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Stefan Niemann - One of the best experts on this subject based on the ideXlab platform.
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role of epistasis in amikacin kanamycin bedaquiline and clofazimine resistance in Mycobacterium Tuberculosis Complex
Antimicrobial Agents and Chemotherapy, 2021Co-Authors: Roger Vargas, Claudio U. Köser, Stefan Niemann, Luca Freschi, Daniela Maria Cirillo, Ivan Barilar, Andrea Spitaleri, Sabira Tahseen, Paolo Miotto, Maha R FarhatAbstract:Antibiotic resistance among bacterial pathogens poses a major global health threat. Mycobacterium Tuberculosis Complex (MTBC) is estimated to have the highest resistance rates of any pathogen globally. Given the low growth rate and the need for a biosafety level 3 laboratory, the only realistic avenue to scale up drug susceptibility testing (DST) for this pathogen is to rely on genotypic techniques. This raises the fundamental question of whether a mutation is a reliable surrogate for phenotypic resistance or whether the presence of a second mutation can completely counteract its effect, resulting in major diagnostic errors (i.e., systematic false resistance results). To date, such epistatic interactions have only been reported for streptomycin that is now rarely used. By analyzing more than 31,000 MTBC genomes, we demonstrated that the eis C-14T promoter mutation, which is interrogated by several genotypic DST assays endorsed by the World Health Organization, cannot confer resistance to amikacin and kanamycin if it coincides with loss-of-function (LoF) mutations in the coding region of eis. To our knowledge, this represents the first definitive example of antibiotic reversion in MTBC. Moreover, we raise the possibility that mmpR (Rv0678) mutations are not valid markers of resistance to bedaquiline and clofazimine if these coincide with an LoF mutation in the efflux pump encoded by mmpS5 (Rv0677c) and mmpL5 (Rv0676c).
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snp it tool for identifying subspecies and associated lineages of Mycobacterium Tuberculosis Complex
Emerging Infectious Diseases, 2019Co-Authors: Sam Lipworth, Rana Jajou, Albert J De Neeling, Phelim Bradley, Wim Van Der Hoek, Gugu Maphalala, Maryline Bonnet, Elizabeth Sanchezpadilla, Roland Diel, Stefan NiemannAbstract:The clinical phenotype of zoonotic Tuberculosis and its contribution to the global burden of disease are poorly understood and probably underestimated. This shortcoming is partly because of the inability of currently available laboratory and in silico tools to accurately identify all subspecies of the Mycobacterium Tuberculosis Complex (MTBC). We present SNPs to Identify TB (SNP-IT), a single-nucleotide polymorphism-based tool to identify all members of MTBC, including animal clades. By applying SNP-IT to a collection of clinical genomes from a UK reference laboratory, we detected an unexpectedly high number of M. orygis isolates. M. orygis is seen at a similar rate to M. bovis, yet M. orygis cases have not been previously described in the United Kingdom. From an international perspective, it is possible that M. orygis is an underestimated zoonosis. Accurate identification will enable study of the clinical phenotype, host range, and transmission mechanisms of all subspecies of MTBC in greater detail.
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mtbseq a comprehensive pipeline for whole genome sequence analysis of Mycobacterium Tuberculosis Complex isolates
PeerJ, 2018Co-Authors: Thomas Kohl, Patrick Beckert, Christian Utpatel, Viola Schleusener, Maria Rosaria De Filippo, Daniela Maria Cirillo, Stefan NiemannAbstract:Analyzing whole-genome sequencing data of Mycobacterium Tuberculosis Complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source.
