Genotypes of Mycobacterium tuberculosis isolates in rural China: Using MIRU-VNTR and spoligotyping methods

Abstract

Background: The genotypes of Mycobacterium tuberculosis (MTB) have been found to be related to the risk of transmission and the development of drug resistance of this pathogen. Thus, exploring the molecular characteristics of MTB is helpful for understanding and controlling the spread of strains in areas with a high incidence of tuberculosis. Methods: We recruited 512 sputum smear-positive tuberculosis patients from 30 counties from 1 April to 30 June 2010; 503 MTB strains were isolated and 497 were successfully genotyped. We genotyped the strains based on a new 15-locus mycobacterial interspersed repetitive unit–variable number of tandem repeats (MIRU-VNTR) method in combination with spacer-oligonucleotide typing (spoligotyping) technology. Results: Based on spoligotyping, 487 strains displayed known patterns, and 10 were absent from the current global spoligotyping database (SpolDB4). The predominant spoligotypes belonged to the Beijing or Beijing-like family (81.1%). When we used the new 15-locus (MIRU-15) set for the MIRU-VNTR analysis, 388 different patterns were identified, including 46 clusters and 342 unique patterns. The combination of spoligotyping and MIRU-15 demonstrated a high discriminatory power. The proportion of clusters varied significantly between the Beijing and non-Beijing family strains, but no significant association was observed between multidrug resistance and Beijing family strains. Conclusions: The present study demonstrated that the Beijing family strains are the most prevalent in rural China. Spoligotyping in combination with the new MIRU-15 technique is useful for the epidemiological analysis of MTB transmission and could be used as a first-line method for the large-scale genotyping of MTB.

Keywords::

• Tuberculosis
• genotyping
• Beijing family
• variable number tandem repeat
• spoligotyping

Acknowledgements

This study was supported in part by the National Nature Science Foundation of China (81302480), Key Personnel of Science and Education Industrial Engineering (JKRC2011005), “Transmission Mode of Tuberculosis” (2008ZX100/03-010-02) of the National Key Program of Mega Infectious Disease, and the project of State Key Laboratory for Infectious Disease Prevention and Control (2011SKLID208). The sponsors had no role in the study design or in the analysis of data.

Declaration of interest: The authors declare that they have no conflict of interest.