This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Klevytska, A. M.
Right arrow Articles by Keim, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Klevytska, A. M.
Right arrow Articles by Keim, P.

 Previous Article  |  Next Article 

Journal of Clinical Microbiology, September 2001, p. 3179-3185, Vol. 39, No. 9
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.9.3179-3185.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Identification and Characterization of Variable-Number Tandem Repeats in the Yersinia pestis Genome

Alexandra M. Klevytska,1,dagger Lance B. Price,1 James M. Schupp,1 Patricia L. Worsham,2 Jane Wong,3 and Paul Keim1,*

Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011-56401; United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702-50112; and Microbial Diseases Laboratory, California Department of Health Services, Berkeley, California 947043

Received 2 April 2001/Returned for modification 26 May 2001/Accepted 6 July 2001

Yersinia pestis, the infamous plague-causing pathogen, appears to have emerged in relatively recent history. Evidence of this fact comes from several studies that document a lack of nucleotide diversity in the Y. pestis genome. In contrast, we report that variable-number tandem repeat (VNTR) sequences are common in the Y. pestis genome and occur frequently in gene coding regions. Larger tandem repeat arrays, most useful for phylogenetic analysis, are present at an average of 2.18 arrays per 10 kbp and are distributed evenly throughout the genome and the two virulence plasmids, pCD1 and pMT1. We examined allelic diversity at 42 chromosomal VNTR loci in 24 selected isolates (12 globally distributed and 12 from Siskiyou County, Calif.). Vast differences in diversity were observed among the 42 VNTR loci, ranging from 2 to 11 alleles. We found that the maximum copy number of repeats in an array was highly correlated with diversity (R = 0.86). VNTR-based phylogenetic analysis of the 24 strains successfully grouped isolates from biovar orientalis and most of the antiqua and mediaevalis strains. Hence, multiple-locus VNTR analysis (MLVA) appears capable of both distinguishing closely related strains and successfully classifying more distant relationships. Harnessing the power of MLVA to establish standardized databases will enable researchers to better understand plague ecology and evolution around the world.

* Corresponding author. Mailing address: Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640. Phone: (520) 523-1078. Fax: (520) 523-7500. E-mail: Paul.Keim{at}nau.edu.

dagger Present address: Johns Hopkins School of Medicine, Department of Pathology, Baltimore, MD 21287-6417.

