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Manaia CM, Rocha J, Scaccia N, Marano R, Radu E, Biancullo F, Cerqueira F, Fortunato G, Iakovides IC, Zammit I, Kampouris I, Vaz-Moreira I, Nunes OC. Antibiotic resistance in wastewater treatment plants: Tackling the black box. ENVIRONMENT INTERNATIONAL 2018; 115:312-324. [PMID: 29626693 DOI: 10.1016/j.envint.2018.03.044] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/05/2018] [Accepted: 03/28/2018] [Indexed: 05/20/2023]
Abstract
Wastewater is among the most important reservoirs of antibiotic resistance in urban environments. The abundance of carbon sources and other nutrients, a variety of possible electron acceptors such as oxygen or nitrate, the presence of particles onto which bacteria can adsorb, or a fairly stable pH and temperature are examples of conditions favouring the remarkable diversity of microorganisms in this peculiar habitat. The wastewater microbiome brings together bacteria of environmental, human and animal origins, many harbouring antibiotic resistance genes (ARGs). Although numerous factors contribute, mostly in a complex interplay, for shaping this microbiome, the effect of specific potential selective pressures such as antimicrobial residues or metals, is supposedly determinant to dictate the fate of antibiotic resistant bacteria (ARB) and ARGs during wastewater treatment. This paper aims to enrich the discussion on the ecology of ARB&ARGs in urban wastewater treatment plants (UWTPs), intending to serve as a guide for wastewater engineers or other professionals, who may be interested in studying or optimizing the wastewater treatment for the removal of ARB&ARGs. Fitting this aim, the paper overviews and discusses: i) aspects of the complexity of the wastewater system and/or treatment that may affect the fate of ARB&ARGs; ii) methods that can be used to explore the resistome, meaning the whole ARB&ARGs, in wastewater habitats; and iii) some frequently asked questions for which are proposed addressing modes. The paper aims at contributing to explore how ARB&ARGs behave in UWTPs having in mind that each plant is a unique system that will probably need a specific procedure to maximize ARB&ARGs removal.
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Affiliation(s)
- Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal.
| | - Jaqueline Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Nazareno Scaccia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Roberto Marano
- Department of Agroecology and Plant Health, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel; Institute of Soil, Water, and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Elena Radu
- University of Technology Vienna, Institute for Water Quality and Resources Management, Karlsplatz 13/226, A-1040 Vienna, Austria; AGES - Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, A-1220 Vienna, Austria
| | - Francesco Biancullo
- Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Adventech-Advanced Environmental Technologies, Centro Empresarial e Tecnológico, Rua de Fundões 151, 3700-121 São João da Madeira, Portugal
| | - Francisco Cerqueira
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain
| | - Gianuário Fortunato
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Iakovos C Iakovides
- NIREAS-International Water Research Center and Department of Civil and Environmental Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Ian Zammit
- Department of Civil Engineering, University of Salerno, SP24a, 84084 Fisciano, SA, Italy
| | - Ioannis Kampouris
- Institute for Hydrobiology, Technische Universität Dresden, 01217 Dresden, Germany
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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252
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Filippitzi ME, Chantziaras I, Devreese M, Dewulf J. Probabilistic risk model to assess the potential for resistance selection following the use of anti-microbial medicated feed in pigs. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2018; 35:1266-1277. [DOI: 10.1080/19440049.2018.1461257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Maria Eleni Filippitzi
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Ilias Chantziaras
- Porcine Health Management Unit, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Mathias Devreese
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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253
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Hall JPJ, Brockhurst MA, Harrison E. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0424. [PMID: 29061896 DOI: 10.1098/rstb.2016.0424] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 12/26/2022] Open
Abstract
In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, Arthur Willis Environment Centre, University of Sheffield, 1 Maxfield Avenue, Sheffield S10 1AE, UK
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254
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Draft Genome Sequence of Mercury-Resistant Pseudomonas putida Strain DRA525. GENOME ANNOUNCEMENTS 2018; 6:6/18/e00370-18. [PMID: 29724843 PMCID: PMC5940961 DOI: 10.1128/genomea.00370-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome sequence of Pseudomonas putida strain DRA525, isolated from mercury-contaminated soil. This strain shows resistance to mercury and multiple antibiotics, and its genome sequence contains several gene sets known to confer resistance to heavy metals enzymatically and through multidrug efflux pumps.
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255
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Hanna N, Sun P, Sun Q, Li X, Yang X, Ji X, Zou H, Ottoson J, Nilsson LE, Berglund B, Dyar OJ, Tamhankar AJ, Stålsby Lundborg C. Presence of antibiotic residues in various environmental compartments of Shandong province in eastern China: Its potential for resistance development and ecological and human risk. ENVIRONMENT INTERNATIONAL 2018; 114:131-142. [PMID: 29501851 DOI: 10.1016/j.envint.2018.02.003] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 05/17/2023]
Abstract
OBJECTIVES To investigate the occurrence of antibiotic residues in different types of environmental samples including water samples in rural Shandong province, China. Further, to characterize the potential ecological risk for development of antibiotic resistance in the environment, and the potential direct human health risk of exposure to antibiotics via drinking water and vegetables. METHODS Environmental samples (n = 214) (river water, waste water, drinking water, sediments, manure, soil and edible parts of vegetables) were collected in twelve villages in Shandong province in eastern China. High performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was used to determine the concentration of antibiotic residues. The ratio of the measured environmental concentrations (MEC) to the predicted no-effect concentrations (PNEC) was used to evaluate the ecological risk (risk quotient, RQ) for development of antibiotic resistance. The potential risks to human health through exposure to antibiotics in drinking water were assessed by comparing measured environmental concentrations (MEC) and predicted no-effect concentration in drinking water (PNECDW), and in vegetables by comparing estimated daily intake (EDI) to ADI. RESULTS Sulfapyridine, sulfamethoxazole, ciprofloxacin, enrofloxacin, levofloxacin, norfloxacin, chloramphenicol, florfenicol, doxycycline, and metronidazole were detected at concentrations ranging between 0.3 and 3.9 ng/L in river water, 1.3 and 12.5 ng/L in waste water, 0.5 and 21.4 ng/L in drinking water, 0.31 and 1.21 μg/kg in river sediment, 0.82 and 1.91 μg/kg in pig manure, 0.1 and 11.68 μg/kg in outlet sediment, 0.5 and 2.5 μg/kg in soil, and 6.3 and 27.2 μg/kg in vegetables. The RQs for resistance development were >1 for enrofloxacin, levofloxacin, and ranged between 0.1 and 1 for ciprofloxacin. MECs/PNECDW ratios were <1 from exposure to antibiotics through drinking water for both adults and children. EDI/ADI ratios were <0.1 from exposure to antibiotics by vegetable consumption. CONCLUSIONS Antibiotic pollutants were ubiquitous in various environmental compartments of Shandong province of China. Risk estimates indicated a potential for the measured levels of enrofloxacin, levofloxacin and ciprofloxacin in waste water to pose an ecological risk for resistance selection, and further studies are needed to validate this finding. The investigated antibiotics did not appear to pose an appreciable direct human health risk from environmental exposure through drinking water or vegetables consumption. However, they might still pose a risk for resistance development.
