Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis
Date
2021
Journal Title
Journal ISSN
Volume Title
Publisher
American Society for Microbiology
Abstract
Pyrazinamide is an important component of both drug-susceptible and
drug-resistant tuberculosis treatment regimens. Although approximately 50% of rifampin-
resistant isolates are also resistant to pyrazinamide, pyrazinamide susceptibility testing
is not routinely performed due to the challenging nature of the assay. We investigated
the diagnostic accuracy of genotypic and phenotypic methods and explored the
occurrence of pyrazinamide heteroresistance. We assessed pyrazinamide susceptibility
among 358 individuals enrolled in the South African EXIT-RIF cohort using Sanger and
targeted deep sequencing (TDS) of the pncA gene, whole-genome sequencing (WGS),
and phenotypic drug susceptibility testing. We calculated the diagnostic accuracy of
the different methods and investigated the prevalence and clinical impact of pncA heteroresistance.
True pyrazinamide susceptibility status was assigned to each isolate using
the Köser classification and expert rules. We observed 100% agreement across genotypic
methods for detection of pncA fixed mutations; only TDS confidently identified
three isolates (0.8%) with minor variants. For the 355 (99.2%) isolates that could be
assigned true pyrazinamide status with confidence, phenotypic DST had a sensitivity of
96.5% (95% confidence interval [CI], 93.8 to 99.3%) and specificity of 100% (95% CI,
100 to 100%), both Sanger sequencing and WGS had a sensitivity of 97.1% (95% CI,
94.6 to 99.6%) and specificity of 97.8% (95% CI, 95.7 to 99.9%), and TDS had sensitivity
of 98.8% (95% CI, 97.2 to 100%) and specificity of 97.8% (95% CI, 95.7 to 99.9%). We
demonstrate high sensitivity and specificity for pyrazinamide susceptibility testing
among all assessed genotypic methods. The prevalence of pyrazinamide heteroresistance
in Mycobacterium tuberculosis isolates was lower than that identified for other
first-line drugs.
Description
CITATION: Whitfield, M. G. et al. 2021. Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis. Journal of Clinical Microbiology 60(1):10 pages.doi.10.1128/JCM.01907-21
The original publication is available at: .asm.org
The original publication is available at: .asm.org
Keywords
Multidrug-resistant tuberculosis, Pyrazinamide, Mycobacterium tuberculosis, Rifampin, Drug resistance
Citation
Whitfield, M. G. et al. 2021. Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis. Journal of Clinical Microbiology 60(1):10 pages.doi.10.1128/JCM.01907-21