scholarly journals Identification of a New DNA Region Specific for Members of Mycobacterium tuberculosis Complex

1998 ◽  
Vol 36 (4) ◽  
pp. 937-943 ◽  
Author(s):  
Juana Magdalena ◽  
Anne Vachée ◽  
Philip Supply ◽  
Camille Locht
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Dna Amplification ◽  
Target Sequence ◽  
Two Component System ◽  
Tuberculosis Complex ◽  
Specific Pcr ◽  
Length Polymorphisms ◽  
Genes Encoding ◽  
Mycobacterium Africanum ◽  
Mycobacterium Microti

The successful use of DNA amplification for the detection of tuberculous mycobacteria crucially depends on the choice of the target sequence, which ideally should be present in all tuberculous mycobacteria and absent from all other bacteria. In the present study we developed a PCR procedure based on the intergenic region (IR) separating two genes encoding a recently identified mycobacterial two-component system named SenX3-RegX3. The senX3-regX3 IR is composed of a novel type of repetitive sequence, called mycobacterial interspersed repetitive units (MIRUs). In a survey of 116Mycobacterium tuberculosis strains characterized by different IS6110 restriction fragment length polymorphisms, 2 Mycobacterium africanum strains, 3 Mycobacterium bovis strains (including 2 BCG strains), and 1Mycobacterium microti strain, a specific PCR fragment was amplified in all cases. This collection included M. tuberculosis strains that lack IS6110 ormtp40, two target sequences that have previously been used for the detection of M. tuberculosis. No PCR fragment was amplified when DNA from other organisms was used, giving a sensitivity of 100% and a specificity of 100% in the confidence limit of this study. The numbers of MIRUs were found to vary among strains, resulting in six different groups of strains on the basis of the size of the amplified PCR fragment. However, the vast majority of the strains (approximately 90%) fell within the same group, containing two 77-bp MIRUs followed by one 53-bp MIRU.

Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 967-978 ◽  
Author(s):  
C. Viana-Niero ◽  
P. E. de Haas ◽  
D. van Soolingen ◽  
S. C. Leão
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Phospholipase C ◽  
Genetic Polymorphisms ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Clinical Isolates ◽  
Significant Similarity ◽  
Genomic Deletions ◽  
Genes Encoding ◽  
Mycobacterium Africanum

The Mycobacterium tuberculosis genome contains four highly related genes which present significant similarity to Pseudomonas aeruginosa genes encoding phospholipase C enzymes. Three of these genes, plcA, plcB and plcC, are organized in tandem (locus plcABC). The fourth gene, plcD, is located in a different region. This study investigates variations in plcABC and plcD genes in clinical isolates of M. tuberculosis, Mycobacterium africanum and ‘Mycobacterium canettii’. Genetic polymorphisms were examined by PCR, Southern blot hybridization, sequence analysis and RT-PCR. Seven M. tuberculosis isolates contain insertions of IS6110 elements within plcA, plcC or plcD. In 19 of 25 M. tuberculosis isolates examined, genomic deletions were identified, resulting in loss of parts of genes or complete genes from the plcABC and/or plcD loci. Partial plcD deletion was observed in one M. africanum isolate. In each case, deletions were associated with the presence of a copy of the IS6110 element and in all occurrences IS6110 was transposed in the same orientation. A mechanism of deletion resulting from homologous recombination of two copies of IS6110 was recognized in a group of genetically related M. tuberculosis isolates. Five M. tuberculosis isolates presented major polymorphisms in the plcABC and plcD regions, along with loss of expression competence that affected all four plc genes. Phospholipase C is a well-known bacterial virulence factor. The precise role of phospholipase C in the pathogenicity of M. tuberculosis is unknown, but considering the potential importance that the plc genes may have in the virulence of the tubercle bacillus, the study of isolates cultured from patients with active tuberculosis bearing genetic variations affecting these genes may provide insights into the significance of phospholipase C enzymes for tuberculosis pathogenicity.

scholarly journals Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

2019 ◽  
Vol 5 (6) ◽  
pp. eaaw3307 ◽  
Author(s):  
Á. Chiner-Oms ◽  
L. Sánchez-Busó ◽  
J. Corander ◽  
S. Gagneux ◽  
S. R. Harris ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Population Genomics ◽  
Mycobacterium Tuberculosis Complex ◽  
Purifying Selection ◽  
Sensor Kinase ◽  
Virulence Determinants ◽  
Two Component System ◽  
Tuberculosis Complex ◽  
Bacterial Speciation ◽  
Two Component

Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.