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2003. Evaluation of genotype MTBC assay for differentiation of clinical Mycobacterium Tuberculosis Complex isolates
2016Co-Authors: Elvira Richter, Michael Weizenegger, Stefan NiemannAbstract:I, and M. microti were unequivocally identified. M. Tuberculosis, M. canetti, and M. africanum subtype II showed a unique hybridization pattern. The Mycobacterium Tuberculosis Complex (MTBC) comprises the closely related species M. Tuberculosis, M. bovis, M. bovis BCG, M. africanum, M. microti, and M. canetti which cause Tuberculosis in humans and animals (23, 24, 25). Despite their close genetic relatedness, as demonstrated, e.g., by DNA-DNA hybridization or by sequencing of the 16S rRNA gene (4, 5, 6, 10, 13, 14, 24), the members of the MTBC differ in host range and pathogenicity (25). The natural hosts of M. Tuberculosis and M. africanum are humans, whereas M. bovis can cause disease in a wide range of domestic or wild animals like cattle or goats, as well as in humans (25). According to their bio-chemical characteristics, two major subgroups of M. africanum, corresponding to their geographic origin in West (subtype I) o
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Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium Tuberculosis Complex
The Journal of antimicrobial chemotherapy, 2014Co-Authors: Silke Feuerriegel, Claudio U. Köser, Stefan NiemannAbstract:OBJECTIVES Sequence analysis of known antibiotic resistance genes of the Mycobacterium Tuberculosis Complex (MTBC) is increasingly being used to infer phenotypic resistance to a variety of antibiotics. However, a clear understanding of the genotype-phenotype relationship is required to interpret genotypic susceptibility results accurately. In this context, it is particularly important to distinguish phylogenetically informative neutral polymorphisms from true resistance-conferring mutations. METHODS Using a collection of 71 strains that encompasses all major MTBC genotypes, we mapped the genetic diversity in 18 genes that are known to be involved or were previously implicated in antibiotic resistance to eight current as well as two novel antibiotics. This included bedaquiline, capreomycin, ethambutol, fluoroquinolones, isoniazid, PA-824, para-aminosalicylic acid, prothionamide, rifampicin and streptomycin. Moreover, we included data from one of our prior studies that focused on two of the three known pyrazinamide resistance genes. RESULTS We found 58 phylogenetic polymorphisms that were markers for the genotypes M. Tuberculosis Beijing, Haarlem, Latin American-Mediterranean (LAM), East African Indian (EAI), Delhi/Central Asian (CAS), Ghana, Turkey (Tur), Uganda I and II, Ural and X-type, as well as for Mycobacterium africanum genotypes West African I (WA I) and II (WA II), Mycobacterium bovis, Mycobacterium caprae, Mycobacterium pinnipedii, Mycobacterium microti and Mycobacterium canettii. CONCLUSIONS This study represents one of the most extensive overviews of phylogenetically informative polymorphisms in known resistance genes to date, and will serve as a resource for the design and interpretation of genotypic susceptibility assays.
Nalin Rastogi - One of the best experts on this subject based on the ideXlab platform.
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TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium Tuberculosis Complex.
Infection Genetics and Evolution, 2012Co-Authors: Amina Shabbeer, Nalin Rastogi, Lauren S Cowan, Cagri Ozcaglar, Scott L Vandenberg, Bülent Yener, Kristin P BennettAbstract:This paper formulates a set of rules to classify genotypes of the Mycobacterium Tuberculosis Complex (MTBC) into major lineages using spoligotypes and MIRU-VNTR results. The rules synthesize prior literature that characterizes lineages by spacer deletions and variations in the number of repeats seen at locus MIRU24 (alias VNTR2687). A tool that efficiently and accurately implements this rule base is now freely available at http://tbinsight.cs.rpi.edu/run_tb_lineage.html. When MIRU24 data is not available, the system utilizes predictions made by a Naïve Bayes classifier based on spoligotype data. This website also provides a tool to generate spoligoforests in order to visualize the genetic diversity and relatedness of genotypes and their associated lineages. A detailed analysis of the application of these tools on a dataset collected by the CDC consisting of 3198 distinct spoligotypes and 5430 distinct MIRU-VNTR types from 37,066 clinical isolates is presented. The tools were also tested on four other independent datasets. The accuracy of automated classification using both spoligotypes and MIRU24 is >99%, and using spoligotypes alone is >95%. This online rule-based classification technique in conjunction with genotype visualization provides a practical tool that supports surveillance of TB transmission trends and molecular epidemiological studies.