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Affiliation(s)
- Nada Hanna
- Global Health-Health Systems and Policy: Medicines, Focusing Antibiotics, Department of Public Health Sciences, Karolinska Institutet, Tomtebodavägen 18 A, 171 77 Stockholm, Sweden
| | - Pan Sun
- Department of Environment and Health, School of Public Health, Shandong University, Jinan 250012, China
| | - Qiang Sun
- School of Health Care Management, Shandong University, Jinan 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Shandong University, Jinan 250012, China.
| | - Xiwei Yang
- Department of Environment and Health, School of Public Health, Shandong University, Jinan 250012, China
| | - Xiang Ji
- Department of Environment and Health, School of Public Health, Shandong University, Jinan 250012, China
| | - Huiyun Zou
- Department of Environment and Health, School of Public Health, Shandong University, Jinan 250012, China
| | - Jakob Ottoson
- National Food Agency, Department of Risk and Benefit Assessment, 751 26 Uppsala, Sweden
| | - Lennart E Nilsson
- Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Björn Berglund
- Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Oliver James Dyar
- Global Health-Health Systems and Policy: Medicines, Focusing Antibiotics, Department of Public Health Sciences, Karolinska Institutet, Tomtebodavägen 18 A, 171 77 Stockholm, Sweden
| | - Ashok J Tamhankar
- Global Health-Health Systems and Policy: Medicines, Focusing Antibiotics, Department of Public Health Sciences, Karolinska Institutet, Tomtebodavägen 18 A, 171 77 Stockholm, Sweden
| | - Cecilia Stålsby Lundborg
- Global Health-Health Systems and Policy: Medicines, Focusing Antibiotics, Department of Public Health Sciences, Karolinska Institutet, Tomtebodavägen 18 A, 171 77 Stockholm, Sweden
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256
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Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain. Antimicrob Agents Chemother 2018. [PMID: 29530862 PMCID: PMC5923176 DOI: 10.1128/aac.00209-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Antimicrobial resistance is a major health care problem, with the intensive use of heavy metals and biocides recently identified as a potential factor contributing to the aggravation of this situation. The present study investigated heavy metal susceptibility and genetic resistance determinants in Escherichia coli isolated from clinical urine samples from Sweden, Germany, and Spain. A total of 186 isolates were tested for their sodium arsenite, silver nitrate, and copper(II) sulfate MICs. In addition, 88 of these isolates were subjected to whole-genome sequencing for characterization of their genetic resistance determinants and epidemiology. For sodium arsenite, the isolates could be categorized into a resistant and a nonresistant group based on MIC values. Isolates of the resistant group exhibited the chromosomal ars operon and belonged to non-B2 phylogenetic groups; in contrast, within the B2 phylogroup, no ars operon was found, and the isolates were susceptible to sodium arsenite. Two isolates also harbored the silver/copper resistance determinant pco/sil, and they belonged to sequence types ST10 (phylogroup A) and ST295 (phylogroup C). The ST295 isolate had a silver nitrate MIC of ≥512 mg/liter and additionally produced extended-spectrum beta-lactamases. To our knowledge, this is the first study to describe the distribution of the arsenic resistance ars operon within phylogroups of E. coli strains isolated from patients with urinary tract infections. The arsenic resistance ars operon was present only in all non-B2 clades, which have previously been associated with the environment and commensalism in both humans and animals, while B2 clades lacked the ars operon.
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257
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Knöppel A, Knopp M, Albrecht LM, Lundin E, Lustig U, Näsvall J, Andersson DI. Genetic Adaptation to Growth Under Laboratory Conditions in Escherichia coli and Salmonella enterica. Front Microbiol 2018; 9:756. [PMID: 29755424 PMCID: PMC5933015 DOI: 10.3389/fmicb.2018.00756] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/04/2018] [Indexed: 11/16/2022] Open
Abstract
Experimental evolution under controlled laboratory conditions is becoming increasingly important to address various evolutionary questions, including, for example, the dynamics and mechanisms of genetic adaptation to different growth and stress conditions. In such experiments, mutations typically appear that increase the fitness under the conditions tested (medium adaptation), but that are not necessarily of interest for the specific research question. Here, we have identified mutations that appeared during serial passage of E. coli and S. enterica in four different and commonly used laboratory media and measured the relative competitive fitness and maximum growth rate of 111 genetically re-constituted strains, carrying different single and multiple mutations. Little overlap was found between the mutations that were selected in the two species and the different media, implying that adaptation occurs via different genetic pathways. Furthermore, we show that commonly occurring adaptive mutations can generate undesired genetic variation in a population and reduce the accuracy of competition experiments. However, by introducing media adaptation mutations with large effects into the parental strain that was used for the evolution experiment, the variation (standard deviation) was decreased 10-fold, and it was possible to measure fitness differences between two competitors as small as |s| < 0.001.
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Affiliation(s)
- Anna Knöppel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michael Knopp
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lisa M Albrecht
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Lundin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ulrika Lustig
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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258
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Evolution of high-level resistance during low-level antibiotic exposure. Nat Commun 2018; 9:1599. [PMID: 29686259 PMCID: PMC5913237 DOI: 10.1038/s41467-018-04059-1] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/29/2018] [Indexed: 12/13/2022] Open
Abstract
It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.
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259
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Wistrand-Yuen E, Knopp M, Hjort K, Koskiniemi S, Berg OG, Andersson DI. Evolution of high-level resistance during low-level antibiotic exposure. Nat Commun 2018; 9:1599. [PMID: 29686259 PMCID: PMC5913237 DOI: 10.1038/s41467-018-04059-1|] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.
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Affiliation(s)
- Erik Wistrand-Yuen
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden
| | - Michael Knopp
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, 75237, Uppsala, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Uppsala University, 75237, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden.