Journal of Clinical Microbiology, September 2001, p. 3179-3185, Vol. 39, No. 9
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.9.3179-3185.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Allix-Beguec, C., Harmsen, D., Weniger, T., Supply, P., Niemann, S. (2008). Evaluation and Strategy for Use of MIRU-VNTRplus, a Multifunctional Database for Online Analysis of Genotyping Data and Phylogenetic Identification of Mycobacterium tuberculosis Complex Isolates. J. Clin. Microbiol. 46: 2692-2699 [Abstract] [Full Text]  
  • Mullane, N. R., Ryan, M., Iversen, C., Murphy, M., O'Gaora, P., Quinn, T., Whyte, P., Wall, P. G., Fanning, S. (2008). Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for the Molecular Subtyping of Enterobacter sakazakii. Appl. Environ. Microbiol. 74: 1223-1231 [Abstract] [Full Text]  
  • Macdonald, T. E., Helma, C. H., Ticknor, L. O., Jackson, P. J., Okinaka, R. T., Smith, L. A., Smith, T. J., Hill, K. K. (2008). Differentiation of Clostridium botulinum Serotype A Strains by Multiple-Locus Variable-Number Tandem-Repeat Analysis. Appl. Environ. Microbiol. 74: 875-882 [Abstract] [Full Text]  
  • Kawamori, F., Hiroi, M., Harada, T., Ohata, K., Sugiyama, K., Masuda, T., Ohashi, N. (2008). Molecular typing of Japanese Escherichia coli O157 : H7 isolates from clinical specimens by multilocus variable-number tandem repeat analysis and PFGE. J Med Microbiol 57: 58-63 [Abstract] [Full Text]  
  • Danin-Poleg, Y., Cohen, L. A., Gancz, H., Broza, Y. Y., Goldshmidt, H., Malul, E., Valinsky, L., Lerner, L., Broza, M., Kashi, Y. (2007). Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats. J. Clin. Microbiol. 45: 736-746 [Abstract] [Full Text]  
  • Boxrud, D., Pederson-Gulrud, K., Wotton, J., Medus, C., Lyszkowicz, E., Besser, J., Bartkus, J. M. (2007). Comparison of Multiple-Locus Variable-Number Tandem Repeat Analysis, Pulsed-Field Gel Electrophoresis, and Phage Typing for Subtype Analysis of Salmonella enterica Serotype Enteritidis. J. Clin. Microbiol. 45: 536-543 [Abstract] [Full Text]  
  • Pasqualotto, A. C., Denning, D. W., Anderson, M. J. (2007). A Cautionary Tale: Lack of Consistency in Allele Sizes between Two Laboratories for a Published Multilocus Microsatellite Typing System. J. Clin. Microbiol. 45: 522-528 [Abstract] [Full Text]  
  • Chang, C.-H., Chang, Y.-C., Underwood, A., Chiou, C.-S., Kao, C.-Y. (2007). VNTRDB: a bacterial variable number tandem repeat locus database. Nucleic Acids Res 35: D416-D421 [Abstract] [Full Text]  
  • Lowell, J. L., Zhansarina, A., Yockey, B., Meka-Mechenko, T., Stybayeva, G., Atshabar, B., Nekrassova, L., Tashmetov, R., Kenghebaeva, K., Chu, M. C., Kosoy, M., Antolin, M. F., Gage, K. L. (2007). Phenotypic and molecular characterizations of Yersinia pestis isolates from Kazakhstan and adjacent regions. Microbiology 153: 169-177 [Abstract] [Full Text]  
  • Van Ert, M. N., Easterday, W. R., Simonson, T. S., U'Ren, J. M., Pearson, T., Kenefic, L. J., Busch, J. D., Huynh, L. Y., Dukerich, M., Trim, C. B., Beaudry, J., Welty-Bernard, A., Read, T., Fraser, C. M., Ravel, J., Keim, P. (2007). Strain-Specific Single-Nucleotide Polymorphism Assays for the Bacillus anthracis Ames Strain. J. Clin. Microbiol. 45: 47-53 [Abstract] [Full Text]  
  • Witonski, D., Stefanova, R., Ranganathan, A., Schutze, G. E., Eisenach, K. D., Cave, M. D. (2006). Variable-Number Tandem Repeats That Are Useful in Genotyping Isolates of Salmonella enterica subsp. enterica Serovars Typhimurium and Newport. J. Clin. Microbiol. 44: 3849-3854 [Abstract] [Full Text]  
