Genetic diversity of drug-resistant Mycobacterium tuberculosis clinical isolates from Khuzestan province, Iran

Bakhtiyariniya, Pejman; Khosravi, Azar Dokht; Hashemzadeh, Mohammad; Savari, Mohammad

doi:10.1186/s13568-022-01425-7

Cited by 3 publications

(5 citation statements)

References 40 publications

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“…Also, in comparison with conventional molecular phenotypic methods, it is the most stable and reliable (Kone et al 2020 ). One of the disadvantages of this method is that it is not suitable for isolates with low copy numbers (Bakhtiyariniya et al 2022 ). In spite of this, semi-automated RFLP has been found to be a robust and promising method for routinely typing MTB (Said et al 2016 ).…”

Section: Assays and Methodsmentioning

confidence: 99%

New insight in molecular detection of Mycobacterium tuberculosis

Mousavi-Sagharchi,

Afrazeh,

Seyyedian-Nikjeh

et al. 2024

AMB Expr

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Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization’s report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.

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Section: Assays and Methodsmentioning

confidence: 99%

New insight in molecular detection of Mycobacterium tuberculosis

Mousavi-Sagharchi,

Afrazeh,

Seyyedian-Nikjeh

et al. 2024

AMB Expr

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“…The integration of tandem gene repeats via a bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation in Saccharomyces cerevisiae Samuel Evans 1,2 , Zeyu Lu 1,2,3 , Liam McDonnell 1,2 , Will Anderson 3 , Francisco Peralta 1,2 , Tyson Watkins 1,2 , Hafna Ahmed 4 , Carlos Horacio Luna-Flores 2 , Thomas Loan 5 , Laura Navone 2,6 , Matt Trau 3,7 , Colin Scott 4 , Robert Speight 1,2,8 , Claudia E. Vickers 1,2 , Bingyin Peng 1,2,3 * Introduction Tandem gene repeats, in the form of an array of two or more copies of a gene, commonly exist in cell genomes, i.e., ribosomal RNA genes (rDNA), 1 oncogenic genes, 2 drug resistant genes, 3,4 secondary metabolite biosynthetic genes, 5,6 and many other trait genes. 7 Their occurrence is generally regarded as the result of gene amplification, which increases gene copy number (gene dosage) and provides a phenotypic advantage during natural or artificial selection.…”

Section: For Table Of Contents Use Onlymentioning

confidence: 99%

Section: For Table Of Contents Use Onlymentioning

confidence: 99%

“…Tandem gene repeats, in the form of an array of two or more copies of a gene, commonly exist in cell genomes, i.e., ribosomal RNA genes (rDNA), 1 oncogenic genes, 2 drug resistant genes, 3, 4 secondary metabolite biosynthetic genes, 5, 6 and many other trait genes. 7 Their occurrence is generally regarded as the result of gene amplification, which increases gene copy number (gene dosage) and provides a phenotypic advantage during natural or artificial selection.…”

Section: Introductionmentioning

confidence: 99%

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The integration of tandem gene repeatsviaa bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation inSaccharomyces cerevisiae

Evans,

Lu,

McDonnell

et al. 2024

Preprint

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Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms, like human diseases and microbial productivities of target bioproducts. Here, we develop a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualise the evolutionary trajectories of gene repeats. We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification (ToxAmp) modules, and accidentally re-visited the high-level capacity of multi-fragment co-transformation in S. cerevisiae. This system delivered the multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection. Inducing the toxin (RelE) expressing via a copper (II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin (RelB) module, resulting in ~40 copies of a green fluorescence reporter (GFP) gene per copy of genome. The copy-number changes, increasing and decreasing, and stable maintenance were visualised using the GFP and blue chromoprotein AeBlue as reporters. Copy-number increasing happened spontaneously not depending on a selection pressure and was quickly enriched through toxin-antitoxin-mediated selection. In summary, the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications.

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“…Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), continues to pose a significant global public health challenge. [1][2][3] In 2021, there were 10.6 million new TB cases worldwide, with China accounting for 780,000 cases, making it the third highest burden country for TB globally. 4 The World Health Organization (WHO) estimates that in 2021, there were 450,000 cases of rifampicin-resistant tuberculosis (RR-TB) globally, of which over 70% were multidrug-resistant tuberculosis (MDR-TB), characterized by resistance to both isoniazid and rifampicin simultaneously.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China

Wang,

Yu,

et al. 2023

IDR

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Given the high burden of Tuberculosis (TB) in China, the prevalence of multidrug-resistant tuberculosis (MDR-TB) is significant. Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) enables the identification of lineages, drugresistant mutations, and transmission patterns, offering valuable insights for TB control, clinical diagnosis, and treatment. Methods: We collected 202 MDR-MTB strains from 3519 suspected pulmonary TB patients treated at The Second Affiliated Hospital of Hainan Medical University between July 2019 and June 2021. Proportional drug-susceptibility testing was performed using 8 common anti-tuberculosis drugs. Subsequently, the genotypic drug resistance and genetic characteristics were analyzed by the WGS. Results: Lineages are identified by TB-profiler revealed 202 MDR-MTB strains, showcasing three predominant lineages, with lineage 2 being the most prevalent. Close genomic relatedness analysis and evidence of MTB transmission led to the formation of 15 clusters comprising 42 isolates, resulting in a clustering rate of 20.8%. Novelty, lineage 2.1 (non-Beijing) accounted for 27.2% of the MDR-MTB strains, which is rare in China and Neighboring countries. Regarding first-line anti-TB drugs, genes associated with rifampicin resistance, primarily the rpoB gene, were detected in 200 strains (99.0%). Genes conferring resistance to isoniazid, ethambutol, and streptomycin were identified in 191 (94.5%), 125 (61.9%), and 100 (49.5%) strains, respectively. Among the second-line drugs, 97 (48.0%) strains exhibited genes encoding resistance to fluoroquinolones. Comparing the results to phenotypic drug susceptibility-based testing, the sensitivity of WGS for detecting resistance to each of the six drugs (rifampicin, isoniazid, ethambutol, ofloxacin, kanamycin, capreomycin) was 90% or higher. With the exception of ethambutol, the specificity of WGS prediction for the remaining drugs exceeded 88%. Conclusion:Our study provides crucial insights into genetic mutation types, genetic diversity, and transmission of MDR-MTB on Hainan Island, serving as a significant reference for MDR-MTB surveillance and clinical decision-making.

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Genetic diversity of drug-resistant Mycobacterium tuberculosis clinical isolates from Khuzestan province, Iran

Cited by 3 publications

References 40 publications

New insight in molecular detection of Mycobacterium tuberculosis

New insight in molecular detection of Mycobacterium tuberculosis

The integration of tandem gene repeatsviaa bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation inSaccharomyces cerevisiae

Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China

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