RESUMEN
The emergence of drug-resistant Mycobacterium tuberculosis strains highlights the need to discover anti-tuberculosis drugs with novel mechanisms of action. Here we discovered a mycobactericidal strategy based on the prodrug activation of selected chemical derivatives classified as nitronaphthofurans (nNFs) mediated by the coordinated action of the sigH and mrx2 genes. The transcription factor SigH is a key regulator of an extensive transcriptional network that responds to oxidative, nitrosative, and heat stresses in M. tuberculosis. The nNF action induced the SigH stress response which in turn induced the mrx2 overexpression. The nitroreductase Mrx2 was found to activate nNF prodrugs, killing replicating, non-replicating and intracellular forms of M. tuberculosis. Analysis of SigH DNA sequences obtained from spontaneous nNF-resistant M. tuberculosis mutants suggests disruption of SigH binding to the mrx2 promoter site and/or RNA polymerase core, likely promoting the observed loss of transcriptional control over Mrx2. Mutations found in mrx2 lead to structural defects in the thioredoxin fold of the Mrx2 protein, significantly impairing the activity of the Mrx2 enzyme against nNFs. Altogether, our work brings out the SigH/Mrx2 stress response pathway as a promising target for future drug discovery programs.
Asunto(s)
Antibacterianos , Mycobacterium tuberculosis , Profármacos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Respuesta al Choque Térmico/genética , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/metabolismo , Profármacos/farmacología , Regiones Promotoras Genéticas , Transcripción Genética , Antibacterianos/farmacologíaRESUMEN
The lungs harbor multiple resident microbial communities, otherwise known as the microbiota. There is an emerging interest in deciphering whether the pulmonary microbiota modulate local immunity, and whether this knowledge could shed light on mechanisms operating in the response to respiratory pathogens. In this study, we investigate the capacity of a pulmonary Lactobacillus strain to modulate the lung T cell compartment and assess its prophylactic potential upon infection with Mycobacterium tuberculosis, the etiological agent of tuberculosis. In naive mice, we report that a Lactobacillus murinus (Lagilactobacillus murinus) strain (CNCM I-5314) increases the presence of lung Th17 cells and of a regulatory T cell (Treg) subset known as RORγt+ Tregs. In particular, intranasal but not intragastric administration of CNCM I-5314 increases the expansion of these lung leukocytes, suggesting a local rather than systemic effect. Resident Th17 and RORγt+ Tregs display an immunosuppressive phenotype that is accentuated by CNCM I-5314. Despite the well-known ability of M. tuberculosis to modulate lung immunity, the immunomodulatory effect by CNCM I-5314 is dominant, as Th17 and RORγt+ Tregs are still highly increased in the lung at 42-d postinfection. Importantly, CNCM I-5314 administration in M. tuberculosis-infected mice results in reduction of pulmonary inflammation, without increasing M. tuberculosis burden. Collectively, our findings provide evidence for an immunomodulatory capacity of CNCM I-5314 at steady state and in a model of chronic inflammation in which it can display a protective role, suggesting that L. murinus strains found in the lung may shape local T cells in mice and, perhaps, in humans.
Asunto(s)
Lactobacillus/fisiología , Pulmón/inmunología , Mycobacterium tuberculosis/fisiología , Miembro 3 del Grupo F de la Subfamilia 1 de Receptores Nucleares/metabolismo , Linfocitos T Reguladores/inmunología , Células Th17/inmunología , Tuberculosis Pulmonar/inmunología , Animales , Células Cultivadas , Modelos Animales de Enfermedad , Humanos , Pulmón/microbiología , Activación de Linfocitos , Ratones , Ratones Endogámicos C57BL , NeumoníaRESUMEN
Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.
Asunto(s)
Genoma Bacteriano , Peste/historia , Peste/microbiología , Yersinia pestis/genética , ADN Bacteriano , Europa (Continente) , Historia del Siglo XVIII , Historia Medieval , Humanos , Pandemias/historia , Filogenia , Peste/genética , Federación de Rusia , Yersinia pestis/clasificaciónRESUMEN
Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.
Asunto(s)
Proteínas Bacterianas/genética , Borrelia/genética , Genoma Bacteriano , Metagenómica , Fiebre Recurrente/genética , Adulto , Animales , Borrelia/clasificación , Borrelia/patogenicidad , Niño , Femenino , Historia del Siglo XV , Humanos , Filogenia , Fiebre Recurrente/historia , Fiebre Recurrente/microbiología , Países Escandinavos y NórdicosRESUMEN
Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.