  • Abele-Horn, M., Vogel, U., Klare, I., Konstabel, C., Trabold, R., Kurihara, R., Witte, W., Kreth, W., Schlegel, P.-G., Claus, H. (2006). Molecular Epidemiology of Hospital-Acquired Vancomycin-Resistant Enterococci. J. Clin. Microbiol. 44: 4009-4013 [Abstract] [Full Text]  
  • Vogler, A. J., Keys, C., Nemoto, Y., Colman, R. E., Jay, Z., Keim, P. (2006). Effect of Repeat Copy Number on Variable-Number Tandem Repeat Mutations in Escherichia coli O157:H7.. J. Bacteriol. 188: 4253-4263 [Abstract] [Full Text]  
  • Chain, P. S. G., Hu, P., Malfatti, S. A., Radnedge, L., Larimer, F., Vergez, L. M., Worsham, P., Chu, M. C., Andersen, G. L. (2006). Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen.. J. Bacteriol. 188: 4453-4463 [Abstract] [Full Text]  
  • Schouls, L. M., van der Ende, A., Damen, M., van de Pol, I. (2006). Multiple-Locus Variable-Number Tandem Repeat Analysis of Neisseria meningitidis Yields Groupings Similar to Those Obtained by Multilocus Sequence Typing. J. Clin. Microbiol. 44: 1509-1518 [Abstract] [Full Text]  
  • Anisimov, A. P., Dentovskaya, S. V., Titareva, G. M., Bakhteeva, I. V., Shaikhutdinova, R. Z., Balakhonov, S. V., Lindner, B., Kocharova, N. A., Senchenkova, S. N., Holst, O., Pier, G. B., Knirel, Y. A. (2005). Intraspecies and Temperature-Dependent Variations in Susceptibility of Yersinia pestis to the Bactericidal Action of Serum and to Polymyxin B. Infect. Immun. 73: 7324-7331 [Abstract] [Full Text]  
  • Vitorino, L., de Sousa, R., Bacellar, F., Ze-Ze, L. (2005). Characterization of a tandem repeat polymorphism in Rickettsia strains. J Med Microbiol 54: 833-841 [Abstract] [Full Text]  
  • de Valk, H. A., Meis, J. F. G. M., Curfs, I. M., Muehlethaler, K., Mouton, J. W., Klaassen, C. H. W. (2005). Use of a Novel Panel of Nine Short Tandem Repeats for Exact and High-Resolution Fingerprinting of Aspergillus fumigatus Isolates. J. Clin. Microbiol. 43: 4112-4120 [Abstract] [Full Text]  
  • Schouls, L. M., van der Ende, A., van de Pol, I., Schot, C., Spanjaard, L., Vauterin, P., Wilderbeek, D., Witteveen, S. (2005). Increase in Genetic Diversity of Haemophilus influenzae Serotype b (Hib) Strains after Introduction of Hib Vaccination in The Netherlands. J. Clin. Microbiol. 43: 2741-2749 [Abstract] [Full Text]  
  • Ablordey, A., Swings, J., Hubans, C., Chemlal, K., Locht, C., Portaels, F., Supply, P. (2005). Multilocus Variable-Number Tandem Repeat Typing of Mycobacterium ulcerans. J. Clin. Microbiol. 43: 1546-1551 [Abstract] [Full Text]  
  • Yazdankhah, S. P., Lindstedt, B.-A., Caugant, D. A. (2005). Use of Variable-Number Tandem Repeats To Examine Genetic Diversity of Neisseria meningitidis. J. Clin. Microbiol. 43: 1699-1705 [Abstract] [Full Text]  
  • Lowell, J. L., Wagner, D. M., Atshabar, B., Antolin, M. F., Vogler, A. J., Keim, P., Chu, M. C., Gage, K. L. (2005). Identifying Sources of Human Exposure to Plague. J. Clin. Microbiol. 43: 650-656 [Abstract] [Full Text]  
  • Foucault, C., La Scola, B., Lindroos, H., Andersson, S. G. E., Raoult, D. (2005). Multispacer Typing Technique for Sequence-Based Typing of Bartonella quintana. J. Clin. Microbiol. 43: 41-48 [Abstract] [Full Text]  
