In order to characterize mutations causing rifampicin and isoniazid resistance of M. tuberculosis in Syria, 69 rifampicin resistant (Rifr) and 72 isoniazid resistant (Inhr) isolates were screened for point mutations in hot spots of the rpoB, katG and inhA genes by DNA sequencing and real time PCR. Of 69 Rifr isolates, 62 (90%) had mutations in the rifampin resistance determining region (RRDR) of the rpoB gene, with codons 531 (61%), 526 (13%), and 516 (8.7%) being the most commonly mutated. We found two new mutations (Asp516Thr and Ser531Gly) described for the first time in the rpoB-RRDR in association with rifampicin resistance. Only one mutation (Ile572Phe) was found outside the rpoB-RRDR. Of 72 Inhr strains, 30 (41.6%) had a mutation in katGcodon 315 (with Ser315Thr being the predominant alteration), and 23 (32%) harbored the inhA−15C→T mutation. While the general pattern of rpoB-RRDR and katG mutations reflected those found worldwide, the prevalence of the inhA−15C→T mutation was above the value found in most other countries, emphasizing the great importance of testing the inhA−15C→T mutation for prediction of isoniazid resistance in Syria. Sensitivity of a rapid test using real time PCR and 3’-Minor groove binder (MGB) probes in detecting Rifr and Inhr isolates was 90% and 69.4%, respectively. This demonstrates that a small set of MGB-probes can be used in real time PCR in order to detect most mutations causing resistance to rifampicin and isoniazid.
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