Asunto(s)
Pandemias/historia , Peste/historia , Yersinia pestis/genética , ADN Bacteriano/genética , ADN Bacteriano/aislamiento & purificación , Europa (Continente)/epidemiología , Evolución Molecular , Fósiles/microbiología , Genoma Bacteriano , Historia Medieval , Humanos , Filogenia , Peste/epidemiología , Peste/microbiología , Polimorfismo de Nucleótido Simple , Factores de Tiempo , Yersinia pestis/clasificaciónRESUMEN
BACKGROUND: Tuberculosis (TB) is caused by Mycobacterium tuberculosis and represents one of the major challenges facing drug discovery initiatives worldwide. The considerable rise in bacterial drug resistance in recent years has led to the need of new drugs and drug regimens. Model systems are regularly used to speed-up the drug discovery process and circumvent biosafety issues associated with manipulating M. tuberculosis. These include the use of strains such as Mycobacterium smegmatis and Mycobacterium marinum that can be handled in biosafety level 2 facilities, making high-throughput screening feasible. However, each of these model species have their own limitations. RESULTS: We report and describe the first complete genome sequence of Mycobacterium aurum ATCC23366, an environmental mycobacterium that can also grow in the gut of humans and animals as part of the microbiota. This species shows a comparable resistance profile to that of M. tuberculosis for several anti-TB drugs. The aims of this study were to (i) determine the drug resistance profile of a recently proposed model species, Mycobacterium aurum, strain ATCC23366, for anti-TB drug discovery as well as Mycobacterium smegmatis and Mycobacterium marinum (ii) sequence and annotate the complete genome sequence of this species obtained using Pacific Bioscience technology (iii) perform comparative genomics analyses of the various surrogate strains with M. tuberculosis (iv) discuss how the choice of the surrogate model used for drug screening can affect the drug discovery process. CONCLUSIONS: We describe the complete genome sequence of M. aurum, a surrogate model for anti-tuberculosis drug discovery. Most of the genes already reported to be associated with drug resistance are shared between all the surrogate strains and M. tuberculosis. We consider that M. aurum might be used in high-throughput screening for tuberculosis drug discovery. We also highly recommend the use of different model species during the drug discovery screening process.
Asunto(s)
Descubrimiento de Drogas , Genómica , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/genética , Fenotipo , Farmacorresistencia Bacteriana/genética , Anotación de Secuencia Molecular , Mycobacterium tuberculosis/metabolismo , Especificidad de la EspecieAsunto(s)
Peste/epidemiología , Yersinia pestis , Brotes de Enfermedades , Historia Medieval , Humanos , Peste/historiaRESUMEN
BACKGROUND: A deeply rooted phylogenetic lineage of Mycobacterium tuberculosis (M. tuberculosis) termed lineage 7 was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was performed. Intra-lineage genome variation was defined and unique characteristics identified with a focus on genes involved in DNA repair, recombination and replication (3R genes). RESULTS: More than 800 mutations specific to M. tuberculosis lineage 7 strains were identified. The proportion of non-synonymous single nucleotide polymorphisms (nsSNPs) in 3R genes was higher after the recent expansion of M. tuberculosis lineage 7 strain started. The proportion of nsSNPs in genes involved in inorganic ion transport and metabolism was significantly higher before the expansion began. A total of 22346 bp deletions were observed. Lineage 7 strains also exhibited a high number of mutations in genes involved in carbohydrate transport and metabolism, transcription, energy production and conversion. CONCLUSIONS: We have identified unique genomic signatures of the lineage 7 strains. The high frequency of nsSNP in 3R genes after the phylogenetic expansion may have contributed to recent variability and adaptation. The abundance of mutations in genes involved in inorganic ion transport and metabolism before the expansion period may indicate an adaptive response of lineage 7 strains to enable survival, potentially under environmental stress exposure. As lineage 7 strains originally were phylogenetically deeply rooted, this may indicate fundamental adaptive genomic pathways affecting the fitness of M. tuberculosis as a species.