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genetic biodiversity of Mycobacterium Tuberculosis Complex strains from patients with pulmonary Tuberculosis in cameroon
Journal of Clinical Microbiology, 2003Co-Authors: Sara Ngo Niobeeyangoh, Nalin Rastogi, Christophe Sola, Veronique Vincent, C Kuaban, Philippe Sorlin, Patrick Cunin, Jocelyn Thonnon, Cristina M GutierrezAbstract:We analyzed DNA polymorphisms in 455 Mycobacterium Tuberculosis Complex isolates from 455 patients to evaluate the biodiversity of tubercle bacilli in Ouest province, Cameroon. The phenotypic and genotypic identification methods gave concordant results for 99.5% of M. Tuberculosis isolates (413 strains) and for 90% of Mycobacterium africanum isolates (41 strains). Mycobacterium bovis was isolated from only one patient. Analysis of regions of difference (RD4, RD9, and RD10) proved to be an accurate and rapid method of distinguishing between unusual members of the M. Tuberculosis Complex. Whereas M. africanum strains were the etiologic agent of Tuberculosis in 56% of cases 3 decades ago, our results showed that these strains now account for just 9% of cases of Tuberculosis. We identified a group of closely genetically related M. Tuberculosis strains that are currently responsible for >40% of smear-positive pulmonary Tuberculosis cases in this region of Cameroon. These strains shared a spoligotype lacking spacers 23, 24, and 25 and had highly related IS6110 ligation-mediated (LM) PCR patterns. They were designated the “Cameroon family.” We did not find any significant association between Tuberculosis-causing species or strain families and patient characteristics (sex, age, and human immunodeficiency virus status). A comparison of the spoligotypes of the Cameroon strains with an international spoligotype database (SpolDB3) containing 11,708 patterns from >90 countries, showed that the predominant spoligotype in Cameroon was limited to West African countries (Benin, Senegal, and Ivory Coast) and to the Caribbean area.
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is Mycobacterium africanum subtype ii uganda i and uganda ii a genetically well defined subspecies of the Mycobacterium Tuberculosis Complex
Journal of Clinical Microbiology, 2003Co-Authors: Christophe Sola, Nalin Rastogi, Cristina M Gutierrez, Veronique Vincent, Roland Brosch, Linda M ParsonsAbstract:In a retrospective study of the population structure of Mycobacterium Tuberculosis Complex strains from a single hospital in Kampala, Uganda, Niemann et al. ([6][1]) reported that M. africanum subtype II is a major cause of human Tuberculosis in this area. The reclassification of strains previously
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characterization of Mycobacterium Tuberculosis Complex dnas from egyptian mummies by spoligotyping
Journal of Clinical Microbiology, 2003Co-Authors: Albert Zink, Nalin Rastogi, Christophe Sola, Udo Reischl, Waltraud Grabner, Hans Wolf, A NerlichAbstract:Bone and soft tissue samples from 85 ancient Egyptian mummies were analyzed for the presence of ancient Mycobacterium Tuberculosis Complex DNA (aDNA) and further characterized by spoligotyping. The specimens were obtained from individuals from different tomb Complexes in Thebes West, Upper Egypt, which were used for upper social class burials between the Middle Kingdom (since ca. 2050 BC) and the Late Period (until ca. 500 BC). A total of 25 samples provided a specific positive signal for the amplification of a 123-bp fragment of the repetitive element IS6110, indicating the presence of M. Tuberculosis DNA. Further PCR-based tests for the identification of subspecies failed due to lack of specific amplification products in the historic tissue samples. Of these 25 positive specimens, 12 could be successfully characterized by spoligotyping. The spoligotyping signatures were compared to those in an international database. They all show either an M. Tuberculosis or an M. africanum pattern, but none revealed an M. bovis-specific pattern. The results from a Middle Kingdom tomb (used exclusively between ca. 2050 and 1650 BC) suggest that these samples bear an M. africanum-type specific spoligotyping signature. The samples from later periods provided patterns typical for M. Tuberculosis. This study clearly demonstrates that spoligotyping can be applied to historic tissue samples. In addition, our results do not support the theory that M. Tuberculosis originated from the M. bovis type but, rather, suggest that human M. Tuberculosis may have originated from a precursor Complex probably related to M. africanum.
