Prevalence of phenotypic pyrazinamide resistance and agreement with PNCA mutations in mycobacterium tuberculosis isolated from the national drug resistance survey in Uganda, 2008-2011.
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Background: Pyrazinamide (PZA) is a pro-drug with high sterilizing effect used to treat both susceptible and multi-drug resistant tuberculosis. PZA susceptibility testing is not commonly done in Uganda because it is expensive and characterized with technical difficulties. Resistance to this drug is commonly associated with mutations in the pncA gene and its promoter region, though the Aspartate 1-decarboxylase precursor and ribosomal protein S1 A genes have also been implicated. This study aimed at establishing the prevalence of PZA resistance in Uganda, the sensitivity of pncA sequencing in detection of phenotypic resistance and ascertain whether PZA resistance is associated with multi-drug resistant (MDR) TB. Methods: It was a cross-sectional study that used archived isolates collected during the Uganda National Drug resistance Survey conducted between 2008- 2011. The isolates were subcultured and PZA resistance tested by BACTEC Mycobacterium Growth inhibition Tube (MGIT) 960 system. Sequence reads were downloaded from the NCBI Library and bioinformatics pipelines were used to call variants. Mutations known to confer PZA resistance from previous literature were considered. Results: The prevalence of PZA resistance was found to be 21% among all isolates. The sensitivity and specificity (95% Confidence intervals) of pncA sequencing were 24% (9.36 45.13%) and 100% (73.54% - 100.00%) respectively. This study found that PZA resistance was significantly associated with multi-drug resistance (p- value of 0.0001, odds ratio 23.8824 (95% CI, 7.0349 – 81.0762). Conclusion: There is a high prevalence of phenotypic PZA resistance among TB patients in Uganda. The prevalence was higher among the multi-drug resistant isolates when compared with their susceptible counterparts. The low sensitivity of pncA gene sequencing confirms the already documented discordances suggesting other mechanisms of PZA resistance in Mycobacterium tuberculosis. Investigations of other resistance mechanisms such as defects in PZA uptake by M. tuberculosis and efflux pumps could be explored to ascertain their role in PZA resistance in Uganda