Asunto(s)
Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/genética , Evolución Biológica , Etiopía , Genoma Bacteriano , Humanos , Mycobacterium tuberculosis/metabolismo , Filogenia , Polimorfismo de Nucleótido Simple , Eliminación de Secuencia , Tuberculosis/microbiologíaRESUMEN
BACKGROUND: As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs. RESULTS: The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress. CONCLUSIONS: Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets.
Asunto(s)
Daño del ADN , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Mycobacterium tuberculosis/genética , Transcriptoma , Análisis por Conglomerados , Daño del ADN/efectos de los fármacos , Perfilación de la Expresión Génica , Humanos , Peróxido de Hidrógeno/toxicidad , Metilnitronitrosoguanidina/toxicidad , Mycobacterium tuberculosis/efectos de los fármacos , Sistemas de Secreción Tipo VII/genéticaRESUMEN
BACKGROUND: MDR Mycobacterium tuberculosis clinical strains that cause large outbreaks, particularly among HIV-negative patients, are likely to have undergone the most successful compensatory evolution. Hence, mutations secondary to the acquisition of drug resistance are worthy of consideration in these highly transmissible strains. Here, we assessed the role of a mutation within rpoB, rpoB V615M, secondary to the rifampicin resistance-conferring mutation rpoB S531L, which is associated with a major MDR tuberculosis outbreak strain that evolved in an HIV-negative context in northern Tunisia. METHODS: Using BCG as a model organism, we engineered strains harbouring either the rpoB S531L mutation alone or the double mutation rpoB S531L, V615M. Individual and competitive in vitro growth assays were performed in order to assess the relative fitness of each BCG mutant. RESULTS: The rpoB V615M mutation was found to be invariably associated with rpoB S531L. Structural analysis mapped rpoB V615M to the same bridge helix region as rpoB compensatory mutations previously described in Salmonella. Compared with the rpoB single-mutant BCG, the double mutant displayed improved growth characteristics and fitness rates equivalent to WT BCG. Strikingly, the rpoB double mutation conferred high-level resistance to rifampicin. CONCLUSIONS: Here, we demonstrated the fitness compensatory role of a mutation within rpoB, secondary to the rifampicin resistance mutation rpoB S531L, which is characteristic of an MDR M. tuberculosis major outbreak strain. The finding that this secondary mutation concomitantly increased the resistance level to rifampicin argues for its significant contribution to the successful transmission of the MDR-TB strain.
Asunto(s)
ARN Polimerasas Dirigidas por ADN/genética , Brotes de Enfermedades , Evolución Molecular , Mutación Missense , Mycobacterium tuberculosis/enzimología , Tuberculosis Resistente a Múltiples Medicamentos/epidemiología , Tuberculosis Resistente a Múltiples Medicamentos/microbiología , Adulto , Femenino , Humanos , Masculino , Mycobacterium bovis/enzimología , Mycobacterium bovis/genética , Mycobacterium bovis/crecimiento & desarrollo , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/crecimiento & desarrollo , Mycobacterium tuberculosis/aislamiento & purificación , Genética Inversa , Tuberculosis Resistente a Múltiples Medicamentos/transmisión , Túnez/epidemiologíaRESUMEN
Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.
Asunto(s)
Variación Genética , Genoma Bacteriano/genética , Mutación , Mycobacterium tuberculosis/genética , Recombinación Genética , Selección Genética , Análisis por Conglomerados , Transferencia de Gen Horizontal , Humanos , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/metabolismo , Filogenia , Polimorfismo de Nucleótido Simple , Especificidad de la Especie , Tuberculosis/microbiologíaRESUMEN
Recent genotyping studies of Mycobacterium tuberculosis in Ethiopia have reported the identification of a new phylogenetically distinct M. tuberculosis lineage, lineage 7. We therefore investigated the genetic diversity and association of specific M. tuberculosis lineages with sociodemographic and clinical parameters among pulmonary TB patients in the Amhara Region, Ethiopia. DNA was isolated from M. tuberculosis-positive sputum specimens (n=240) and analyzed by PCR and 24-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) analysis and spoligotyping. Bioinformatic analysis assigned the M. tuberculosis genotypes to global lineages, and associations between patient characteristics and genotype were evaluated using logistic regression analysis. The study revealed a high diversity of modern and premodern M. tuberculosis lineages, among which approximately 25% were not previously reported. Among the M. tuberculosis strains (n=138) assigned to seven subgroups, the largest cluster belonged to the lineage Central Asian (CAS) (n=60; 26.0%), the second largest to lineage 7 (n=36; 15.6%), and the third largest to the lineage Haarlem (n=35; 15.2%). Four sublineages were new in the MIRU-VNTRplus database, designated NW-ETH3, NW-ETH1, NW-ETH2, and NW-ETH4, which included 24 (10.4%), 18 (7.8%), 8 (3.5%), and 5 (2.2%) isolates, respectively. Notably, patient delay in seeking treatment was significantly longer among patients infected with lineage 7 strains (Mann-Whitney test, P<0.008) than in patients infected with CAS strains (adjusted odds ratio [AOR], 4.7; 95% confidence interval [CI], 1.6 to 13.5). Lineage 7 strains also grew more slowly than other M. tuberculosis strains. Cases of Haarlem (OR, 2.8; 95% CI, 1.2 to 6.6) and NW-ETH3 (OR, 2.8; 95% CI, 1.0 to 7.3) infection appeared in defined clusters. Intensified active case finding and contact tracing activities in the study region are needed to expedite diagnosis and treatment of TB.
