Whole Genome Sequence Typing and Analysis of Non-O157 Stec
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Antimicrobial Resistant Escherichia Coli in Alberta's Rural Well Water
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2017 Antimicrobial Resistant Escherichia coli in Alberta's Rural Well Water Meyer, Kelsey Meyer, K. (2017). Antimicrobial Resistant Escherichia coli in Alberta's Rural Well Water (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/24938 http://hdl.handle.net/11023/3976 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Antimicrobial Resistant Escherichia coli in Alberta’s Rural Well Water by Kelsey Meyer A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN MICROBIOLOGY AND INFECTIOUS DISEASES CALGARY, ALBERTA JULY, 2017 © Kelsey Meyer 2017 Abstract The consumption of rural well water (RWW) contaminated with antimicrobial resistant (AMR) Escherichia coli has been linked to human carriage of resistance. Our objective was to determine whether AMR and extended spectrum beta lactamase (ESBL) producing E.coli are present in Alberta’s RWW. Resistant isolates were detected with an agar screen on (up to) 20 isolates from each sample, and AMR was measured with NARMS Sensititre™ panels. Disk diffusion assays detected ESBL-producing E.coli, and spatial clusters of AMR E.coli were assessed using ArcGIS (version 10.4.1) and SaTScan™ (version 9.4.4). -
University of Cape Town
Town The copyright of this thesis rests with the University of Cape Town. No quotation from it or information derivedCape from it is to be published without full acknowledgement of theof source. The thesis is to be used for private study or non-commercial research purposes only. University Isolation And Molecular CharacterizationTown Of Shiga Toxin Producing Escherichia coli In Cattle, Water And Diarrhoeal Children From The PastoralCape Systems Of Southwesternof Uganda Samuel Majalija UniversityThesis presented for the degree of DOCTOR OF PHILOSOPHY Faculty of Health Sciences UNIVERSITY OF CAPE TOWN February 2009 Town Isolation and Molecular Characterisation of Shiga Toxin Producing Escherichia coli in Cattle, Water and Diarrhoeal Children from the Pastoral Systems of SouthwesternCape Uganda Copyright c Samuel Majalija 2009. of All right reserved. No part of this thesis may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or in any information storage and retrieval system, without permission in writing from the author or the University of Cape Town. Typeset using PDFLATEX as implemented in MIKTEX. Printed in SouthUniversity Africa at: University of Cape Town, Private Bag, 7700, Rondebosch. Cape Town. Specially dedicated to my parents Town Methuselah andCape Glads Majalija of and wife Mabel Majalija University Declaration I...................................................................... declare that the work presented in this thesis is my original work, except where indicated, and that it has not been submitted before for any degree or examination at any university. Town Signed: ........................................... Date: Cape of University Acknowledgements This study was conducted under the supervision of associate Professor Gay B. Elisha and co-supervisor Dr Segal Heidi both of University of Cape Town, and associate Professor Francis Ejobi from Makerere University. -
The Correlation Between Tolerance to Low Water Activity and High Hydrostatic Pressure in Shiga Toxin Producing Escherichia Coli
The Correlation between Tolerance to Low Water Activity and High Hydrostatic Pressure in Shiga Toxin Producing Escherichia coli BY Fahad Bazaid A Thesis Presented to The University of Guelph In partial fulfillment of requirements for the degree of Doctor of Philosophy in Food Science Guelph, Ontario, Canada © Fahad Bazaid, March 2019 ABSTRACT THE CORRELATION BETWEEN TOLERANCE TO LOW WATER ACTIVITY AND HIGH HYDROSTATIC PRESSURE IN SHIGA TOXIN PRODUCING ESCHERICHIA COLI Fahad Bazaid University of Guelph, 2019 Advisors: Dr. Keith Warriner Dr. Andrew Kropinski Dr. Don Mercer Dr. Tatiana Koutchma High hydrostatic