Global Infectious Disease Risks Associated with Occupational
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Coxiella Burnetii
SENTINEL LEVEL CLINICAL LABORATORY GUIDELINES FOR SUSPECTED AGENTS OF BIOTERRORISM AND EMERGING INFECTIOUS DISEASES Coxiella burnetii American Society for Microbiology (ASM) Revised March 2016 For latest revision, see web site below: https://www.asm.org/Articles/Policy/Laboratory-Response-Network-LRN-Sentinel-Level-C ASM Subject Matter Expert: David Welch, Ph.D. Medical Microbiology Consulting Dallas, TX [email protected] ASM Sentinel Laboratory Protocol Working Group APHL Advisory Committee Vickie Baselski, Ph.D. Barbara Robinson-Dunn, Ph.D. Patricia Blevins, MPH University of Tennessee at Department of Clinical San Antonio Metro Health Memphis Pathology District Laboratory Memphis, TN Beaumont Health System [email protected] [email protected] Royal Oak, MI BRobinson- Erin Bowles David Craft, Ph.D. [email protected] Wisconsin State Laboratory of Penn State Milton S. Hershey Hygiene Medical Center Michael A. Saubolle, Ph.D. [email protected] Hershey, PA Banner Health System [email protected] Phoenix, AZ Christopher Chadwick, MS [email protected] Association of Public Health Peter H. Gilligan, Ph.D. m Laboratories University of North Carolina [email protected] Hospitals/ Susan L. Shiflett Clinical Microbiology and Michigan Department of Mary DeMartino, BS, Immunology Labs Community Health MT(ASCP)SM Chapel Hill, NC Lansing, MI State Hygienic Laboratory at the [email protected] [email protected] University of Iowa [email protected] Larry Gray, Ph.D. Alice Weissfeld, Ph.D. TriHealth Laboratories and Microbiology Specialists Inc. Harvey Holmes, PhD University of Cincinnati College Houston, TX Centers for Disease Control and of Medicine [email protected] Prevention Cincinnati, OH om [email protected] [email protected] David Welch, Ph.D. -
Host-Adaptation in Legionellales Is 2.4 Ga, Coincident with Eukaryogenesis
bioRxiv preprint doi: https://doi.org/10.1101/852004; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Host-adaptation in Legionellales is 2.4 Ga, 2 coincident with eukaryogenesis 3 4 5 Eric Hugoson1,2, Tea Ammunét1 †, and Lionel Guy1* 6 7 1 Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, 8 Uppsala University, Box 582, 75123 Uppsala, Sweden 9 2 Department of Microbial Population Biology, Max Planck Institute for Evolutionary 10 Biology, D-24306 Plön, Germany 11 † current address: Medical Bioinformatics Centre, Turku Bioscience, University of Turku, 12 Tykistökatu 6A, 20520 Turku, Finland 13 * corresponding author 14 1 bioRxiv preprint doi: https://doi.org/10.1101/852004; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 15 Abstract 16 Bacteria adapting to living in a host cell caused the most salient events in the evolution of 17 eukaryotes, namely the seminal fusion with an archaeon 1, and the emergence of both the 18 mitochondrion and the chloroplast 2. A bacterial clade that may hold the key to understanding 19 these events is the deep-branching gammaproteobacterial order Legionellales – containing 20 among others Coxiella and Legionella – of which all known members grow inside eukaryotic 21 cells 3. -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
Validation and Annotation of Virus Sequence Submissions to Genbank Alejandro A
Schäffer et al. BMC Bioinformatics (2020) 21:211 https://doi.org/10.1186/s12859-020-3537-3 SOFTWARE Open Access VADR: validation and annotation of virus sequence submissions to GenBank Alejandro A. Schäffer1,2, Eneida L. Hatcher2, Linda Yankie2, Lara Shonkwiler2,3,J.RodneyBrister2, Ilene Karsch-Mizrachi2 and Eric P. Nawrocki2* *Correspondence: [email protected] Abstract 2National Center for Biotechnology Background: GenBank contains over 3 million viral sequences. The National Center Information, National Library of for Biotechnology Information (NCBI) previously made available a tool for validating Medicine, National Institutes of Health, Bethesda, MD, 20894 USA and annotating influenza virus sequences that is used to check submissions to Full list of author information is GenBank. Before this project, there was no analogous tool in use for non-influenza viral available at the end of the article sequence submissions. Results: We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. -
Bats: Important Reservoir Hosts of Emerging Viruses