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rapid differentiation of Mycobacterium canettii from other Mycobacterium Tuberculosis Complex organisms by pcr restriction analysis of the hsp65 gene
Journal of Clinical Microbiology, 2001Co-Authors: Khye Seng Goh, Christophe Sola, Eric Legrand, Nalin RastogiAbstract:A total of 102 isolates of the Mycobacterium Tuberculosis Complex, including available “ M. canettii ” isolates, were studied by PCR-restriction analysis of a 441-bp fragment of the hsp65 gene. PRA upon Hha I enzyme digestion (GCGC) allowed easy differentiatiation of “ M. canettii ” from other members of the M. Tuberculosis Complex (three bands of 260, 105, and 60 bp for “ M. canetti ,” compared to four bands of 185, 105, 75, and 60 bp for other members of the M. Tuberculosis Complex). Sequencing of the 441-bp hsp65 fragment of “ M. canettii ” isolates showed the disappearance of an Hha I site at position 235 due to a C-to-T transition that corresponded to position 631 of the homologous hsp65 gene of M. Tuberculosis H37Rv. Considering that “ M. canettii ” may also exist as a stable rough morphotype, we suggest that the true number of “ M. canettii ” isolates may be underestimated in clinical microbiology laboratories.
Silke Feuerriegel - One of the best experts on this subject based on the ideXlab platform.
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Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium Tuberculosis Complex.
Antimicrobial Agents and Chemotherapy, 2019Co-Authors: Chloé Loiseau, Daniela Brites, Irmgard Moser, Francesc Coll, Christine Pourcel, Suelee Robbe-austerman, Vincent E. Escuyer, Kimberlee A. Musser, Sharon J. Peacock, Silke FeuerriegelAbstract:Using 894 phylogenetically diverse genomes of the Mycobacterium Tuberculosis Complex (MTBC), we simulated in silico the ability of the Hain Lifescience GenoType MTBC assay to differentiate the causative agents of Tuberculosis. Here, we propose a revised interpretation of this assay to reflect its strengths (e.g., it can distinguish some strains of Mycobacterium canettii and variants of Mycobacterium bovis that are not intrinsically resistant to pyrazinamide) and limitations (e.g., Mycobacterium orygis cannot be differentiated from Mycobacterium africanum).
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Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium Tuberculosis Complex
The Journal of antimicrobial chemotherapy, 2014Co-Authors: Silke Feuerriegel, Claudio U. Köser, Stefan NiemannAbstract:OBJECTIVES Sequence analysis of known antibiotic resistance genes of the Mycobacterium Tuberculosis Complex (MTBC) is increasingly being used to infer phenotypic resistance to a variety of antibiotics. However, a clear understanding of the genotype-phenotype relationship is required to interpret genotypic susceptibility results accurately. In this context, it is particularly important to distinguish phylogenetically informative neutral polymorphisms from true resistance-conferring mutations. METHODS Using a collection of 71 strains that encompasses all major MTBC genotypes, we mapped the genetic diversity in 18 genes that are known to be involved or were previously implicated in antibiotic resistance to eight current as well as two novel antibiotics. This included bedaquiline, capreomycin, ethambutol, fluoroquinolones, isoniazid, PA-824, para-aminosalicylic acid, prothionamide, rifampicin and streptomycin. Moreover, we included data from one of our prior studies that focused on two of the three known pyrazinamide resistance genes. RESULTS We found 58 phylogenetic polymorphisms that were markers for the genotypes M. Tuberculosis Beijing, Haarlem, Latin American-Mediterranean (LAM), East African Indian (EAI), Delhi/Central Asian (CAS), Ghana, Turkey (Tur), Uganda I and II, Ural and X-type, as well as for Mycobacterium africanum genotypes West African I (WA I) and II (WA II), Mycobacterium bovis, Mycobacterium caprae, Mycobacterium pinnipedii, Mycobacterium microti and Mycobacterium canettii. CONCLUSIONS This study represents one of the most extensive overviews of phylogenetically informative polymorphisms in known resistance genes to date, and will serve as a resource for the design and interpretation of genotypic susceptibility assays.
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importance of the genetic diversity within the Mycobacterium Tuberculosis Complex for the development of novel antibiotics and diagnostic tests of drug resistance
Antimicrobial Agents and Chemotherapy, 2012Co-Authors: Silke Feuerriegel, Claudio U. Köser, David K Summers, John A C Archer, Stefan NiemannAbstract:Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium Tuberculosis Complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.
