to investigate this issue , we determined sequences of ospc and igs1 loci , and in selected cases the ospa and igs2 loci , in 1,522 dna extracts from b. burgdorferi  infected ixodes scapularis nymphs collected from the northeastern , mid - atlantic , and north - central united states during the summers of 2004 , 2005 , 2006 , and 2007 , as described ( 4,11 ) . we also included results from 214 infected i. pacificus nymphs collected in mendocino county , california ( 5 ) ; 20 infected i. pacificus adults from contra costa county , california ( j. bunikis and a.g . data ) ; and 10 b. burgdorferi genomes ( strains b31 , zs7 , 156a , 64b , 72a , 118a , wi91 - 23 , 94a , 29805 , and ca-11.2a ) , for which sequences are publicly available ( www.ncbi.nlm.nih.gov ) . multilocus sequence typing ( mlst ) , based on 8 chromosomal housekeeping genes , had been carried out for several strains represented in the extracts ( table ) ( 4,12 ) . the corresponding mlst types of the 10 genome sequences were assigned by reference to a b. burgdorferi mlst database ( http://borrelia.mlst.net ) ( 12 ) . the methods for 1 ) dna extraction from ticks ( 11 ) , 2 ) pcr amplification of ospc , ospa , and igs1 ( 7 ) , 3 ) amplification of igs2 ( 8) , and 4 ) amplification of 8 chromosomal loci for mlst ( 12 ) have been described . sequences for both strands were determined from either pcr products or cloned fragments with custom primers ( 7 ) . ( 13 ) until , after exhausting the alphabet , we assigned both a letter and , arbitrarily , the number 3 ( e.g. , c3 ) when a new nucleotide sequence differed by > 8% from known ospc alleles . we distinguished ospc variants with < 1% sequence difference by adding a lowercase letter , e.g. , da and db . except for ospc d3 and oa , novel polymorphisms were confirmed in at least 1 other sample . to simplify igs1 nomenclature , we numbered types sequentially , beginning with the original 9 types ( 7 ) ; ospa alleles ( 7 ) and igs2 loci were likewise sequentially numbered . the table a1 provides accession numbers for all sequences , as well as original and revised names for igs1 sequences . for 741 ixodes ticks from northeastern and north - central united states or from northern california , 1 ospc allele was identified and sequenced . in the remaining samples , we found a mixture of strains or evidence of > 2 ospc and/or > 2 igs sequences ( 9 ) . in 678 ( 91% ) of the 741 samples with a single ospc , the allele could be matched with particular igs1 ( table ) . we identified 9 unique ospc sequences : fc , ob , ub , a3 , b3 , c3 , d3 , e3 , and f3 , all from the north - central united states . ( 5 ) . of 32 codon - aligned ospc sequences , 6 pairs and 1 trio ( fa , fb , and fc ) differed in sequence by < nine novel igs1 sequences , numbered 2431 and 33 , were discovered in samples from which ospc alleles were determined . a ) bayesian and maximum - likelihood phylogenetic inference of outer surface protein c ( ospc ) gene sequences and b ) concatenated multilocus sequence typing ( mlst ) sequences of borrelia burgdorferi . labels at the tips refer to ospc alleles ( a ) or mlst ( st ) and linked ospc alleles ( b ; table ) . nodes with posterior probabilities of > 0.5 are indicated by values above the branches . below the branches are integer values for nodes with support of > 500 of 1,000 bootstrap iterations of the maximum - likelihood method , as carried out with the phyml 3.0 algorithm ( www.atgc-montpellier.fr/phyml ) . for both data sets and both algorithms , the models were general time reversible with empirical estimations of the proportions of invariant sites and gamma shape parameters . genbank accession numbers for sequences are given in the table a1 . when we confined analysis to samples from northeastern states , we confirmed linkage disequilibrium between ospc and igs1 loci ( 7,10,14 ) . however , when results from north - central states and california were included , a different picture emerged ( table , figure , panel b ) . most of the ospc alleles showed concordance with the chromosomal loci ; monophyletic mlst showed either the same ospc allele or a minor variant of it . however , in several instances , the ospc alleles were linked to different igs1 sequences , different ospa sequences , and/or different mlst with internal nodes in common . we observed this linkage for ospc alleles a , g , hb , and n. in the case of ospc hb , the shared internal node was deep . we applied the simpson index of diversity , as implemented by hunter and gaston ( 15 ) , to the data in the table to compare the discriminatory power ( dp ) of genotyping on the basis of a combination of ospc and igs1 sequences with genotyping by 8-locus mlst ( 12 ) . for double - locus typing , there were 43 types were found for 678 strains ; dp value was 0.96 . for mlst in this data set , 36 types were shown for 554 strains ; dp was 0.95 . in the study of hoen et al . in which selection was made for geographic isolation , 37 types were distributed among 78 strains ; dp was 0.97 ( 4 ) . dependence on a single locus for typing may falsely identify different lineages as the same , especially when the samples come from different regions . other loci may be as informative as ospc or igs1 , but the abundance of extant sequences for these loci justifies their continued use . uncertainties about the linkage of ospc and igs1 usually can be resolved by sequencing the ospa allele ( table ) . one interpretation of these findings is that lateral gene transfer of all or nearly all of an ospc gene has occurred between different genetic lineages . we previously had not detected recombination at the igs1 locus on the chromosome ( 7 ) , but there may be recombination at other chromosomal loci , as well as plasmid loci ( 6 ) . besides extending the understanding of the geographic structuring of the b. burgdorferi population , the results indicate that the ospc allele does not fully represent the complexity of b. burgdorferi lineages ; thus , inferring phenotypes on the basis of this single locus should be made with caution .
borrelia burdorferi genotype in the northeastern united states is associated with lyme borreliosis severity . 
 analysis of dna sequences of the outer surface protein c gene and rrs - rrla intergenic spacer from extracts of ixodes spp . 
 ticks in 3 us regions showed linkage disequilibrium between the 2 loci within a region but not consistently between regions .