1. Xpert MTB/RIF Ultra-resistant and MTBDR plus- susceptible rifampicin results in people with tuberculosis: utility of FluoroType MTBDR and deep sequencing.
- Author
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Ghebrekristos Y, Ahmed A, Beylis N, Singh S, Opperman C, Naufal F, Folkerts M, Engelthaler D, Auma E, Venter R, Booley G, Metcalfe J, Warren R, and Theron G
- Subjects
- Humans, Microbial Sensitivity Tests methods, Antitubercular Agents pharmacology, Oxidoreductases genetics, Antibiotics, Antitubercular pharmacology, South Africa, Catalase genetics, Drug Resistance, Multiple, Bacterial genetics, Rifampin pharmacology, Mycobacterium tuberculosis drug effects, Mycobacterium tuberculosis genetics, Tuberculosis, Multidrug-Resistant drug therapy, Tuberculosis, Multidrug-Resistant microbiology, High-Throughput Nucleotide Sequencing methods, Sputum microbiology, Bacterial Proteins genetics, DNA-Directed RNA Polymerases genetics
- Abstract
Xpert MTB/RIF Ultra (Ultra)-detected rifampicin-resistant tuberculosis (TB) is often programmatically confirmed using MTBDR plus . There are limited data on discordant results, including when re-tested using newer methods, like FluoroType MTBDR (FT-MTBDR) and targeted deep sequencing. MTBDR plus rifampicin-susceptible isolates from people with Ultra rifampicin-resistant sputum were identified from a South African programmatic laboratory. FT-MTBDR and single molecule-overlapping reads (SMOR; rpoB , inhA , katG ) on isolate DNA were done (SMOR was used as a reference standard). Between 1 April 2021 and 30 September 2022, 8% (109/1347) of Ultra rifampicin-resistant specimens were MTBDR plus -susceptible. Of 89% (97/109) isolates with a sequenceable rpoB , SMOR resolved most in favor of Ultra (79% [77/97]). Sputum with lower mycobacterial load was associated with Ultra false-positive resistance (46% [11/24] of "very low" Ultra had false resistance vs 12% [9/73; P = 0.0004] of ≥"low"), as were Ultra heteroresistance calls (all wild-type probes, ≥1 mutant probe) (62% [23/37 vs 25% 15/60] for Ultra without heteroresistance calls; P = 0.0003). Of the 91% (88/97) of isolates successfully tested by FT-MTBDR, 55% (48/88) were FT-MTBDR rifampicin-resistant and 45% (40/88) susceptible, translating to 69% (47/68) sensitivity and 95% (19/20) specificity. In the 91% (99/109) of isolates with inhA and katG sequenced, 62% (61/99) were SMOR isoniazid-susceptible. When Ultra and MTBDR plus rifampicin results are discordant, Ultra is more likely to be correct, and FT-MTBDR agrees more with Ultra than MTBDR plus ; however, lower load and the Ultra heteroresistance probe pattern were risk factors for Ultra false rifampicin-resistant results. Most people with Ultra-MTBDR plus discordant resistance results were isoniazid-susceptible. These data have implications for drug-resistant TB diagnosis., Competing Interests: The authors declare no conflict of interest.
- Published
- 2025
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