Guidelines for Drinking-Water Quality - Second Edition - Volume 2 - Health Criteria and Other Supporting Information
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IDENTIFIKASI BAKTERI PATOGEN PADA IKAN BARONANG (Siganus Canaliculatus) YANG DIDARATKAN DI TEMPAT PELELANGAN IKAN PAOTERE MAKASSAR
IDENTIFIKASI BAKTERI PATOGEN PADA IKAN BARONANG (Siganus canaliculatus) YANG DIDARATKAN DI TEMPAT PELELANGAN IKAN PAOTERE MAKASSAR SKRIPSI ANDI RISMA AMIRUDDIN PROGRAM STUDI ILMU KELAUTAN FAKULTAS ILMU KELAUTAN DAN PERIKANAN UNIVERSITAS HASANUDDIN MAKASSAR 2020 IDENTIFIKASI BAKTERI PATOGEN PADA IKAN BARONANG (Siganus canaliculatus) YANG DIDARATKAN DI TEMPAT PELELANGAN IKAN PAOTERE MAKASSAR ANDI RISMA AMIRUDDIN L111 13 015 SKRIPSI Sebagai salah satu syarat untuk memperoleh gelar sarjana pada Fakultas Ilmu Kelautan dan Perikanan PROGRAM STUDI ILMU KELAUTAN FAKULTAS ILMU KELAUTAN DAN PERIKANAN UNIVERSITAS HASANUDDIN MAKASSAR 2020 ii iii iii iv ABSTRAK ANDI RISMA AMIRUDDIN. Identifikasi Bakteri Patogen pada Ikan Baronang (Siganus canaliculatus) yang Didaratkan Di Tempat Pelelangan Ikan Paotere Makassar. Dibimbing oleh Arniati Massinai sebagai Pembimbing utama dan Andi Iqbal Burhanuddin sebagai Pembimbing pendamping. Bakteri patogen merupakan bakteri yang dapat menyebabkan penyakit. Bakteri patogen detemukan pada setiap habitat, seperti di tanah, air tawar, air laut, perakaran tanaman, dan jaringan hewan. Penelitian ini bertujuan untuk mengetahui keberadaan jenis bakteri patogen pada ikan baronang Siganus canaliculatus yang didaratkan (belum dicuci ai laut) dan dipasarkan (telah dicuci air laut), serta kaitannya terhadap air pencucian di Tempat Pelelangan Ikan (TPI) Paotere Kota Makassar. Pengambilan sampel dilakukan di pelabuhan TPI Paotere, dengan mengambil sampel air dan sampel ikan; daging, insang, usus masing-asing 10 gr yang kemudian -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
Post-Cesarean Surgical Site Infection Due to Buttiauxella Agrestis
International Journal of Infectious Diseases 22 (2014) 65–66 Contents lists available at ScienceDirect International Journal of Infectious Diseases jou rnal homepage: www.elsevier.com/locate/ijid Short Communication Post-cesarean surgical site infection due to Buttiauxella agrestis a, a b Vicente Sperb Antonello *, Jessica Dalle´ , Guilherme Campos Domingues , c c d Jorge Alberto Santiago Ferreira , Maria do Carmo Queiroz Fontoura , Fa´bio Borges Knapp a Department of Infection Prevention and Control, Hospital Feˆmina, Rua Mostardeiro, 17, Bairro: Independeˆncia, Porto Alegre, RS 90430-001, Brazil b Department of Infectious Diseases, Hospital Nossa Senhora da Conceic¸a˜o, Porto Alegre, RS, Brazil c Department of Microbiology, Hospital Nossa Senhora da Conceic¸a˜o, Porto Alegre, Brazil d bioMe´rieux, Sa˜o Paulo, Brazil A R T I C L E I N F O S U M M A R Y Article history: Surgical site infections (SSI) are postoperative complications that constitute a major public health Received 27 September 2013 problem. We present a rare case report of infection by Buttiauxella agrestis, a member of the Received in revised form 26 January 2014 Enterobacteriaceae family, occurring after a cesarean delivery in a young woman with no comorbidities. Accepted 28 January 2014 The authors further discuss the origin of this infection. Corresponding Editor: Eskild Petersen, ß 2014 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. Aarhus, Denmark This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by- nc-nd/3.0/). Keywords: Surgical site infection Buttiauxella agrestis Obstetric infection Cesarean delivery 1. -
The Quest for Novel Extracellular Polymers Produced by Soil-Borne Bacteria
Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. Bioprospecting: The quest for novel extracellular polymers produced by soil-borne bacteria A thesis presented in partial fulfilment of the requirements for the degree of Master of Science In Microbiology at Massey University, Palmerston North, New Zealand Jason Smith 2017 i Dedication This thesis is dedicated to my dad. Vaughan Peter Francis Smith 13 July 1955 – 27 April 2002 Though our time together was short you are never far from my mind nor my heart. ii Abstract Bacteria are ubiquitous in nature, and the surrounding environment. Bacterially produced extracellular polymers, and proteins are of particular value in the fields of medicine, food, science, and industry. Soil is an extremely rich source of bacteria with over 100 million per gram of soil, many of which produce extracellular polymers. Approximately 90% of soil-borne bacteria are yet to be cultured and classified. Here we employed an exploratory approach and culture based method for the isolation of soil-borne bacteria, and assessed their capability for extracellular polymer production. Bacteria that produced mucoid (of a mucous nature) colonies were selected for identification, imaging, and polymer production. Here we characterised three bacterial isolates that produced extracellular polymers, with a focus on one isolate that formed potentially novel proteinaceous cell surface appendages. These appendages have an unknown function, however, I suggest they may be important for bacterial communication, signalling, and nutrient transfer. -
Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES .............................................................................................................................. -
Isolation and Characterization of Cultivable Fermentative Bacteria from the Intestine of Two Edible Snails, Helix Pomatia and Cornu Aspersum (Gastropoda: Pulmonata)
CHARRIER ET AL. Biol Res 39, 2006, 669-681 669 Biol Res 39: 669-681, 2006 BR Isolation and characterization of cultivable fermentative bacteria from the intestine of two edible snails, Helix pomatia and Cornu aspersum (Gastropoda: Pulmonata) MARYVONNE CHARRIER*, 1, GÉRARD FONTY2, 3, BRIGITTE GAILLARD-MARTINIE2, KADER AINOUCHE1 and GÉRARD ANDANT2 1 Université de Rennes I, UMR CNRS 6553 EcoBio, 263, Avenue du Général Leclerc, CS 74205, F-35042 Rennes Cedex, France. 2 Unité de Microbiologie, CR INRA de Clermont-Ferrand - Theix, F-63122 Saint Genès-Champanelle, France. 3 Laboratoire de Biologie des Protistes, UMR CNRS 6023, Université Clermont II, 63177 Aubière, France. ABSTRACT The intestinal microbiota of the edible snails Cornu aspersum (Syn: H. aspersa), and Helix pomatia were investigated by culture-based methods, 16S rRNA sequence analyses and phenotypic characterisations. The study was carried out on aestivating snails and two populations of H. pomatia were considered. The cultivable bacteria dominated in the distal part of the intestine, with up to 5.109 CFU g -1, but the Swedish H. pomatia appeared significantly less colonised, suggesting a higher sensitivity of its microbiota to climatic change. All the strains, but one, shared ≥ 97% sequence identity with reference strains. They were arranged into two taxa: the Gamma Proteobacteria with Buttiauxella, Citrobacter, Enterobacter, Kluyvera, Obesumbacterium, Raoultella and the Firmicutes with Enterococcus, Lactococcus, and Clostridium. According to the literature, these genera are mostly assigned to enteric environments or to phyllosphere, data in favour of culturing snails in contact with soil and plants. None of the strains were able to digest filter paper, Avicel cellulose or carboxymethyl cellulose (CMC). -
Microorganism in Concrete