Asunto(s)
Diagnóstico Tardío , Genotipo , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/aislamiento & purificación , Tuberculosis Pulmonar/diagnóstico , Tuberculosis Pulmonar/microbiología , Adulto , Estudios Transversales , ADN Bacteriano/genética , ADN Bacteriano/aislamiento & purificación , Etiopía/epidemiología , Femenino , Variación Genética , Humanos , Masculino , Epidemiología Molecular , Tipificación Molecular , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/crecimiento & desarrollo , Esputo/microbiología , Tuberculosis Pulmonar/epidemiología , VirulenciaRESUMEN
BACKGROUND: Drug susceptibility testing (DST) remains an important concern for implementing treatment of MDR tuberculosis patients. Implementation of molecular tests for drug resistance identification would facilitate DST particularly in developing countries where culturing is difficult to perform. We have characterized multidrug resistant strains in Cambodia using MDTDRsl tests, drug target sequencing and phenotypic tests. METHODS: A total of 65 non-MDR and 101 MDR TB isolates collected between May 2007 and June 2009 were tested for resistance to fluoroquinolones and aminoglycosides/cyclic peptides using the GenoType® MTBDRsl assay and gene sequencing. Rifampicin resistance (RMP-R) was tested using gene sequencing and genotyping was assessed by spoligotyping. RESULTS: A total of 95 of the 101 MDR strains were confirmed to be RMP-R by rpoB gene sequencing. Fourteen of the 101 MDR isolates (14%) carried a gyrA mutation associated with fluoroquinolone-resistance (FQ-R) (detected by the MTBDRsl assay and sequencing) compared with only 1 (1.5%) of the 65 non-MDR strains. Only 1 (1%) of the MDR isolates was found to be XDR TB. The MDR group contained a higher proportion of Beijing or Beijing like strains (58%) than the non MDR group (28%). This percentage is higher in MDR FQ-R strains (71%). CONCLUSIONS: The new GenoType® MTBDRsl assay combined with molecular tests to detect RMP-R and isoniazid resistance (INH-R) represents a valuable tool for the detection of XDR TB. In Cambodia there is a low rate of XDR amongst MDR TB including MDR FQ-R TB. This suggests a low association between FQ-R and XDR TB. Strain spoligotyping confirms Beijing strains to be more prone to accumulate antibiotic resistance.
Asunto(s)
Antituberculosos/farmacología , Fluoroquinolonas/farmacología , Genes Bacterianos , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/genética , Tuberculosis Resistente a Múltiples Medicamentos/microbiología , Cambodia , Girasa de ADN/genética , ADN Bacteriano/química , ADN Bacteriano/genética , ARN Polimerasas Dirigidas por ADN/genética , Genotipo , Humanos , Pruebas de Sensibilidad Microbiana/métodos , Mycobacterium tuberculosis/aislamiento & purificación , Fenotipo , Análisis de Secuencia de ADNRESUMEN
BACKGROUND. The progenitors of multidrug-resistant tuberculosis (MDR-TB) outbreak strains might evolve into new outbreak strains. We hypothesized that these strains could re-emerge among post-outbreak patients with TB and must thus be tracked. METHODS. To identify the progenitors of the outbreak strain, we first determined the precise IS6110 genomic insertion locations of a Haarlem3 strain that caused a severe MDR-TB outbreak in Tunisia. Next, we searched by polymerase chain reaction for these outbreak-specific IS6110 transposition sites in all the Haarlem3 post-outbreak isolates recovered in the epidemic region. RESULTS. By analyzing the distribution of the outbreak-specific IS6110 transposition sites, we were able to trap, among isolates recovered from post-outbreak new patients, drug-susceptible and drug-resistant isolates that are likely to represent the very close progenitors of the outbreak strain. Mycobacterial interspersed repetitive units-variable number of tandem repeats typing and sequential accumulation of rifampicin resistance-associated rpoB mutations further confirmed the identity of the outbreak's progenitor strains. CONCLUSIONS. The data of the current study show that the progenitors of an MDR-TB outbreak strain could re-emerge among post-outbreak TB cases. We provide an IS6110 insertion site-based approach to better trace back the events preceding the emergence of MDR-TB outbreaks, irrespective of the availability of a pre-outbreak strain collection.
