List of the Pathogens Intended to Be Controlled Under Section 18 B.E
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Food Or Beverage Product, Or Probiotic Composition, Comprising Lactobacillus Johnsonii 456
(19) TZZ¥¥¥ _T (11) EP 3 536 328 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 11.09.2019 Bulletin 2019/37 A61K 35/74 (2015.01) A61K 35/66 (2015.01) A61P 35/00 (2006.01) (21) Application number: 19165418.5 (22) Date of filing: 19.02.2014 (84) Designated Contracting States: • SCHIESTL, Robert, H. AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Encino, CA California 91436 (US) GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO • RELIENE, Ramune PL PT RO RS SE SI SK SM TR Los Angeles, CA California 90024 (US) • BORNEMAN, James (30) Priority: 22.02.2013 US 201361956186 P Riverside, CA California 92506 (US) 26.11.2013 US 201361909242 P • PRESLEY, Laura, L. Santa Maria, CA California 93458 (US) (62) Document number(s) of the earlier application(s) in • BRAUN, Jonathan accordance with Art. 76 EPC: Tarzana, CA California 91356 (US) 14753847.4 / 2 958 575 (74) Representative: Müller-Boré & Partner (71) Applicant: The Regents of the University of Patentanwälte PartG mbB California Friedenheimer Brücke 21 Oakland, CA 94607 (US) 80639 München (DE) (72) Inventors: Remarks: • YAMAMOTO, Mitsuko, L. This application was filed on 27-03-2019 as a Alameda, CA California 94502 (US) divisional application to the application mentioned under INID code 62. (54) FOOD OR BEVERAGE PRODUCT, OR PROBIOTIC COMPOSITION, COMPRISING LACTOBACILLUS JOHNSONII 456 (57) The present invention relates to food products, beverage products and probiotic compositions comprising Lacto- bacillus johnsonii 456. EP 3 536 328 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 536 328 A1 Description CROSS-REFERENCE TO RELATED APPLICATIONS 5 [0001] This application claims the benefit of U.S. -
Identification by 16S Ribosomal RNA Gene Sequencing of an Enterobacteriaceae Species from a Bone Marrow Transplant Recipient
J Clin Pathol: Mol Pathol 2000;53:211–215 211 Identification by 16S ribosomal RNA gene sequencing of an Enterobacteriaceae species from Mol Path: first published as 10.1136/mp.53.4.211 on 1 August 2000. Downloaded from a bone marrow transplant recipient PCYWoo,PKLLeung, K W Leung, K Y Yuen Abstract with biochemical characteristics that do not fit Aims—To ascertain the clinical relevance into patterns of any known genus and species. of a strain of Enterobacteriaceae isolated Since the discovery of the polymerase chain from the stool of a bone marrow trans- reaction (PCR) and DNA sequencing, the plant recipient with diarrhoea. The isolate genomes of some bacteria have been se- could not be identified to the genus level quenced completely.1 A comparison of the by conventional phenotypic methods and genomic sequences of bacterial species showed required 16S ribosomal RNA (rRNA) gene that the 16S ribosomal RNA (rRNA) gene is sequencing for full identification. highly conserved within a species and among Methods—The isolate was investigated species of the same genus, and hence can be phenotypically by standard biochemical used as the new gold standard for the methods using conventional biochemical speciation of bacteria. Using this new standard, tests and two commercially available sys- phylogenetic trees based on base diVerences tems, the Vitek (GNI+) and API (20E) sys- between species are constructed; bacteria are tems. Genotypically, the 16S bacterial classified and re-classified into new genera;23 rRNA gene was amplified by the polymer- and classifications of non-cultivable micro- ase chain reaction (PCR) and sequenced. -
BD-CS-057, REV 0 | AUGUST 2017 | Page 1
