Biology subjects

Soualhine, H.

Publications and source records attributed to Soualhine, H..

2 recordsLinked to original sources

bioRxiv2023

Mutations in embB406 are associated with low-level ethambutol resistance in Canadian Mycobacterium tuberculosis isolates

BackgroundIn Mycobacterium tuberculosis, molecular predictions of ethambutol resistance rely primarily on the detection of mutations within embB. However, discordance between embB406 mutations and phenotypic drug sensitivity questions its clinical significance. This study aims to decipher the association of embB406 mutations with ethambutol resistance in M. tuberculosis. MethodsAll M. tuberculosis isolates from our culture collection containing embB406 mutations (n=16) and pan-sensitive control isolates (n=10) were selected for this study. Phenotypic drug susceptibility testing for ethambutol was performed in duplicate on the BACTEC MGIT 960 at concentrations of 2, 3, 4, and 5 g/mL with strain H37Rv as assay control. Whole genome sequencing was performed on Illumina Miseq for drug resistance predictions (MyKrobe Predictor v.0.7.0), phylogenomics (SNVPhyl v.1.2.3) and single nucleotide polymorphism analysis (Snippy). ResultsTwo embB406 mutation subtypes were found among 16 strains: Gly406Asp and Gly406Ala. MyKrobe predicted all strains of either subtype to be ethambutol resistant. However, 12 of 16 strains appear phenotypically sensitive at 5 g/mL but exhibit variable resistance between 2-4 g/mL. Of these 12 strains, a newly described frameshift mutation in regulator embR (Gln258fs) was found in 9 strains. ConclusionsMutations in embB406 are associated with low-level ethambutol resistance currently undetectable by the critical concentration of 5 g/mL for ethambutol. Novel mutations are predicted to exacerbate variability in ethambutol resistance. We suggest amendment to molecular and phenotypic drug susceptibility testing to improve ethambutol DST sensitivity and specificity as well as concordance between rapid and gold standard methods.

microbiology↗

bioRxiv2023

Challenges of Whole Genome Sequencing based Molecular Identification of Zoonotic Tuberculosis caused by Mycobacterium orygis

A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphisms (SNPs) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of MTBC species. WGS-based SNPs analysis was performed for 61 isolates from different Provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB277 (A[->]G), gyrB1478 (T[->]C), leuS1064 (A[->]T), mmpL6486 (T[->]C), and mmpS6334 (C[->]G) are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.

microbiology↗