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Variable-Number Tandem Repeats That Are Useful in Genotyping Isolates of Salmonella enterica subsp. enterica Serovars Typhimurium and Newport

D. Witonski,^4,6 R. Stefanova,^1,4,6, A. Ranganathan,^4,6 G. E. Schutze,^1,3,5 K. D. Eisenach,^1,2,6 and M. D. Cave^4,6*

Departments of Pathology,¹ Microbiology and Immunology,² Pediatrics,³ Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences,⁴ Arkansas Childrens Hospital,⁵ Medical Research Service, Central Arkansas Veterans Healthcare System, Little Rock, Arkansas 72205⁶

Received 3 March 2006/ Returned for modification 16 June 2006/ Accepted 15 August 2006

The genome of Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 was analyzed for direct repeats, and 54 sequences containing variable-number tandem repeat loci were identified. Ten primer pairs that anneal upstream and downstream of each selected locus were designed and used to amplify PCR targets in isolates of S. enterica serovars Typhimurium and Newport. Four of the 10 loci did not show polymorphism in the length of products. Six loci were selected for analysis. Isolates of S. enterica serovars Typhimurium and Newport that were related to specific outbreaks and showed identical pulsed-field gel electrophoresis patterns were indistinguishable by the length of the six variable-number tandem repeats. Isolates that differed in their pulsed-field gel electrophoresis patterns showed polymorphism in variable-number tandem repeat profiles. Length of the products was confirmed by DNA sequence analysis. Only 2 of the 10 loci contained exact integers of the direct repeat. Eight loci contained partial copies. The partial copies were maintained at the ends of the variable-number tandem repeat loci in all isolates. In spite of having partial copies that were maintained in all isolates, the number of direct repeats at a locus was polymorphic. Six variable-number tandem repeat loci were useful in distinguishing isolates of S. enterica serovars Typhimurium and Newport that had different pulsed-field gel electrophoresis patterns and in identifying outbreak-associated cases that shared a common pulsed-field gel pattern.

Published ahead of print on 30 August 2006.

Present address: Public Health Laboratories, Arkansas Department of Health and Human Services, Little Rock, AR 72207.

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