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260
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Cairns J, Ruokolainen L, Hultman J, Tamminen M, Virta M, Hiltunen T. Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Commun Biol 2018; 1:35. [PMID: 30271921 PMCID: PMC6123812 DOI: 10.1038/s42003-018-0041-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 03/28/2018] [Indexed: 01/20/2023] Open
Abstract
Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of predation. The strong effects of antibiotic treatment on community composition depend on the presence of predation and spatial structuring that have strong community effects on their own. Overall, we find plasmid transfer to diverse recipient taxa. Plasmid transfer is likely to occur to abundant strains, occurs to a higher number of strains in the presence of antibiotic, and also occurs to low-abundance strains in the presence of spatial structures. These results fill knowledge gaps concerning the effects of low antibiotic concentrations in complex ecological settings.
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Affiliation(s)
- Johannes Cairns
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Lasse Ruokolainen
- Department of Biosciences, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Manu Tamminen
- Department of Aquatic Ecology, Eawag, Dubendorf, 8600, Zurich, Switzerland.,Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Marko Virta
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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261
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Zhu YG, Gillings M, Simonet P, Stekel D, Banwart S, Penuelas J. Human dissemination of genes and microorganisms in Earth's Critical Zone. GLOBAL CHANGE BIOLOGY 2018; 24:1488-1499. [PMID: 29266645 DOI: 10.1111/gcb.14003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.
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Affiliation(s)
- Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Université de Lyon, Lyon, France
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Steven Banwart
- Department of Geography, The University of Sheffield, Sheffield, UK
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Barcelona, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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262
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Gustave CA, Tristan A, Martins-Simões P, Stegger M, Benito Y, Andersen PS, Bes M, Le Hir T, Diep BA, Uhlemann AC, Glaser P, Laurent F, Wirth T, Vandenesch F. Demographic fluctuation of community-acquired antibiotic-resistant Staphylococcus aureus lineages: potential role of flimsy antibiotic exposure. ISME JOURNAL 2018; 12:1879-1894. [PMID: 29599521 DOI: 10.1038/s41396-018-0110-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/03/2018] [Accepted: 03/12/2018] [Indexed: 01/28/2023]
Abstract
Community-acquired (CA)- as opposed to hospital acquired- methicillin-resistant Staphylococcus aureus (MRSA) lineages arose worldwide during the 1990s. To determine which factors, including selective antibiotic pressure, govern the expansion of two major lineages of CA-MRSA, namely "USA300" in Northern America and "European ST80" in North Africa, Europe and Middle-East, we explored virulence factor expression, and fitness levels with or without antibiotics. The sampled strains were collected in a temporal window representing various steps of the epidemics, reflecting predicted changes in effective population size as inferred from whole-genome analysis. In addition to slight variations in virulence factor expression and biofilm production that might influence the ecological niches of theses lineages, competitive fitness experiments revealed that the biological cost of resistance to methicillin, fusidic acid and fluoroquinolones is totally reversed in the presence of trace amount of antibiotics. Our results suggest that low-level antibiotics exposure in human and animal environments contributed to the expansion of both European ST80 and USA300 lineages in community settings. This surge was likely driven by antibiotic (ab)use promoting the accumulation of antibiotics as environmental pollutants. The current results provide a novel link between effective population size increase of a pathogen and a selective advantage conferred by antibiotic resistance.
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Affiliation(s)
- Claude-Alexandre Gustave
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Anne Tristan
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Patricia Martins-Simões
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Marc Stegger
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Yvonne Benito
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Paal Skytt Andersen
- Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, Frederiksberg, Denmark
| | - Michèle Bes
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Typhanie Le Hir
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Binh An Diep
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York City, NY, USA
| | - Philippe Glaser
- Institut Pasteur - APHP - Université Paris Sud, Unité Ecologie et Evolution de la Résistance aux Antibiotiques Paris, France, CNRS UMR3525, Paris, France
| | - Frédéric Laurent
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité (ISYEB - UMR 7205, CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France.,EPHE, PSL University, Paris, France
| | - François Vandenesch
- CIRI - Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France. .,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France.
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263
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Frost I, Smith WPJ, Mitri S, Millan AS, Davit Y, Osborne JM, Pitt-Francis JM, MacLean RC, Foster KR. Cooperation, competition and antibiotic resistance in bacterial colonies. ISME JOURNAL 2018; 12:1582-1593. [PMID: 29563570 DOI: 10.1038/s41396-018-0090-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/09/2018] [Accepted: 01/26/2018] [Indexed: 12/22/2022]
Abstract
Bacteria commonly live in dense and genetically diverse communities associated with surfaces. In these communities, competition for resources and space is intense, and yet we understand little of how this affects the spread of antibiotic-resistant strains. Here, we study interactions between antibiotic-resistant and susceptible strains using in vitro competition experiments in the opportunistic pathogen Pseudomonas aeruginosa and in silico simulations. Selection for intracellular resistance to streptomycin is very strong in colonies, such that resistance is favoured at very low antibiotic doses. In contrast, selection for extracellular resistance to carbenicillin is weak in colonies, and high doses of antibiotic are required to select for resistance. Manipulating the density and spatial structure of colonies reveals that this difference is partly explained by the fact that the local degradation of carbenicillin by β-lactamase-secreting cells protects neighbouring sensitive cells from carbenicillin. In addition, we discover a second unexpected effect: the inducible elongation of cells in response to carbenicillin allows sensitive cells to better compete for the rapidly growing colony edge. These combined effects mean that antibiotic treatment can select against antibiotic-resistant strains, raising the possibility of treatment regimes that suppress sensitive strains while limiting the rise of antibiotic resistance. We argue that the detailed study of bacterial interactions will be fundamental to understanding and overcoming antibiotic resistance.
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Affiliation(s)
- Isabel Frost
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.,Center for Disease Dynamics, Economics & Policy, New Delhi, 110020, India
| | - William P J Smith
- Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Sara Mitri
- Département de Microbiologie Fondamentale (DMF), Université de Lausanne, Lausanne, 1015, Switzerland
| | - Alvaro San Millan
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, 28034, Spain
| | - Yohan Davit
- Institut de Mécanique des Fluides de Toulouse (IMFT)-Université de Toulouse, CNRS-INPT-UPS, Toulouse, France
| | - James M Osborne
- School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Joe M Pitt-Francis
- Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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264
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Abstract
Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.