MICROORGANISMS IN CONCRETE A THESIS SUBMITTED FOR THE DEGREE OF ENVIRONMENTAL ENGINEERING BY ÁNGELA MARCELA QUINTERO MARTÍNEZ DIRECTOR MAURICIO SÁNCHEZ SILVA, PH.D. ADVISOR AIDA JULIANA MARTÍNEZ LEÓN, MSC. UNIVERSIDAD DE LOS ANDES FACULTY OF ENGINEERING DEPARTMENT OF CIVIL AND ENVIRONMENTAL ENGINEERING BOGOTÁ, COLOMBIA 2011 Dedicated to my parents and my sister… Acknowledgements The author would like to acknowledge the supervision, suggestions and ideas about the investigation, provided by the engineer Mauricio Sánchez Silva and the collaboration, contributions, explanations and advices of the microbiologist Juliana Martínez. Many thanks are extended to the proofreader, the philologist Laura Ontibón; the people that collaborated in the field work (transportation and photographs), Mr. José Manuel Quintero and Mrs. Rocío Martínez; the company which realized the sequencing of DNA samples, Macrogen –Korea Inc.; and the persons of the laboratory of electrophoresis of Universidad de los Andes Abstract This study reports the use of culture dependent and independent techniques to identify indigenous and naturally occurring bacteria in deteriorate concrete surfaces. In the field work was sampled a total of 6 bridges located in via Bogotá – Villeta. Genomic DNA was isolated to the samples in two different ways: indirect and direct. The indirect way involves the cultivation of microorganisms, while the direct way does not. PCR amplification of bacterial ribosomal DNA (16S rDNA) was conducted with subsequent DNA sequencing to identify the microbes. Three bacteria genus was recognized Pseudomonas, Rahnella and Buttiauxella corresponding to four distinct DNA samples (Pseudomonas was found twice) occurring at two bridges. Of these genuses, only Pseudomonas was reported in the scientific articles related to deterioration of concrete. -
Cyanobacterial Blooms Contribute to the Diversity of Antibiotic-Resistance Genes in Aquatic Ecosystems
ARTICLE https://doi.org/10.1038/s42003-020-01468-1 OPEN Cyanobacterial blooms contribute to the diversity of antibiotic-resistance genes in aquatic ecosystems Qi Zhang1,10, Zhenyan Zhang1,10, Tao Lu 1, W. J. G. M. Peijnenburg 2,3, Michael Gillings 4, Xiaoru Yang5, ✉ ✉ 1234567890():,; Jianmeng Chen1, Josep Penuelas 6,7, Yong-Guan Zhu5,8, Ning-Yi Zhou9, Jianqiang Su5 & Haifeng Qian 1 Cyanobacterial blooms are a global ecological problem that directly threatens human health and crop safety. Cyanobacteria have toxic effects on aquatic microorganisms, which could drive the selection for resistance genes. The effect of cyanobacterial blooms on the dispersal and abundance of antibiotic-resistance genes (ARGs) of concern to human health remains poorly known. We herein investigated the effect of cyanobacterial blooms on ARG compo- sition in Lake Taihu, China. The numbers and relative abundances of total ARGs increased obviously during a Planktothrix bloom. More pathogenic microorganisms were present during this bloom than during a Planktothrix bloom or during the non-bloom period. Microcosmic experiments using additional aquatic ecosystems (an urban river and Lake West) found that a coculture of Microcystis aeruginosa and Planktothrix agardhii increased the richness of the bacterial community, because its phycosphere provided a richer microniche for bacterial colonization and growth. Antibiotic-resistance bacteria were naturally in a rich position, successfully increasing the momentum for the emergence and spread of ARGs. These results demonstrate that cyanobacterial blooms are a crucial driver of ARG diffusion and enrichment in freshwater, thus providing a reference for the ecology and evolution of ARGs and ARBs and for better assessing and managing water quality. -
Pseudomonas Aeruginosa Diego Carriel
Structure-function relationships of the lysine decarboxylase from Pseudomonas aeruginosa Diego Carriel To cite this version: Diego Carriel. Structure-function relationships of the lysine decarboxylase from Pseudomonas aerug- inosa. Biomolecules [q-bio.BM]. Université Grenoble Alpes, 2017. English. NNT : 2017GREAV011. tel-02130621 HAL Id: tel-02130621 https://tel.archives-ouvertes.fr/tel-02130621 Submitted on 16 May 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour obtenir le grade de DOCTEUR DE LA COMMUNAUTÉ UNIVERSITÉ GRENOBLE ALPES Spécialité : Biologie Structurale et Nanobiologie Arrêté ministériel : 25 mai 2016 Présentée par Diego CARRIEL Thèse dirigée par Irina GUTSCHE et Co-dirigée par Sylvie ELSEN préparée au sein de