Mycobacterium tuberculosis Intra-Host Evolution Among Drug-Resistant Tuberculosis Patients Failing Treatment

Abstract

Background Understanding Mycobacterium tuberculosis ( Mtb ) intra-host evolution of drug resistance is important for successful drug-resistant tuberculosis (DR-TB) treatment and control strategies. This study aimed to characterise the acquisition of genetic mutations and low-frequency variants associated with treatment-emergent Mtb drug resistance in longitudinally profiled clinical isolates from patients who experienced DR-TB treatment failure. Patients and Methods We performed deep Whole Genome Sequencing on 23 clinical isolates obtained longitudinally across nine timepoints from five patients who experienced DR-TB treatment failure enrolled in the CAPRISA 020 InDEX study. The minimum inhibitory concentrations (MICs) were established on the BACTEC™ MGIT 960™ instrument on 15/23 longitudinal clinical isolates for eight anti-TB drugs (rifampicin, isoniazid, ethambutol, levofloxacin, moxifloxacin, linezolid, clofazimine, bedaquiline). Results In total, 22 resistance associated mutations/variants were detected. We observed four treatment-emergent mutations in two out of the five patients. Emerging resistance to the fluoroquinolones was associated with 16- and 64-fold elevated levofloxacin (2–8 mg/L) and moxifloxacin (1–2 mg/L) MICs, respectively, resulting from the D94G/N and A90V variants in the gyrA gene. We identified two novel mutations associated with elevated bedaquiline MICs (>66-fold): an emerging frameshift variant (D165) on the Rv0678 gene and R409Q variant on the Rv1979c gene present from baseline. Conclusion Genotypic and phenotypic resistance to the fluoroquinolones and bedaquiline was acquired in two out of five patients who experienced DR-TB treatment failure. Deep sequencing of multiple longitudinal clinical isolates for resistance-associated mutations coupled with phenotypic MIC testing confirmed intra-host Mtb evolution.

The positivity rates and drug resistance patterns of Mycobacterium tuberculosis using nucleotide MALDI-TOF MS assay among suspected tuberculosis patients in Shandong, China: a multi-center prospective study

“…Additionally, it is noteworthy that the resistance rate to fluoroquinolones is also relatively high, ranking third after rifampicin and isoniazid, although the proportion of patients with monoreistance to it is not very high. Fluoroquinolones are widely used not only for treating TB but also for other types of infectious diseases ( 22 ), which might contribute to the high fluoroquinolone resistance rate. Considering that fluoroquinolones are core drugs for treating DR-TB patients, we need to pay attention to and strengthen monitoring of its drug resistance.…”

“…Faye et al, have found the phenomenon of heteroresistance rate in the Rural Eastern Cape Province increased over time, from 9.6% in 2018 to 32.2% in 2020 ( 27 ). Recent study has characterized the trend of MTB drug resistance changes in a few TB patients during the treatment process and the proportion of drug-resistant strains indeed increases in some cases as treatment progresses, leading to complete drug resistance in later stages ( 22 ). If very low proportions of drug-resistant strains can be detected early and appropriate measures are taken to eliminate these strains, it may improve the success rate of subsequent treatment.…”