THETHE MULTIPLEMULTIPLE ROLESROLES OFOF ANTIBIOTICSANTIBIOTICS ANDAND ANTIBIOTICANTIBIOTIC RESISTANCERESISTANCE ININ NATURENATURE TopicTopic EditorEditor FionaFiona WalshWalsh MICROBIOLOGY FRONTIERS COPYRIGHT STATEMENT ABOUT FRONTIERS © Copyright 2007-2015 Frontiers is more than just an open-access publisher of scholarly articles: it is a pioneering Frontiers Media SA. All rights reserved. approach to the world of academia, radically improving the way scholarly research is managed. All content included on this site, such as The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share text, graphics, logos, button icons, images, and generate knowledge. 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ISBN 978-2-88919-525-1 Find out more on how to host your own Frontiers Research Topic or contribute to one as an DOI 10.3389/978-2-88919-525-1 author by contacting the Frontiers Editorial Office: [email protected] Frontiers in Microbiology April 2015 | The Multiple Roles of Antibiotics and Antibiotic Resistance in Nature | 1 THE MULTIPLE ROLES OF ANTIBIOTICS AND ANTIBIOTIC RESISTANCE IN NATURE Topic Editor: Fiona Walsh, National University of Ireland Maynooth, Ireland Antibiotics and antibiotic resistance have most commonly been viewed in the context of human use and effects. However, both have co-existed in nature for millennia. Recently the roles of antibiotics and antibiotic resistance genes have started to be discussed in terms of functions other than bacterial inhibition and protection. This special topic will focus on both the traditional role of antibiotics as warfare mechanisms and their alternative roles and uses within nature such as antibiotics Antibiotic susceptibility testing of bacteria as signals or communication mechanisms, isolated from soil antibiotic selection at low concentrations, the non-specific role of resistance mechanisms in nature: e.g. efflux pumps, evolution of antibiotic resistance and the role of persisters in natural antibiotic resistance. Frontiers in Microbiology April 2015 | The Multiple Roles of Antibiotics and Antibiotic Resistance in Nature | 2 Table of Contents 04 The Multiple Roles of Antibiotics and Antibiotic Resistance in Nature Fiona Walsh 05 Investigating Antibiotic Resistance in Non-Clinical Environments Fiona Walsh 10 A Brief Multi-Disciplinary Review on Antimicrobial Resistance in Medicine and Its Linkage to the Global Environmental Microbiota L. Cantas, Syed Q. A. Shah, L. M. Cavaco, C. M. Manaia, F. Walsh, M. Popowska, H. Garelick, H. Bürgmann and H. Sørum 24 Antibiotic Resistance Shaping Multi-Level Population Biology of Bacteria Fernando Baquero, Ana P. Tedim and Teresa M. Coque 39 Antibiotics as Selectors and Accelerators of Diversity in the Mechanisms of Resistance: From the Resistome to Genetic Plasticity in the β-Lactamases World Juan-Carlos Galán, Fernando González-Candelas, Jean-Marc Rolain and Rafael Cantón 56 Evolutionary Consequences of Antibiotic Use for the Resistome, Mobilome, and Microbial Pangenome Michael R. Gillings 66 “Stormy Waters Ahead”: Global Emergence of Carbapenemases Gopi Patel and Robert A. Bonomo 83 The Multifaceted Roles of Antibiotics and Antibiotic Resistance in Nature Saswati Sengupta, Madhab K. Chattopadhyay and Hans-Peter Grossart 96 Broad-Host-Range IncP-1 Plasmids and Their Resistance Potential Magdalena Popowska and Agata Krawczyk-Balska 104 RND Multidrug Efflux Pumps: What are they Good for? Carolina Alvarez-Ortega, Jorge Olivares and José L. Martínez 115 Extracellular DNA-Induced Antimicrobial Peptide Resistance Mechanisms in Pseudomonas Aeruginosa Shawn Lewenza 121 Concentration-Dependent Activity of Antibiotics in Natural Environments Steve P. Bernier and Michael G. Surette Frontiers in Microbiology April 2015 | The Multiple Roles of Antibiotics and Antibiotic Resistance in Nature | 3 EDITORIAL published: 27 August 2013 doi: 10.3389/fmicb.2013.00255 The multiple roles of antibiotics and antibiotic resistance in nature Fiona Walsh* Agroscope Changins Wädenswil, Wädenswil, Switzerland *Correspondence: fi[email protected] Edited by: Rustam I. Aminov, University of the West Indies, Jamaica Keywords: antibiotic resistance, environment, clinical pathogens, soil, plasmids, intrinsic factor There have been many calls for more information about the nat- and diversification of antibiotic resistance mechanisms, in partic- ural resistome and these have also highlighted the importance of ular using the β-lactamasesasmodels(Galán et al., 2013; Patel understanding the environmental resistome in the preservation of and Bonomo, 2013; Popowska and Krawczyk-Balska, 2013). The antibiotics for the treatment of infections. However, to date there β-lactamases constitute the most widespread mechanism of resis- have been few studies which have investigated the roles of antibi- tance, at least among pathogenic bacteria, with more than 1000 otics and resistances outside of the clinical environment. This lack enzymes identified in the literature. We present some examples of data also highlights the difficulties faced by microbiologists in of the alternative functions for the multi-drug resistance mecha- designingtheseexperimentstoproducemeaningfuldata.Antibiotics nisms of efflux, that range from bacterial interactions with plant and antibiotic resistance have most commonly been viewed in the or animal hosts, to the detoxification of metabolic intermediates context of human use and effects. However, both have co-existed in or the maintenance of cellular homeostasis and also the poten- nature for millennia. Recently the roles of antibiotics and antibiotic tial role of extracellular DNA in antibiotic resistance and virulence resistance genes have started to be discussed in terms of functions (Alvarez-Ortega et al., 2013). Bacterial responses to antibiotics other than bacterial inhibition and protection. This special topic may be concentration dependent and so we discuss the different has focused on both the traditional role of antibiotics as warfare types of interactions mediated by antibiotics