Genitsaris S.,CNRS Laboratory of Oceanology and Geosciences |
Monchy S.,CNRS Laboratory of Oceanology and Geosciences |
Viscogliosi E.,University of Lille Nord de France |
Sime-Ngando T.,CNRS Microorganisms Laboratory: Genome and Environment |
And 2 more authors.
FEMS Microbiology Ecology | Year: 2015
Previous microscopy-based studies in the eastern English Channel have revealed it to be a productive meso-eutrophic coastal ecosystem, characterized by strong repeating patterns in microplankton succession. The present study examines the seasonal structure of the entire protistan community from March 2011 to July 2013, using tag pyrosequencing of the V2-V3 hypervariable region of the 18S rRNA gene. A total of 1242 OTUs and 28 high-level taxonomic groups, which included previously undetected taxa in the area, were identified. The detected OTUs were considered according to taxon-specific traits, which included their trophic role, abundance and specialization level. Taxa differentiation based on specialization level rather than abundance was more informative in describing community organization. While generalists were always abundant, numerous specialists that were either rare or absent in most samples, increased in abundance for short periods, appearing to be overall abundant. Statistical and network analyses showed that the protistan seasonal organization was influenced by environmental parameters. It also highlighted that in addition to grazers, fungi and parasites played potentially significant roles during phytoplankton blooms. Overall, while the protistan succession was mainly shaped by environmental variations, biotic interactions among co-occurring taxa were the main structural drivers of the temporal assemblages. © FEMS 2015. Source
Genoscreen | Date: 2016-06-21
Chemicals, other than for use in immunodiagnostics and HIV tests, for use in industry, science, as well as in agriculture, horticulture and forestry except fungicides, herbicides, insecticides and parasiticides; chemical preparations for making diagnoses in laboratories other than for medical or veterinary purposes and other than immunodiagnostics and HIV tests; chemical reagents, other than those used for medical, veterinary, immunodiagnostic and HIV tests; biological, biochemical, and chemical reagents for non-medical purposes for the improvement of molecules, other than those used for HIV and immunodiagnostics tests; biological preparations other than for medical or veterinary use for use for identifying and testing various complex microbiological samples, including human micro biota, soils, water, air and food; chemical products for creating genetic marker libraries in order to genotype a complex micro biota population and for making diagnoses in laboratories other than for medical or veterinary purposes for use in the fields of biology, biotechnology, biochemistry, genomics, proteomics, transcriptomics, genetics and life sciences, other than those used for HIV and immunodiagnostics tests; diagnostic kits comprised of bio chemicals, namely, cells, antibodies, antigens, and gene banks containing bio technologically formed genes, as well as mutation and molecular variant banks containing bio technologically formed genes for in vitro scientific research use and for diagnostics not for medical or veterinary purposes. Pharmaceutical products, namely, pharmaceutical products for treatment of cancer, infectious diseases, tuberculosis and for Alzheimer detection and treatment; veterinary products, namely, veterinary products for treatment of cancer, infectious diseases, tuberculosis and Alzheimer detection and treatment; chemical preparations for medical use in the treatment of cancer, infectious diseases, tuberculosis and Alzheimer detection and treatment; diagnostic preparations for medical and veterinary use but not for immunodiagnostic and HIV tests; diagnostic products for medical use, namely, reagents and assays; chemical reagents for medical or veterinary purposes but not for immunodiagnostic and HIV tests; preparations of microorganisms for medical and veterinary use. Measuring instruments and devices, namely, research laboratory analyzers for measuring, testing and analyzing blood and other bodily fluids; computer programs for research and analysis in the fields of science, biology, biotechnology, biochemistry, genomics, proteomics, transcriptomics, genetics, life sciences, cloning, human health, diagnostics and in the processing of biological data; software for scientific analysis of genetic sequences and biological platelets for use in the scientific research industry and in the field of genetics; computer programs and software incorporating algorithms designed for research and analysis in the fields of science, biology, biotechnology, biochemistry, genomics, proteomics, transcriptomics, genetics, life sciences, cloning, human health, diagnostics and in the processing of biological data; computer programs designed for scientific analysis of genetic sequences and biological platelets for use in scientific research; computer programs designed to identify DNA, detect diseases, test and develop drugs; analysis apparatus, not for medical use, namely, scales, sequencers, analyzers and captors; apparatus for testing air, water, food, namely, scales, sequencers, analyzers and captors; chemistry apparatus and instruments, namely, sequencers, chemistry analyzers and captors ;diagnostic apparatus, not for medical use, namely, sequencers, analyzers and captors; electronic quantity indicators for measuring blood and other bodily fluids; measuring instruments, namely, scales, analyzers and captors; DNA chips. Evaluations, analyses, scientific research and technological testing services of flora, metagenomes, microorganisms, micro biota or transcriptomics in the field of pharmacy, chemistry, biotechnology, biochemistry, genomics, bacteriology, transcriptomics, genetics, and