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Volume 14, Number 3—March 2008

Research

Discovering and Differentiating New and Emerging Clonal Populations of Chlamydia trachomatis with a Novel Shotgun Cell Culture Harvest Assay

Naraporn Somboonna*†, Sally Mead*, Jessica Liu†, and Deborah Dean*†‡Comments to Author 
Author affiliations: *Children’s Hospital Oakland Research Institute, Oakland, California, USA; †University of California, Berkeley, California, USA; ‡University of California School of Medicine, San Francisco, California, USA;

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Table 1

Results of the modified plaque assay for Chlamydia reference strains and shotgun cell culture harvest technique for clinical strains representing acute and persistent infections*

Strain Days p.i. to plaque formation or harvest No. plaques or shotgun harvested areas ompA genotype (no.) Location of nucleotide substitutions in ompA (amino acid substitution location) 16S rRNA (no.)
Reference D/UW-3 and E/Bour 1:1† 9 25 D (13)
E (9)
D/E (3) –
–
– Chlamydia trachomatis D (13)
C. trachomatis E (9)
C. trachomatis D/E (3)
Reference D/UW-3 and E/Bour 3:‡ 9 9 D (9)
E (0) –
– C. trachomatis D (9)
C. trachomatis E (0)
D/UW-3/E/Bour mixed infection§ 9 11 D (7)
E (4) C. trachomatis D (7)
C. trachomatis E (4)
Acute clinical Ja 8 11 Ja (11) C. trachomatis Ja (11)
Acute clinical K 10 11 K (11) C. trachomatis K (11)
Persistent H 7 5 H (5) C. trachomatis H (5)
Persistent G 14 7 G (7) C. trachomatis G (7)
Persistent F 10 5 F (5) C. trachomatis F (5)
Persistent clinical F and G strains 1:1† 10 13 F (1)
G (12) –
– C. trachomatis F (1)
C. trachomatis G (12)
A/SA-1 10
10¶ 18
21 A (14)
Chlamydophila abortus (4)
A/C. abortus (21) –
– C. trachomatis A (14)
C. abortus (4)
C. trachomatis A/C. abortus (21)
B/TW-5 9 15 B (15) C. trachomatis B (15)
Ba/Apache-2 8 14 Ba (9)
Ba1 (1)
Ba2 (1)
Ba3 (1) –
C662T (P221L)C662T (P221L) 
G673A (E225K)C662T (P221L)
A717C (K239N) C. trachomatis Ba (14)
C/TW-3 12 13 C (13) C. trachomatis C (13)
D/UW-3 9 11 D (11) C. trachomatis D (11)
Da/TW-448 10 12 Da (12) C. trachomatis Da (12)
E/Bour 9 9 E (9) C. trachomatis E (9)
F/IC-Cal3 9 13 F (10)
F-III (3) –
G269A (G90E)# C. trachomatis F (13)
G/UW57/Cx 7 10 G (10) C. trachomatis G (10)
H/UW-4 12 12 H (10) C. trachomatis H(10)
I/UW-12 11 14 I (14) C. trachomatis I (14)
Ia/IU-4168 12 11 Ia (12) C. trachomatis Ia (12)
J/UW-36 11 15 J (15) C. trachomatis J (15)
Ja/UW-92 12 12 Ja (12) C. trachomatis Ja (12)
K/UW-31 11 13 K (13) C. trachomatis K (13)
L1/440 9 11 L1 (11) C. trachomatis L1 (11)
L2/434 9 11 L2 (8)
L2’ (3) –
C471G,
G496A (A166T)¶ C. trachomatis L2 (10)
C. trachomatis L2a (1)
L2a/TW-396 9 13 L2a (13) C. trachomatis L2 (13)
L3/404 9 14 L3 (14) C. trachomatis L3 (14)

*p.i.,.postinoculation; ompA, outer membrane protein A; –, no evidence for nucleotide substitution.
†Represents an equal mixture of inclusion-forming units (IFUs) of each strain.
‡Represents a 3:1 mixture of IFUs of reference strains D/UW-3 and E/Bour.
§Represents the plaques from the 1:1 mixture of D/UW-3 and E/Bour when both reference strains were found in 3 plaques.
¶Represents the plaques that were harvested from the wells with 10–8 dilution.
#Boldface denotes nonconservative amino acid substitution (17).

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