TY - JOUR
T1 - Variants associated with Bedaquiline (BDQ) resistance identified in Rv0678 and efflux pump genes in Mycobacterium tuberculosis isolates from BDQ naïve TB patients in Pakistan
AU - Saeed, Dania Khalid
AU - Shakoor, Sadia
AU - Razzak, Safina Abdul
AU - Hasan, Zahra
AU - Sabzwari, Saba Faraz
AU - Azizullah, Zahida
AU - Kanji, Akbar
AU - Nasir, Asghar
AU - Shafiq, Samreen
AU - Ghanchi, Najia Karim
AU - Hasan, Rumina
N1 - Funding Information:
We would like to thank Health Security Partners (HSP)-USA for funding the project and Ms. Jessica McLean for her generous assistance and support throughout the course of this study. We would also like to acknowledge and thank Janssen Research & Development, Titusville, NJ, United States, for providing us with microtitre plates that were used for performing BMD susceptibility testing. We also extend our gratitude to Andrea Cabbibe, TB Supranational Reference Laboratory Emerging Bacterial Pathogens Unit Ospedale San Raffaele, Milan, Italy for sharing DNA extraction protocol and giving technical insight in our early days of sequencing. We would also like to thank Ms. Maliha Yameen, Dr. Nazish Jabeen, Sarah Ehtesham, and the microbiologists working in our clinical Mycobacteriology Laboratory for their cooperation and facilitation in using BSL-3 resources.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - Background: Mutations in the Rv0678, pepQ and atpE genes of Mycobacterium tuberculosis (MTB) have been reported to be associated with reduced antimycobacterial susceptibility to bedaquiline (BDQ). Resistance conferring mutations in treatment naïve MTB strains is likely to have implications for BDQ based new drug regimen that aim to shorten treatment duration. We therefore investigated the genetic basis of resistance to BDQ in MTB clinical isolates from BDQ naïve TB patients from Pakistan. In addition, mutations in genes associated with efflux pumps were investigated as an alternate mechanism of resistance. Methods: Based on convenience sampling, we studied 48 MTB clinical isolates from BDQ naïve TB patients. These isolates (from our strain bank) included 38 MDR/pre-XDR/XDR (10 BDQ resistant, 8 BDQ intermediate and 20 BDQ susceptible) and 10 pan drug susceptible MTB isolates. All strains were subjected to whole genome sequencing and genomes were analysed to identify variants in Rv0678, pepQ, atpE, Rv1979c, mmpLS and mmpL5 and drug resistance associated efflux pump genes. Results: Of the BDQ resistant and intermediate strains 44% (8/18) had variants in Rv0678 including; two reported mutations S63R/G, six previously unreported variants; L40F, R50Q and R107C and three frameshift mutations; G25fs, D64fs and D109fs. Variants in efflux pumps; Rv1273c (G462K), Rv0507c (R426H) and Rv1634c (E198R) were found to be present in drug resistant isolates including BDQ resistant and intermediate isolates. E198R in efflux pump gene Rv1634c was the most frequently occurring variant in BDQ resistant and intermediate isolates (n = 10). Conclusion: We found RAVs in Rv0678 to be commonly associated with BDQ resistance. Further confirmation of the role of variants in efflux pump genes in resistance is required so that they may be incorporated in genome-based diagnostics for drug resistant MTB.
AB - Background: Mutations in the Rv0678, pepQ and atpE genes of Mycobacterium tuberculosis (MTB) have been reported to be associated with reduced antimycobacterial susceptibility to bedaquiline (BDQ). Resistance conferring mutations in treatment naïve MTB strains is likely to have implications for BDQ based new drug regimen that aim to shorten treatment duration. We therefore investigated the genetic basis of resistance to BDQ in MTB clinical isolates from BDQ naïve TB patients from Pakistan. In addition, mutations in genes associated with efflux pumps were investigated as an alternate mechanism of resistance. Methods: Based on convenience sampling, we studied 48 MTB clinical isolates from BDQ naïve TB patients. These isolates (from our strain bank) included 38 MDR/pre-XDR/XDR (10 BDQ resistant, 8 BDQ intermediate and 20 BDQ susceptible) and 10 pan drug susceptible MTB isolates. All strains were subjected to whole genome sequencing and genomes were analysed to identify variants in Rv0678, pepQ, atpE, Rv1979c, mmpLS and mmpL5 and drug resistance associated efflux pump genes. Results: Of the BDQ resistant and intermediate strains 44% (8/18) had variants in Rv0678 including; two reported mutations S63R/G, six previously unreported variants; L40F, R50Q and R107C and three frameshift mutations; G25fs, D64fs and D109fs. Variants in efflux pumps; Rv1273c (G462K), Rv0507c (R426H) and Rv1634c (E198R) were found to be present in drug resistant isolates including BDQ resistant and intermediate isolates. E198R in efflux pump gene Rv1634c was the most frequently occurring variant in BDQ resistant and intermediate isolates (n = 10). Conclusion: We found RAVs in Rv0678 to be commonly associated with BDQ resistance. Further confirmation of the role of variants in efflux pump genes in resistance is required so that they may be incorporated in genome-based diagnostics for drug resistant MTB.
KW - Bedaquiline resistance
KW - Extensively drug resistant Mycobacterium tuberculosis
KW - Resistance associated variants
KW - Whole genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85125340872&partnerID=8YFLogxK
U2 - 10.1186/s12866-022-02475-4
DO - 10.1186/s12866-022-02475-4
M3 - Article
C2 - 35209842
AN - SCOPUS:85125340872
SN - 1471-2180
VL - 22
JO - BMC Microbiology
JF - BMC Microbiology
IS - 1
M1 - 62
ER -