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Other Publications in Zoonotics and Wildlife Disease Wildlife Disease and Zoonotics 2006 Bats: Important Reservoir Hosts of Emerging Viruses Charles H. Calisher Colorado State University James E. Childs Yale University School of Medicine, [email protected] Hume E. Field Department of Primary Industries and Fisheries, Brisbane, Queensland Tony Schountz University of Northern Colorado Kathryn V. Holmes University of Colorado Health Sciences Center Follow this and additional works at: https://digitalcommons.unl.edu/zoonoticspub Part of the Veterinary Infectious Diseases Commons Calisher, Charles H.; Childs, James E.; Field, Hume E.; Schountz, Tony; and Holmes, Kathryn V., "Bats: Important Reservoir Hosts of Emerging Viruses" (2006). Other Publications in Zoonotics and Wildlife Disease. 60. https://digitalcommons.unl.edu/zoonoticspub/60 This Article is brought to you for free and open access by the Wildlife Disease and Zoonotics at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Other Publications in Zoonotics and Wildlife Disease by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. CLINICAL MICROBIOLOGY REVIEWS, July 2006, p. 531–545 Vol. 19, No. 3 0893-8512/06/$08.00ϩ0 doi:10.1128/CMR.00017-06 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Bats: Important Reservoir Hosts of Emerging Viruses Charles H. Calisher,1* James E. Childs,2 Hume E. Field,3 Kathryn V. Holmes,4 -
Coxiella Burnetii Utilizes Both Glutamate and Glucose During Infection with Glucose Uptake Mediated by Multiple Transporters
Biochemical Journal (2019) 476 2851–2867 https://doi.org/10.1042/BCJ20190504 Research Article Coxiella burnetii utilizes both glutamate and glucose during infection with glucose uptake mediated by multiple transporters Miku Kuba1, Nitika Neha2,3, David P. De Souza2, Saravanan Dayalan2, Joshua P. M. Newson1, Dedreia Tull2, Malcolm J. McConville2, Fiona M. Sansom3* and Hayley J. Newton1* Downloaded from https://portlandpress.com/biochemj/article-pdf/476/19/2851/856758/bcj-2019-0504.pdf by guest on 07 April 2020 1Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; 2Metabolomics Australia, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; 3Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia Correspondence: Fiona M. Sansom ([email protected]) or Hayley J. Newton ([email protected]) Coxiella burnetii is a Gram-negative bacterium which causes Q fever, a complex and life- threatening infection with both acute and chronic presentations. C. burnetii invades a variety of host cell types and replicates within a unique vacuole derived from the host cell lysosome. In order to understand how C. burnetii survives within this intracellular niche, we have investigated the carbon metabolism of both intracellular and axenically cultivated bacteria. Both bacterial populations were shown to assimilate exogenous [13C]glucose or [13C]glutamate, with concomitant labeling of intermediates in glycolysis and gluconeo- genesis, and in the TCA cycle. Significantly, the two populations displayed metabolic pathway profiles reflective of the nutrient availabilities within their propagated environ- ments. -
Molecular Detection of Pathogens in Ticks and Fleas Collected From
Nguyen et al. Parasites Vectors (2020) 13:420 https://doi.org/10.1186/s13071-020-04288-8 Parasites & Vectors RESEARCH Open Access Molecular detection of pathogens in ticks and feas collected from companion dogs and cats in East and Southeast Asia Viet‑Linh Nguyen1, Vito Colella1,2, Grazia Greco1, Fang Fang3, Wisnu Nurcahyo4, Upik Kesumawati Hadi5, Virginia Venturina6, Kenneth Boon Yew Tong7, Yi‑Lun Tsai8, Piyanan Taweethavonsawat9, Saruda Tiwananthagorn10, Sahatchai Tangtrongsup10, Thong Quang Le11, Khanh Linh Bui12, Thom Do13, Malaika Watanabe14, Puteri Azaziah Megat Abd Rani14, Filipe Dantas‑Torres1,15, Lenaig Halos16, Frederic Beugnet16 and Domenico Otranto1,17* Abstract Background: Ticks and feas are considered amongst the most important arthropod vectors of medical and veteri‑ nary concern due to their ability to transmit pathogens to a range of animal species including dogs, cats and humans. By sharing a common environment with humans, companion animal‑associated parasitic arthropods may potentially transmit zoonotic vector‑borne pathogens (VBPs). This study aimed to molecularly detect pathogens from ticks and feas from companion dogs and cats in East and Southeast Asia. Methods: A total of 392 ticks and 248 feas were collected from 401 infested animals (i.e. 271 dogs and 130 cats) from China, Taiwan, Indonesia, Malaysia, Singapore, Thailand, the Philippines and Vietnam, and molecularly screened for the presence of pathogens. Ticks were tested for Rickettsia spp., Anaplasma spp., Ehrlichia spp., Babesia spp. and Hepato- zoon spp. while feas were screened for the presence of Rickettsia spp. and Bartonella spp. Result: Of the 392 ticks tested, 37 (9.4%) scored positive for at least one pathogen with Hepatozoon canis being the most prevalent (5.4%), followed by Ehrlichia canis (1.8%), Babesia vogeli (1%), Anaplasma platys (0.8%) and Rickettsia spp. -