EXPLIFY RESPIRATORY PATHOGENS BY NEXT GENERATION SEQUENCING Limitations Negative results do not rule out viral, bacterial, or fungal infections. Targeted, PCR-based tests are generally more sensitive and are preferred when specific pathogens are suspected, especially for DNA viruses (Adenovirus, CMV, HHV6, HSV, and VZV), mycobacteria, and fungi. The analytical sensitivity of this test depends on the cellularity of the sample and the concentration of all microbes present. Analytical sensitivity is assessed using Internal Controls that are added to each sample. Sequencing data for Internal Controls is quantified. Samples with Internal Control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as ‘Reduced Analytical Sensitivity’. Additional respiratory pathogens to those reported cannot be excluded in samples with ‘Reduced Analytical Sensitivity’. Due to the complexity of next generation sequencing methodologies, there may be a risk of false-positive results. Contamination with organisms from the upper respiratory tract during specimen collection can also occur. The detection of viral, bacterial, and fungal nucleic acid does not imply organisms causing invasive infection. Results from this test need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases. Validated Organisms BACTERIA Achromobacter -
Lpr0050 and Lpr0024 in Legionella Pneumophila
Characterization of the role of the small regulatory RNA (sRNAs) lpr0050 and lpr0024 in Legionella pneumophila Malak Sadek Natural Resource Sciences Department McGill University Montreal, Canada Supervisor: Prof. Sébastien P. Faucher June , 2019 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master of Science © Malak Sadek 2019 1 Abstract Legionella pneumophila is a facultative intracellular pathogen, and it is the causative agent of Legionnaires’ disease, a life-threatening form of pneumonia. L. pneumophila is commonly found in most water systems including freshwater bodies, rivers, and lakes as well as in engineered water systems and man-made water distribution systems such as cooling towers. Free-living amoeba in aquatic environments are the primary reservoir of L. pneumophila. Following inhalation of contaminated water droplets by humans, L. pneumophila infects and replicates within lung alveolar macrophages and potentially causes Legionnaires’ disease (LD) in susceptible individuals. The bacterium establishes its intracellular niche by forming the Legionella-containing vacuoles (LCVs). L. pneumophila governs the formation of the LCV and intracellular growth through the Icm/Dot type IVB secretion system. Icm/Dot is able to translocate around 300 protein effectors in the host cell allowing L. pneumophila to modulate many signalling and metabolic pathways of the host to its benefit. It is believed that Small Regulatory RNAs (sRNAs) are major players of regulation of virulence-related genes in L. pneumophila. We investigated the regulatory role of the two sRNA Lpr0050 and Lpr0024. Lpr0050 is encoded on the complementary strand of the effector SdeA. Using northern blot we showed that the cis-encoded sRNALpr0050 is expressed in the Exponential (E) phase and Post-Exponential (PE) phase in the wild-type, ΔcpxR and ΔletS. -
Review and Meta-Analysis of the Environmental Biology and Potential Invasiveness of a Poorly-Studied Cyprinid, the Ide Leuciscus Idus
REVIEWS IN FISHERIES SCIENCE & AQUACULTURE https://doi.org/10.1080/23308249.2020.1822280 REVIEW Review and Meta-Analysis of the Environmental Biology and Potential Invasiveness of a Poorly-Studied Cyprinid, the Ide Leuciscus idus Mehis Rohtlaa,b, Lorenzo Vilizzic, Vladimır Kovacd, David Almeidae, Bernice Brewsterf, J. Robert Brittong, Łukasz Głowackic, Michael J. Godardh,i, Ruth Kirkf, Sarah Nienhuisj, Karin H. Olssonh,k, Jan Simonsenl, Michał E. Skora m, Saulius Stakenas_ n, Ali Serhan Tarkanc,o, Nildeniz Topo, Hugo Verreyckenp, Grzegorz ZieRbac, and Gordon H. Coppc,h,q aEstonian Marine Institute, University of Tartu, Tartu, Estonia; bInstitute of Marine Research, Austevoll Research Station, Storebø, Norway; cDepartment of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Łod z, Poland; dDepartment of