Utility of line probe assay in detecting drug resistance and the associated mutations in patients with extrapulmonary tuberculosis in Addis Ababa, Ethiopia

Getu Diriba; Abebaw Kebede; Habteyes Hailu Tola; Ayinalem Alemu; Bazezew Yenew; Shewki Moga; Desalegn Addise; Zemedu Mohammed; Muluwork Getahun; Mengistu Fantahun; Mengistu Tadesse; Biniyam Dagne; Misikir Amare; Gebeyehu Assefa; Dessie Abera; Kassu Desta

doi:10.1177/20503121221098241

Utility of line probe assay in detecting drug resistance and the associated mutations in patients with extrapulmonary tuberculosis in Addis Ababa, Ethiopia

SAGE Open Med. 2022 May 20:10:20503121221098241. doi: 10.1177/20503121221098241. eCollection 2022.

Authors

Getu Diriba^{1

2}, Abebaw Kebede^{1

3}, Habteyes Hailu Tola¹, Ayinalem Alemu^{1

4}, Bazezew Yenew¹, Shewki Moga¹, Desalegn Addise¹, Zemedu Mohammed¹, Muluwork Getahun¹, Mengistu Fantahun⁵, Mengistu Tadesse¹, Biniyam Dagne¹, Misikir Amare¹, Gebeyehu Assefa⁶, Dessie Abera², Kassu Desta²

Affiliations

¹ Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
² Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
³ Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
⁴ Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
⁵ St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.
⁶ Armauer Hansen Research Institute, Addis Ababa, Ethiopia.

Abstract

Introduction: Molecular tests allow rapid detection of Mycobacterium tuberculosis and drug resistance in a few days. Identifying the mutations in genes associated with drug resistance may contribute to the development of appropriate interventions to improve tuberculosis control. So far, there is little information in Ethiopia about the diagnostic performance of line probe assay (LPA) and the M. tuberculosis common gene mutations associated with drug resistance in extrapulmonary tuberculosis. Thus, this study aimed to assess the frequency of drug resistance-associated mutations in patients with extrapulmonary tuberculosis (EPTB) and to compare the agreement and determine the utility of the genotypic in the detection of drug resistance in Addis Ababa, Ethiopia.

Methods: A cross-sectional study was conducted on stored M. tuberculosis isolates. The genotypic and phenotypic drug susceptibility tests were performed using LPA and BACTEC-MGIT-960, respectively. The common mutations were noted, and the agreement and the utility of the LPA were determined using the BACTEC-MGIT-960 as a gold standard.

Results: Of the 151 isolates, the sensitivity and specificity of MTBDRplus in detecting isoniazid resistance were 90.9% and 100%, respectively. While for rifampicin, it was 100% and 99.3% for sensitivity and specificity, respectively. The katG S315Tl was the most common mutation observed in 85.7% of the isoniazid-resistant isolates. In the case of rifampicin, the most common mutation (61.9%) was observed at position rpoB S531L. Mutations in the gyrA promoter region were strongly associated with Levofloxacin and Moxifloxacin resistance.

Conclusion: Line probe assay has high test performance in detecting resistance to anti-TB drugs in EPTB isolates. The MTBDRplus test was slightly less sensitive for the detection of isoniazid resistance as compared to the detection of rifampicin. The most prevalent mutations associated with isoniazid and rifampicin resistance were observed at katG S315Tl and rpoB S531L respectively. Besides, all the fluoroquinolone-resistant cases were associated with gyrA gene. Finally, a validation study with DNA sequencing is recommended.

Keywords: Extrapulmonary tuberculosis; mutation; performance characteristics.

Grants and funding

D43 TW009127/TW/FIC NIH HHS/United States