Virusscope – Inside a Virus Testing Lab
VirusSCOPE – Inside a virus testing lab Viruses are too small to be seen. There are different kinds of tests to find out whether someone has a virus in their body. These tests are carried out in specialized laboratories. One kind of test uses so-called antibodies. Antibodies are tiny recognition tools, which our body uses to recognize and fight viruses. Each antibody has a different shape, which makes it recognize a certain virus. In the lab, such antibodies are used to find and distinguish viruses in patients. Now, this is your task! Can you find out, which viruses are in your patients' bodies? Here’s what you’ll learn: In the lab, people find out which virus someone has by using antibodies. The shape of these antibodies matches perfectly with one specific virus. Antibodies have several parts. Material for print-out (4 pages): - Viruses (16 purple fields) - Antibodies (4 red and 4 blue parts with QR-Codes and letters) – cut these out! - Samples from 9 patients (green flasks with QR-Codes and numbers) - Laboratory report You can play this game on your own or in pairs. If you play this game in pairs, one person can find the matching parts, while the other documents your findings in the laboratory report. Alternatively, print out the materials twice and compete against each other to diagnose all patients correctly as quickly as possible! Note: The QR-Codes are not needed in this game. If you have access to a 3D-printer you can also 3D-print the parts of this game: https://www.prusaprinters.org/prints/28554-virusscope-educational-game-about-covid-19- diagnos 1st step: Assign antibodies to viruses Each antibody consists of two pieces, a „light chain“ (red) and a „heavy chain” (red). -
Vero Cell Upstream Bioprocess Development for the Production of Viral Vectors and Vaccines T ⁎ Sascha Kiesslich, Amine A
Biotechnology Advances 44 (2020) 107608 Contents lists available at ScienceDirect Biotechnology Advances journal homepage: www.elsevier.com/locate/biotechadv Research review paper Vero cell upstream bioprocess development for the production of viral vectors and vaccines T ⁎ Sascha Kiesslich, Amine A. Kamen Department of Bioengineering, McGill University, 817 Sherbrooke Street West, Montreal, Quebec H3A 0C3, Canada ARTICLE INFO ABSTRACT Keywords: The Vero cell line is considered the most used continuous cell line for the production of viral vectors and Vero vaccines. Historically, it is the first cell line that was approved by the WHO for the production of human vac- Cell culture cines. Comprehensive experimental data on the production of many viruses using the Vero cell line can be found Process development in the literature. However, the vast majority of these processes is relying on the microcarrier technology. While Virus production this system is established for the large-scale manufacturing of viral vaccine, it is still quite complex and labor Optimization intensive. Moreover, scale-up remains difficult and is limited by the surface area given by the carriers. To Vaccines ffi Bioreactor overcome these and other drawbacks and to establish more e cient manufacturing processes, it is a priority to Microcarrier further develop the Vero cell platform by applying novel bioprocess technologies. Especially in times like the Suspension culture current COVID-19 pandemic, advanced and scalable platform technologies could provide more efficient and cost-effective solutions to meet the global vaccine demand. Herein, we review the prevailing literature on Vero cell bioprocess development for the production of viral vectors and vaccines with the aim to assess the recent advances in bioprocess development. -
Emerging Issues in Virus Taxonomy Marc H.V
PERSPECTIVES Emerging Issues in Virus Taxonomy Marc H.V. van Regenmortel* and Brian W.J. Mahy† Viruses occupy a unique position in biology. Although are nonliving infectious entities that can be said, at best, to they possess some of the properties of living systems such lead a kind of borrowed life. as having a genome, they are actually nonliving infectious entities and should not be considered microorganisms. A Viruses versus Virus Particles or Virions clear distinction should be drawn between the terms virus, A virus is a general term which denotes any number of virion, and virus species. Species is the most fundamental taxonomic category used in all biological classification. In concrete objects that possess various relational properties 1991, the International Committee on Taxonomy of Viruses (for instance, its host, vector, and