Ecology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; eDepartment of Basic Medical Sciences, USP-CEU University, Madrid, Spain; fMolecular Parasitology Laboratory, School of Life Sciences, Pharmacy and Chemistry, Kingston University, Kingston-upon-Thames, Surrey, UK; gDepartment of Life and Environmental Sciences, Bournemouth University, Dorset, UK; hCentre for Environment, Fisheries & Aquaculture Science, Lowestoft, Suffolk, UK; iAECOM, Kitchener, Ontario, Canada; jOntario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada; kDepartment of Zoology, Tel Aviv University and Inter-University Institute for Marine Sciences in Eilat, Tel Aviv, -
Legionella Shows a Diverse Secondary Metabolism Dependent on a Broad Spectrum Sfp-Type Phosphopantetheinyl Transferase
Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase Nicholas J. Tobias1, Tilman Ahrendt1, Ursula Schell2, Melissa Miltenberger1, Hubert Hilbi2,3 and Helge B. Bode1,4 1 Fachbereich Biowissenschaften, Merck Stiftungsprofessur fu¨r Molekulare Biotechnologie, Goethe Universita¨t, Frankfurt am Main, Germany 2 Max von Pettenkofer Institute, Ludwig-Maximilians-Universita¨tMu¨nchen, Munich, Germany 3 Institute of Medical Microbiology, University of Zu¨rich, Zu¨rich, Switzerland 4 Buchmann Institute for Molecular Life Sciences, Goethe Universita¨t, Frankfurt am Main, Germany ABSTRACT Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict Submitted 29 June 2016 some novel compounds that are probably involved in cell-cell communication, Accepted 25 October 2016 Published 24 November 2016 differing to known communication systems. -
Virulence Determinants, Drug Resistance and Mobile Genetic
Lau et al. Cell & Bioscience 2011, 1:17 http://www.cellandbioscience.com/content/1/1/17 Cell & Bioscience RESEARCH Open Access Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis Susanna KP Lau1,2,3,4*†, Gilman KM Wong4†, Alan KL Tsang4†, Jade LL Teng4, Rachel YY Fan4, Herman Tse1,2,3,4, Kwok-Yung Yuen1,2,3,4 and Patrick CY Woo1,2,3,4* Abstract Background: Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler’s diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements. Results: For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to b-lactam (n = 10) and multidrug efflux (n = 54). -
Genomics of Helicobacter Species 91
Genomics of Helicobacter Species 91 6 Genomics of Helicobacter Species Zhongming Ge and David B. Schauer Summary Helicobacter pylori was the first bacterial species to have the genome of two independent strains completely sequenced. Infection with this pathogen, which may be the most frequent bacterial infec- tion of humanity, causes peptic ulcer disease and gastric cancer. Other Helicobacter species are emerging as causes of infection, inflammation, and cancer in the intestine, liver, and biliary tract, although the true prevalence of these enterohepatic Helicobacter species in humans is not yet known. The murine pathogen Helicobacter hepaticus was the first enterohepatic Helicobacter species to have its genome completely sequenced. Here, we consider functional genomics of the genus Helico- bacter, the comparative genomics of the genus Helicobacter, and the related genera Campylobacter and Wolinella. Key Words: Cytotoxin-associated gene; H-Proteobacteria; gastric cancer; genomic evolution; genomic island; hepatobiliary; peptic ulcer disease; type IV secretion system. 1. Introduction The genus Helicobacter belongs to the family Helicobacteriaceae, order Campylo- bacterales, and class H-Proteobacteria, which is also known as the H subdivision of the phylum Proteobacteria. The H-Proteobacteria comprise of a relatively small and recently recognized line of descent within this extremely large and phenotypically diverse phy- lum. Other genera that colonize and/or infect humans and animals include Campylobac- ter, Arcobacter, and Wolinella. These organisms are all microaerophilic, chemoorgano- trophic, nonsaccharolytic, spiral shaped or curved, and motile with a corkscrew-like motion by means of polar flagella. Increasingly, free living H-Proteobacteria are being recognized in a wide range of environmental niches, including seawater, marine sedi- ments, deep-sea hydrothermal vents, and even as symbionts of shrimp and tubeworms in these environments. -
