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

Jana M. U'Ren, James M. Schupp, Talima R Pearson, Heidie Hornstra, Christine Friedman, Kimothy L. Smith, Rebecca Daugherty, Shane D. Rhoton, Ben Leadem, Shalamar Georgia, Michelle Cardon, Lynn Y. Huynh, David Deshazer, Steven P. Harvey, Richard Robison, Daniel Gal, Mark J. Mayo, David M Wagner, Bart J. Currie, Paul S Keim

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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.

Original languageEnglish (US)
Article number23
JournalBMC Microbiology
Volume7
DOIs
StatePublished - 2007

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

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

Cite this

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. / U'Ren, Jana M.; Schupp, James M.; Pearson, Talima R; Hornstra, Heidie; Friedman, Christine; Smith, Kimothy L.; Daugherty, Rebecca; Rhoton, Shane D.; Leadem, Ben; Georgia, Shalamar; Cardon, Michelle; Huynh, Lynn Y.; Deshazer, David; Harvey, Steven P.; Robison, Richard; Gal, Daniel; Mayo, Mark J.; Wagner, David M; Currie, Bart J.; Keim, Paul S.

In: BMC Microbiology, Vol. 7, 23, 2007.

Research output: Contribution to journalArticle

U'Ren, JM, Schupp, JM, Pearson, TR, Hornstra, H, Friedman, C, Smith, KL, Daugherty, R, Rhoton, SD, Leadem, B, Georgia, S, Cardon, M, Huynh, LY, Deshazer, D, Harvey, SP, Robison, R, Gal, D, Mayo, MJ, Wagner, DM, Currie, BJ & Keim, PS 2007, 'Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping', BMC Microbiology, vol. 7, 23. https://doi.org/10.1186/1471-2180-7-23
U'Ren, Jana M. ; Schupp, James M. ; Pearson, Talima R ; Hornstra, Heidie ; Friedman, Christine ; Smith, Kimothy L. ; Daugherty, Rebecca ; Rhoton, Shane D. ; Leadem, Ben ; Georgia, Shalamar ; Cardon, Michelle ; Huynh, Lynn Y. ; Deshazer, David ; Harvey, Steven P. ; Robison, Richard ; Gal, Daniel ; Mayo, Mark J. ; Wagner, David M ; Currie, Bart J. ; Keim, Paul S. / Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. In: BMC Microbiology. 2007 ; Vol. 7.
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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.",
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T1 - Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

AU - U'Ren, Jana M.

AU - Schupp, James M.

AU - Pearson, Talima R

AU - Hornstra, Heidie

AU - Friedman, Christine

AU - Smith, Kimothy L.

AU - Daugherty, Rebecca

AU - Rhoton, Shane D.

AU - Leadem, Ben

AU - Georgia, Shalamar

AU - Cardon, Michelle

AU - Huynh, Lynn Y.

AU - Deshazer, David

AU - Harvey, Steven P.

AU - Robison, Richard

AU - Gal, Daniel

AU - Mayo, Mark J.

AU - Wagner, David M

AU - Currie, Bart J.

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.

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.

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