infectivity) that arise by (ICTV) decided that the category of virus species should be virtue of a relation with other objects. These relational used in virus classification together with the categories of properties, also called emergent properties, are characteris- genus and family. More than 50 ICTV study groups were tic of the viral biosystem as a whole and are not present in given the task of demarcating the 1,550 viral species that its constituent parts. When a virus undergoes its so-called were recognized in the 7th ICTV report, which was pub- life cycle, it takes on various forms and manifestations, for lished in 2000. We briefly describe the changes in virus instance, as a replicating nucleic acid in the host cell or classification that were introduced in that report. -
Host Cell-Free Growth of the Q Fever Bacterium Coxiella Burnetii
Host cell-free growth of the Q fever bacterium Coxiella burnetii Anders Omslanda, Diane C. Cockrella, Dale Howea, Elizabeth R. Fischerb, Kimmo Virtanevac, Daniel E. Sturdevantc, Stephen F. Porcellac, and Robert A. Heinzena,1 aCoxiella Pathogenesis Section, Laboratory of Intracellular Parasites, bElectron Microscopy Unit, and cGenomics Unit, Research Technology Section, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840 Edited by Emil C. Gotschlich, The Rockefeller University, New York, NY, and approved January 22, 2009 (received for review November 26, 2008) The inability to propagate obligate intracellular pathogens under tified a potential nutritional deficiency of this medium. More- axenic (host cell-free) culture conditions imposes severe experi- over, using genomic reconstruction and metabolite typing, we mental constraints that have negatively impacted progress in defined C. burnetii as a microaerophile. These data allowed understanding pathogen virulence and disease mechanisms. Cox- development of a medium that supports axenic growth of iella burnetii, the causative agent of human Q (Query) fever, is an infectious C. burnetii under microaerobic conditions. obligate intracellular bacterial pathogen that replicates exclusively in an acidified, lysosome-like vacuole. To define conditions that Results support C. burnetii growth, we systematically evaluated the or- C. burnetii Exhibits Reduced Ribosomal Gene Expression in CCM. As an ganism’s metabolic requirements using expression microarrays, initial step to identify nutritional deficiencies of CCM that could genomic reconstruction, and metabolite typing. This led to devel- preclude C. burnetii cell division, a comparison of genome wide opment of a complex nutrient medium that supported substantial transcript profiles between organisms replicating in Vero cells growth (approximately 3 log10)ofC. -
Legionnaires' Disease and Pontiac Fever
Legionnaires’ Disease and 232 Pontiac Fever Paul H. Edelstein and Craig R. Roy SHORT VIEW SUMMARY Definition } Pontiac fever is associated with inhalation of highly sensitive in all settings. Urine antigen } Legionnaires’ disease is a noncontagious type Legionellaa spp.–containing water but not testing, the most commonly used test, is about of bacterial pneumonia caused by Legionella necessarily caused by the bacterium. It occurs 70% and 30% sensitive in spp. bacteria, most commonly Legionella in sporadic and epidemic form at apparently community-acquired and nosocomial disease, pneumophila. low incidence but may be more common than respectively. is reported. } Pontiac fever is a several-day-long, Therapy nonpneumonic, febrile, influenza-like illness Microbiology } Macrolides, tetracyclines, and quinolone associated with exposure to Legionellaa spp. } Constituted of more than 60 known species, the antimicrobials can all be used to successfully that resolves spontaneously. Legionellaa bacteria are ubiquitous in the treat the disease, with azithromycin and Legionellosis includes legionnaires’ disease, } aqueous environment and probably moist soils. levofloxacin being the most active. Pontiac fever, and extrapulmonary Legionella } Optimal bacterial growth requires specialized Tetracyclines may not be active for L. spp. infection not associated with pneumonia. media that contain cysteine and iron. longbeachaee–caused disease. Epidemiology } The bacteria are facultative intracellular } For cure, 3 to 14 days’ therapy is required, } Legionnaires’ disease is acquired by inhaling a parasites of free-living amebae and human depending on disease severity, host factors, water aerosol containing Legionellaa spp. monocytes and macrophages that use hostlike and type of therapy used. proteins to masquerade as host and to avail bacteria, and possibly by microaspirating Prevention Legionellaa spp.–containing water.