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265
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Modeling the Emergence of Antibiotic Resistance in the Environment: an Analytical Solution for the Minimum Selection Concentration. Antimicrob Agents Chemother 2018; 62:AAC.01686-17. [PMID: 29263062 DOI: 10.1128/aac.01686-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Environmental antibiotic risk management requires an understanding of how subinhibitory antibiotic concentrations contribute to the spread of resistance. We develop a simple model of competition between sensitive and resistant bacterial strains to predict the minimum selection concentration (MSC), the lowest level of antibiotic at which resistant bacteria are selected. We present an analytical solution for the MSC based on the routinely measured MIC, the selection coefficient (sc) that expresses fitness differences between strains, the intrinsic net growth rate, and the shape of the bacterial growth dose-response curve with antibiotic or metal exposure (the Hill coefficient [κ]). We calibrated the model by optimizing the Hill coefficient to fit previously reported experimental growth rate difference data. The model fit varied among nine compound-taxon combinations examined but predicted the experimentally observed MSC/MIC ratio well (R2 ≥ 0.95). The shape of the antibiotic response curve varied among compounds (0.7 ≤ κ ≤ 10.5), with the steepest curve being found for the aminoglycosides streptomycin and kanamycin. The model was sensitive to this antibiotic response curve shape and to the sc, indicating the importance of fitness differences between strains for determining the MSC. The MSC can be >1 order of magnitude lower than the MIC, typically by the factor scκ This study provides an initial quantitative depiction and a framework for a research agenda to examine the growing evidence of selection for resistant bacterial communities at low environmental antibiotic concentrations.
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266
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Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo. Antimicrob Agents Chemother 2018; 62:AAC.02091-17. [PMID: 29311089 DOI: 10.1128/aac.02091-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/29/2017] [Indexed: 12/21/2022] Open
Abstract
Although KPC enzymes are most common among carbapenemases produced by Enterobacter cloacae complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing E. cloacae complex isolates collected from three hospitals in central Tokyo using whole-genome sequencing. Seventy-one isolates were classified into several sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei ST78. Isolates of ST78 were divided into three clades by core-genome single nucleotide polymorphism (SNP)-based phylogenetic analysis. Whereas isolates of clade 3 were isolated from only one hospital, isolates of clade 1 and 2 were identified from multiple hospitals. Ten of 12 clade 1 isolates and 1 of 4 clade 2 isolates carried blaIMP-1 on IncHI2 plasmids, with high similarity of genetic structures. In addition, these plasmids shared backbone structures with IncHI2 plasmids carrying blaIMP reported from other countries of the Asia-Pacific region. All isolates of clade 3 except one carried blaIMP-1 in In1426 on IncW plasmids. An isolate of clade 3, which lacked IncW plasmids, carried blaIMP-1 in In1426 on an IncFIB plasmid. These observations suggest that IMP-producing E. cloacae complex isolates with a diversity of host genomic backgrounds have spread in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids toward this phenomenon.
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267
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Slipski CJ, Zhanel GG, Bay DC. Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae. J Membr Biol 2018; 251:15-33. [PMID: 29063140 PMCID: PMC5840245 DOI: 10.1007/s00232-017-9992-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/04/2017] [Indexed: 02/03/2023]
Abstract
Bacterial resistance to biocides used as antiseptics, dyes, and disinfectants is a growing concern in food preparation, agricultural, consumer manufacturing, and health care industries, particularly among Gram-negative Enterobacteriaceae, some of the most common community and healthcare-acquired bacterial pathogens. Biocide resistance is frequently associated with antimicrobial cross-resistance leading to reduced activity and efficacy of both antimicrobials and antiseptics. Multidrug resistant efflux pumps represent an important biocide resistance mechanism in Enterobacteriaceae. An assortment of structurally diverse efflux pumps frequently co-exist in these species and confer both unique and overlapping biocide and antimicrobial selectivity. TolC-dependent multicomponent systems that span both the plasma and outer membranes have been shown to confer clinically significant resistance to most antimicrobials including many biocides, however, a growing number of single component TolC-independent multidrug resistant efflux pumps are specifically associated with biocide resistance: small multidrug resistance (SMR), major facilitator superfamily (MFS), multidrug and toxin extruder (MATE), cation diffusion facilitator (CDF), and proteobacterial antimicrobial compound efflux (PACE) families. These efflux systems are a growing concern as they are rapidly spread between members of Enterobacteriaceae on conjugative plasmids and mobile genetic elements, emphasizing their importance to antimicrobial resistance. In this review, we will summarize the known biocide substrates of these efflux pumps, compare their structural relatedness, Enterobacteriaceae distribution, and significance. Knowledge gaps will be highlighted in an effort to unravel the role that these apparent "lone wolves" of the efflux-mediated resistome may offer.
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Affiliation(s)
- Carmine J Slipski
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
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268
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Amos GCA, Ploumakis S, Zhang L, Hawkey PM, Gaze WH, Wellington EMH. The widespread dissemination of integrons throughout bacterial communities in a riverine system. ISME JOURNAL 2018; 12:681-691. [PMID: 29374269 PMCID: PMC5864220 DOI: 10.1038/s41396-017-0030-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/01/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Anthropogenic inputs increase levels of antimicrobial resistance (AMR) in the environment, however, it is unknown how these inputs create this observed increase, and if anthropogenic sources impact AMR in environmental bacteria. The aim of this study was to characterise the role of waste water treatment plants (WWTPs) in the dissemination of class 1 integrons (CL1s) in the riverine environment. Using sample sites from upstream and downstream of a WWTP, we demonstrate through isolation and culture-independent analysis that WWTP effluent significantly increases both CL1 abundance and antibiotic resistance in the riverine environment. Characterisation of CL1-bearing isolates revealed that CL1s were distributed across a diverse range of bacteria, with identical complex genetic resistance determinants isolated from both human-associated and common environmental bacteria across connected sites. Over half of sequenced CL1s lacked the 3′-conserved sequence ('atypical’ CL1s); surprisingly, bacteria carrying atypical CL1s were on average resistant to more antibiotics than bacteria carrying 3′-CS CL1s. Quaternary ammonium compound (QAC) resistance genes were observed across 75% of sequenced CL1 gene cassette arrays. Chemical data analysis indicated high levels of boron (a detergent marker) downstream of the WWTP. Subsequent phenotypic screening of CL1-bearing isolates demonstrated that ~90% were resistant to QAC detergents, with in vitro experiments demonstrating that QACs could solely select for the transfer of clinical antibiotic resistance genes to a naive Escherichia coli recipient. In conclusion, this study highlights the significant impact of WWTPs on environmental AMR, and demonstrates the widespread carriage of clinically important resistance determinants by environmentally associated bacteria.
