title: Comparison of restriction fragment length polymorphism with the polymorphic guanine-cytosine-rich sequence and spoligotyping for differentiation of Mycobacterium tuberculosis isolates with five or fewer copies of IS6110.
abstract: The use of IS6110 as a marker for molecular epidemiological studies is limited when a Mycobacterium tuberculosis isolate has five or fewer copies of IS6110. Restriction fragment length polymorphism analysis with a highly polymorphic GC-rich repetitive sequence located in the plasmid pTBN12 (PGRS RFLP) and spoligotyping (based on the polymorphism of the DR region) are two frequently used secondary typing methods. The aim of this study was to compare the performance of these two methods in a population-based study in San Francisco. We included all patients with culture-positive tuberculosis from 1999 to 2007 with IS6110 RFLP results presenting five or fewer bands. PGRS RFLP and spoligotyping were performed using standardized methods. We determined the concordance between the two methods regarding cluster status and the risk factors for an isolate to be in a cluster with each of the methods. Our data indicate that both methods had similar discriminatory power and that the risk factors associated with clustering by either method were the same. Although the cluster/unique status was concordant in 84% of the isolates, patients were clustered differently depending on the method. Therefore, the methods are not interchangeable, and the same method should be used for longitudinal studies.
authors.affiliation: Francis J. Curry National Tuberculosis Center, Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, Department of Medicine, University of California, San Francisco, San Francisco, California 94110, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Flores
authors.forename: Leah G
authors.initials: LG
authors.lastname: Jarlsberg
authors.forename: Elizabeth Y
authors.initials: EY
authors.lastname: Kim
authors.forename: Dennis
authors.initials: D
authors.lastname: Osmond
authors.forename: Jennifer
authors.initials: J
authors.lastname: Grinsdale
authors.forename: Masae
authors.initials: M
authors.lastname: Kawamura
authors.forename: Ed
authors.initials: E
authors.lastname: Desmond
authors.forename: Philip C
authors.initials: PC
authors.lastname: Hopewell
authors.forename: Midori
authors.initials: M
authors.lastname: Kato-Maeda
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics*; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D012495:San Francisco; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial