51
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Day WA, Fernández RE, Maurelli AT. Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp. Infect Immun 2001; 69:7471-80. [PMID: 11705922 PMCID: PMC98836 DOI: 10.1128/iai.69.12.7471-7480.2001] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2001] [Accepted: 08/29/2001] [Indexed: 11/20/2022] Open
Abstract
Pathoadaptive mutations improve the fitness of pathogenic species by modification of traits that interfere with factors (virulence and ancestral) required for survival in host tissues. A demonstrated pathoadaptive mutation is the loss of lysine decarboxylase (LDC) expression in Shigella species that have evolved from LDC-expressing Escherichia coli. Previous studies demonstrated that the product of LDC activity, cadaverine, blocks the action of Shigella enterotoxins and that the gene encoding LDC, cadA, was abolished by large chromosomal deletions in each Shigella species. To better understand the nature and evolution of these pathoadaptive mutations, remnants of the cad region were sequenced from the four Shigella species. These analyses reveal novel gene arrangements in this region of the pathogens' chromosomes. Insertion sequences, a phage genome, and/or loci from different positions on the ancestral E. coli chromosome displaced the cadA locus to form distinct genetic linkages that are unique to each Shigella species. Hybridization studies, using an E. coli K-12 microarray, indicated that the genes displaced to form the novel linkages still remain in the Shigella genomes. None of these novel gene arrangements were observed in representatives of all E. coli phylogenies. Collectively, these observations indicate that inactivation of the cadA antivirulence gene occurred independently in each Shigella species. The convergent evolution of these pathoadaptive mutations demonstrates that, following evolution from commensal E. coli, strong pressures in host tissues selected Shigella clones with increased fitness and virulence through the loss of an ancestral trait (LDC). These observations strongly support the role of pathoadaptive mutation as an important pathway in the evolution of pathogenic organisms.
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Affiliation(s)
- W A Day
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799, USA
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52
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Vera-Cabrera L, Hernández-Vera MA, Welsh O, Johnson WM, Castro-Garza J. Phospholipase region of Mycobacterium tuberculosis is a preferential locus for IS6110 transposition. J Clin Microbiol 2001; 39:3499-504. [PMID: 11574563 PMCID: PMC88379 DOI: 10.1128/jcm.39.10.3499-3504.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymes with phospholipase C activity in Mycobacterium tuberculosis have been recently described. The three genes encoding these proteins, plcA, plcB, and plcC, are located at position 2351 of the genomic map of M. tuberculosis H37Rv and are arranged in tandem. We have previously described the presence of variations in the restriction fragment length polymorphism patterns of the plcA and plcB genes in M. tuberculosis clinical isolates. In the present work we investigated the origin of this polymorphism by sequence analysis of the phospholipase-encoding regions of 11 polymorphic M. tuberculosis clinical isolates. To do so, a long-PCR assay was used to amplify a 5,131-bp fragment that contains the plcA and plcB genes and part of the plcC gene. In the M. tuberculosis strains studied the production of an amplicon approximately 1,400 bp larger than anticipated was observed. Sequence analysis of the PCR products indicated the presence of a foreign sequence that corresponded to an IS6110 element. We observed insertion elements in the plcA, plcB, and plcC genes. One site in plcB had the highest incidence of transposition (5 out of 11 strains). In two strains the insertion element was found in plcA in the same nucleotide position. In all the cases, IS6110 was transposed in the same direction. The high level of transposition in the phospholipase region can lead to the excision of fragments of genomic DNA by recombination of neighboring IS6110 elements, as demonstrated by finding the deletion, in two strains, of a 2,837-bp fragment that included plcA and most of plcB. This can explain the negative results obtained by some authors when detecting the mtp40 sequence (plcA) by PCR. Given the high polymorphism in this region, the use of the mtp40 sequence as a genetic marker for M. tuberculosis sensu stricto is very restricted.
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Affiliation(s)
- L Vera-Cabrera
- Servicio de Dermatología, Hospital Universitario José E. González, Madero y Gonzalitos, Col Mitras Centro, Monterrey, México.
