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Background  Strains of the endosymbiotic bacterium  Wolbachia pipientis  are extremely diverse both genotypically and in terms of their induced phenotypes in invertebrate hosts. Despite extensive molecular characterisation of  Wolbachia  diversity, little is known about the actual genomic diversity within or between closely related strains that group tightly on the basis of existing gene marker systems, including Multiple Locus Sequence Typing (MLST). There is an urgent need for higher resolution fingerprinting markers of  Wolbachia  for studies of population genetics, horizontal transmission and experimental evolution.    Results  The genome of the  w Mel  Wolbachia  strain that infects  Drosophila melanogaster  contains inter- and intragenic tandem repeats that may evolve through expansion or contraction. We identified hypervariable regions in  w Mel, including intergenic Variable Number Tandem Repeats (VNTRs), and genes encoding ankyrin (ANK) repeat domains. We amplified these markers from 14 related  Wolbachia  strains belonging to supergroup A and were successful in differentiating size polymorphic alleles. Because of their tandemly repeated structure and length polymorphism, the markers can be used in a PCR-diagnostic multilocus typing approach, analogous to the Multiple Locus VNTR Analysis (MLVA) established for many other bacteria and organisms. The isolated markers are highly specific for supergroup A and not informative for other supergroups. However,  in silico  analysis of completed genomes from other supergroups revealed the presence of tandem repeats that are variable and could therefore be useful for typing target strains.    Conclusions   Wolbachia  genomes contain inter- and intragenic tandem repeats that evolve through expansion or contraction. A selection of polymorphic tandem repeats is a novel and useful PCR diagnostic extension to the existing MLST typing system of  Wolbachia , as it allows rapid and inexpensive high-throughput fingerprinting of closely related strains for which polymorphic markers were previously lacking.

Tandem repeat markers as novel diagnostic tools for high resolution fingerprinting of Wolbachia