Rapid detection of the Mycobacterium tuberculosis Beijing genotype and its ancient and modern sublineages by IS6110-based inverse PCR

Abstract

The Mycobacterium tuberculosis Beijing genotype strains appear to be hypervirulent and associated with multidrug-resistant tuberculosis. Therefore, the development of a both rapid and simple method to detect the M. tuberculosis Beijing genotype is of clinical interest per se. Previously, we described a simple and fast approach to detect the Beijing genotype based on IS6110 inverse-PCR typing. Here, we evaluated this method against a large, diverse, and recent collection of strains. The study sample included 866 M. tuberculosis strains representing but not limited to the regions in Russia, Europe, and East Asia where the Beijing genotype is endemic. Based on a spoligotyping method, 408 strains were identified as Beijing genotypes; they were additionally subdivided into ancient and modern sublineages based on the analysis of the NTF locus. All strains were further subjected to the IS6110-based inverse PCR. All of the Beijing genotype strains were found to have identical two-band (ancient sublineage) or three-band (modern sublineage) profiles that were easily recognizable and distinct from the profiles of the non-Beijing strains. Therefore, we suggest using IS6110-based inverse-PCR typing for the correct identification of the Beijing genotype and its major sublineages. The method is fast and inexpensive and does not require additional experiments but instead is implemented in the routine typing method of M. tuberculosis.

FIG. 1.

Schematic presentation of the M. tuberculosis spoligoprofiles. *, A local code used in the present study. The numbers of ancient Beijing strains (in case of the Beijing genotypes) are given in parentheses. An initial Excel file is available upon request.

FIG. 1.

Schematic presentation of the M. tuberculosis spoligoprofiles. *, A local code used in the present study. The numbers of ancient Beijing strains (in case of the Beijing genotypes) are given in parentheses. An initial Excel file is available upon request.

FIG. 2.

Examples of IS6110 inverse-PCR profiles of M. tuberculosis strains from China (a), Vietnam (b), Bulgaria (c), and Russia (d). Bj, Beijing genotype strains; ancient Beijing strains are also marked by an asterisk. M, 100-bp DNA ladder. Arrows indicate the PCR fragments specific for the Beijing genotypes (two- or three-band profile).