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53
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Fang Z, Kenna DT, Doig C, Smittipat DN, Palittapongarnpim P, Watt B, Forbes KJ. Molecular evidence for independent occurrence of IS6110 insertions at the same sites of the genome of Mycobacterium tuberculosis in different clinical isolates. J Bacteriol 2001; 183:5279-84. [PMID: 11514510 PMCID: PMC95409 DOI: 10.1128/jb.183.18.5279-5284.2001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several characteristics of Mycobacterium tuberculosis (e.g., conserved genome and low growth rate) have severely restricted the study of the microorganism. The discovery of IS6110 raised hopes of overcoming these obstacles. However, our knowledge of this IS element is relatively limited; even its two basic characteristics (transposition mechanism and target site selection) are far from well understood. In this study, IS6110 insertions in ipl loci (iplA and iplB) in two collections of clinical isolates of M. tuberculosis from different geographic locations, one from Scotland and the other from Thailand, were investigated. Five different IS6110 insertions in the loci were identified: ipl-4::IS6110, ipl-5::IS6110, ipl-11::IS6110, ipl-12::IS6110, and ipl-13::IS6110. An attempt to establish the phylogenetic relationship of the isolates containing these insertions was unsuccessful, suggesting that some of these insertions may have arisen from more than one event. This possibility is further supported by the observation that IS6110 copies existed in the same site but with different orientations in different isolates, and the insertion site of ipl-1::IS6110 harbored IS6110 copies in both iplA and iplB in different strains. All these suggest the independent occurrence of IS6110 insertions at the same sites of the genome of M. tuberculosis in different clinical isolates. The implications of this finding are discussed.
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Affiliation(s)
- Z Fang
- Public Health Laboratory Services Mycobacteria Reference Unit and Department of Infection, Guy's, King's and St. Thomas' School of Medicine, London, United Kingdom.
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54
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Brosch R, Pym AS, Gordon SV, Cole ST. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol 2001; 9:452-8. [PMID: 11553458 DOI: 10.1016/s0966-842x(01)02131-x] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Comparative genomics, and related technologies, are helping to unravel the molecular basis of the pathogenesis, host range, evolution and phenotypic differences of the slow-growing mycobacteria. In the highly conserved Mycobacterium tuberculosis complex, where single-nucleotide polymorphisms are rare, insertion and deletion events (InDels) are the principal source of genome plasticity. InDels result from recombinational or insertion sequence (IS)-mediated events, expansion of repetitive DNA sequences, or replication errors based on repetitive motifs that remove blocks of genes or contract coding sequences. Comparative genomic analyses also suggest that loss of genes is part of the ongoing evolution of the slow-growing mycobacterial pathogens and might also explain how the vaccine strain BCG became attenuated.
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Affiliation(s)
- R Brosch
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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55
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Abstract
The standard method for the typing of Mycobacterium tuberculosis is still IS6110 restriction fragment length polymorphism (RFLP). This method has been widely used and has provided information on the variety and distribution of tuberculosis strain types across the globe. Recently, IS6110 RFLP has been used to investigate the question of reinfection versus reactivation, examine the existence of multiple infection, and track the spread of multidrug-resistant tuberculosis. There have also been efforts to increase our understanding of the biologic characteristics of IS6110. These studies have resulted in a clearer understanding of fingerprinting data and increased our understanding of the evolution and pathogenicity of this organism.
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Affiliation(s)
- H A Fletcher
- University College London, Center for Infectious Diseases, Royal Free and University College Medical School, Windeyer Institute of Medical Sciences, London, UK.
