Antimicrobial Resistance and Food Safety: Methods and Techniques PDF
Preview Antimicrobial Resistance and Food Safety: Methods and Techniques
Antimicrobial Resistance and Food Safety Antimicrobial Resistance and Food Safety Methods and Techniques Editors Chin-Yi Chen US Department of Agriculture, Agricultural Research Service, Wyndmoor, PA, USA Xianghe Yan US Department of Agriculture, Agricultural Research Service, Wyndmoor, PA, USA Charlene R. Jackson US Department of Agriculture, Agricultural Research Service, Athens, GA, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 32 Jamestown Road, London NW1 7BY, UK 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 225 Wyman Street, Waltham, MA 02451, USA The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK Copyright © 2015 Elsevier Inc. All rights reserved. Portions of this book were written and prepared by officers and/or employees of the U.S. Government as part of their official duties and are not copyrightable. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. ISBN: 978-0-12-801214-7 British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress For information on all Academic Press publications visit our website at http://store.elsevier.com/ Typeset by MPS Limited, Chennai, India www.adi-mps.com Printed and bound in the USA List of Contributors María Ángeles Argudín Laboratoire de Référence MRSA-Staphylocoques, Department of Microbiology, Hôpital Erasme, Brussels, Belgium Craig Baker-Austin Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK Clara Ballesté-Delpierre ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic – Universitat de Barcelona, Barcelona, Spain Robert A. Bonomo Department of Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH, USA; Department of Medicine, Case Western Reserve University, Cleveland, OH, USA Patrick Butaye Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St Kitts and Nevis, West Indies; Department of Pathology, Bacteriology and Poultry diseases, Ghent University, Salisburlylaan, Merelbeke, Belgium Juliany Rivera Calo Center for Food Safety and Department of Food Science, University of Arkansas, Fayetteville, AR, USA Chin-Yi Chen US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA, USA Jinru Chen Department of Food Science and Technology, The University of Georgia, Griffin, GA, USA H. Gregg Claycamp Center for Veterinary Medicine, US Food and Drug Administration, Rockville, MD, USA Louis Anthony (Tony) Cox NextHealth Technologies, Cox Associates and University of Colorado, Denver, CO, USA Philip G. Crandall Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, USA Emily Crarey Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD, USA Andrea Endimiani Institute for Infectious Diseases, University of Bern, Bern, Switzerland Anna Fàbrega ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic – Universitat de Barcelona, Barcelona, Spain xv xvi List of Contributors Andrea T. Feßler Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany Anuradha Ghosh Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA Marja-Liisa Hänninen Department of Food Hygiene and Environmental Health, University of Helsinki, Finland Lee H. Harrison Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA Pei-Ying Hong Water Desalination and Reuse Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia Charlene R. Jackson US Department of Agriculture, Agricultural Research Service, Russell Research Center, Athens, GA, USA Nathan A. Jarvis Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, USA Yangjin Jung Department of Food Science, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA Claudine Kabera Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD, USA Kristina Kadlec Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany Vinayak Kapatral Igenbio, Inc., Chicago, IL, USA Rauni Kivistö Department of Food Hygiene and Environmental Health, University of Helsinki, Finland Keith A. Lampel Food and Drug Administration, Laurel, MD, USA Agnese Lupo Institute for Infectious Diseases, University of Bern, Bern, Switzerland Jane W. Marsh Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA Karl R. Matthews Department of Food Science, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA Corliss A. O’Bryan Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, USA Satu Olkkola Department of Food Hygiene and Environmental Health, University of Helsinki, Finland Krisztina M. Papp-Wallace Department of Medicine, Case Western Reserve, University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veteran Affairs Medical Center, Cleveland, OH, USA Steven C. Ricke Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, USA List of Contributors xvii Mati Roasto Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi, Tartu, Estonia Mirko Rossi Department of Food Hygiene and Environmental Health, University of Helsinki, Finland Stefan Schwarz Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany Heather Tate Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD, USA John Threlfall European Food Safety Agency (EFSA) Biological Hazards (BIOHAZ) Panel, Parma, Italy Jordi Vila ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic – Universitat de Barcelona, Barcelona, Spain; Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain Guangshun Wang Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA Siyun Wang Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada Sarah