pressure processing (HHP) is extensively applied for the non-thermal pasteurization of foods. One notable feature of HHP mediated inactivation of microbes is the large variation in lethality between strains and the influence of the food matrix. In the following it was hypothesized that the barotolerance of Shiga Toxin producing Escherichia coli could be correlated to tolerance to low water activity environments. The study evaluated the barotolerance of members of the Top 6 STEC serotypes and found variation with O26: H11 and O45: H2 exhibiting higher tolerance to pressure compared to the other bacterial types tested. A negative correlation was found between resistance to high pressure and the NaCl concentration under which E. coli could grow under. For example, E. coli O26: H11 exhibited the highest tolerance to pressure, within 300 MPa, but could only grow under NaCl up to 2.4% w/v. In contrast, E. coli O121: H19 was sensitive to pressure, but could grow in the presence of 6% NaCl. The results suggested ii that the induction of the stress-response was the likely reason for high barotolerance in salt sensitive strains vs resistant. -
The Shiga Toxin Producing Escherichia Coli
microorganisms Review An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli Panagiotis Sapountzis 1,* , Audrey Segura 1,2 , Mickaël Desvaux 1 and Evelyne Forano 1 1 Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; [email protected] (A.S.); [email protected] (M.D.); [email protected] (E.F.) 2 Chr. Hansen Animal Health & Nutrition, 2970 Hørsholm, Denmark * Correspondence: [email protected] Received: 22 May 2020; Accepted: 7 June 2020; Published: 10 June 2020 Abstract: For approximately 10,000 years, cattle have been our major source of meat and dairy. However, cattle are also a major reservoir for dangerous foodborne pathogens that belong to the Shiga toxin-producing Escherichia coli (STEC) group. Even though STEC infections in humans are rare, they are often lethal, as treatment options are limited. In cattle, STEC infections are typically asymptomatic and STEC is able to survive and persist in the cattle GIT by escaping the immune defenses of the host. Interactions with members of the native gut microbiota can favor or inhibit its persistence in cattle, but research in this direction is still in its infancy. Diet, temperature and season but also industrialized animal husbandry practices have a profound effect on STEC prevalence and the native gut microbiota composition. Thus, exploring the native cattle gut microbiota in depth, its interactions with STEC and the factors that affect them could offer viable solutions against STEC carriage in cattle. Keywords: cattle; STEC colonization; microbiota; bacterial interactions 1. Introduction The domestication of cattle, approximately 10,000 years ago [1], brought a stable supply of protein to the human diet, which was instrumental for the building of our societies. -
Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Rachel Gilroy1, Anuradha Ravi1, Maria Getino2, Isabella Pursley2, Daniel L. Horton2, Nabil-Fareed Alikhan1, Dave Baker1, Karim Gharbi3, Neil Hall3,4, Mick Watson5, Evelien M. Adriaenssens1, Ebenezer Foster-Nyarko1, Sheikh Jarju6, Arss Secka7, Martin Antonio6, Aharon Oren8, Roy R. Chaudhuri9, Roberto La Ragione2, Falk Hildebrand1,3 and Mark J. Pallen1,2,4 1 Quadram Institute Bioscience, Norwich, UK 2 School of Veterinary Medicine, University of Surrey, Guildford, UK 3 Earlham Institute, Norwich Research Park, Norwich, UK 4 University of East Anglia, Norwich, UK 5 Roslin Institute, University of Edinburgh, Edinburgh, UK 6 Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia 7 West Africa Livestock Innovation Centre, Banjul, The Gambia 8 Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel 9 Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK ABSTRACT Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from Submitted 4 December 2020 two breeds and analysed these, alongside all (n = 582) relevant publicly available Accepted 22 January 2021 chicken metagenomes, to cluster over 20 million non-redundant genes and to Published 6 April 2021 construct over 5,500 metagenome-assembled bacterial genomes. -