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56
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Sander P, Papavinasasundaram KG, Dick T, Stavropoulos E, Ellrott K, Springer B, Colston MJ, Böttger EC. Mycobacterium bovis BCG recA deletion mutant shows increased susceptibility to DNA-damaging agents but wild-type survival in a mouse infection model. Infect Immun 2001; 69:3562-8. [PMID: 11349014 PMCID: PMC98336 DOI: 10.1128/iai.69.6.3562-3568.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic microorganisms possess antioxidant defense mechanisms for protection from reactive oxygen metabolites which are generated during the respiratory burst of phagocytic cells. These defense mechanisms include enzymes such as catalase, which detoxifies reactive oxygen species, and DNA repair systems, which repair damage resulting from oxidative stress. To (i) determine the relative importance of the DNA repair system when oxidative stress is encountered by the Mycobacterium tuberculosis complex during infection of the host and to (ii) provide improved mycobacterial hosts as live carriers to express foreign antigens, the recA locus was inactivated by allelic exchange in Mycobacterium bovis BCG. The recA mutants are sensitive to DNA-damaging agents and show increased susceptibility to metronidazole, the first lead compound active against the dormant M. tuberculosis complex. Surprisingly, the recA genotype does not affect the in vitro dormancy response, nor does the defect in the DNA repair system lead to attenuation as determined in a mouse infection model. The recA mutants will be a valuable tool for further development of BCG as an antigen delivery system to express foreign antigens and as a source of a genetically stable vaccine against tuberculosis.
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Affiliation(s)
- P Sander
- Institut für Medizinische Mikrobiologie, Medizinische Hochschule Hannover, Germany.
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57
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Sola C, Filliol I, Gutierrez MC, Mokrousov I, Vincent V, Rastogi N. Spoligotype Database ofMycobacterium tuberculosis: Biogeographic Distribution of Shared Types and Epidemiologic and Phylogenetic Perspectives. Emerg Infect Dis 2001. [DOI: 10.3201/10.3201/eid0703.0107304] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
| | - Ingrid Filliol
- Institut Pasteur de Guadeloupe, Pointe à Pitre, Guadeloupe
| | | | - Igor Mokrousov
- Institut Pasteur de Guadeloupe, Pointe à Pitre, Guadeloupe
| | - Véronique Vincent
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
| | - Nalin Rastogi
- Institut Pasteur de Guadeloupe, Pointe à Pitre, Guadeloupe
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58
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Legrand E, Filliol I, Sola C, Rastogi N. Use of spoligotyping to study the evolution of the direct repeat locus by IS6110 transposition in Mycobacterium tuberculosis. J Clin Microbiol 2001; 39:1595-9. [PMID: 11283094 PMCID: PMC87977 DOI: 10.1128/jcm.39.4.1595-1599.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Based on the variability of 43 spacers within the direct repeat (DR) locus of Mycobacterium tuberculosis complex organisms, spoligotyping is a rapid method that aids in the study of the epidemiology of tuberculosis. It was recently hypothesized that despite its presence in the DR locus, spacer 31 could not be amplified in M. tuberculosis clinical isolates belonging to spoligotype 50 due to the insertion of an extra copy of IS6110 between spacers 31 and 32 that could lead to an asymmetrical split of the primer targets (I. Filliol, C. Sola, and N. Rastogi, J. Clin. Microbiol. 38:1231--1234, 2000). In the present investigation, previous observations were extended to 25 clinical isolates of type 50 showing that the primer set IS6-DRb that selectively amplified the left and central DR regions was indeed able to demonstrate the presence of spacer 31. IS6110-restriction fragment length polymorphism (RFLP) and DR-RFLP showed that type 50 isolates were characterized by the presence of two copies of IS6110 associated with the DR locus and an additional double IS6110 band of 1.4 kb. The primer set IS3-IS6 was then used to selectively amplify a 750-bp inter-IS6110 fragment within the DR locus. The sequencing of the central DR region corroborated our previous findings and showed that the absence of spacer 31 among the type 50 isolates was due to the asymmetric insertion of an extra copy of IS6110 between spacers 31 and 32, leading to an unequal split of the DRa-DRb target into two portions, of 6 and 30 bp, respectively. These results show that the DR locus constitutes an ideal IS6110 preferential locus (ipl), permitting the insertion of two or more copies of IS6110, and provide new clues for epidemiological and phylogenetic interpretation of changes in IS6110-RFLP and spoligotyping profiles.
