequencing mononucleotide repeats limit its application, as Sanger sequencing often fails to resolve poly(G) repeats exceeding 11 bp (10,15).…”

CRISPRs: Molecular Signatures Used for Pathogen Subtyping

“…As mentioned previously, data from early work in GAS suggested that PCR/CRISPR array size correlated with RFLP typing results (66). Following this work, Vergnaud and colleagues used the YPa (Yp1) locus as a VNTR marker for MLVA in Y. pestis (33,90). More recently, using both outbreak and control isolates, two groups have shown that "CRISPR size typing" can be successfully implemented in Salmonella serovar Typhimurium and Salmonella serovar Newport (49,69).…”