Table 4. SNPs and combinations of SNPs that correlate 100% with designated cluster and disease phenotype group*.
| Gene locus | SNP no. | Cluster III | Cluster II | Subcluster I† |
|---|---|---|---|---|
|
glyA
|
1–5 |
|
4‡ |
|
|
mdhC
|
6–8 |
|
|
|
|
pdhA
|
9–14 |
|
|
|
|
yhbG
|
15–35 |
15§
20
22–26
30 |
29‡
31
33
34 |
|
|
pykF
|
36–42 |
|
|
38¶ |
|
lysS
|
43–51 |
|
|
|
|
leuS
|
52–61 |
52§
56
61 |
|
54
55
57 |
| Total no. SNPs | 61 | 15 | 5 | 4 |
*SNP, single nucleotide polymorphism. Each SNP is 100% specific for designated cluster and disease group (e.g., SNP 15 identifies cluster III but all 15 SNPs are specific to cluster III). Cluster III comprises all clinical and reference lymphogranuloma venereum (LGV) strains; cluster II comprises all reference and clinical D, Da, E, F, and recombinant clinical Ja strains except recombinant clinical D2s, D43nl, E87e, and reference Ja strains; Subcluster I comprises all reference and clinical trachoma A, B, Ba and C strains except reference strains A and Ba. Disease phenotype groups: invasive LGV strains (cluster III); trachoma A, B, Ba and C strains (Subcluster I); and noninvasive globally prevalent STI D/Da, E, and F strains (cluster II). Clinical Ja strains likley acquired a Ja ompA gene by recombination. †SNPs 54, 55, and 57 together (not independently) are specific for all trachoma strains except reference A strain. ‡p<0.01 for classification index. §p<0.001 for classification index. ¶p = 0.008 for classification index.