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Affiliation(s)
- E Legrand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, 97165 Pointe-à-Pitre Cedex, Guadeloupe
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59
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Sola C, Filliol I, Gutierrez MC, Mokrousov I, Vincent V, Rastogi N. Spoligotype database of Mycobacterium tuberculosis: biogeographic distribution of shared types and epidemiologic and phylogenetic perspectives. Emerg Infect Dis 2001; 7:390-6. [PMID: 11384514 PMCID: PMC2631784 DOI: 10.3201/eid0703.010304] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We give an update on the worldwide spoligotype database, which now contains 3,319 spoligotype patterns of Mycobacterium tuberculosis in 47 countries, with 259 shared types, i.e., identical spoligotypes shared by two or more patient isolates. The 259 shared types contained a total of 2,779 (84%) of all the isolates. Seven major genetic groups represented 37% of all clustered isolates. Two types (119 and 137) were found almost exclusively in the USA and accounted for 9% of clustered isolates. The remaining 1,517 isolates were scattered into 252 different spoligotypes. This database constitutes a tool for pattern comparison of M. tuberculosis clinical isolates for global epidemiologic studies and phylogenetic purposes.
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Affiliation(s)
- C Sola
- Institut Pasteur de Guadeloupe, Pointe poundà Pitre, Guadeloupe.
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60
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Abstract
Inversions and translocations distinguish the genomes of closely related bacterial species, but most of these rearrangements preserve the relationship between the rearranged fragments and the axis of chromosome replication. Within species, such rearrangements are found less frequently, except in the case of clinical isolates of human pathogens, where rearrangements are very frequent.
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Affiliation(s)
- D Hughes
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden.
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61
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Affiliation(s)
- A S Pym
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 75724 Paris, CEDEX 15, France
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62
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de Boer AS, Kremer K, Borgdorff MW, de Haas PE, Heersma HF, van Soolingen D. Genetic heterogeneity in Mycobacterium tuberculosis isolates reflected in IS6110 restriction fragment length polymorphism patterns as low-intensity bands. J Clin Microbiol 2000; 38:4478-84. [PMID: 11101583 PMCID: PMC87624 DOI: 10.1128/jcm.38.12.4478-4484.2000] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to originate from the same ancestral strain and thus to reflect ongoing transmission. In this study, we investigated 1,277 IS6110 RFLP patterns for the presence of multiple low-intensity bands (LIBs), which may indicate infections with multiple M. tuberculosis strains. We did not find any multiple LIBs, suggesting that multiple infections are rare in the Netherlands. However, we did observe a few LIBs in 94 patterns (7.4%) and examined the nature of this phenomenon. With single-colony cultures it was found that LIBs mostly represent mixed bacterial populations with slightly different RFLP patterns. Mixtures were expressed in RFLP patterns as LIBs when 10 to 30% of the DNA analyzed originated from a bacterial population with another RFLP pattern. Presumably, a part of the LIBs did not represent mixed bacterial populations, as in some clusters all strains exhibited LIBs in their RFLP patterns. The occurrence of LIBs was associated with increased age in patients. This may reflect either a gradual change of the bacterial population in the human body over time or IS6110-mediated genetic adaptation of M. tuberculosis to changes in the environmental conditions during the dormant state or reactivation thereafter.
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Affiliation(s)
- A S de Boer
- Department of Infectious Disease Epidemiology, National Institute of Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands.
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63
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Eckstein TM, Inamine JM, Lambert ML, Belisle JT. A genetic mechanism for deletion of the ser2 gene cluster and formation of rough morphological variants of Mycobacterium avium. J Bacteriol 2000; 182:6177-82. [PMID: 11029440 PMCID: PMC94754 DOI: 10.1128/jb.182.21.6177-6182.2000] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major phenotypic trait of the Mycobacterium avium complex is the ability to produce rough and smooth colony variants. The chemical basis of this morphological variation is the loss of an antigenic surface structure, termed glycopeptidolipid (GPL), by rough variants. Using M. avium serovar 2 strain 2151 as a model system, this laboratory previously reported that rough variants arise via the deletion of large genomic regions encoding GPL biosynthesis. One such deletion encompasses the gene cluster (ser2) responsible for production of the serovar 2 GPL haptenic oligosaccharide. In this study, nucleotide sequencing revealed that both ends of the ser2 gene cluster are flanked by a novel insertion sequence (IS1601) oriented as direct repeats. Detailed analyses of the site of deletion in the genome of M. avium 2151 Rg-1 demonstrated that a single copy of IS1601 remained and that the ser2 gene cluster was deleted by homologous recombination. This same deletion pattern was observed for 10 out of 15 rough colony variants tested. Additionally, these studies revealed that IS1601 contains portions of three independent insertion sequences. This report is the first to define the precise genetic basis of colony variation in Mycobacterium spp. and provides further evidence that homologous recombination between insertion sequence elements can be a primary determinant of genome plasticity in these bacteria.
