title: Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore.
abstract: Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The Hunter-Gaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.
authors.affiliation: Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Republic of Singapore. Yong_Jiang_Sun@ttsh.com.sg
authors.forename: Yong-Jiang
authors.initials: YJ
authors.lastname: Sun
authors.forename: Richard
authors.initials: R
authors.lastname: Bellamy
authors.forename: Ann S G
authors.initials: AS
authors.lastname: Lee
authors.forename: Sze Ta
authors.initials: ST
authors.lastname: Ng
authors.forename: Sindhu
authors.initials: S
authors.lastname: Ravindran
authors.forename: Sin-Yew
authors.initials: SY
authors.lastname: Wong
authors.forename: Camille
authors.initials: C
authors.lastname: Locht
authors.forename: Philip
authors.initials: P
authors.lastname: Supply
authors.forename: Nicholas I
authors.initials: NI
authors.lastname: Paton
mesh_terms: D000483:Alleles; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D014644:Genetic Variation; D006801:Humans; D020071:Interspersed Repetitive Sequences; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D015203:Reproducibility of Results; D012846:Singapore / Q000453:epidemiology; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology / Q000382:microbiology
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial