Corporacion CorpoGen

Bogotá, Colombia

Corporacion CorpoGen

Bogotá, Colombia

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Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-2.3.2-3 | Award Amount: 3.64M | Year: 2008

Tuberculosis (TB) continues being a leading cause of death due to a single infectious disease agent. The HIV/AIDS pandemic and the emergence of drug resistance are compounding factors that hinder the control of the disease. Associated with this problem is the emergence of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis, defined as strains resistant to at least isoniazid and rifampicin, the most valuable drugs in the treatment of the disease. More recently, the appearance of extensively drug resistant (XDR) strains has been reported. These strains, in addition to being MDR, are also resistant to key second-line drugs. Patients, especially HIV patients, harbouring XDR strains have virtually no treatment options. New and improved methods for fast detection of drug resistance are urgently needed. This project will develop a twofold-approach system for the fast and simultaneous detection of MDR and XDR strains based on a rapid phenotypic assay and a genotypic test. Colorimetric methods, which have been previously validated by our group for first-line drug susceptibility testing, will be developed for key second-line drugs involved in XDRTB. Once set up, these methods will be further elaborated for direct application to sputum specimens. The molecular tool will be based on a modification of the novel technology named detection of immobilized amplified product in one phase system. This single step amplification method will be developed in a versatile microtitre well strip format for detection first of MDR and then of XDR strains. The tools will be then validated in different settings and prospectively evaluated in target populations. The project will contribute to the currently available armamentarium for rapid detection of drug resistant TB and will introduce new tools for the detection of the recently-described and highly-lethal XDRTB. It will also contribute to our knowledge on the mechanisms of M. tuberculosis resistance to second-line drugs.


PubMed | Microbiomas Foundation, Helmholtz Center for Infection Research and Corporacion CorpoGen
Type: Journal Article | Journal: Genome announcements | Year: 2016

Bacillus licheniformis strain CG-B52 was isolated as the etiological agent producing a self-limited outbreak of high mortalities in commercial Litopenaeus vannamei culture ponds on the Colombian Caribbean coast in 2005. Here, we report its draft genome and three novel extrachromosomal elements that it harbors.


Garcia-Betancur J.C.,Corporacion Corpogen | Menendez M.C.,Autonomous University of Madrid | Del Portillo P.,Corporacion Corpogen | Garcia M.J.,Autonomous University of Madrid
Infection, Genetics and Evolution | Year: 2012

To more accurately define the taxonomic relationships among species belonging to the genus Mycobacterium we have applied and compared three complete genome sequence comparison procedures to existing systems. These included a nucleotide sequence comparison including both coding and no-coding regions of the genome and two genomic-order comparisons using MAUVE and M-GCAT software to provide comparative gene synteny. These methods clearly differentiated a panel of genomes from reference mycobacterial species. Overall, the speciation of bacteria through determination of gene rearrangements were consistent with the gold standard method for species definition in bacteria, DNA-DNA hybridization however within the context of this system, individual components of the Mycobacterium tuberculosis complex (MTBC) did not show sufficient diversity to classify them as a separate species. The high number of gene rearrangements observed between the species tested suggests that gene reorganization of the genome represents an important contributor to speciation within the genus Mycobacterium and other related genera. The absence of rearrangements amongst MTBC supports their consideration as a single genospecies. Some gene rearrangements provided clear internal synteny between genomes of mycobacterial strains belonging to a same species and we suggest these could be used to classify subspecies. © 2011 Elsevier B.V..


Rodriguez J.G.,Corporacion CorpoGen | Hernandez A.C.,Corporacion CorpoGen | Helguera-Repetto C.,National Polytechnic Institute of Mexico | Ayala D.A.,National Polytechnic Institute of Mexico | And 7 more authors.
mBio | Year: 2014

Strong evidence supports the idea that fatty acids rather than carbohydrates are the main energy source of Mycobacterium tuberculosis during infection and latency. Despite that important role, a complete scenario of the bacterium's metabolism when lipids are the main energy source is still lacking. Here we report the development of an in vitro model to analyze adaptation of M. tuberculosis during assimilation of long-chain fatty acids as sole carbon sources. The global lipid transcriptome revealed a shift toward the glyoxylate cycle, the overexpression of main regulators whiB3, dosR, and Rv0081, and the increased expression of several genes related to reductive stress. Our evidence showed that lipid storage seems to be the selected mechanism used by M. tuberculosis to ameliorate the assumed damage of reductive stress and that concomitantly the bacilli acquired a slowed-growth and drug-tolerant phenotype, all characteristics previously associated with the dormant stage. Additionally, intergenic regions were also detected, including the unexpected upregulation of tRNAs that suggest a new role for these molecules in the acquisition of a drug-tolerant phenotype by dormant bacilli. Finally, a set of lipid signature genes for the adaptation process was also identified. This in vitro model represents a suitable condition to illustrate the participation of reductive stress in drugs' activity against dormant bacilli, an aspect scarcely investigated to date. This approach provides a new perspective to the understanding of latent infection and suggests the participation of previously undetected molecules. © 2014 Rodríguez et al.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-2.3.2-2;HEALTH-2007-2.3.2-3 | Award Amount: 3.59M | Year: 2008

Although the definition of latency under a clinical point of view seems clear, the bacterial biology behind that clinical situation remains poorly understood. While dormant, the tubercle bacilli are considered to be under non-replicating (NR) stage. In such a condition, bacilli are not only difficult to be detected but also refractory to the standard treatments avoiding their clearance from the infected tissues. The proposal has been built with the intend of providing tools to understand the bacterial mechanisms that leads to metabolic stage of M. tuberculosis during dormancy as the basis of sorting out the detection and treatment of latent infection. Several models of analysis have been developed trying to characterize dormant tubercle bacilli. Those models are ranging from in vitro conditions, such as hypoxia or starvation, to in vivo analysis, such as the animal model. We propose not only to study a complete range of those previously tested conditions, but also checking some other putative newly described, such as the recently described adipocytes ex vivo model, the new developments of the classical model of hypoxia, and the use of guinea-pigs as more adequate animal model of latent infection. Moreover, a set of drug combinations will be applied to determine their capability of clearance of the bacterial load. Due to its central role in the bacterial metabolism and growth we will analyze the non-replicating stage of the M. tuberculosis bacilli by determining the pre-rRNA synthesis. Finally, the cellular and tissue distribution of dormant bacilli will be also tested during in vivo latent infection both in the animal model and in clinical human samples. Research on the metabolic conditions of the dormant bacilli inside hosts, will provide important and invaluable insight into the biology of M. tuberculosis. That knowledge may lead to the development of novel strategies targeted at the control of the latent infection.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: KBBE-2009-3-5-01 | Award Amount: 4.52M | Year: 2010

MAGICPAH aims to explore, understand and exploit the catalytic activities of microbial communities involved in the degradation of persistent PAHs. It will integrate (meta-) genomic studies with in-situ activity assessment based on stable isotope probing particularly in complex matrices of different terrestrial and marine environments. PAH degradation under various conditions of bioavailability will be assessed as to improve rational exploitation of the catalytic properties of bacteria for the treatment and prevention of PAH pollution. We will generate a knowledge base not only on the microbial catabolome for biodegradation of PAHs in various impacted environmental settings based on genome gazing, retrieval and characterization of specific enzymes but also on systems related bioavailability of contaminant mixtures. MAGICPAH takes into account the tremendous undiscovered metagenomic resources by the direct retrieval from genome/metagenome libraries and consequent characterization of enzymes through activity screens. These screens will include a high-end functional small-molecule fluorescence screening platform and will allow us to directly access novel metabolic reactions followed by their rational exploitation for biocatalysis and the re-construction of biodegradation networks. Results from (meta-) genomic approaches will be correlated with microbial in situ activity assessments, specifically dedicated to identifying key players and key reactions involved in anaerobic PAH metabolism. Key processes for PAH metabolism particularly in marine and composting environments and the kinetics of aerobic degradation of PAH under different conditions of bioavailability will be assessed in model systems, the rational manipulation of which will allow us to deduce correlations between system performance and genomic blueprint. The results will be used to improve treatments of PAH-contaminated sites.


Jimenez A.,National University of Colombia | Tibata V.,National University of Colombia | Junca H.,Corporacion CorpoGen | Ariza F.,National University of Colombia | And 2 more authors.
Aquaculture | Year: 2011

Streptococcosis caused by Streptococcus agalactiae is an important disease affecting the world-wide fish industry; developing sensitive diagnostic tools for its rapid identification has thus become an urgent need. A nested PCR technique was implemented in this study for detecting S. agalactiae in frozen and paraffin-wax-embedded tilapia tissue. S. agalactiae was successfully detected in several samples taken from naturally-infected adult fish whereas larvae and fry tissue all proved negative. Such observations were consistent with previous studies by our group where the presence of S. agalactiae was detected by histopathology and immunohistochemistry in tissue taken from adult animals but not from tilapia having less than 20. g body weight. The results suggested that the microorganism's vertical transmission may not occur in the farm conditions pertaining to this study, thereby making S. agalactiae-free breeding farms feasible. © 2011 Elsevier B.V.


Martin A.,Institute of Tropical Medicine | Bombeeck D.,Institute of Tropical Medicine | Fissette K.,Institute of Tropical Medicine | de Rijk P.,Institute of Tropical Medicine | And 3 more authors.
Journal of Microbiological Methods | Year: 2011

The BACTEC MGIT 960 system is increasingly used to culture Mycobacterium tuberculosis. We evaluated the performance of the new immunochromatographic assay BD MGIT TBc Identification Test (TBc ID) for the rapid identification of M. tuberculosis complex in clinical samples when performed directly from BACTEC MGIT 960 culture positive for acid-fast bacilli (AFB). Of 92 cultures evaluated, the sensitivity and specificity of the TBc ID test was 98.5% and 100%, respectively compared to sequencing of the 16S rRNA gene. One culture that was TBc ID test negative but that was identified as M. tuberculosis by 16S rRNA sequencing was confirmed to have a mutation in the mpt64 gene.The TBc ID test is an easy and sensitive method for the identification of M. tuberculosis complex in liquid culture medium, does not require a high level of skills, neither any additional specific equipment and gives results in 15. min, which provide a good alternative for the rapid identification of M. tuberculosis complex in liquid medium. © 2010 Elsevier B.V.


Martin A.,Institute of Tropical Medicine | Paasch F.,Institute of Tropical Medicine | Docx S.,Institute of Tropical Medicine | Fissette K.,Institute of Tropical Medicine | And 13 more authors.
Journal of Antimicrobial Chemotherapy | Year: 2011

Objectives: To perform a multicentre study to evaluate the performance of the colorimetric redox indicator (CRI) assay and to establish the MICs and critical concentrations of rifampicin, isoniazid, ofloxacin, kanamycin and capreomycin. Methods: The study was carried out in two phases. Phase I determined the MIC of each drug. Phase II established critical concentrations for the five drugs tested by the CRI assay compared with the conventional proportion method. Results: Phase I: a strain was considered resistant by the CRI assay if the MIC was ≥0.5 mg/L for rifampicin, ≥0.25 mg/L for isoniazid, ≥4.0 mg/L for ofloxacin and ≥5.0 mg/L for kanamycin and capreomycin. Sensitivity was 99.1% for isoniazid and 100% for the other drugs and specificity was 97.9% for capreomycin and 100% for the other drugs. Phase II: the critical concentration was 0.5 mg/L for rifampicin, 0.25 mg/L for isoniazid, 2.0 mg/L for ofloxacin and 2.5 mg/L for kanamycin and capreomycin giving an overall accuracy of 98.4%, 96.6%, 96.7%, 98.3% and 90%, respectively. Conclusions: Results demonstrate that the CRI assay is an accurate method for the rapid detection of XDR Mycobacterium tuberculosis. The CRI assay is faster than the conventional drug susceptibility testing method using solid medium, has the same turnaround time as the BACTEC MGIT 960 system, but is less expensive, and could be an adequate method for low-income countries. © The Author 2011. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved.


Salmonellosis outbreaks in Europe, the United States, and Latin America have been associated with contaminated food derivatives including meat from the poultry industry. Salmonella grown under iron-limiting conditions has the capability to increase concentration of several iron-regulated outer-membrane proteins to augment the acquisition of the metal. These proteins have been proved to have immunogenic properties. Our aim was to increase the relative expression of iroN, fepA, and cirA in Salmonella Enteritidis domestic strain. Furthermore, we proposed a 3-dimensional structure model for each protein to predict and locate antigenic peptides. Our eventual objective is to produce an effective vaccine against regional avian salmonellosis. Two simple factorial designs were carried out to discriminate between 2 nitrogen sources and determine chelating-agent addition timing to augment relative gene expression. Two antigenic peptides located at the external face of each protein and 2 typical domains of iron-regulated outer-membrane proteins, plug and TonB-dep-Rec, were identified from the 3-dimensional models. Tryptone was selected as the best nitrogen source based on growth rate (x = 0.36 h(-1)) and biomass productivity (Px = 0.9 gh(-1)L(-1)) as determined by a general factorial design. Optimum timing for chelating agent addition was in the middle of the log phase, which allowed relative expressions at 4 h of culture. Increase in iroN, fepA, and cirA relative expression was favored by the length of log phase and the addition of chelating agent, which decreased chelating toxicity and enhanced cell growth rate.

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