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Affiliation(s)
- T M Eckstein
- Mycobacteria Research Laboratories, Department of Microbiology, Colorado State University, Fort Collins, Colorado 80523-1677, USA
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64
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Warren RM, Sampson SL, Richardson M, Van Der Spuy GD, Lombard CJ, Victor TC, van Helden PD. Mapping of IS6110 flanking regions in clinical isolates of Mycobacterium tuberculosis demonstrates genome plasticity. Mol Microbiol 2000; 37:1405-16. [PMID: 10998172 DOI: 10.1046/j.1365-2958.2000.02090.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Southern hybridization was used in combination with IS6110 insertion-locus-specific probes in a comparative study to determine the structure of chromosomal domains flanking IS6110 elements in clinical isolates of Mycobacterium tuberculosis. The resulting restriction fragment length polymorphism (RFLP) data demonstrated three mutational mechanisms responsible for the polymorphisms observed: IS6110 insertion, chromosomal mutation and deletion. The frequency of IS6110 insertion within many of the chromosomal regions demonstrates that preferential integration regions are common in M. tuberculosis. Mapping the IS6110 insertion positions and chromosomal deletions in relation to the M. tuberculosis H37Rv and M. bovis BCG genome sequences reveals numerous disruptions of predicted open reading frames (ORFs). A phylogenetic tree, based on the mutational data, showed a number of independently evolving lineages of M. tuberculosis, while analysis of the mutational events occurring at each branch point suggests both divergent and convergent evolution. A significant positive correlation was demonstrated between the mutation rate and the frequency of occurrence of different isolates in families of strains, suggesting that evolution may impact on strain 'fitness' or that strain proliferation may increase the chance of mutation. We conclude that the genome of clinical isolates of M. tuberculosis continues to evolve.
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Affiliation(s)
- R M Warren
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, University of Stellenbosch, PO Box 19063, Tygerberg, 7505, South Africa
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65
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Sampson SL, Warren RM, Richardson M, van der Spuy GD, van Helden PD. Disruption of coding regions by IS6110 insertion in Mycobacterium tuberculosis. TUBERCLE AND LUNG DISEASE : THE OFFICIAL JOURNAL OF THE INTERNATIONAL UNION AGAINST TUBERCULOSIS AND LUNG DISEASE 2000; 79:349-59. [PMID: 10694979 DOI: 10.1054/tuld.1999.0218] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
SETTING The insertion sequence IS6110 is widely used as a DNA fingerprinting probe for the classification of Mycobacterium tuberculosis strains. This study has focused on the characterization of regions disrupted by insertion of the IS6110 element. OBJECTIVE To characterize IS6110 insertion loci in clinical isolates of M. tuberculosis, in terms of their genomic location and genetic identity, to ascertain whether IS6110 transposition could be a mechanism driving phenotypic change. DESIGN Thirty-three IS6110 insertion loci were cloned from 8 clinical isolates of M. tuberculosis. Clones representing DR locus insertions were identified by hybridization (n = 4), and all other clones were characterized by DNA sequencing (n = 29). The sequence data was analyzed in conjunction with that of 43 other insertion loci identified in published literature and DNA sequence databases. RESULTS The 76 sequences analyzed represented 66 unique insertion loci (including 9 unique insertions into the ipl locus). When mapped to the H37Rv genome, the majority of unique insertion loci demonstrated disruption of coding regions by IS6110 (n = 42; including the ipl insertions), while the remainder either occurred within intergenic regions (n = 17), or could not be mapped to the H37Rv genome sequence (n = 7). Mapping of the insertion loci reveals distribution throughout the chromosome, with isolated preferential insertion loci. CONCLUSIONS This study has demonstrated the occurrence of 66 unique IS6110 insertion loci dispersed throughout the M. tuberculosis genome, with an unexpectedly high incidence of IS6110 insertions occurring within coding regions. However, the IS6110-mediated coding region disruptions identified here may only have limited impact on phenotype, as most of the coding regions disrupted are members of multiple gene families. Disruption of individual members of a family of genes may have no effect on phenotype or could have a minor or major impact, depending on the specificity and activity of the encoded protein.