Ocorrência De Fatores De Virulência Em Estirpes De Escherichia Coli Isoladas De Fezes De Cães Errantes
Ocorrência de fatores de virulência em estirpes de Escherichia coli isoladas de fezes de cães errantes. 401 OCORRÊNCIA DE FATORES DE VIRULÊNCIA EM ESTIRPES DE ESCHERICHIA COLI ISOLADAS DE FEZES DE CÃES ERRANTES A.C.M.D.G. von Sydow, J.A. Coogan, A.M. Moreno, P.A. Melville, N.R. Benites Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Medicina Veterinária Preventiva e Saúde Animal, Av. Prof. Dr. Orlando Marques de Paiva, 87, CEP 05508-000, São Paulo, SP, Brasil. E-mail: [email protected] RESUMO Escherichia coli pode causar doenças em humanos e animais, tais como infecções do trato urinário, septicemia, meningites e gastroenterites. Cães assintomáticos podem participar da cadeia epidemiológica como reservatório de E. coli patogênica ao homem. Este estudo objetivou avaliar a ocorrência de E. coli patogênica ao homem em fezes de cães errantes sem sintomas de colibacilose e assim averiguar a participação do cão como fonte de infecção de colibacilose humana. Foram coletadas 220 amostras de fezes de animais capturados por diferentes Centros de Controle de Zoonoses do Estado de São Paulo. As amostras foram submetidas a exames microbiológicos sendo isoladas 196 (89,09%) estirpes de E. coli, cujos genes de fatores de virulência foram detectados por PCR. Cento e vinte e três (62,75%) estirpes apresentaram um ou mais dos fatores de virulência estudados. Dezesseis (8,16%) foram positivas para afa, 54 (27,55%) para sfa, 38 (19,38%) para pap, 66 (33,67%) para aer, 31 (15,81%) para cnf, 13 (6,63%) para hly, 1 (0,51%) para VT2 e nenhuma das linhagens foi positiva para LT, STa e STb. -
Axel Janssen Mechanisms and Evolution of Colistin Resistance in Clinical Enterobacteriaceae
Mechanisms and evolution of colistin resistance in clinical Enterobacteriaceae Axel Janssen Mechanisms and evolution of colistin resistance in clinical Enterobacteriaceae Axel B. Janssen Mechanisms and evolution of colistin resistance in clinical Enterobacteriaceae PhD thesis, Utrecht University, Utrecht, the Netherlands Author: Axel B. Janssen Cover design: Axel B. Janssen Lay-out: Axel B. Janssen Printing: ProefschriftMaken ISBN: 978-94-6380-950-4 © Axel B. Janssen, 2020, Utrecht, the Netherlands. All rights reserved. No parts of this thesis may be reproduced, stored in a retrieval system, or transmitted in any form or by any means without prior permission of the author. The copyright of articles that have been published has been transferred to the respective journals. Printing of this thesis was financially supported by: the Netherlands Society of Medical Microbiology, the Royal Netherlands Society for Microbiology, Infection & Immunity Utrecht, and the University Medical Center Utrecht. Mechanisms and evolution of colistin resistance in clinical Enterobacteriaceae Mechanismen en evolutie van colistin resistentie in klinische Enterobacteriaceae (met een samenvatting in het Nederlands) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof. dr. H.R.B.M. Kummeling, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op dinsdag 3 november 2020 des middags te 12.45 uur door Absalom Benjamin Janssen geboren op 31 oktober 1991 te Nijmegen Promotoren: Prof. dr. R.J.L. Willems Prof. dr. ir. W. van Schaik Beoordelingscommissie: Prof. dr. J.A.J.W. Kluytmans Prof. dr. S.H.M. Rooijakkers Prof. dr. J.W.A. Rossen Prof. -
Molecular Evaluation and Antimicrobial Susceptibility Testing of Escherichia Coli Isolates Collected from Various Food Products in Turkey
