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The survey is based on a total of 1263 records (738 isolations and 525 molecular DNA detections) of five Borrelia burgdorferi s.l. genomic groups available from 26 European countries: B. burgdorferi sensu stricto, B. afzelii, B. garinii, B. valaisiana (= VS116) and B. lusitaniae (= PoTiB2). It shows the geographic distribution, the source (ixodid ticks 802 records, fleas 2 records, mosquitoes 2 records, wild mammals 66 records, human patients 391 records) and the association of the genomic groups with particular clinical manifestations of Lyme borreliosis in humans (B. afzelii significantly prevails in skin lesions whereas B. garinii is more often associated with neuroborreliosis). The most frequent genomic groups in Europe are B. garinii (501 records) and B. afzelii (469 records). They occur across the continent and islands, whereas the third frequent genomic group, B. burgdorferi s.s. (201 records), has only rarely been isolated in eastern Europe. The remaining genomic groups, i.e. B. valaisiana (85 records) and B. lusitaniae (7 records) have only been isolated from, or detected in, Ixodes ricinus ticks in a few European countries.