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Affiliation(s)
- S L Sampson
- Department of Medical Biochemistry, University of Stellenbosch Medical School, Tygerberg
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66
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Filliol I, Sola C, Rastogi N. Detection of a previously unamplified spacer within the DR locus of Mycobacterium tuberculosis: epidemiological implications. J Clin Microbiol 2000; 38:1231-4. [PMID: 10699028 PMCID: PMC86384 DOI: 10.1128/jcm.38.3.1231-1234.2000] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spoligotyping, a method based on the variability of distribution of the 43 inter-direct repeat (DR) spacers of Mycobacterium tuberculosis and Mycobacterium bovis BCG, is useful to study the molecular epidemiology of bovine and human tuberculosis. Recently, a major family of M. tuberculosis clinical isolates named the Haarlem family, which did not contain spacers 31 and 33 to 36, was reported in a multicenter study. Independently, a data bank containing all the published spoligotypes showed that the two most prevalent spoligotypes in the world differed only by the presence or absence of spacer 31. A careful analysis of the DR locus sequence led us to hypothesize that spacer 31 may not have been amplified in some isolates with the primer sets DRa and DRb currently used for spoligotyping. Consequently, a modified spoligotyping method based on different combinations of the 36-bp DR and IS6110 primers was devised that was able to discriminate between the left and the right parts of the DR locus and demonstrated the presence of the previously unamplified spacer 31 for some of the clinical isolates. By analogy, we suggest that a single-spacer difference in some epidemiologically linked cases of tuberculosis may simply arise due to the insertion of an extra copy of IS6110 within the DR locus, leading to its asymmetrical disruption and subsequent lack of the DRa or DRb targets. The influence of the IS6110 preferential insertion sites within the DR locus on spoligotyping results should be further investigated.
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Affiliation(s)
- I Filliol
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur, F-97165 Pointe à Pitre Cedex, Guadeloupe
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67
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Ho TB, Robertson BD, Taylor GM, Shaw RJ, Young DB. Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates. Yeast 2000; 17:272-82. [PMID: 11119304 PMCID: PMC2448390 DOI: 10.1002/1097-0061(200012)17:4<272::aid-yea48>3.0.co;2-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mycobacterium tuberculosis complex is associated with a remarkably low level of structural gene polymorphism. As part of a search for alternative forms of genetic variation that may act as a source of biological diversity in M. tuberculosis, we have identified a region of the genome that is highly variable amongst a panel of unrelated clinical isolates. Fifteen of 24 isolates examined contained one or more copies of the M. tuberculosis-specific IS6110 insertion element within this 20 kb variable region. In nine of the isolates, including the laboratory-passaged strain H37Rv, genomic deletions were identified, resulting in loss of between two and 13 genes. In each case, deletions were associated with the presence of a copy of the IS6110 element. Absence of flanking tri- or tetra-nucleotide repeats identified homologous recombination between adjacent IS6110 elements as the most likely mechanism of the deletion events. IS6110 insertion into hot-spots within the genome of M. tuberculosis provides a mechanism for generation of genetic diversity involving a high frequency of insertions and deletions.
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Affiliation(s)
- T B Ho
- Department of Infectious Diseases and Microbiology, Imperial College School of Medicine, Norfolk Place, London W2 1PG, UK.