life sciences; biomedical research, and biological, medical and veterinary product development; providing laboratory research services in the field of gene expression and protein profiling, namely, cancer infectious diseases, tuberculosis, Alzheimer biology; genotyping services for research and analysis purposes for genotyping based on biological markers; design and development of programming databases in the field of pharmaceuticals, biotechnology, biology, biochemistry, genomics, transcriptomics, genetics, and life sciences; clinical laboratory testing services, namely, gene sequencing-based testing services with a view to research relating to genome sequencing of plants and animals, micro-organisms, sequencing of DNA or RNA and epigenetic sequencing; development and updating of computer programs designed for scientific analysis of genetic sequences, genetic sequencing of the genes of individuals and cohorts; electronic data storage and computer programming services for publishing data in a computer science environment designed for bioinformatics; bioinformatics computer engineering; laboratory research services in the field of large-scale DNA sequencing; development and updating of data management systems; database design and development applications in general of biological data processing; scientific development and technical validation of micro-satellite and mini-satellite markers; scientific services in the field of genomics for use in laboratories working on all kinds genomes, including human, animal and micro-organisms, namely, scientific development and validation of micro-satellite and mini-satellite markers; scientific services in the field of genomics for use in laboratories working on all kinds genomes, including human, animal and micro-organisms, namely, identification, typing, tracing, analysis and creation of a bank and a database, treatments resistance prediction, whole genome sequencing and complete flora; scientific research, mutation detection and identification of microorganisms; scientific research, namely, mutation detection and identification of microorganisms; genotyping services for research or analyses purposes; development and testing of computer databases, software, algorithms and computing methods for generating and analyzing biological, genetic and epidemiological data; scientific research and development services in the fields of diagnostic methods, antibody technology, and gene expression systems; rental of software and computer databases; scientific research and development services; medical laboratory services.
Varghese B.,King Faisal Specialist Hospital And Research Center |
Supply P.,GenoScreen |
Supply P.,French Institute of Health and Medical Research |
Supply P.,French National Center for Scientific Research |
And 7 more authors.
PLoS ONE | Year: 2013
Background: The phylogeographical structure of Mycobacterium tuberculosis is generally bimodal in low tuberculosis (TB) incidence countries, where genetic lineages of the isolates generally differ with little strain clustering between autochthonous and foreign-born TB patients. However, less is known on this structure in Saudi Arabia-the most important hub of human migration as it hosts a total population of expatriates and pilgrims from all over the world which is equal to that of its citizens. Methodology: We explored the mycobacterial phylogenetic structure and strain molecular clustering in Saudi Arabia by genotyping 322 drug-resistant clinical isolates collected over a 12-month period in a national drug surveillance survey, using 24 locus-based MIRU-VNTR typing and spoligotyping. Principal Findings: In contrast to the cosmopolitan population of the country, almost all the known phylogeographic lineages of M. tuberculosis complex (with noticeable exception of Mycobacterium africanum/West-African 1 and 2) were detected, with Delhi/CAS (21.1%), EAI (11.2%), Beijing (11.2%) and main branches of the Euro-American super-lineage such as Ghana (14.9%), Haarlem (10.6%) and Cameroon (7.8%) being represented. Statistically significant associations of strain lineages were observed with poly-drug resistance and multi drug resistance especially among previously treated cases (p value of < = 0.001 for both types of resistance), with relative over-representation of Beijing strains in the latter category. However, there was no significant difference among Saudi and non-Saudi TB patients regarding distribution of phylogenetic lineages (p = 0.311). Moreover, 59.5% (22/37) of the strain molecular clusters were shared between the Saudi born and immigrant TB patients. Conclusions: Specific distribution of M. tuberculosis phylogeographic lineages is not observed between the autochthonous and foreign-born populations. These observations might reflect both socially favored ongoing TB transmission between the two population groups, and historically deep-rooted, prolonged contacts and trade relations of the peninsula with other world regions. More vigorous surveillance and strict adherence to tuberculosis control policies are urgently needed in the country. © 2013 Varghese et al. Source
Allix-Beguec C.,GenoScreen |
Wahl C.,GenoScreen |
Hanekom M.,Stellenbosch University |
Nikolayevskyy V.,PHE National Mycobacterial Reference Laboratory and Clinical TB and HIV Group |
And 17 more authors.
Journal of Clinical Microbiology | Year: 2014
Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/ 24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single- locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing.Copyright © 2014, American Society for Microbiology. All Rights Reserved. Source
Merker M.,Research Center Borstel |
Blin C.,EPHE Paris |
Mona S.,EPHE Paris |
Duforet-Frebourg N.,CNRS Complex Medical Engineering Laboratory |
And 51 more authors.
Nature genetics | Year: 2015
Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage. Source