Profiling and identification of novel rpoB mutations in rifampicin-resistant Mycobacterium tuberculosis clinical isolates from Pakistan

Mehmood Qadir; Sabira Tahseen; Timothy D McHugh; Alamdar Hussain; Faisal Masood; Niaz Ahmed; Rani Faryal

doi:10.1016/j.jiac.2021.06.020

Profiling and identification of novel rpoB mutations in rifampicin-resistant Mycobacterium tuberculosis clinical isolates from Pakistan

J Infect Chemother. 2021 Nov;27(11):1578-1583. doi: 10.1016/j.jiac.2021.06.020. Epub 2021 Jul 7.

Authors

Mehmood Qadir¹, Sabira Tahseen², Timothy D McHugh³, Alamdar Hussain², Faisal Masood², Niaz Ahmed², Rani Faryal⁴

Affiliations

¹ Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
² National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan.
³ Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK.
⁴ Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan. Electronic address: ranifaryal@qau.edu.pk.

PMID: 34244055
DOI: 10.1016/j.jiac.2021.06.020

Abstract

Introduction: Rifampicin (RIF) is one of the most effective anti-tuberculosis first-line drugs prescribed along with isoniazid. However, the emergence of RIF resistance Mycobacterium tuberculosis (MTB) isolates is a major issue towards tuberculosis (TB) control program in high MDR TB-burdened countries including Pakistan. Molecular data behind phenotypic resistance is essential for better management of RIF resistance which has been linked with mutations in rpoB gene. Since molecular studies on RIF resistance is limited in Pakistan, the current study was aimed to investigate the molecular data of mutations in rpoB gene behind phenotypic RIF resistance isolates in Pakistan.

Method: A total of 322 phenotypically RIF-resistant isolates were randomly selected from National TB Reference Laboratory, Pakistan for sequencing while 380 RIF resistance whole-genome sequencing (WGS) of Pakistani isolates (BioProject PRJEB25972), were also analyzed for rpoB mutations.

Result: Among the 702 RIF resistance samples, 675 (96.1%) isolates harbored mutations in rpoB in which 663 (94.4%) were detected within the Rifampicin Resistance Determining Region (RRDR) also known as a mutation hot spot region, including three novel. Among these mutations, 657 (97.3%) were substitutions including 603 (89.3%) single nucleotide polymorphism, 49 (7.25%) double and five (0.8%) triple. About 94.4% of Phenotypic RIF resistance strains, exhibited mutations in RRDR, which were also detectable by GeneXpert.

Conclusion: Mutations in the RRDR region of rpoB is a major mechanism of RIF resistance in MTB circulating isolates in Pakistan. Molecular detection of drug resistance is a faster and better approach than phenotypic drug susceptibility testing to reduce the time for transmission of RIF resistance strains in population. Such insights will inform the deployment of anti-TB drug regimens and disease control tools and strategies in high burden settings, such as Pakistan.

Keywords: Anti-TB drug; Mutations; Mycobacterium tuberculosis; Rifampicin-resistant; rpoB.

MeSH terms

Antitubercular Agents / pharmacology
Bacterial Proteins / genetics
DNA-Directed RNA Polymerases / genetics
Humans
Microbial Sensitivity Tests
Mutation
Mycobacterium tuberculosis* / genetics
Pakistan
Rifampin / pharmacology
Tuberculosis, Multidrug-Resistant* / drug therapy

Substances

Antitubercular Agents
Bacterial Proteins
DNA-Directed RNA Polymerases
Rifampin