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Mahghani GA, Kargar M, Ghaemi EA, Kafilzadeh F, Davoodi H. Role of ESAT-6 in pathogenicity of Beijing and non-Beijing Mycobacterium tuberculosis isolates. Microb Pathog 2021; 162:105366. [PMID: 34968645 DOI: 10.1016/j.micpath.2021.105366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Mycobacterium tuberculosis Beijing genotype was associated with tuberculosis outbreaks and increased transmissibility. To understand the variation in virulence between Beijing and non-Beijing clinical isolates of M.tuberculosis genotypes, the esat-6 gene sequencing, and its expression was compared in the macrophage environment. MATERIALS & METHODS Among 64 nonrepetitive, culture-positive M.tuberculosis, DNA extraction of 24 and 40 pure confirmed Beijing and non-Beijing isolates was accompanied by the boiling method. esat-6 gene PCR amplification and their sequencing were carried out by specific primers and its expression was performed on human macrophage cell line U937 after 6, 12, and 18 h of exposure to bacilli. The esat-6 mRNA transcription and expression in M. tuberculosis treated macrophage by Real-Time PCR and Western blot method. RESULTS Data analysis based on sequencing of the east-6 gene PCR product showed that this gene exists in all isolates and there are no changes or single nucleotide variation between the Beijing and non-Beijing isolates. In Beijing strains, the esat-6 expression was increased during the study times, but it was constant in non-Beijing isolates. esat-6 gene expression in Beijing isolates reached to about 44.9 times more than non-Beijing isolates after 18 h incubation on the macrophages cell line. CONCLUSION esat-6 is a conserved gene both in Beijing and non-Beijing isolates of M.tuberculosis. More expression of the east-6 gene in the macrophage model may indicate that this gene is likely to play a more important role in increasing the pathogenicity of Beijing strains.
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Affiliation(s)
- Ghorban Ali Mahghani
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Mohammad Kargar
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran.
| | - Ezzat Allah Ghaemi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Farshid Kafilzadeh
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Homa Davoodi
- Cancer Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Yar AM, Zaman G, Hussain A, Changhui Y, Rasul A, Hussain A, Bo Z, Bokhari H, Ibrahim M. Comparative Genome Analysis of 2 Mycobacterium Tuberculosis Strains from Pakistan: Insights Globally Into Drug Resistance, Virulence, and Niche Adaptation. Evol Bioinform Online 2018; 14:1176934318790252. [PMID: 30083049 PMCID: PMC6075610 DOI: 10.1177/1176934318790252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/18/2018] [Indexed: 12/02/2022] Open
Abstract
Multidrug-resistant Mycobacterium tuberculosis is a global
threat particularly in developing countries like Pakistan. In this study, we
identified 2 M tuberculosis strains, mnpk and swlpk, by 16S RNA
genes, sequenced their draft genome, and compared the 2 genomes with reference
strain H37Rv and gene expression analysis of selected virulent genes.
Phylogenetic analysis of M tuberculosis strains, mnpk and
swlpk, using 16S RNA genes revealed that the strains are closely related with
reference strain H37Rv. The draft genome sequence of mnpk and swlpk contains
4305 and 4295 protein-coding genes, respectively, having 99.9% with high
collinearity when compared with H37Rv. Although some important drug-resistant
genes such as fabG, faDE24, and
iniA were missing, genome mining also revealed key
drug-resistant genes such as katG, inhA,
rpoA, rpoB, and rpoC
against first-line isoniazid and rifampicin drug. The strain mnpk and swlpk
encodes 257 putative and 86 verified virulent genes including type 7 secretion
system (T7SS) key genes. The variation in the expression profile of selected
T7SS genes, particularly low expression level of EspK, raised
concern that the mechanism of virulence of mnpk and swlpk might be different
from H37Rv strains as espK is associated with ATPase
EccC1a and EccC1b which showed high
expression level. Briefly, this study shows that the strains mnpk and swlpk are
linked with H37Rv having 99% similarity in genomes, but the absence of
drug-resistant genes and variation in key genes’ expression profile
espK, EccE1, PPE41, and
espC provide a rationale for the future investigation of
M tuberculosis mnpk and swlpk pathogenesis via RNA
sequencing, single-nucleotide polymorphisms, as well as gene manipulation.
