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Volume 15, Number 9—September 2009

Research

Predicting Phenotype and Emerging Strains among Chlamydia trachomatis Infections

Deborah DeanComments to Author , William J. Bruno, Raymond Wan, João P. Gomes, Stéphanie Devignot, Tigist Mehari, Henry J.C. de Vries, Servaas A. Morré, Garry Myers, Timothy D. Read, and Brian G. Spratt
Author affiliations: Children’s Hospital Oakland Research Institute, Oakland, California, USA (D. Dean, R. Wan, T. Mehari); University of California, San Francisco, California, USA (D. Dean); University of California, Berkeley, California, USA (D. Dean); Los Alamos National Laboratories, Los Alamos, New Mexico, USA (W.J. Bruno); National Institute of Health, Lisbon, Portugal (J.P. Gomes); Institut de Médecine Tropicale du Service de Santé des Armées, Marseille, France (S. Devignot); University of Amsterdam, the Netherlands (H.J.C. de Vries); Vrije Universiteit Medical Center, Amsterdam (S.A. Morré); University of Maryland School of Medicine, Baltimore, Maryland, USA (G. Myers); Emory University, Atlanta, Georgia, USA (T.D. Read); Imperial College, London, UK (B.G. Spratt)

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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.

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