Wendlandt Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany Xianghe Yan US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA, USA Ludek Zurek Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA; Department of Entomology, Kansas State University, Manhattan, KS, USA Chapter 1 Introduction to Antimicrobial- Resistant Foodborne Pathogens Patrick Butaye1, María Ángeles Argudín2 and John Threlfall3 1Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St Kitts and Nevis, West Indies; Department of Pathology, Bacteriology and Poultry diseases, Ghent University, Salisburlylaan, Merelbeke, Belgium, 2Laboratoire de Référence MRSA-Staphylocoques, Department of Microbiology, Hôpital Erasme, Brussels, Belgium, 3European Food Safety Agency (EFSA) Biological Hazards (BIOHAZ) Panel, Parma, Italy Chapter Outline How Antimicrobial Resistance Conclusion 14 Is Defined? 2 References 15 How Does Resistance Spread Between Ecosystems? 8 Antimicrobial resistance is no longer just a potential threat, it is a serious health problem that is rapidly increasing across the world. Since the discov- ery of penicillin, resistance has been described. With the advent of the mas- sive use of antibiotics, appropriate or not, resistances have been continuously selected, both in commensal bacteria, zoonotic bacteria, and pathogenic bacteria. According to the report of the European Centre for Disease Prevention and Control (ECDC) and the European Medicines Agency (EMA), in Europe, each year 400,000 patients suffer from infections caused by multidrug-resistant bacteria, and 25,000 die (Anonymous, 2009a). The ECDC, as well as the World Health Organization, considers antimicrobial drug resistance to be one of the major health threats in Europe in the twenty-first century (Anonymous, 2011a, 2013a,b). In addition to direct healthcare costs, infectious diseases caused by drug-resistant bacteria result in indirect costs such as days away from work and lost output. The report by ECDC/EMA (Anonymous, 2009a) estimates the overall cost to society at €1.5 billion each year. Antimicrobial resistance is an ever-growing problem, but what is an anti- microbial agent? The term “antimicrobial agent” includes all compounds that kill microorganisms or inhibit their growth. The antibiotics are included within these agents. Antibiotics are natural substances and are produced by fungi or bacteria. Next to these antimicrobial agents, there are purely chemically derived products that are named synthetic antibacterial drugs or chemotherapeutics. At Antimicrobial Resistance and Food Safety.DOI:http://dx.doi.org/10.1016/B978-0-12-801214-7.00001-6 © 2015 Elsevier Inc. All rights reserved. 1 2 Antimicrobial Resistance and Food Safety the microbiological level, they exert the same activity. Against both chemo- therapeutics and antibiotics, resistances have been selected. Currently, the term antibiotic is so extended that it is often used as synonym of the general term “antimicrobial agent”. In this chapter we first deal with the different criteria of determining how antimicrobial resistance is defined. The aim is to provide guidance for under- standing how people discuss resistance, whilst they are using different defini- tions. We will then discuss how resistance is spreading between ecosystems and determine the importance of each for foodborne pathogens. HOW ANTIMICROBIAL RESISTANCE IS DEFINED? Antimicrobial resistance is a complex item in which several ways of measuring are applied. Resistance in bacteria can be determined according to several dif- ferent criteria. First, there is the microbiological or epidemiological criterion. This is subdivided into a phenotypic determination or genotypic determination. The latter can also be seen as a separate criterion, since the phenotype does not always accord with the genotype. Secondly there is the pharmacological crite- rion; and finally, there is the clinical criterion. The phenotypic criterion for the determination of antimicrobial resistance relates to the characteristics of the bacterium itself and relies only on in vitro testing. It deals with the minimal inhibitory concentrations (MICs) or inhibition zones of antibiotics for bacteria of one species and looks at how the bacteria are distributed over the MICs/inhibition zones, which are normally doubling dilutions of the respective antibiotics. As such, when in a specific bacterial pop- ulation, the strains are distributed as a normal Gaussian distribution over the doubling dilutions, this should be regarded as the normal, susceptible, or wild- type population (Figure 1.1). 45 Wild-type population 40 s 35 m s 30 ni ga 25 or Non-wild-type o 20 cr population Mi 15 % 10 5 0 2 4 8 6 2 4 5 5 5 1 2 8 6 2 4 8 6 0.00 0.00 0.00 0.01 0.03 0.06 0.12 0.2 0. 