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Affiliation(s)
| | | | - Lihong Zhang
- School of Life Sciences, University of Warwick, Coventry, UK.,European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, UK
| | | | - William H Gaze
- School of Life Sciences, University of Warwick, Coventry, UK.,European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, UK
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269
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Washington MT, Moorman TB, Soupir ML, Shelley M, Morrow AJ. Monitoring tylosin and sulfamethazine in a tile-drained agricultural watershed using polar organic chemical integrative sampler (POCIS). THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:358-367. [PMID: 28854391 DOI: 10.1016/j.scitotenv.2017.08.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
This study evaluated the influence of temporal variation on the occurrence, fate, and transport of tylosin (TYL) and sulfamethazine (SMZ); antibiotics commonly used in swine production. Atrazine (ATZ) was used as a reference analyte to indicate the agricultural origin of the antibiotics. We also assessed the impact of season and hydrology on antibiotic concentrations. A reconnaissance study of the South Fork watershed of the Iowa River (SFIR), was conducted from 2013 to 2015. Tile drain effluent and surface water were monitored using polar organic integrative sampler (POCIS) technology. Approximately 169 animal feeding operations (AFOs) exist in SFIR, with 153 of them being swine facilities. All analytes were detected, and detection frequencies ranged from 69 to 100% showing the persistence in the watershed. Antibiotics were detected at a higher frequency using POCIS compared to grab samples. We observed statistically significant seasonal trends for SMZ and ATZ concentrations during growing and harvest seasons. Time weighted average (TWA) concentrations quantified from the POCIS were 1.87ngL-1 (SMZ), 0.30ngL-1 (TYL), and 754.2ngL-1 (ATZ) in the watershed. SMZ and TYL concentrations were lower than the minimum inhibitory concentrations (MIC) for E. coli. All analytes were detected in tile drain effluent, confirming tile drainage as a pathway for antibiotic transport. Our results identify the episodic occurrence of antibiotics, and highlights the importance identifying seasonal fate and occurrence of these analytes.
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Affiliation(s)
- Maurice T Washington
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1340 Elings Hall, 605 Bissell Road Ames, Iowa, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Boulevard Ames Iowa, 50011, USA.
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1340 Elings Hall, 605 Bissell Road Ames, Iowa, USA
| | - Mack Shelley
- Department of Political Science and Department of Statistics, 503 Ross Hall, Iowa State University, Ames, Iowa, USA
| | - Amy J Morrow
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Boulevard Ames Iowa, 50011, USA
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270
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Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev 2018; 42:4563583. [PMID: 29069382 PMCID: PMC5812547 DOI: 10.1093/femsre/fux053] [Citation(s) in RCA: 496] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/19/2017] [Indexed: 11/25/2022] Open
Abstract
Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans.
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Affiliation(s)
- Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
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271
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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272
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Hrenovic J, Ivankovic T, Ivekovic D, Repec S, Stipanicev D, Ganjto M. The fate of carbapenem-resistant bacteria in a wastewater treatment plant. WATER RESEARCH 2017; 126:232-239. [PMID: 28961491 DOI: 10.1016/j.watres.2017.09.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/11/2017] [Accepted: 09/02/2017] [Indexed: 06/07/2023]
Abstract
Wastewater treatment plants have been considered potential sources of antibiotic resistance gene exchange and release into the environment. The aim of our study was to quantify environmental and human-associated carbapenem-resistant bacterial populations (CRBPs) across wastewater treatment stages and correlate bacterial counts to physicochemical and other bacteriological parameters in order to see their behaviour in wastewater and sludge and their potential dissemination in the environment. Samples were taken from five sites (treatment stages) of the largest Croatian wastewater treatment plant (20 per site) over 10 months of monitoring. CRBPs were found at all wastewater treatment stages save for the lime-treated, stabilised sludge, which underlines the importance of effluent and digested sludge disinfection. Secondary sludge settling removed 99% of CRBP from the effluent, but the relative proportion of CRBP in the total bacterial count significantly increased in the effluent (0.0020%) and digested sludge (0.0019%) compared to the influent (0.0006%), indicating selection for resistant bacteria in these settings. CRBP counts did not correlate with measured carbapenem concentrations in wastewater, which suggests that antibiotic concentrations were not the reason for CRBP selection. Negative correlation between activated sludge retention time and CRBP indicated that their number could be reduced by increasing the retention time during secondary treatment. Despite the indications that WWTPs select for antibiotic-resistant bacteria, wastewater treatment is very efficient in reducing their absolute numbers, and proper effluent and sludge disinfection can significantly reduce dissemination of antibiotic-resistant bacteria into the environment.
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Affiliation(s)
- Jasna Hrenovic
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov Trg 6, 10000 Zagreb, Croatia
| | - Tomislav Ivankovic
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov Trg 6, 10000 Zagreb, Croatia.
| | - Damir Ivekovic
- University of Zagreb, Faculty of Food Technology and Biotechnology, Pierottijeva 6, Zagreb, Croatia
| | - Sinisa Repec
- Croatian Waters, Ulica Grada Vukovara 220, Zagreb, Croatia
| | | | - Marin Ganjto
- Zagreb Wastewater - Management and Operation Ltd., Culinecka Cesta 287, 10000 Zagreb, Croatia
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273
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Le Page G, Gunnarsson L, Snape J, Tyler CR. Integrating human and environmental health in antibiotic risk assessment: A critical analysis of protection goals, species sensitivity and antimicrobial resistance. ENVIRONMENT INTERNATIONAL 2017; 109:155-169. [PMID: 28964562 DOI: 10.1016/j.envint.2017.09.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/04/2017] [Accepted: 09/10/2017] [Indexed: 05/21/2023]
Abstract
Antibiotics are vital in the treatment of bacterial infectious diseases but when released into the environment they may impact non-target organisms that perform vital ecosystem services and enhance antimicrobial resistance development with significant consequences for human health. We evaluate whether the current environmental risk assessment regulatory guidance is protective of antibiotic impacts on the environment, protective of antimicrobial resistance, and propose science-based protection goals for antibiotic manufacturing discharges. A review and meta-analysis was conducted of aquatic ecotoxicity data for antibiotics and for minimum selective concentration data derived from clinically relevant bacteria. Relative species sensitivity was investigated applying general linear models, and predicted no effect concentrations were generated for toxicity to aquatic organisms and compared with predicted no effect concentrations for resistance development. Prokaryotes were most sensitive to antibiotics but the range of sensitivities spanned up to several orders of magnitude. We show reliance on one species of (cyano)bacteria and the 'activated sludge respiration inhibition test' is not sufficient to set protection levels for the environment. Individually, neither traditional aquatic predicted no effect concentrations nor predicted no effect concentrations suggested to safeguard for antimicrobial resistance, protect against environmental or human health effects (via antimicrobial resistance development). Including data from clinically relevant bacteria and also more species of environmentally relevant bacteria in the regulatory framework would help in defining safe discharge concentrations for antibiotics for patient use and manufacturing that would protect environmental and human health. It would also support ending unnecessary testing on metazoan species.