MOLECULAR EVALUATION AND ANTIMICROBIAL SUSCEPTIBILITY TESTING OF ESCHERICHIA COLI ISOLATES COLLECTED FROM VARIOUS FOOD PRODUCTS IN TURKEY A THESIS SUBMITTED TO THE GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCES OF MIDDLE EAST TECHNICAL UNIVERSITY BY EMMANUEL OWUSU KYERE IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN BIOTECHNOLOGY JULY 2014 ii Approval of the thesis: MOLECULAR EVALUATION AND ANTIMICROBIAL SUSCEPTIBILITY TESTING OF ESCHERICHIA COLI ISOLATES COLLECTED FROM VARIOUS FOOD PRODUCTS IN TURKEY Submitted by EMMANUEL OWUSU KYERE in partial fulfillment of the requirements for the degree of Master of Science in Biotechnology Department, Middle East Technical University by, Prof. Dr. Canan Özgen _____________ Dean, Graduate School of Natural and Applied Sciences Prof. Dr. Filiz Bengü Dilek _____________ Head of Department, Biotechnology Asist. Prof. Dr. Yeşim Soyer _____________ Supervisor, Food Engineering Dept., METU Asist. Prof. Dr. Dilek Avşaroğlu Erkan _____________ Co-supervisor, Agric. Biotech. Dept., Ahi Evran University Examining Committee Members: Assoc. Prof. Dr. Çağdaş Son _____________ Biology Dept., METU Asist. Prof. Dr. Yeşim Soyer _____________ Food Engineering Dept., METU Asist. Prof. Dr. Mecit H. Öztop _____________ Food Engineering Dept., METU Asist. Prof. Dr. Tuba H. Ergüder _____________ Environmental Engineering Dept., METU Asist. Prof. Dr. Umut Yücel _____________ Food Engineering Dept., METU Date: 23.07.2014 iii I hereby declare that all information in this document has been obtained and presented in accordance with academic rules and ethical conduct. I also declare that, as required by these rules and conduct, I have fully cited and referenced all materials and results that are not original to this work. -
Molecular Characterization of Cytolethal
Hinenoya et al. BMC Microbiology 2014, 14:97 http://www.biomedcentral.com/1471-2180/14/97 RESEARCH ARTICLE Open Access Molecular characterization of cytolethal distending toxin gene-positive Escherichia coli from healthy cattle and swine in Nara, Japan Atsushi Hinenoya1, Kensuke Shima1,5, Masahiro Asakura1, Kazuhiko Nishimura1, Teizo Tsukamoto1, Tadasuke Ooka2, Tetsuya Hayashi2, Thandavarayan Ramamurthy3, Shah M Faruque4 and Shinji Yamasaki1* Abstract Background: Cytolethal distending toxin (CDT)-producing Escherichia coli (CTEC) has been isolated from patients with gastrointestinal or urinary tract infection, and sepsis. However, the source of human infection remains unknown. In this study, we attempted to detect and isolate CTEC strains from fecal specimens of healthy farm animals and characterized them phenotypically and genotypically. Results: By PCR analysis, the cdtB gene was detected in 90 and 14 out of 102 and 45 stool specimens of healthy cattle and swine, respectively, and none from 45 chicken samples. Subtypes of the cdtB genes (I to V) were further examined by restriction fragment length polymorphism analysis of the amplicons and by type-specific PCRs for the cdt-III and cdt-V genes. Of the 90 cdtB gene-positive cattle samples, 2 cdt-I,25cdt-III,1cdt-IV,52cdt-V and 1 both cdt-III and cdt-V gene-positive strains were isolated while 1 cdt-II and 6 cdt-V gene-positive were isolated from 14 cdtB positive swine samples. Serotypes of some isolates were identical to those of human isolates. Interestingly, a cdt-II gene-positive strain isolated from swine was for the first time identified as Escherichia albertii. Phylogenetic analysis grouped 87 E. -
Toxin E. Coli Serogroups on Fresh Produce
Development of a Phage Cocktail to Control the Top 7 Shiga -toxin E. coli Serogroups on Fresh Produce by Yiran Ding A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfilment of the requirement of the degree of MASTER OF SCIENCE Department of Food and Nutritional Sciences University of Manitoba Winnipeg Copyright © 2018 by Yiran Ding I I hereby declare that I am the sole author of this thesis. I authorize the University of Manitoba to lend this thesis to other institutions or individuals for the purpose of scholarly research. Yiran Ding I further authorize the University of Manitoba to reproduce this thesis by photocopying or by other means in total or in part, at the request of other institutions or individuals for the purpose of scholarly research. Yiran Ding II ACKNOWLEDGMENTS First of all, I want to thank my parents, Luosi Ding and Xu Li, for their encouragements and supports in every way I can think about throughout my life. I would never have been able to achieve anything without their love and care. I also would like to thank my grandparents for believing in me and encouraging me to go through the difficult times. I owe my sincerest gratitude to my relatives back home, for staying in touch and warming my heart in the coldest winter. I am extremely thankful to my Advisor, Dr. Narvaez, for her generous, knowledge, patience, encouragement, and inspiration for me to explore deeper into the topics. She provided me many chances to learn and triggered my passion for food and microbiology. -
