Spoligotyping analysis of Mycobacterium tuberculosis with TB-sprint technology

Spoligotyping is a highly reproducible, fast polymerase chain reaction (PCR)-based approach for identification of different strains of Mycobacterium tuberculosis through genotyping of Mycobacterium tuberculosis complex (MTB). Molecular typing of MTB is helpful for understanding and controlling TB epidemics. Spoligotyping was performed on 166 strains of MTB collected from 25 districts of Khyber Pakhtunkhwa, Pakistan. Results were analyzed using online database, SITVIT2, developed by the Institute Pasteur de Guadeloupe, France and SPSS software V.15 (IMB Inc). Drug susceptibility test (DST) was performed on all strains using commercial liquid media in BACTECMGIT 960 instrument. Spoligotyping results showed that 145 (88%) strains displayed known patterns while 21 (12%) were new. Central Asian strain (CAS) was the predominant family (73%, x2=19.9, P=0.001) followed by Beijing (5.4) and T1 (4.2%). CAS1-Dehli was the major sub-family (82%) among the CAS family (x2=664, P=0.0001). Furthermore, new spoligotyping patterns were clustered using the maximum parsimony (MP) test to find any evolutionary relationship with pre-published genotypes. Analysis showed that the majority of the strains with unknown pattern have an evolutionary link with CAS strain, and 9 (5.4%) of the unknown strains were epidemiologically linked and named CAS-KPK (Khyber Pakhtunkhwa). The present study demonstrated that CAS is a predominant strain of MTB prevailing in different areas of the Khyber Pakhtunkhwa province of Pakistan. Spoligotyping pattern of some strains could not match other reported pattern in the international database. Other tools, like MIRU/ VNTR, can be helpful to perform investigation of its epidemiological characteristics in future.