  • Achtman, M., Morelli, G., Zhu, P., Wirth, T., Diehl, I., Kusecek, B., Vogler, A. J., Wagner, D. M., Allender, C. J., Easterday, W. R., Chenal-Francisque, V., Worsham, P., Thomson, N. R., Parkhill, J., Lindler, L. E., Carniel, E., Keim, P. (2004). Microevolution and history of the plague bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. USA 101: 17837-17842 [Abstract] [Full Text]  
  • Young, S. K., Taylor, G. M., Jain, S., Suneetha, L. M., Suneetha, S., Lockwood, D. N. J., Young, D. B. (2004). Microsatellite Mapping of Mycobacterium leprae Populations in Infected Humans. J. Clin. Microbiol. 42: 4931-4936 [Abstract] [Full Text]  
  • Johansson, A., Farlow, J., Larsson, P., Dukerich, M., Chambers, E., Bystrom, M., Fox, J., Chu, M., Forsman, M., Sjostedt, A., Keim, P. (2004). Worldwide Genetic Relationships among Francisella tularensis Isolates Determined by Multiple-Locus Variable-Number Tandem Repeat Analysis. J. Bacteriol. 186: 5808-5818 [Abstract] [Full Text]  
  • Schouls, L. M., van der Heide, H. G. J., Vauterin, L., Vauterin, P., Mooi, F. R. (2004). Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s. J. Bacteriol. 186: 5496-5505 [Abstract] [Full Text]  
  • van der Woude, M. W., Baumler, A. J. (2004). Phase and Antigenic Variation in Bacteria. Clin. Microbiol. Rev. 17: 581-611 [Abstract] [Full Text]  
  • Girard, J. M., Wagner, D. M., Vogler, A. J., Keys, C., Allender, C. J., Drickamer, L. C., Keim, P. (2004). From The Cover: Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proc. Natl. Acad. Sci. USA 101: 8408-8413 [Abstract] [Full Text]  
  • Anisimov, A. P., Lindler, L. E., Pier, G. B. (2004). Intraspecific Diversity of Yersinia pestis. Clin. Microbiol. Rev. 17: 434-464 [Abstract] [Full Text]  
  • Groathouse, N. A., Rivoire, B., Kim, H., Lee, H., Cho, S.-N., Brennan, P. J., Vissa, V. D. (2004). Multiple Polymorphic Loci for Molecular Typing of Strains of Mycobacterium leprae. J. Clin. Microbiol. 42: 1666-1672 [Abstract] [Full Text]  
  • Noller, A. C., McEllistrem, M. C., Pacheco, A. G. F., Boxrud, D. J., Harrison, L. H. (2003). Multilocus Variable-Number Tandem Repeat Analysis Distinguishes Outbreak and Sporadic Escherichia coli O157:H7 Isolates. J. Clin. Microbiol. 41: 5389-5397 [Abstract] [Full Text]  
  • Feldgarden, M., Byrd, N., Cohan, F. M. (2003). Gradual evolution in bacteria: evidence from Bacillus systematics. Microbiology 149: 3565-3573 [Abstract] [Full Text]  
  • Liu, Y., Lee, M.-A., Ooi, E.-E., Mavis, Y., Tan, A.-L., Quek, H.-H. (2003). Molecular Typing of Salmonella enterica Serovar Typhi Isolates from Various Countries in Asia by a Multiplex PCR Assay on Variable-Number Tandem Repeats. J. Clin. Microbiol. 41: 4388-4394 [Abstract] [Full Text]  
  • Lindstedt, B.-A., Heir, E., Gjernes, E., Kapperud, G. (2003). DNA Fingerprinting of Salmonella enterica subsp. enterica Serovar Typhimurium with Emphasis on Phage Type DT104 Based on Variable Number of Tandem Repeat Loci. J. Clin. Microbiol. 41: 1469-1479 [Abstract] [Full Text]  
  • Savine, E., Warren, R. M., van der Spuy, G. D., Beyers, N., van Helden, P. D., Locht, C., Supply, P. (2002). Stability of Variable-Number Tandem Repeats of Mycobacterial Interspersed Repetitive Units from 12 Loci in Serial Isolates of Mycobacterium tuberculosis. J. Clin. Microbiol. 40: 4561-4566 [Abstract] [Full Text]  
  • Farlow, J., Smith, K. L., Wong, J., Abrams, M., Lytle, M., Keim, P. (2001). Francisella tularensis Strain Typing Using Multiple-Locus, Variable-Number Tandem Repeat Analysis. J. Clin. Microbiol. 39: 3186-3192 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»