l’Institut de Biologie Structurale dans l'École Doctorale de Chimie et Sciences du Vivant Structure-function relationships of the lysine decarboxylase LdcA from Pseudomonas aeruginosa Thèse soutenue le 15 Mai 2017, devant le jury composé de : M. Axel HARTKE Professeur des Universités, UCBN, Caen (Rapporteur) Mme. Anne-Marie DI GUILMI Ingénieur-chercheur, CEA Paris-Saclay (Rapporteur) M. Bertrand TOUSSAINT Professeur des Universités, UGA, Grenoble (Président) Mme. Patricia RENESTO Directeur de Recherche, CNRS, Grenoble (Examinateur) Mme. Irina GUTSCHE Directeur de Recherche, CNRS, Grenoble (Directeur de thèse) Mme. -
Margarita Elvira-Recuenco SUSTAINABLE CONTROL of PEA
Margarita Elvira-Recuenco SUSTAINABLE CONTROL OF PEA BACTERIAL BLIGHT Approaches for durable genetic resistance and biocontrol by endophytic bacteria Proefschrift terverkrijgin g van degraa d van doctor opgeza g van derecto r magnificus vanWageninge n Universiteit, dr.ir .L .Speelman , inhe t openbaar te verdedigen opvrijda g 6oktobe r 2000 desnamiddag so m 13.30uu ri nd eAul a 2> Elvira-Recuenco,M . Sustainable control of pea bacterial blight: approaches for durable genetic resistance andbiocontro l byendophyti c bacteria Thesis Wageningen University, the Netherlands - With references - With summaries inEnglish , Dutch and Spanish. ISBN 90-5808-291-1 Subject headings: pea / Pseudomonas syringae pv. pisi I genetic resistance / endophytic bacteria/ biocontrol Printed byPonse n &Looye n BV, Wageningen The research described in this thesis (April 1995-October 2000) was conducted at Plant Research International, Wageningen, The Netherlands and at Horticulture Research International, Wellesbourne, UK.I n 1999par t of the research was also done atJoh n InnesCentre ,Norwich , UK. This PhD study was funded by Instituto Nacional de Investigation y Tecnologia Agraria yAlimentari a (INIA),Ministr y of Science andTechnology , Spain. BIBl.lOTHi-FK LANDBOl WUMVHK; VVAGT^N.'NGFNJ SUSTAINABLE CONTROL OF PEA BACTERIAL BLIGHT Approaches for durable genetic resistance and biocontrol byendophyti c bacteria Promoter: Dr.M.J .Jege r Hoogleraar in deecologisch e fytopathologie Co-promotoren: Dr.J.W.L .va n Vuurde Senior onderzoeker PlantResearc h International, Wageningen Dr.J.D .Taylo r Senior scientist Horticulture Research International, Wellesbourne,U K STELLINGEN/PROPOSITIONS 1. The combination of race specific resistance and race non-specific resistance is the optimal genetic background for a potentially durable resistance to pea bacterial blight. -
Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances. -
Antibiotic Resistance in Gram Negative Bacteria Isolated from Fish Sold in Western Australia
Edith Cowan University Research Online Theses: Doctorates and Masters Theses 2018 Antibiotic resistance in Gram negative bacteria isolated from fish sold in Western Australia Hannah Kathleen Robinson Edith Cowan University Follow this and additional works at: https://ro.ecu.edu.au/theses Part of the Food Science Commons, Nutrition Commons, and the Public Health Commons Recommended Citation Robinson, H. K. (2018). Antibiotic resistance in Gram negative bacteria isolated from fish sold in esternW Australia. https://ro.ecu.edu.au/theses/2161 This Thesis is posted at Research Online. https://ro.ecu.edu.au/theses/2161 Edith Cowan University Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorize you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. Where the reproduction of such material is done without attribution of authorship, with false attribution of authorship or the authorship is treated in a derogatory manner, this may be a breach of the author’s moral rights contained in Part IX of the Copyright Act 1968 (Cth). Courts have the power to impose a wide range of civil and criminal sanctions for infringement of copyright, infringement of moral rights and other offences under the Copyright Act 1968 (Cth). Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form.