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Affiliation(s)
- Gareth Le Page
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Lina Gunnarsson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Jason Snape
- AstraZeneca, Global Environment, Alderley Park, Macclesfield, Cheshire SK10 4TF, UK; School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK.
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274
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Lopatkin AJ, Meredith HR, Srimani JK, Pfeiffer C, Durrett R, You L. Persistence and reversal of plasmid-mediated antibiotic resistance. Nat Commun 2017; 8:1689. [PMID: 29162798 PMCID: PMC5698434 DOI: 10.1038/s41467-017-01532-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/22/2017] [Indexed: 02/07/2023] Open
Abstract
In the absence of antibiotic-mediated selection, sensitive bacteria are expected to displace their resistant counterparts if resistance genes are costly. However, many resistance genes persist for long periods in the absence of antibiotics. Horizontal gene transfer (primarily conjugation) could explain this persistence, but it has been suggested that very high conjugation rates would be required. Here, we show that common conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics in Escherichia coli. The notion is applicable to nine plasmids from six major incompatibility groups and mixed populations carrying multiple plasmids. These results suggest that reducing antibiotic use alone is likely insufficient for reversing resistance. Therefore, combining conjugation inhibition and promoting plasmid loss would be an effective strategy to limit conjugation-assisted persistence of antibiotic resistance. It is unclear whether the transfer of plasmids carrying antibiotic resistance genes can explain their persistence when antibiotics are not present. Here, Lopatkin et al. show that conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics.
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Affiliation(s)
- Allison J Lopatkin
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Hannah R Meredith
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jaydeep K Srimani
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Connor Pfeiffer
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Rick Durrett
- Department of Mathematics, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
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275
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Alotaibi SMI, Ayibiekea A, Pedersen AF, Jakobsen L, Pinholt M, Gumpert H, Hammerum AM, Westh H, Ingmer H. Susceptibility of vancomycin-resistant and -sensitive Enterococcus faecium obtained from Danish hospitals to benzalkonium chloride, chlorhexidine and hydrogen peroxide biocides. J Med Microbiol 2017; 66:1744-1751. [PMID: 29134935 DOI: 10.1099/jmm.0.000642] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
PURPOSE In Danish hospitals, the number of infections caused by vancomycin-resistant Enterococcus faecium (VRE faecium) has dramatically increased in recent years. Hospital disinfectants are essential in eliminating pathogenic microorganisms, and reduced susceptibility may contribute to hospital-associated infections. We have addressed whether clinical VRE faecium display decreased biocide susceptibility when compared to vancomycin-sensitive Enterococcus faecium (VSE faecium) isolates. METHODOLOGY In total 12 VSE faecium and 37 VRE faecium isolates obtained from Danish hospitals over an extended time period were tested for susceptibility towards three commonly applied biocides, namely benzalkonium chloride, chlorhexidine and hydrogen peroxide. RESULTS For benzalkonium chloride, 89 % of VRE faecium strains had a minimal inhibitory concentration (MIC) of 8 mg l-1, whereas for VSE faecium, only 25 % of the strains had an MIC of 8 mg l-1. For chlorhexidine, the MIC of 95 % of VRE faecium strains was 4 mg l-1 or higher, while only 33 % of VSE faecium strains displayed MIC values at the same level. In contrast, both VRE and VSE faecium displayed equal susceptibility to hydrogen peroxide, but a higher minimal bactericidal concentration (MBC) was found for the former. The efflux activity was also assessed, and this was generally higher for the VRE faecium strains compared to VSE faecium. CONCLUSION VRE faecium from Danish hospitals demonstrated decreased susceptibility towards benzalkonium chloride and chlorhexidine compared to VSE faecium, where the use of chlorhexidine is particularly heavy in the hospital environment. These findings suggest that biocide tolerance may characterize VRE faecium isolated in Danish hospitals.