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Affiliation(s)
- Asma Muhammad Yar
- Genomics and Computational Biology Laboratory, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Ghanva Zaman
- Genomics and Computational Biology Laboratory, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Annam Hussain
- Genomics and Computational Biology Laboratory, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Yan Changhui
- Department of Computer Science, North Dakota State University, Fargo, ND, USA
| | - Azhar Rasul
- Department of Zoology, Government College University, Faisalabad, Pakistan
| | - Abrar Hussain
- Genomics and Computational Biology Laboratory, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Zhu Bo
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Habib Bokhari
- Laboratories of Microbiology and Public Health, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Ibrahim
- Genomics and Computational Biology Laboratory, COMSATS University Islamabad, Sahiwal Campus, Pakistan
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The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040782. [PMID: 29673235 PMCID: PMC5923824 DOI: 10.3390/ijerph15040782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI) value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%). By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP), and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%). By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.
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Pan XL, Zhang CL, Nakajima C, Fu J, Shao CX, Zhao LN, Cui JY, Jiao N, Fan CL, Suzuki Y, Hattori T, Li D, Ling H. A quantitative and efficient approach to select MIRU-VNTR loci based on accumulation of the percentage differences of strains for discriminating divergent Mycobacterium tuberculosis sublineages. Emerg Microbes Infect 2017; 6:e68. [PMID: 28745309 PMCID: PMC5567172 DOI: 10.1038/emi.2017.58] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/11/2017] [Accepted: 06/04/2017] [Indexed: 11/09/2022]
Abstract
Although several optimal mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) loci have been suggested for genotyping homogenous Mycobacterium tuberculosis, including the Beijing genotype, a more efficient and convenient selection strategy for identifying optimal VNTR loci is needed. Here 281 M. tuberculosis isolates were analyzed. Beijing genotype and non-Beijing genotypes were identified, as well as Beijing sublineages, according to single nucleotide polymorphisms. A total of 22 MIRU-VNTR loci were used for genotyping. To efficiently select optimal MIRU-VNTR loci, we established accumulations of percentage differences (APDs) between the strains among the different genotypes. In addition, we constructed a minimum spanning tree for clustering analysis of the VNTR profiles. Our findings showed that eight MIRU-VNTR loci displayed disparities in h values of ≥0.2 between the Beijing genotype and non-Beijing genotype isolates. To efficiently discriminate Beijing and non-Beijing genotypes, an optimal VNTR set was established by adding loci with APDs ranging from 87.2% to 58.8%, resulting in the construction of a nine-locus set. We also found that QUB11a is a powerful locus for separating ST10s (including ST10, STF and STCH1) and ST22s (including ST22 and ST8) strains, whereas a combination of QUB11a, QUB4156, QUB18, Mtub21 and QUB26 could efficiently discriminate Beijing sublineages. Our findings suggested that two nine-locus sets were not only efficient for distinguishing the Beijing genotype from non-Beijing genotype strains, but were also suitable for sublineage genotyping with different discriminatory powers. These results indicate that APD represents a quantitative and efficient approach for selecting MIRU-VNTR loci to discriminate between divergent M. tuberculosis sublineages.
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Affiliation(s)
- Xin-Ling Pan
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Chun-Lei Zhang
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 0010020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo 0600808, Japan
| | - Jin Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150026, China
| | - Chang-Xia Shao
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Li-Na Zhao
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Jia-Yi Cui
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Na Jiao
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Chang-Long Fan
- Department of Clinical Laboratory, Harbin Chest Hospital, Harbin 150081, China
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 0010020, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo 0600808, Japan
| | - Toshio Hattori
- Graduate School of Health Science Studies, Kibi International University, Takahashi 7168508, Japan
| | - Di Li
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
| | - Hong Ling
- Department of Microbiology, Wu Lien-Teh Institute, Harbin Medical University, Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin 150081, China
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