| Summary: | <p>Abstract</p> <p>Background</p> <p>Drug resistance displays a problem for the therapy of <it>Mycobacterium tuberculosis</it> infections. For molecular resistance testing, it is essential to have precise knowledge on genomic variations involved in resistance development. However, data from high-incidence settings are only sparely available. Therefore we performed a systematic approach and analyzed a total of 97 <it>M. tuberculosis</it> strains from previously treated patients in Sierra Leone for mutations in <it>kat</it>G, <it>rpo</it>B, <it>rrs</it>, <it>rps</it>L, <it>gid</it>B, <it>emb</it>B, <it>pnc</it>A and where applicable in <it>inh</it>A and <it>ahp</it>C. Of the strains investigated 50 were either mono- or poly-resistant to isoniazid, rifampin, streptomycin, ethambutol and pyrazinamide or MDR and 47 fully susceptible strains served as controls.</p> <p>Results</p> <p>The majority of isoniazid and rifampin resistant strains had mutations in <it>kat</it>G315 (71.9%) and <it>rpo</it>B531 (50%). However, <it>rpo</it>B mutations in codons 511, 516 and 533 were also detected in five rifampin susceptible strains. MIC determinations revealed low-level rifampin resistance for those strains. Thus, the sensitivity and specificity of sequencing of <it>kat</it>G for detection of drug resistance were 86.7% and 100% and for sequencing of <it>rpo</it>B 100% and 93.8%, respectively.</p> <p>Strikingly, none of the streptomycin resistant strains had mutations in <it>rrs</it>, but 47.5% harboured mutations in <it>rps</it>L. Further changes were detected in <it>gid</it>B. Among ethambutol resistant strains 46.7% had mutations at <it>emb</it>B306. Pyrazinamide resistant strains displayed a variety of mutations throughout <it>pnc</it>A. The specificities of sequencing of <it>rps</it>L, <it>emb</it>B and <it>pnc</it>A for resistance detection were high (96-100%), whereas sensitivities were lower (48.8%, 73.3%, 70%).</p> <p>Conclusions</p> <p>Our study reveals a good correlation between data from molecular and phenotypic resistance testing in this high-incidence setting. However, the fact that particular mutations in <it>rpo</it>B are not linked to high-level resistance is challenging and demonstrates that careful interpretation of molecular resistance assays is mandatory. In addition, certain variations, especially in <it>gid</it>B, appear to be phylogenetically informative polymorphisms rather than markers for drug resistance.</p>
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