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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 3

Allele frequencies by geographic region by locus

Gene locus No. alleles Allele frequency, no. (%)*
Classification index
p value
Africa
(n = 11) Northern Europe (n = 14) Southern Europe (n = 10) Asia
(n = 13) North America
(n = 33) South America
(n = 6)
glyA
7
3 (90.9)
6 (9.1)
1 (7.1)
3 (42.9)
4 (7.1)5 (14.3)
6 (28.6)
3 (60)
6 (40)
3 (30.8)
6 (7.7)
7 (61.5)
1 (15.1)
2 (3.0)
3 (54.6)
6 (27.3)
3 (33.3)
6 (66.7)
<0.001
mdhC
4
3 (90.9)
4 (9.1)
1 (7.1)
2 (14.3)
3 (64.3)
4 (14.3)
3 (80)
4 (20)
3 (100)
1 (18.2)
3 (72.7)
4 (9.1)
3 (50.0)
4 (50.0)
<0.001
pdhA
7
1 (9.1)
3 (90.9)
2 (7.1)
3 (92.9)
3 (60)
4 (30)7 (10)
3 (100)
3 (94.0)
5 (3.0)
6 (3.0)
3 (100.0)
<0.001
yhbG
8
2 (9.1)
6 (90.9)
2 (28.6)
3 (7.1)
6 (42.7)
8 (21.4)
2 (40)
6 (50)
7 (10)
1 (7.7)4 (7.7)
5 (7.7)
6 (76.9)
2 (21.2)
3 (3.0)
5 (3.0)
6 (57.6)
8 (15.2)
2 (66.7)
6 (33.3)
<0.001
pykF
7
3 (81.8)
6 (9.1)
7 (8.1)
1 (12.5)
6 (50)
7 (37.5)
6 (60)
7 (40)
3 (92.3)
7 (7.7)
1 (18.2)
2 (9.1)4 (3.0)5 (3.0)
6 (39.4)
7 (27.3)
6 (33.3)
7 (66.7)
<0.001
lysS
8
4 (15.2)
5 (72.7)
7 (9.1)
1 (14.3)
4 (78.6)
8 (7.1)
4 (70)
8 (30)
4 (7.7)
5 (30.8)
6 (61.5)
1 (3.0)
3 (3.0)
4 (75.8)
8 (18.2)
2 (16.7)
4 (66.7)
8 (16.7)
<0.001
leuS
11
2 (9,1)
3 (9.1)
9 (81.8)
3 (57.1)
6 (21.4)
11(21.4)
3 (80)
4 (10)5 (10)
2 (7.7)
7 (84.6)10 (7.7)
1 (3.0)
3 (48.5)
8 (30.3)
9 (3.0)
11 (15.2)
3 (100.0)
<0.001
Total no. alleles 52 17 24 17 17 31 13

*Numbers are arranged vertically for each locus to represent the individual alleles (e.g., glyA, alleles are assigned 1, 2, 3, 4, 5, 6 and 7 because there are 7 alleles for this locus). Alleles marked in boldface are specific for a single geographic region. n values indicate number of samples.

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