Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis

Abstract

Five different genetic elements have been found to be associated with genetic rearrangements in Mycobacterium tuberculosis complex strains. Of these elements, the insertion sequence IS6110 is presently the most frequently used genetic marker for strain differentiation ofM. tuberculosis. In the present study we compared five genetic elements for their potentials to differentiate a given cluster ofM. tuberculosis strains. Because of the presence of only a single copy of IS6110 or two IS6110 copies at the same chromosomal locus, a large number of strains could not be differentiated by IS6110 fingerprinting. Most strains, including the low-copy-number IS6110 strains, could be differentiated by fingerprinting with the 36-bp direct repeat or the polymorphic GC-rich repetitive DNA element. Less discriminative power was obtained with the major polymorphic tandem repeat and the insertion element IS1081. One strain which did not contain IS6110 DNA was encountered. Until now, this element has invariantly been found to be present in all M. tuberculosis complex strains. On the basis of classical taxonomic criteria and sequencing of the 16S rRNA gene, this strain was shown to be a genuline M. tuberculosis strain. Therefore, the use of this element as a target for polymerase chain reaction-facilitated detection of M. tuberculosis should be reconsidered.

Multiplex Polymerase Chain Reaction for diagnosis of gastrointestinal tuberculosis

“…The absence of IS6110 copies in some of Indian M. tuberculosis strains, as observed by some earlier studies, was also evident in the present study. 27,28 The strengths of our study include a prospective analysis of cases of suspected GITB using strict inclusion and exclusion criteria using three primers, IS6110, MPB64, and Protein b, versus single or two primers used in previous studies. The present study has also made an attempt to use composite reference standard for the comparative evaluation of multiplex PCR instead of using only culture or histopathology as the gold standard.…”

Comparison of loop-mediated isothermal amplification and real-time PCR for the diagnosis of tuberculous pleurisy

“…The reason to choose IS1081 as amplification target in the study is that this insertion element is carried by all M. tuberculosis complex strains investigated, with stable 5-6 copies (Collins and Stephens 1991;van Soolingen et al 1992van Soolingen et al , 1993Dziadek et al 2001). IS6110 has high copy numbers in most M. tuberculosis strains and is used as target by many nucleic acid amplification assays; however, strains with low copies or lacking IS6110 completely have been identified (van Soolingen et al 1993;Flores et al 2010). Recently, an IS6110-related element in a strain of M. smegmatis was identified and it has 67% amino acid identity and 79% similarity (Coros et al 2008).…”

Evaluation of Amplicor‐ and IS6110‐PCR for direct detection of Mycobacterium tuberculosis complex in Singapore

“…These studies, however, were mainly carried out in the West and rarely involved Asian strains. A study conducted by von Soolingen et al (1993) revealed that many M. tuberculosis strains from Asia harbour relatively fewer copies of IS6110, and that a strain which lacked IS6110-DNA was isolated from India. Albeit the occurrence of IS6110-deleted tuberculosis strain in Singapore has not been reported, we suspected that it could have occurred in sample #25250.…”