Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

J U'ren, James Schupp, Talima Pearson, Heidie Hornstra, C Friedman, K Smith, R Daugherty, S Rhoton, Benjamin Leadem, Shalamar Georgia, M Cardon, L Huynh, D Deshazer, S Harvey, R Robison, D Gal, Mark Mayo, David M Wagner, Bart Currie, Paul S Keim

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    Background. The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ?18,000 generations. Results. B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10(-5 )per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion. The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen. � 2007 U'Ren et al; licensee BioMed Central Ltd.
    Original languageEnglish
    Pages (from-to)1-20
    Number of pages20
    JournalBMC Microbiology
    Volume7
    Publication statusPublished - 2007

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    Burkholderia pseudomallei
    Tandem Repeat Sequences
    Genome
    Malleus
    Minisatellite Repeats
    Melioidosis
    Bacteria
    Intergenic DNA
    Livestock
    Mutation Rate
    Communicable Diseases
    Alleles

    Cite this

    U'ren, J., Schupp, J., Pearson, T., Hornstra, H., Friedman, C., Smith, K., ... Keim, P. S. (2007). Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. BMC Microbiology, 7, 1-20.
    U'ren, J ; Schupp, James ; Pearson, Talima ; Hornstra, Heidie ; Friedman, C ; Smith, K ; Daugherty, R ; Rhoton, S ; Leadem, Benjamin ; Georgia, Shalamar ; Cardon, M ; Huynh, L ; Deshazer, D ; Harvey, S ; Robison, R ; Gal, D ; Mayo, Mark ; Wagner, David M ; Currie, Bart ; Keim, Paul S. / Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. In: BMC Microbiology. 2007 ; Vol. 7. pp. 1-20.
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    title = "Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping",
    abstract = "Background. The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ?18,000 generations. Results. B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10(-5 )per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion. The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen. � 2007 U'Ren et al; licensee BioMed Central Ltd.",
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    author = "J U'ren and James Schupp and Talima Pearson and Heidie Hornstra and C Friedman and K Smith and R Daugherty and S Rhoton and Benjamin Leadem and Shalamar Georgia and M Cardon and L Huynh and D Deshazer and S Harvey and R Robison and D Gal and Mark Mayo and Wagner, {David M} and Bart Currie and Keim, {Paul S}",
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    U'ren, J, Schupp, J, Pearson, T, Hornstra, H, Friedman, C, Smith, K, Daugherty, R, Rhoton, S, Leadem, B, Georgia, S, Cardon, M, Huynh, L, Deshazer, D, Harvey, S, Robison, R, Gal, D, Mayo, M, Wagner, DM, Currie, B & Keim, PS 2007, 'Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping', BMC Microbiology, vol. 7, pp. 1-20.

    Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. / U'ren, J; Schupp, James; Pearson, Talima; Hornstra, Heidie; Friedman, C; Smith, K; Daugherty, R; Rhoton, S; Leadem, Benjamin; Georgia, Shalamar; Cardon, M; Huynh, L; Deshazer, D; Harvey, S; Robison, R; Gal, D; Mayo, Mark; Wagner, David M; Currie, Bart; Keim, Paul S.

    In: BMC Microbiology, Vol. 7, 2007, p. 1-20.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

    AU - U'ren, J

    AU - Schupp, James

    AU - Pearson, Talima

    AU - Hornstra, Heidie

    AU - Friedman, C

    AU - Smith, K

    AU - Daugherty, R

    AU - Rhoton, S

    AU - Leadem, Benjamin

    AU - Georgia, Shalamar

    AU - Cardon, M

    AU - Huynh, L

    AU - Deshazer, D

    AU - Harvey, S

    AU - Robison, R

    AU - Gal, D

    AU - Mayo, Mark

    AU - Wagner, David M

    AU - Currie, Bart

    AU - Keim, Paul S

    PY - 2007

    Y1 - 2007

    N2 - Background. The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ?18,000 generations. Results. B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10(-5 )per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion. The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen. � 2007 U'Ren et al; licensee BioMed Central Ltd.

    AB - Background. The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ?18,000 generations. Results. B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10(-5 )per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion. The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen. � 2007 U'Ren et al; licensee BioMed Central Ltd.

    KW - article

    KW - bacterial genome

    KW - bacterium isolate

    KW - Burkholderia

    KW - Burkholderia mallei

    KW - Burkholderia pseudomallei

    KW - Burkholderia thailandensis

    KW - clone

    KW - gene mutation

    KW - genetic line

    KW - genetic screening

    KW - genotype

    KW - geographic distribution

    KW - microbial diversity

    KW - molecular epidemiology

    KW - mutational analysis

    KW - nonhuman

    KW - nucleotide sequence

    KW - polymorphic locus

    KW - variable number of tandem repeat

    KW - chemistry

    KW - DNA sequence

    KW - genetics

    KW - polymerase chain reaction

    KW - tandem repeat

    KW - Animalia

    KW - Bacteria (microorganisms)

    KW - bacterial DNA

    KW - DNA, Bacterial

    KW - Genome, Bacterial

    KW - Genotype

    KW - Polymerase Chain Reaction

    KW - Sequence Analysis, DNA

    KW - Tandem Repeat Sequences

    M3 - Article

    VL - 7

    SP - 1

    EP - 20

    JO - BMC Microbiology

    JF - BMC Microbiology

    SN - 1471-2180

    ER -