Co-Infection Associated with Diarrhea in a Colony of <I>Scid
Laboratory Animal Science Vol 48, No 5 Copyright 1998 October 1998 by the American Association for Laboratory Animal Science Helicobacter bilis/Helicobacter rodentium Co-Infection Associated with Diarrhea in a Colony of scid Mice Nirah H. Shomer,* Charles A. Dangler, Robert P. Marini, and James G. Fox† Abstract _ An outbreak of diarrhea spanning 3 months occurred in a breeding colony of scid/Trp53 knockout mice. Approximately a third of the 150 mice were clinically affected, with signs ranging from mucoid or watery diarrhea to severe hemorrhagic diarrhea with mortality. Helicobacter bilis and the newly recognized urease-negative organ- ism H. rodentium were isolated from microaerobic culture of feces or cecal specimens from affected mice. Dual infection with H. bilis and H. rodentium were confirmed by culture and polymerase chain reaction (PCR) in several animals. Both Helicobacter species rapidly colonized immunocompetent sentinel mice exposed to bedding from cages containing affected mice, but the sentinel remained asymptomatic. Mice with diarrhea had multifocal to segmental proliferative typhlitis, colitis, and proctitis. Several affected mice had multifocal mucosal necrosis with a few focal ulcers in the cecum, colon, and rectum. Mice with diarrhea were treated with antibiotic food wafers (1.5 mg of amoxicillin, 0.69 mg of metronidazole, and 0.185 mg of bismuth/mouse per day) previously shown to eradi- cate H. hepaticus in immunocompetent mice. Antibiotic treatment resulted in resolution of diarrhea, but not eradication of H. bilis and H. rodentium; mice continued to have positive PCR results after a 2-week treatment regimen, and clinical signs of diarrhea returned in some mice when treatment was suspended. -
Diagnostic Assay for Helicobacter Hepaticus Based on Nucleotide Sequence of Its 16S Rrna Gene JANE K
JOURNAL OF CLINICAL MICROBIOLOGY, May 1995, p. 1344–1347 Vol. 33, No. 5 0095-1137/95/$04.0010 Copyright q 1995, American Society for Microbiology Diagnostic Assay for Helicobacter hepaticus Based on Nucleotide Sequence of Its 16S rRNA Gene JANE K. BATTLES,1 JAMES C. WILLIAMSON,1 KRISTEN M. PIKE,1 PETER L. GORELICK,2 3 1 JERROLD M. WARD, AND MATTHEW A. GONDA * Laboratory of Cell and Molecular Structure1 and Laboratory Animal Sciences Program,2 Program Resources, Inc./DynCorp, and Veterinary and Tumor Pathology Section, Office of Laboratory Animal Science,3 National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, Maryland 21702-1201 Received 17 November 1994/Returned for modification 3 January 1995/Accepted 7 February 1995 Conserved primers were used to PCR amplify 95% of the Helicobacter hepaticus 16S rRNA gene. Its sequence was determined and aligned to those of related bacteria, enabling the selection of primers to highly diverged regions of the 16S rRNA gene and an oligonucleotide probe for the development of a PCR-liquid hybridization assay. This assay was shown to be both sensitive and specific for H. hepaticus 16S rRNA gene sequences. Helicobacter hepaticus is a recently identified species of Helicobacter canis (34). Many PCR-based techniques have gram-negative, microaerophilic, urease-positive, spiral bacte- been developed to amplify 16S rRNA sequences of H. pylori rium that was originally isolated from the livers of mice with and related organisms (3, 6, 15, 16, 20, 24, 39, 44). chronic active hepatitis at the National Cancer Institute-Fred- In the present report, the objective was to develop a species- erick Cancer Research and Development Center. -