Asunto(s)
Brotes de Enfermedades , Farmacorresistencia Bacteriana Múltiple/genética , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/genética , Tuberculosis Resistente a Múltiples Medicamentos/epidemiología , Tuberculosis Resistente a Múltiples Medicamentos/microbiología , Genotipo , Humanos , Túnez/epidemiologíaRESUMEN
Typing analyses of 378 Mycobacterium tuberculosis isolates collected between the years 2001 and 2005 from three northern representative regions of Tunisia revealed a highly homogeneous population. Indeed, 84.9 % of all tuberculosis (TB) cases were attributed to the Haarlem, LAM or T families. Strikingly, within each family, more than 60 % of TB cases were due to a single genotype. ST50 (Haarlem3) and ST42 (LAM9) genotypes were exceptionally predominant, representing 46.3 % of all typed isolates. ST50 showed an increased tendency for clustering and was more predominant in the extreme north of the country. By contrast, the more widespread ST42, which was apparently prevalent 17 years ago, displayed weak cluster individualization and a low transmission rate, consistent with its stable association with the Tunisian population. It is believed that both mass BCG vaccination, strictly applied for four decades, and the high endogamy rate that characterizes the Tunisian population could have profoundly shaped the population structure of M. tuberculosis by concurrently favouring the selection and accommodation of particular genotypes.
Asunto(s)
Variación Genética , Epidemiología Molecular , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/genética , Tuberculosis Pulmonar/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Antituberculosos/farmacología , Técnicas de Tipificación Bacteriana , Farmacorresistencia Bacteriana , Femenino , Genotipo , Humanos , Masculino , Persona de Mediana Edad , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/aislamiento & purificación , Tuberculosis Pulmonar/microbiología , Túnez/epidemiologíaRESUMEN
Neisseria meningitidis (Nm) is a Gram-negative nasopharyngeal commensal that can cause septicaemia and meningitis. The neisserial DNA damage-inducible protein DinG is a helicase related to the mammalian helicases XPD and FANCJ. These helicases belong to superfamily 2, are ATP dependent and exert 5' â 3' directionality. To better understand the role of DinG in neisserial genome maintenance, the Nm DinG (DinGNm) enzymatic activities were assessed in vitro and phenotypical characterization of a dinG null mutant (NmΔdinG) was performed. Like its homologues, DinGNm possesses 5' â 3' directionality and prefers DNA substrates containing a 5'-overhang. ATPase activity of DinGNm is strictly DNA-dependent and DNA unwinding activity requires nucleoside triphosphate and divalent metal cations. DinGNm directly binds SSBNm with a Kd of 313 nM. Genotoxic stress analysis demonstrated that NmΔdinG was more sensitive to double-strand DNA breaks (DSB) induced by mitomycin C (MMC) than the Nm wildtype, defining the role of neisserial DinG in DSB repair. Notably, when NmΔdinG cells grown under MMC stress assessed by quantitative mass spectrometry, 134 proteins were shown to be differentially abundant (DA) compared to unstressed NmΔdinG cells. Among the DNA replication, repair and recombination proteins affected, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly down regulated while TopA and SSB were upregulated under stress condition. Most of the other DA proteins detected are involved in metabolic functions. The present study shows that the helicase DinG is probably involved in regulating metabolic pathways as well as in genome maintenance.
