Drug resistant Mycobacterium tuberculosis in Oman: resistance-conferring mutations and lineage diversity

Abstract

Background: The Sultanate of Oman is country a low TB-incidence, with less than seven cases per 10⁵ population detected in 2020. Recent years have witnessed a persistence in TB cases, with sustained incidence rate among expatriates and limited reduction among Omanis. This pattern suggests transmission from the migrant population. The present study examined the genetic profile and drug resistance-conferring mutations in Mycobacterium tuberculosis collected from Omanis and expatriates to recognise possible causes of disease transmission.

Methods: We examined M. tuberculosis cultured positive samples, collected from Omanis (n = 1,344) and expatriates (n = 1,203) between 2009 and 2018. These isolates had a known in vitro susceptibility profile to first line anti-TB, Streptomycin (SM), Isoniazid (INH), Rifampicin (RIF), Ethambutol (EMB) and Pyrazinamide (PZA). The diversity of the isolates was assessed by spacer oligo-typing (spoligotyping). Drug resistance-conferring mutations resulted from full-length sequence of nine genes (katG, inhA, ahpc, rpoB, rpsL, rrs, embB, embC, pncA) and their phenotypic relationship were analysed.

Results: In total, 341/2192 (13.4%), M. tuberculosis strains showed resistance to any drug, comprising mono-resistance (MR) (242, 71%), poly-resistance (PR) (40, 11.7%) and multi-drug resistance (MDR) (59, 17.3%). The overall rate of resistance among Omanis and expatriates was similar; however, MDR and PZA^R were significantly higher among Omanis, while INH^R was greater among expatriates. Mutations rpsL K43R and rpoB S450L were linked to Streptomycin (SM^R) and Rifampicin resistance (RIF^R) respectively. Whereas, katG S315T and inhA -C15T/G-17T were associated with Isoniazid resistance (INH^R). The resistance patterns (mono-resistant, poly-resistant and MDR) and drug resistance-conferring mutations were found in different spoligo-lineages. rpsL K43R, katG S315T and rpoB S450L mutations were significantly higher in Beijing strains.

Conclusions: Diverse drug resistant M. tuberculosis strains exist in Oman, with drug resistance-conferring mutations widespread in multiple spoligo-lineages, indicative of a large resistance reservoir. Beijing's M. tuberculosis lineage was associated with MDR, and multiple drug resistance-conferring mutations, favouring the hypothesis of migration as a possible source of resistant lineages in Oman.

Keywords: Drug resistance genes; Mycobacterium tuberculosis; Oman; Spoligotypes.

Figure 1. Odds ratio and 95% confidence interval of PZA^R-TB and MDR-TB to evaluate the strength of association between DST profiles and provinces with > 10 reported TB cases.

Figure 2. Drug susceptibility test (DST) profiles of M. tuberculosis isolates collected between 2009 and 2018.

MDR pattern (A), mono-resistance (B), poly-resistance (C) and pattern of INH^R (D), PZA^R (E), RIF^R (F) SM^R (G). Black dots are the observed data with 0 being negative and 1 being positive for drug resistance response. Lines represent estimated prevalence overtime based on logistic regression models, gray shade around the line is the 95% confidence intervals. P and logistic regression model and odd ratio (OR) correspond to time of significant change in prevalence compared to the reference year (2009).

Figure 3. Distribution of drug resistance-conferring mutations among M. tuberculosis obtained from Omanis and expatriates.