Clinical Significance of Escherichia Albertii
DISPATCHES biochemical properties (6–9). A large number of E. albertii Clinical strains might have been misidentifi ed as EPEC or EHEC Signifi cance of because they possess the eae gene. The Study Escherichia albertii We collected 278 eae-positive strains that were Tadasuke Ooka, Kazuko Seto, Kimiko Kawano, originally identifi ed by routine diagnostic protocols Hideki Kobayashi, Yoshiki Etoh, as EPEC or EHEC. They were isolated from humans, Sachiko Ichihara, Akiko Kaneko, Junko Isobe, animals, and the environment in Japan, Belgium, Brazil, Keiji Yamaguchi, Kazumi Horikawa, and Germany during 1993–2009 (Table 1; online Technical Tânia A.T. Gomes, Annick Linden, Appendix, wwwnc.cdc.gov/pdfs/11-1401-Techapp.pdf). Marjorie Bardiau, Jacques G. Mainil, To characterize the strains, we fi rst determined their Lothar Beutin, Yoshitoshi Ogura, intimin subtypes by sequencing the eae gene as described and Tetsuya Hayashi (online Technical Appendix). Of the 275 strains examined, 267 possessed 1 of the 26 known intimin subtypes (4 Discriminating Escherichia albertii from other subtypes—η, ν, τ, and a subtype unique to C. rodentium— Enterobacteriaceae is diffi cult. Systematic analyses were not found). In the remaining 8 strains, we identifi ed showed that E. albertii represents a substantial portion 5 new subtypes; each showed <95% nt sequence identity of strains currently identifi ed as eae-positive Escherichia to any known subtype, and they were tentatively named coli and includes Shiga toxin 2f–producing strains. subtypes N1–N5. For subtype N1, 3 variants were identifi ed Because E. albertii possesses the eae gene, many strains might have been misidentifi ed as enterohemorrhagic or (N1.1, N1.2, and N1.3, with >95% sequence identity among enteropathogenic E. -
Survival of Acid-Adapted Escherichia Coli O157:H7 and Non-O157:H7
The Pennsylvania State University The Graduate School College of Agricultural Sciences SURVIVAL OF ACID-ADAPTED ESCHERICHIA COLI O157:H7 AND NON-O157:H7 SHIGA TOXIN-PRODUCING E. COLI (STEC) DURING PROCESSING OF DRY, FERMENTED SAUSAGES A Dissertation in Food Science by Minerva Rivera © 2017 Minerva Rivera Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2017 i The dissertation of Minerva Rivera was reviewed and approved* by the following: Catherine N. Cutter Professor of Food Science Food Safety Extension Specialist – Muscle Foods Dissertation Advisor Chair of Committee Jonathan A. Campbell Assistant Professor of Meat Science Extension Meat Specialist Edward G. Dudley Associate Professor of Food Science Sara Milillo Food Science Faculty Director of Math and Science at Bay Path University Robert F. Roberts Professor of Food Science Head of the Department of Food Science *Signatures are on file in the Graduate School ii Abstract Escherichia coli O157:H7 was first recognized as a human pathogen following outbreaks of hemorrhagic colitis in the early 1980s. Due to the infectious dose of E. coli O157:H7, the severity of the disease, and the possibility of lifelong sequalae, the U. S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS) declared it as an adulterant in raw ground beef in 1994. In 2012, non-O157:H7 Shiga toxin-producing E. coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) also were declared adulterants in raw beef products by USDA- FSIS. Until recently, the majority of the research done on interventions used to control STEC has been done on E.