The Trematode Parasites of Marine Mammals
THE TREMATODE PARASITES OF MARINE MAMMALS By Emmett W. Pkice Parasitologist, Zoological Division, Bureau of Animal Industry United States Department of Agriculture The internal parasites of marine mammals have not been exten- sively studied, although a fairly large number of species have been described. In attempting to identify the trematodes from mammals of the orders Cetacea, Pinnipedia, and Sirenia, as represented by specimens in the United States National Museum helminthological collection, it was necessary to review the greater part of the litera- ture dealing with this group of parasitic worms. In view of the fact that there is not in existence a single comprehensive paper on the trematodes of these mammals, and that many of the descrip- tions of species have appeared in publications having more or less limited circulation, the writer has undertaken to assemble descriptions of all trematodes reported from these hosts, with the hope that such a paper may serve a useful purpose in aiding other workers in de- termining specimens at their disposal. In addition to compiling the descriptions of species not available to the writer, two new species, one of which represents a new genus, have been described. Specimens representing 10 of the previously described species have been studied and emendations or additions have been made to the existing descriptions; in a few instances the species have been completely reclescribed. Three species, Distoinwni pallassil Poirier, D. vaUdwim von Lin- stow, and D. am/pidlacewni Buttel-Reepen, have been omitted from this paper despite the fact that they have been reported from ceta- ceans. These species belong in the family Hemiuridae, and since all species of this family are parasites of fishes, the writer feels that their reported occurrence in mammals may be regarded as either errors of some sort or cases of accidental parasitism in which fishes have been eaten by mammals and the fish parasites found in the mammal post-mortem. -
Assessment of the Risk to Norwegian Biodiversity and Aquaculture from Pink Salmon
VKM Report 2020: 01 Assessment of the risk to Norwegian biodiversity and aquaculture from pink salmon (Oncorhynchus gorbuscha) Scientific Opinion of the Panel on Alien Organisms and Trade in Endangered Species of the Norwegian Scientific Committee for Food and Environment Report from the Norwegian Scientific Committee for Food and Environment (VKM) 2020: 01 Assessment of the risk to Norwegian biodiversity and aquaculture from pink salmon (Oncorhynchus gorbuscha). Scientific Opinion of the Panel on Alien Organisms and Trade in Endangered Species (CITES) of the Norwegian Scientific Committee for Food and Environment. 15.01.2020 ISBN: 978-82-8259-334-2 ISSN: 2535-4019 Norwegian Scientific Committee for Food and Environment (VKM) Po 222 Skøyen N – 0213 Oslo Norway Phone: +47 21 62 28 00 Email: [email protected] vkm.no vkm.no/english Cover photo: Colourbox Suggested citation: VKM, Kjetil Hindar, Lars Robert Hole, Kyrre Kausrud, Martin Malmstrøm, Espen Rimstad, Lucy Robertson, Odd Terje Sandlund, Eva B. Thorstad, Knut Wiik Vollset, Hugo de Boer, Katrine Eldegard, Johanna Järnegren, Lawrence Kirkendall, Inger Måren, Anders Nielsen, Erlend B. Nilsen, Eli Rueness and Gaute Velle (2020). Assessment of the risk to Norwegian biodiversity and aquaculture from pink salmon (Oncorhynchus gorbuscha). Scientific Opinion of the Panel on Alien Organisms and Trade in Endangered Species (CITES). VKM report 2020:01, ISBN: 978-82-8259-334-2, ISSN: 2535-4019. Norwegian Scientific Committee for Food and Environment (VKM), Oslo, Norway. VKM Report 2020: 01 Assessment of the risk to Norwegian biodiversity and aquaculture from pink salmon (Oncorhynchus gorbuscha) Preparation of the opinion The Norwegian Scientific Committee for Food and Environment (Vitenskapskomiteen for mat og miljø, VKM) appointed a project group to ansver the mandate.