Asunto(s)
Roturas del ADN de Doble Cadena , ADN Helicasas/metabolismo , ADN Bacteriano/metabolismo , Neisseria meningitidis/crecimiento & desarrollo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , ADN Helicasas/química , Regulación del Desarrollo de la Expresión Génica , Inestabilidad Genómica , Mitomicina/efectos adversos , Modelos Moleculares , Neisseria meningitidis/enzimología , Neisseria meningitidis/genética , Filogenia , Estructura Terciaria de ProteínaRESUMEN
The objective of this study was to find molecules with anti-mycobacterial activity from a natural compounds library, investigate their mechanisms of resistance, and assess their synergy with antibiotics. We screened a library of 2582 natural compounds with Mycobacterium aurum with the aim of identifying molecules with anti-mycobacterial activity. The hits with the lowest MICs in M. aurum were also tested for their antimicrobial activity in other mycobacterial species including M. tuberculosis complex strains. The chequerboard titration assay was chosen for determining drug interactions in vitro. Spontaneous resistant mutants were isolated and their whole genome sequences compared to wild type and resistant mutants to identify resistance mechanisms. We found that ionophores show anti-mycobacterial activity in vitro. Resistance mechanism to ionophores is mediated by the MmpL5-MmpS5 transporter overexpression. Ionophore A23187 enhanced beta-lactam activity in M. tuberculosis infected macrophage. It will help in the investigation of new drug combinations against bacterial infections including tuberculosis.
Asunto(s)
Antibióticos Antituberculosos/farmacología , Calcimicina/farmacología , Ionóforos de Calcio/farmacología , Carbapenémicos/farmacología , Mycobacterium tuberculosis/efectos de los fármacos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Células Cultivadas , Relación Dosis-Respuesta a Droga , Farmacorresistencia Bacteriana/genética , Sinergismo Farmacológico , Genotipo , Humanos , Macrófagos/microbiología , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/metabolismo , Pruebas de Sensibilidad Microbiana , Mutación , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/crecimiento & desarrolloRESUMEN
BACKGROUND: The highly homologous PE_PGRS (Proline-glutamic acid_polymorphic GC-rich repetitive sequence) genes are members of the PE multigene family which is found only in mycobacteria. PE genes are particularly abundant within the genomes of pathogenic mycobacteria where they seem to have expanded as a result of gene duplication events. PE_PGRS genes are characterized by their high GC content and extensive repetitive sequences, making them prone to recombination events and genetic variability. RESULTS: Comparative sequence analysis of Mycobacterium tuberculosis genes PE_PGRS17 (Rv0978c) and PE_PGRS18 (Rv0980c) revealed a striking genetic variation associated with this typical tandem duplicate. In comparison to the M. tuberculosis reference strain H37Rv, the variation (named the 12/40 polymorphism) consists of an in-frame 12-bp insertion invariably accompanied by a set of 40 single nucleotide polymorphisms (SNPs) that occurs either in PE_PGRS17 or in both genes. Sequence analysis of the paralogous genes in a representative set of worldwide distributed tubercle bacilli isolates revealed data which supported previously proposed evolutionary scenarios for the M. tuberculosis complex (MTBC) and confirmed the very ancient origin of "M. canettii" and other smooth tubercle bacilli. Strikingly, the identified polymorphism appears to be coincident with the emergence of the post-bottleneck successful clone from which the MTBC expanded. Furthermore, the findings provide direct and clear evidence for the natural occurrence of gene conversion in mycobacteria, which appears to be restricted to modern M. tuberculosis strains. CONCLUSION: This study provides a new perspective to explore the molecular events that accompanied the evolution, clonal expansion, and recent diversification of tubercle bacilli.
Asunto(s)
Reordenamiento Génico , Genes Bacterianos , Genes Duplicados , Mycobacterium tuberculosis/genética , Evolución Molecular , Variación Genética , Análisis de Secuencia de ADNRESUMEN
Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band.
Asunto(s)
Mapeo Cromosómico/métodos , Elementos Transponibles de ADN/genética , Genoma Bacteriano/genética , Mycobacterium tuberculosis/genética , Tuberculosis/microbiología , Clonación Molecular , ADN Bacteriano/química , ADN Bacteriano/genética , Desoxirribonucleasas de Localización Especificada Tipo II/metabolismo , Biblioteca Genómica , Humanos , Mycobacterium tuberculosis/clasificación , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Transformación GenéticaRESUMEN
Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.