Institution
Defence Science and Technology Laboratory
Government•Salisbury, United Kingdom•
About: Defence Science and Technology Laboratory is a government organization based out in Salisbury, United Kingdom. It is known for research contribution in the topics: Burkholderia pseudomallei & Francisella tularensis. The organization has 926 authors who have published 1242 publications receiving 30091 citations. The organization is also known as: Dstl & [dstl].
Papers published on a yearly basis
Papers
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University of Birmingham1, Bernhard Nocht Institute for Tropical Medicine2, Ontario Institute for Cancer Research3, University of Toronto4, Public Health England5, European Centre for Disease Prevention and Control6, University of Edinburgh7, Robert Koch Institute8, Swiss Tropical and Public Health Institute9, University College London10, Paul Ehrlich Institute11, University of Liverpool12, Rega Institute for Medical Research13, Kenya Medical Research Institute14, Friedrich Loeffler Institute15, Janssen-Cilag16, Technische Universität München17, Public Health Agency of Canada18, Pasteur Institute19, Sandia National Laboratories20, MRIGlobal21, World Health Organization22, University of London23, Norwegian Institute of Public Health24, Defence Science and Technology Laboratory25, Bundeswehr Institute of Microbiology26, National Institutes of Health27
TL;DR: This paper presents sequence data and analysis of 142 EBOV samples collected during the period March to October 2015 and shows that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
Abstract: A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection. This paper reports the use of nanopore DNA sequencers (known as MinIONs) for real-time genomic surveillance of the Ebola virus epidemic, in the field in Guinea. The authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection. The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths1. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 and 1.42 × 10−3 mutations per site per year. This is equivalent to 16–27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic2,3,4,5,6,7. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions8. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities9. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15–60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
1,187 citations
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TL;DR: It is proposed that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species.
Abstract: Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic areas of the world and accounts for 20% of community-acquired septicaemias in northeastern Thailand where half of those affected die. Here we report the complete genome of B. pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase pairs, showing significant functional partitioning of genes between them. The large chromosome encodes many of the core functions associated with central metabolism and cell growth, whereas the small chromosome carries more accessory functions associated with adaptation and survival in different niches. Genomic comparisons with closely and more distantly related bacteria revealed a greater level of gene order conservation and a greater number of orthologous genes on the large chromosome, suggesting that the two replicons have distinct evolutionary origins. A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species.
726 citations
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Swedish Defence Research Agency1, Defence Science and Technology Laboratory2, Lawrence Livermore National Laboratory3, Centers for Disease Control and Prevention4, Uppsala University5, SRI International6, Walter Reed Army Institute of Research7, Umeå University8, Wellcome Trust Sanger Institute9, University of London10
TL;DR: The complete genome sequence of a highly virulent isolate of F. tularensis is reported and an unexpectedly high proportion of disrupted pathways are found, explaining the fastidious nutritional requirements of the bacterium.
Abstract: Francisella tularensis is one of the most infectious human pathogens known. In the past, both the former Soviet Union and the US had programs to develop weapons containing the bacterium. We report the complete genome sequence of a highly virulent isolate of F. tularensis (1,892,819 bp). The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems. Several virulence-associated genes were located in a putative pathogenicity island, which was duplicated in the genome. More than 10% of the putative coding sequences contained insertion-deletion or substitution mutations and seemed to be deteriorating. The genome is rich in IS elements, including IS630 Tc-1 mariner family transposons, which are not expected in a prokaryote. We used a computational method for predicting metabolic pathways and found an unexpectedly high proportion of disrupted pathways, explaining the fastidious nutritional requirements of the bacterium. The loss of biosynthetic pathways indicates that F. tularensis is an obligate host-dependent bacterium in its natural life cycle. Our results have implications for our understanding of how highly virulent human pathogens evolve and will expedite strategies to combat them.
473 citations
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United States Department of Agriculture1, Washington University in St. Louis2, Hungarian Academy of Sciences3, National Institutes of Health4, Georgia State University5, United States Army Medical Research Institute of Infectious Diseases6, Commonwealth Scientific and Industrial Research Organisation7, Columbia University8, University of Texas Medical Branch9, Colorado State University10, Yeshiva University11, Huazhong Agricultural University12, University of Queensland13, University of Marburg14, University of Illinois at Urbana–Champaign15, University of Warwick16, Empresa Brasileira de Pesquisa Agropecuária17, World Health Organization18, Erasmus University Rotterdam19, New York University20, University of Kentucky21, Public Health England22, Kagoshima University23, Murdoch University24, University of São Paulo25, Public Health Agency of Canada26, Okayama University27, United States Geological Survey28, Northwestern University29, Centers for Disease Control and Prevention30, University of Cambridge31, Boston University32, Novosibirsk State University33, University of Veterinary Medicine Vienna34, University of Medicine and Health Sciences35, Texas Biomedical Research Institute36, Texas A&M University37, University of St Andrews38, Queen's University Belfast39, University of Freiburg40, Chinese Center for Disease Control and Prevention41, Defence Science and Technology Laboratory42, Hokkaido University43, Kyoto University44, Pasteur Institute45, Wageningen University and Research Centre46, University of Lyon47, National University of Singapore48, Kansas State University49, University of Hong Kong50
TL;DR: The updated taxonomy of the order Mononegavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Abstract: In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
404 citations
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TL;DR: Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
Abstract: Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique "genomic islands" identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
315 citations
Authors
Showing all 928 results
Name | H-index | Papers | Citations |
---|---|---|---|
Richard W. Titball | 79 | 410 | 22484 |
Andrew D. Griffiths | 72 | 152 | 37590 |
Alan D.T. Barrett | 71 | 341 | 17136 |
Jim Haywood | 67 | 213 | 20503 |
Philip N. Bartlett | 58 | 293 | 12798 |
Alan C. Newell | 58 | 209 | 17820 |
David A. Rand | 57 | 223 | 12157 |
Michael P. O'Donnell | 49 | 301 | 8762 |
James Hill | 47 | 216 | 6837 |
Franz Worek | 46 | 262 | 8754 |
Petra C. F. Oyston | 45 | 127 | 7155 |
K. Ravi Acharya | 45 | 161 | 7405 |
Horst Thiermann | 43 | 298 | 7091 |
Leigh T. Canham | 42 | 160 | 18268 |
Mark J. Midwinter | 39 | 180 | 5330 |