Chloé Loiseau - One of the best experts on this subject based on the ideXlab platform.
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A sister lineage of the Mycobacterium Tuberculosis Complex discovered in the African Great Lakes region
Nature Communications, 2020Co-Authors: Jean Claude Semuto Ngabonziza, Chloé Loiseau, Michael Marceau, Agathe Jouet, Fabrizio Menardo, Oren Tzfadia, Rudy Antoine, Esdras Belamo Niyigena, Wim Mulders, Kristina FissetteAbstract:The human-and animal-adapted lineages of the Mycobacterium Tuberculosis Complex (MTBC) are thought to have expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug resistant Tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region-involved in the cobalamin/vitamin B12 synthesis-and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle.
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a sister lineage of the Mycobacterium Tuberculosis Complex discovered in the african great lakes region
bioRxiv, 2020Co-Authors: Jean Claude Semuto Ngabonziza, Chloé Loiseau, Michael Marceau, Agathe Jouet, Fabrizio Menardo, Oren Tzfadia, Rudy Antoine, Esdras Belamo Niyigena, Wim Mulders, Kristina FissetteAbstract:The human- and animal-adapted lineages of the Mycobacterium Tuberculosis Complex (MTBC) are thought to have clonally expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug-resistant Tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle.
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Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium Tuberculosis Complex.
Antimicrobial Agents and Chemotherapy, 2019Co-Authors: Chloé Loiseau, Daniela Brites, Irmgard Moser, Francesc Coll, Christine Pourcel, Suelee Robbe-austerman, Vincent E. Escuyer, Kimberlee A. Musser, Sharon J. Peacock, Silke FeuerriegelAbstract:Using 894 phylogenetically diverse genomes of the Mycobacterium Tuberculosis Complex (MTBC), we simulated in silico the ability of the Hain Lifescience GenoType MTBC assay to differentiate the causative agents of Tuberculosis. Here, we propose a revised interpretation of this assay to reflect its strengths (e.g., it can distinguish some strains of Mycobacterium canettii and variants of Mycobacterium bovis that are not intrinsically resistant to pyrazinamide) and limitations (e.g., Mycobacterium orygis cannot be differentiated from Mycobacterium africanum).
William R Jacobs - One of the best experts on this subject based on the ideXlab platform.
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genome wide mutational biases fuel transcriptional diversity in the Mycobacterium Tuberculosis Complex
Nature Communications, 2019Co-Authors: Alvaro Chineroms, Michael Berney, Christine J Boinett, Fernando Gonzalezcandelas, Douglas Young, Sebastien Gagneux, William R JacobsAbstract:The Mycobacterium Tuberculosis Complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methylome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics. A variety of biological differences exist between strains and phylogenetic lineages in the Mycobacterium Tuberculosis Complex (MTBC). Here, the authors perform RNAseq and methylome analysis of the main clades of the MTBC and show variation in transcriptional profiles is mainly due to mutations in transcriptional start sites.
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mutation of the principal sigma factor causes loss of virulence in a strain of the Mycobacterium Tuberculosis Complex
Proceedings of the National Academy of Sciences of the United States of America, 1995Co-Authors: D M Collins, Riku Pamela Kawakami, G W De Lisle, Lisa Pascopella, Barry R Bloom, William R JacobsAbstract:Abstract Tuberculosis continues to be responsible for the deaths of millions of people, yet the virulence factors of the causative pathogens remain unknown. Genetic complementation experiments with strains of the Mycobacterium Tuberculosis Complex have identified a gene from a virulent strain that restores virulence to an attenuated strain. The gene, designated rpoV, has a high degree of homology with principal transcription or sigma factors from other bacteria, particularly Mycobacterium smegmatis and Streptomyces griseus. The homologous rpoV gene of the attenuated strain has a point mutation causing an arginine-->histidine change in a domain known to interact with promoters. To our knowledge, association of loss of bacterial virulence with a mutation in the principal sigma factor has not been previously reported. The results indicate either that Tuberculosis organisms have an alternative principal sigma factor that promotes virulence genes or, more probably, that this particular mutant principal sigma factor is unable to promote expression of one or more genes required for virulence. Study of genes and proteins differentially regulated by the mutant transcription factor should facilitate identification of further virulence factors.
