A Molecular Typing Methodology of Mycobacterium tuberculosis using Small Genomic Islet Patterns (TB-SGIP): A Novel Genotyping Methodology to Discriminate Clinical Strains between Beijing Family and T3-OSAKA

Abstract

Tuberculosis remains a leading cause of infectious disease morbidity and mortality worldwide. Therefore, the ability to discriminate between strains of the causative agent, Mycobacterium tuberculosis (M. tuberculosis), is an important issue for public health epidemiologists when tracking transmission of the disease. Several molecular typing methods are in use; however, some are labor intensive and technically demanding, while others require expensive equipment. Recently, a novel analysis of the presence or absence of genomic signatures in open reading frames (ORFs) was demonstrated to have several advantages over conventional typing methods: it uses a simple and rapid polymerase chain reaction (PCR)-based method, and the results are stable and easily comparable among institutions. We used this technology to develop a novel molecular typing method to assess the composition of small genomic islets (SGIs) derived from ORFs in the genomic sequences of M. tuberculosis. Analyses of the whole genome sequences of five M. tuberculosis complex strains led to the selection of nine SGIs. The conservation of each SGI was investigated in 40 clinical isolates from several different groups. The SGI patterns exhibited a clear difference between Beijing family members and T3-OSAKA, suggesting that the analysis of SGIs is useful for the discrimination of these strains.