1 3 6 12 25 < MIC (mg/L) FIGURE 1.1 Example of a hypothetical MIC distribution, in which the epidemiological cutoff is set in 0.5 mg/L. The wild-type (from 0.032 to 0.5 mg/L), as well as the non-wild-type (from 2 to 32 mg/L), populations follow normal Gaussian distributions. Introduction to Antimicrobial-Resistant Foodborne Pathogens Chapter | 1 3 The in vitro tests generally rely on two different kinds of tests. One is a “dilution test”, which may be in broth or agar, and the other is the diffusion test. Both tests are widely used as antimicrobial susceptibility testing methods in clinical laboratories. They are suitable for testing the majority of bacterial path- ogens, including the more common fastidious bacteria, are versatile in the range of antimicrobial agents that can be tested, and require no special equipment. In the dilution tests, agar plates or tubes or microtiter trays with twofold dilutions of antibiotics in agar or broth, respectively, are inoculated with a standardized quantity of bacteria and incubated. After 24 h the MIC is recorded as the lowest concentration of the antimicrobial agent with no visible growth. In contrast, diffusion tests are primarily qualitative methods, in which a known quantity of bacteria is grown on an appropriate culture plate (such as Mueller–Hinton agar) in the presence of antibiotic-impregnated filter paper disks or tablets. During incubation the antimicrobial agent diffuses into the agar and inhibits growth of the bacteria if sensitive. The presence or absence of growth around the disks or tablets is an indirect measure of the ability of that compound to inhibit that organism. There exists also a quantitative diffusion test, the E-test. This test also allows determination of the MIC because a con- centration gradient of the antibiotic is made in the medium. Apart from the above classical methods, different approaches have been published regarding the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as a tool for resistance detec- tion (Kostrzewa et al., 2013). MALDI-TOF MS was applied as a fast moni- toring tool for the different effects of an antibiotic to resistant or susceptible strains, with the advantage, in contrast to established standard methods, of a reduction of time results. This technology has been suitable for yeast profiling, as well as antimicrobial tests based on enzymatic activities including the beta (β)-lactamase and aminoglycoside-modifying enzyme tests. This technique is still evolving and new developments are underway. The phenotypic criterion is thus focused on one specific bacterial species, and in most cases may not be extrapolated to other species, since different bacterial species may have different susceptibilities to a particular antibiotic. Typically, within a species, the normal susceptibility, as measured by pheno- typic means, is distributed over a specific concentration range. This range can be larger or smaller, depending on the bacterial species and the chemical char- acteristics of the antimicrobial agent. The normal susceptibility is dependent on the test methods used and for some antibiotics, even small differences may have an effect on the normal susceptibility of the bacteria (Butaye et al., 1998, 1999, 2000, 2003). Therefore standardized methods have been developed for phenotypic susceptibility testing. Different standardized methods are in use (e.g., CLSI, EUCAST, BSAC). Because of this the results (in the case of disk diffusion, the mm, and in the case of dilution tests, the MIC) may differ and as such require specific breakpoints/cutoff values. These differences have led to discussions in the interpretation of what is regarded as “sensitive” or “resistant”, particularly in relation to fluoroquinolone antibiotics (see later). 4 Antimicrobial Resistance and Food Safety The breakpoints for the microbiological criterion indicate the differences between the normal susceptible population (wild-type population) and the resistant population (non-wild-type population) (Figure 1.1). The wild-type cutoff, used for the microbiological criterion, is commonly named the epide- miological cutoff value (ECOFF) and is determined for both disk diffusion and broth dilution tests by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). This breakpoint may differ from the clinical breakpoints set by EUCAST and most other methods. For some bacteria–antimicrobial agent combinations the wild-type and non- wild-type populations may overlap, making it very hard to define an accurate breakpoint and, if one is defined, the sensitivity will not be 100% for the deter- mination of a resistant strain. This phenomenon is known as “tailing”, and is shown in Figure 1.2. In fact, this tailing is caused by an overlap of the suscep- tible and resistant populations. This has also been found for disinfectants and makes it difficult to determine resistance against disinfectants. Here, till now, only genetic detection of known resistance genes is possible. It should be clear that this method of determination of the susceptibility may not always have a clinical implication. It may even be the case that a strain defined as having no acquired resistance may not be treatable by the antibiotic and a strain defined as being “resistant” may still be treatable when using this microbiological break- point (Aarestrup et al., 2003). 40 % 6 20 7 Microorganisms 8 9 10 11 Zone 1213 0 diameter (mm) 14 0,5 15 16 17 4 MIC (mg/L) 18 19 20 32 21 22 FIGURE 1.2 Hypothetical example of overlapping of wild-type and non-wild-type populations. In this example the MIC epidemiological cutoff is set at 8 mg/L, and the resistance breakpoint diameter is set at 11 mm. The non-wild-type or resistant population (with zone diameter from 6, to 11 mm and MIC of 32 mg/L), as well as the wild-type or susceptible population (with zone diameter from 11 to 22 mm and MIC of 0.5-4 mg/L), follows both criteria. However, there is a part of the population (with zone diameter of 12 mm but MIC of 32 mg/L) that could not be classified as either non-wild type or wild type.
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