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Affiliation(s)
- Sulaiman M I Alotaibi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Foodborne Diseases Surveillance Center, Executive Department of Surveillance Centers & Crisis Management, Saudi Food & Drug Authority, Riyadh, Saudi Arabia
| | - Alafate Ayibiekea
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Annemette Frøling Pedersen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lotte Jakobsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Heidi Gumpert
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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276
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Heat Resistance Mediated by pLM58 Plasmid-Borne ClpL in Listeria monocytogenes. mSphere 2017; 2:mSphere00364-17. [PMID: 29104933 PMCID: PMC5663981 DOI: 10.1128/msphere.00364-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/24/2017] [Indexed: 01/15/2023] Open
Abstract
Listeria monocytogenes is a dangerous food pathogen causing the severe illness listeriosis that has a high mortality rate in immunocompromised individuals. Although destroyed by pasteurization, L. monocytogenes is among the most heat-resistant non-spore-forming bacteria. This poses a risk to food safety, as listeriosis is commonly associated with ready-to-eat foods that are consumed without thorough heating. However, L. monocytogenes strains differ in their ability to survive high temperatures, and comprehensive understanding of the genetic mechanisms underlying these differences is still limited. Whole-genome-sequence analysis and phenotypic characterization allowed us to identify a novel plasmid, designated pLM58, and a plasmid-borne ATP-dependent protease (ClpL), which mediated heat resistance in L. monocytogenes. As the first report on plasmid-mediated heat resistance in L. monocytogenes, our study sheds light on the accessory genetic mechanisms rendering certain L. monocytogenes strains particularly capable of surviving high temperatures—with plasmid-borne ClpL being a potential predictor of elevated heat resistance. Listeria monocytogenes is one of the most heat-resistant non-spore-forming food-borne pathogens and poses a notable risk to food safety, particularly when mild heat treatments are used in food processing and preparation. While general heat stress properties and response mechanisms of L. monocytogenes have been described, accessory mechanisms providing particular L. monocytogenes strains with the advantage of enhanced heat resistance are unknown. Here, we report plasmid-mediated heat resistance of L. monocytogenes for the first time. This resistance is mediated by the ATP-dependent protease ClpL. We tested the survival of two wild-type L. monocytogenes strains—both of serotype 1/2c, sequence type ST9, and high sequence identity—at high temperatures and compared their genome composition in order to identify genetic mechanisms involved in their heat survival phenotype. L. monocytogenes AT3E was more heat resistant (0.0 CFU/ml log10 reduction) than strain AL4E (1.4 CFU/ml log10 reduction) after heating at 55°C for 40 min. A prominent difference in the genome compositions of the two strains was a 58-kb plasmid (pLM58) harbored by the heat-resistant AT3E strain, suggesting plasmid-mediated heat resistance. Indeed, plasmid curing resulted in significantly decreased heat resistance (1.1 CFU/ml log10 reduction) at 55°C. pLM58 harbored a 2,115-bp open reading frame annotated as an ATP-dependent protease (ClpL)-encoding clpL gene. Introducing the clpL gene into a natively heat-sensitive L. monocytogenes strain (1.2 CFU/ml log10 reduction) significantly increased the heat resistance of the recipient strain (0.4 CFU/ml log10 reduction) at 55°C. Plasmid-borne ClpL is thus a potential predictor of elevated heat resistance in L. monocytogenes. IMPORTANCEListeria monocytogenes is a dangerous food pathogen causing the severe illness listeriosis that has a high mortality rate in immunocompromised individuals. Although destroyed by pasteurization, L. monocytogenes is among the most heat-resistant non-spore-forming bacteria. This poses a risk to food safety, as listeriosis is commonly associated with ready-to-eat foods that are consumed without thorough heating. However, L. monocytogenes strains differ in their ability to survive high temperatures, and comprehensive understanding of the genetic mechanisms underlying these differences is still limited. Whole-genome-sequence analysis and phenotypic characterization allowed us to identify a novel plasmid, designated pLM58, and a plasmid-borne ATP-dependent protease (ClpL), which mediated heat resistance in L. monocytogenes. As the first report on plasmid-mediated heat resistance in L. monocytogenes, our study sheds light on the accessory genetic mechanisms rendering certain L. monocytogenes strains particularly capable of surviving high temperatures—with plasmid-borne ClpL being a potential predictor of elevated heat resistance.
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277
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Kraemer SA, Böndel KB, Ness RW, Keightley PD, Colegrave N. Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii. Evolution 2017; 71:2918-2929. [PMID: 28884790 PMCID: PMC5765464 DOI: 10.1111/evo.13360] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 01/08/2023]
Abstract
Although all genetic variation ultimately stems from mutations, their properties are difficult to study directly. Here, we used multiple mutation accumulation (MA) lines derived from five genetic backgrounds of the green algae Chlamydomonas reinhardtii that have been previously subjected to whole genome sequencing to investigate the relationship between the number of spontaneous mutations and change in fitness from a nonevolved ancestor. MA lines were on average less fit than their ancestors and we detected a significantly negative correlation between the change in fitness and the total number of accumulated mutations in the genome. Likewise, the number of mutations located within coding regions significantly and negatively impacted MA line fitness. We used the fitness data to parameterize a maximum likelihood model to estimate discrete categories of mutational effects, and found that models containing one to two mutational effect categories (one neutral and one deleterious category) fitted the data best. However, the best‐fitting mutational effects models were highly dependent on the genetic background of the ancestral strain.
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Affiliation(s)
- Susanne A Kraemer
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| | - Katharina B Böndel
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| | - Robert W Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississuaga L5L1C6, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| | - Nick Colegrave
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
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278
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Garner E, Benitez R, von Wagoner E, Sawyer R, Schaberg E, Hession WC, Krometis LAH, Badgley BD, Pruden A. Stormwater loadings of antibiotic resistance genes in an urban stream. WATER RESEARCH 2017; 123:144-152. [PMID: 28662396 DOI: 10.1016/j.watres.2017.06.046] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/16/2017] [Accepted: 06/17/2017] [Indexed: 06/07/2023]
Abstract
Antibiotic resistance presents a critical public health challenge and the transmission of antibiotic resistance via environmental pathways continues to gain attention. Factors driving the spread of antibiotic resistance genes (ARGs) in surface water and sources of ARGs in urban stormwater have not been well-characterized. In this study, five ARGs (sul1, sul2, tet(O), tet(W), and erm(F)) were quantified throughout the duration of three storm runoff events in an urban inland stream. Storm loads of all five ARGs were significantly greater than during equivalent background periods. Neither fecal indicator bacteria measured (E. coli or enterococci) was significantly correlated with sul1, sul2, or erm(F), regardless of whether ARG concentration was absolute or normalized to 16S rRNA levels. Both E. coli and enterococci were correlated with the tetracycline resistance genes, tet(O) and tet(W). Next-generation shotgun metagenomic sequencing was conducted to more thoroughly characterize the resistome (i.e., full complement of ARGs) and profile the occurrence of all ARGs described in current databases in storm runoff in order to inform future watershed monitoring and management. Between 37 and 121 different ARGs were detected in each stream sample, though the ARG profiles differed among storms. This study establishes that storm-driven transport of ARGs comprises a considerable fraction of overall downstream loadings and broadly characterizes the urban stormwater resistome to identify potential marker ARGs indicative of impact.