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68
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Ho TBL, Robertson BD, Taylor GM, Shaw RJ, Young DB. Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates. Yeast 2000. [PMID: 11119304 PMCID: PMC2448390 DOI: 10.1002/1097-0061(200012)17:4<272::aid-yea48>3.0.co;2-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mycobacterium tuberculosis complex is associated with a remarkably low level of structural gene polymorphism. As part of a search for alternative forms of genetic variation that may act as a source of biological diversity in M. tuberculosis, we have identified a region of the genome that is highly variable amongst a panel of unrelated clinical isolates. Fifteen of 24 isolates examined contained one or more copies of the M. tuberculosis-specific IS6110 insertion element within this 20 kb variable region. In nine of the isolates, including the laboratory-passaged strain H37Rv, genomic deletions were identified, resulting in loss of between two and 13 genes. In each case, deletions were associated with the presence of a copy of the IS6110 element. Absence of flanking tri- or tetra-nucleotide repeats identified homologous recombination between adjacent IS6110 elements as the most likely mechanism of the deletion events. IS6110 insertion into hot-spots within the genome of M. tuberculosis provides a mechanism for generation of genetic diversity involving a high frequency of insertions and deletions.
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Affiliation(s)
- Timothy B. L. Ho
- Department of Infectious Diseases and Microbiology
Imperial College School of MedicineNorfolk PlaceLondonW2 1PGUK,Department of Respiratory MedicineImperial College School of MedicineNorfolk PlaceLondonW2 1PGUK
| | - Brian D. Robertson
- Department of Infectious Diseases and Microbiology
Imperial College School of MedicineNorfolk PlaceLondonW2 1PGUK
| | - G. Michael Taylor
- Department of Infectious Diseases and Microbiology
Imperial College School of MedicineNorfolk PlaceLondonW2 1PGUK
| | - Rory J. Shaw
- Department of Respiratory MedicineImperial College School of MedicineNorfolk PlaceLondonW2 1PGUK
| | - Douglas B. Young
- Department of Infectious Diseases and Microbiology
Imperial College School of MedicineNorfolk PlaceLondonW2 1PGUK
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Brosch R, Philipp WJ, Stavropoulos E, Colston MJ, Cole ST, Gordon SV. Genomic analysis reveals variation between Mycobacterium tuberculosis H37Rv and the attenuated M. tuberculosis H37Ra strain. Infect Immun 1999; 67:5768-74. [PMID: 10531227 PMCID: PMC96953 DOI: 10.1128/iai.67.11.5768-5774.1999] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis H37Ra is an attenuated tubercle bacillus closely related to the virulent type strain M. tuberculosis H37Rv. Despite extensive study, the reason for the decreased virulence of M. tuberculosis H37Ra has not been determined. A genomic approach was therefore initiated to identify genetic differences between M. tuberculosis H37Rv and M. tuberculosis H37Ra as a means of pinpointing the attenuating mutation(s). Digestion with the rare-cutting restriction endonuclease DraI revealed two polymorphisms between the strains: a 480-kb fragment in M. tuberculosis H37Rv was replaced by two fragments of 220 and 260 kb in M. tuberculosis H37Ra, while there was a approximately 7.9-kb DraI fragment in M. tuberculosis H37Ra that had no counterpart in M. tuberculosis H37Rv. As the M. tuberculosis insertion sequence IS6110 contains a single DraI restriction site, it was considered possible that these polymorphisms were the result of IS6110 transposition events in M. tuberculosis H37Ra, events that may have inactivated virulence genes. The 7.9-kb polymorphism was found to be due to the presence of the previously described H37Rv RvD2 deletion in M. tuberculosis H37Ra, with sequence analysis suggesting an IS6110-mediated deletion mechanism for loss of RvD2. Three other IS6110-catalyzed deletions from the M. tuberculosis H37Rv chromosome (RvD3 to RvD5) were also identified, suggesting that this mechanism plays an important role in genome plasticity in the tubercle bacilli. Comparative mapping and sequencing revealed that the 480-kb polymorphism was due to an IS6110 insertion in M. tuberculosis H37Ra near oriC. Complementation of M. tuberculosis H37Ra with a 2.9-kb restriction fragment from M. tuberculosis H37Rv that encompassed the IS6110 insertion did not increase the survival of recombinant M. tuberculosis H37Ra in mice. In conclusion, this study describes the presence and mechanisms of genomic variation between M. tuberculosis H37Ra and M. tuberculosis H37Rv, although the role that they play in the attenuation of M. tuberculosis H37Ra is unclear.
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Affiliation(s)
- R Brosch
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 75724 Paris, Cedex 15, France
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