Spoligotyping is a molecular typing method that is used to differentiate M.tuberculosis complex. The method is based on polymorphism of the chromosomal DR locus consisting of identical 36-bp DRs alternating with 35-41 unique spacers. In this study, the spoligotyping was applied to Ziehl-Neelsen stained smears and its utility in smears with different positivity rate was assessed. DNA were extracted from smears (n=115) with different positivity rate [3+ (39; 33%), 2+ (28; 24), 1+ (33; 28%) and Scanty (15; 13%)]. Thirty negative smear slides were also used as a control. PCR was performed with primers specific for direct repeats and the product was detected by ECL hybridization kit. The obtained data entered the X-file and were analyzed with previously published database (spolDB4).

The utility rate in 3+, 2+ and 1+ smears were 84.6%, 71.4%, 36.4% respectively (p<0.01). The smears with scanty results could not produce any patterns.  In overall, the spoligopatterns was observed in 56.5% of samples. The predominant spoligopatterns identified as Haarlem (47.6%), CAS (26%) and T (15.3%). Spoligotyping can be reliable in smears with high positivity rate. Therefore, the method may be the best option to identify the circulating strains within limited resources laboratories.