scholarly journals Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Qingtian Guan ◽  
Musa Garbati ◽  
Sara Mfarrej ◽  
Talal AlMutairi ◽  
Thomas Laval ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Tuberculosis Complex ◽  
Evolutionary Relationship ◽  
Type I ◽  
Dna Sensors ◽  
Mycobacterial Species ◽  
Tuberculosis Complex ◽  
Genes Encoding ◽  
Cumulative Process ◽  
Comparative Transcriptomic Analysis

Abstract Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.

scholarly journals Novel Genetic Polymorphisms That Further Delineate the Phylogeny of the Mycobacterium tuberculosis Complex

2006 ◽  
Vol 188 (12) ◽  
pp. 4271-4287 ◽  
Author(s):  
Richard C. Huard ◽  
Michel Fabre ◽  
Petra de Haas ◽  
Luiz Claudio Oliveira Lazzarini ◽  
Dick van Soolingen ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Deletions ◽  
History Of ◽  
Species Specific ◽  
Mycobacterium Africanum ◽  
Mycobacterium Microti ◽  
First Time ◽  
Fine Tune

ABSTRACT In a previous report, we described a PCR protocol for the differentiation of the various species of the Mycobacterium tuberculosis complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol. 41:1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (n = 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various Mycobacterium tuberculosis strains, new species-specific SNPs were identified for “Mycobacterium canettii,” Mycobacterium microti, and Mycobacterium pinnipedii, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two Mycobacterium africanum subtype I variants. Surprisingly, coincident polymorphisms linked one M. africanum subtype I genotype with the dassie bacillus and M. microti with M. pinnipedii, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.

Mycobacteria

2012 ◽  
pp. 126-137
Author(s):  
Irene G. Sia
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Chest Pain ◽  
Physical Examination ◽  
Mycobacterial Infection ◽  
Milk Products ◽  
Natural Reservoir ◽  
Unpasteurized Milk ◽  
Hilar Adenopathy ◽  
Mycobacterium Africanum ◽  
Mycobacterium Microti

Mycobacterium tuberculosis complex is made up of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium microti. Humans are the only natural reservoir of M tuberculosis. Mycobacterium bovis is caused by consumption of unpasteurized milk products from an infected cow. Cattle-to-human transmission also occurs. Patients with tuberculosis (TB) usually present with fever; less commonly, pleuritic chest pain, retrosternal or interscapular pain. Physical examination findings are usually normal. Hilar adenopathy is typical, often resolving in 1 year or more. Disease manifestations of other mycobacterial infection are also reviewed.

scholarly journals Detection of Mycobacterium tuberculosis complex by nested polymerase chain reaction in pulmonary and extrapulmonary specimens

2013 ◽  
Vol 39 (6) ◽  
pp. 711-718 ◽  
Author(s):  
Adriana Antônia da Cruz Furini ◽  
Heloisa da Silveira Paro Pedro ◽  
Jean Francisco Rodrigues ◽  
Lilian Maria Lapa Montenegro ◽  
Ricardo Luiz Dantas Machado ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Mycobacterium Tuberculosis ◽  
Mycobacterium Tuberculosis Complex ◽  
Extrapulmonary Tuberculosis ◽  
Laboratory Data ◽  
Target Sequence ◽  
Tuberculosis Complex ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Polymerase Chain

OBJECTIVE: To compare the performance of nested polymerase chain reaction (NPCR) with that of cultures in the detection of the Mycobacterium tuberculosis complex in pulmonary and extrapulmonary specimens.METHODS: We analyzed 20 and 78 pulmonary and extrapulmonary specimens, respectively, of 67 hospitalized patients suspected of having tuberculosis. An automated microbial system was used for the identification of Mycobacterium spp. cultures, and M. tuberculosis IS6110 was used as the target sequence in the NPCR. The kappa statistic was used in order to assess the level of agreement among the results.RESULTS: Among the 67 patients, 6 and 5, respectively, were diagnosed with pulmonary and extrapulmonary tuberculosis, and the NPCR was positive in all of the cases. Among the 98 clinical specimens, smear microscopy, culture, and NPCR were positive in 6.00%, 8.16%, and 13.26%, respectively. Comparing the results of NPCR with those of cultures (the gold standard), we found that NPCR had a sensitivity and specificity of 100% and 83%, respectively, in pulmonary specimens, compared with 83% and 96%, respectively, in extrapulmonary specimens, with good concordance between the tests (kappa, 0.50 and 0.6867, respectively).CONCLUSIONS: Although NPCR proved to be a very useful tool for the detection of M. tuberculosis complex, clinical, epidemiological, and other laboratory data should also be considered in the diagnosis and treatment of pulmonary and extrapulmonary tuberculosis.

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