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Background  Deer tick-transmitted human babesiosis due to  Babesia microti  appears to be expanding its distribution and prevalence in the northeastern United States. One hypothesis for this emergence is the introduction of parasites into new sites from areas of long-standing transmission, such as Nantucket Island, Massachusetts.    Methods  We developed a typing system based on variable number tandem repeat loci that distinguished individual  B. microti  genotypes. We thereby analyzed the population structure of parasites from 11 sites, representing long-standing and newly emerging transmission in southern New England (northeastern United States), and compared their haplotypes and allele frequencies to determine the most probable number of  B. microti  populations represented by our enzootic collections. We expected to find evidence for a point source introduction across southern New England, with all parasites clearly derived from Nantucket, the site with the most intense longstanding transmission.    Results   B. microti  in southern New England comprises at least two major populations, arguing against a single source. The Nantucket group comprises Martha's Vineyard, Nantucket and nearby Cape Cod. The Connecticut/Rhode Island (CT/RI) group consists of all the samples from those states along with samples from emerging sites in Massachusetts.    Conclusions  The expansion of  B. microti  in the southern New England mainland is not due to parasites from the nearby terminal moraine islands (Nantucket group), but rather from the CT/RI group. The development of new  B. microti  foci is likely due to a mix of local intensification of transmission within relict foci across southern New England as well as long distance introduction events.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-014-0546-y) contains supplementary material, which is available to authorized users.

Not “out of Nantucket”: Babesia microti in southern New England comprises at least two major populations