Characterization of ancestral Mycobacterium tuberculosis by multiple genetic markers and proposal of genotyping strategy.
Sixty-eight ancestral Mycobacterium tuberculosis isolates were previously identified by using the tuberculosis-specific deletion 1 (TbD1) PCR and mycobacterial interspersed-repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing (Y. J. Sun, R. Bellamy, A. S. G. Lee, S. T. Ng, S. Ravindran, S.-Y. Wong, C. Locht, P. Supply, and N. I. Paton, J. Clin. Microbiol. 42:1986-1993, 2004). These TbD1(+) ancestral isolates were further characterized and typed in this study by IS6110 restriction fragment length polymorphism (RFLP) typing, VNTR typing using exact tandem repeats (VNTR-ETR), and spoligotyping of the direct-repeat region. To our knowledge, this is the first characterization of this genogroup by multiple genetic markers based on a fairly large sample size. In this genogroup, all spoligotypes were characterized by the absence of spacers 29 to 32 and 34. In addition, VNTR-ETR typing could add further resolution to the clustered isolates identified by MIRU-VNTR, and the combination of MIRU-VNTR and VNTR-ETR, called MIRU-ETR, showed the highest discriminatory power for these strains compared to IS6110 RFLP typing and spoligotyping alone. However, MIRU-ETR appeared to still cluster some probably epidemiologically unrelated strains, as judged by IS6110 RFLP divergence. Therefore, a typing strategy based on stepwise combination of MIRU-ETR and IS6110 RFLP is proposed to achieve maximal discrimination for unrelated TbD1(+) strains. This typing strategy may be useful in areas where TbD1(+) ancestral strains are prevalent.
Sun
Yong-Jiang
YJ
Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore 308433. Yong_Jiang_Sun@ttsh.com.sg
Lee
Ann S G
AS
Ng
Sze Ta
ST
Ravindran
Sindhu
S
Kremer
Kristin
K
Bellamy
Richard
R
Wong
Sin-Yew
SY
van Soolingen
Dick
D
Supply
Philip
P
Paton
Nicholas I
NI
D015373:Bacterial Typing Techniques; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics; D009841:Oligonucleotides / Q000032:analysis; D012150:Polymorphism, Restriction Fragment Length; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D020080:Tandem Repeat Sequences / Q000235:genetics
D004251:DNA Transposable Elements; D005819:Genetic Markers; D009841:Oligonucleotides