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Affiliation(s)
- Emily Garner
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States.
| | - Romina Benitez
- Department of Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Emily von Wagoner
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Richard Sawyer
- Department of Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Erin Schaberg
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - W Cully Hession
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Leigh-Anne H Krometis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Brian D Badgley
- Department of Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
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279
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Peeters L, De Mulder T, Van Coillie E, Huygens J, Smet A, Daeseleire E, Dewulf J, Imberechts H, Butaye P, Haesebrouck F, Croubels S, Heyndrickx M, Rasschaert G. Selection and transfer of an IncI1-tet
(A) plasmid of Escherichia coli
in an ex vivo
model of the porcine caecum at doxycycline concentrations caused by crosscontaminated feed. J Appl Microbiol 2017; 123:1312-1320. [DOI: 10.1111/jam.13561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 07/18/2017] [Accepted: 08/04/2017] [Indexed: 11/29/2022]
Affiliation(s)
- L.E.J. Peeters
- Department of General Bacteriology; Veterinary and Agrochemical Research centre; Brussels Belgium
- Department of Pathology, Bacteriology and Avian Diseases; Ghent University; Merelbeke Belgium
| | - T. De Mulder
- Technology and Food Science Unit; Institute for Agricultural and Fisheries Research; Melle Belgium
| | - E. Van Coillie
- Technology and Food Science Unit; Institute for Agricultural and Fisheries Research; Melle Belgium
| | - J. Huygens
- Technology and Food Science Unit; Institute for Agricultural and Fisheries Research; Melle Belgium
| | - A. Smet
- Laboratory Experimental Medicine and Pediatrics; Faculty of Medicine and Health Sciences; University of Antwerp; Antwerp Belgium
| | - E. Daeseleire
- Technology and Food Science Unit; Institute for Agricultural and Fisheries Research; Melle Belgium
| | - J. Dewulf
- Veterinary Epidemiology Unit; Department of Reproduction; Obstetrics and Herd health; Ghent University; Merelbeke Belgium
| | - H. Imberechts
- Department of General Bacteriology; Veterinary and Agrochemical Research centre; Brussels Belgium
| | - P. Butaye
- Department of Pathology, Bacteriology and Avian Diseases; Ghent University; Merelbeke Belgium
- Department of Biosciences; Ross University School of Veterinary Medicine; St Kitts and Nevis West Indies
| | - F. Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases; Ghent University; Merelbeke Belgium
| | - S. Croubels
- Department of Pharmacology, Toxicology and Biochemistry; Ghent University; Merelbeke Belgium
| | - M. Heyndrickx
- Department of Pathology, Bacteriology and Avian Diseases; Ghent University; Merelbeke Belgium
- Technology and Food Science Unit; Institute for Agricultural and Fisheries Research; Melle Belgium
| | - G. Rasschaert
- Technology and Food Science Unit; Institute for Agricultural and Fisheries Research; Melle Belgium
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280
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Vibrio Pathogens: A Public Health Concern in Rural Water Resources in Sub-Saharan Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14101188. [PMID: 28991153 PMCID: PMC5664689 DOI: 10.3390/ijerph14101188] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 09/29/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Abstract
Members of the Vibrio genus are autochthonous inhabitants of aquatic environments and play vital roles in sustaining the aquatic milieu. The genus comprises about 100 species, which are mostly of marine or freshwater origin, and their classification is frequently updated due to the continuous discovery of novel species. The main route of transmission of Vibrio pathogens to man is through drinking of contaminated water and consumption inadequately cooked aquatic food products. In sub-Saharan Africa and much of the developing world, some rural dwellers use freshwater resources such as rivers for domestic activities, bathing, and cultural and religious purposes. This review describes the impact of inadequately treated sewage effluents on the receiving freshwater resources and the associated risk to the rural dwellers that depends on the water. Vibrio infections remain a threat to public health. In the last decade, Vibrio disease outbreaks have created alertness on the personal, economic, and public health uncertainties associated with the impact of contaminated water in the aquatic environment of sub-Saharan Africa. In this review, we carried out an overview of Vibrio pathogens in rural water resources in Sub-Saharan Africa and the implication of Vibrio pathogens on public health. Continuous monitoring of Vibrio pathogens among environmental freshwater and treated effluents is expected to help reduce the risk associated with the early detection of sources of infection, and also aid our understanding of the natural ecology and evolution of Vibrio pathogens.
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281
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Horizontal Dissemination of Antimicrobial Resistance Determinants in Multiple Salmonella Serotypes following Isolation from the Commercial Swine Operation Environment after Manure Application. Appl Environ Microbiol 2017; 83:AEM.01503-17. [PMID: 28802274 DOI: 10.1128/aem.01503-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farm environment after manure application on land. Manure and soil samples were collected on day 0 before and after manure application on six farms in North Carolina, and sequential soil samples were recollected on days 7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella, and their plasmid contents were further characterized. A total of 14 isolates including Salmonella enterica serotypes Johannesburg (n = 2), Ohio (n = 2), Rissen (n = 1), Typhimurium var5- (n = 5), Worthington (n = 3), and 4,12:i:- (n = 1), representing different farms, were selected for plasmid analysis. Antimicrobial susceptibility testing was done by broth microdilution against a panel of 14 antimicrobials on the 14 confirmed transconjugants after conjugation assays. The plasmids were isolated by modified alkaline lysis, and PCRs were performed on purified plasmid DNA to identify the AMR determinants and the plasmid replicon types. The plasmids were sequenced for further analysis and to compare profiles and create phylogenetic trees. A class 1 integron with an ANT(2″)-Ia-aadA2 cassette was detected in the 50-kb IncN plasmids identified in S Worthington isolates. We identified 100-kb and 90-kb IncI1 plasmids in S Johannesburg and S Rissen isolates carrying the blaCMY-2 and tet(A) genes, respectively. An identical 95-kb IncF plasmid was widely disseminated among the different serotypes and across different farms. Our study provides evidence on the importance of horizontal dissemination of resistance determinants through plasmids of multiple Salmonella serotypes distributed across commercial swine farms after manure application.IMPORTANCE The horizontal gene transfer of antimicrobial resistance (AMR) determinants located on plasmids is considered to be the main reason for the rapid proliferation and spread of drug resistance. The deposition of manure generated in swine production systems into the environment is identified as a potential source of AMR dissemination. In this study, AMR gene-carrying plasmids were detected in multiple Salmonella serotypes across different commercial swine farms in North Carolina. The plasmid profiles were characterized based on Salmonella serotype donors and incompatibility (Inc) groups. We found that different Inc plasmids showed evidence of AMR gene transfer in multiple Salmonella serotypes. We detected an identical 95-kb plasmid that was widely distributed across swine farms in North Carolina. These conjugable resistance plasmids were able to persist on land after swine manure application. Our study provides strong evidence of AMR determinant dissemination present in plasmids of multiple Salmonella serotypes in the environment after manure application.
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282
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Huseby DL, Pietsch F, Brandis G, Garoff L, Tegehall A, Hughes D. Mutation Supply and Relative Fitness Shape the Genotypes of Ciprofloxacin-Resistant Escherichia coli. Mol Biol Evol 2017; 34:1029-1039. [PMID: 28087782 PMCID: PMC5400412 DOI: 10.1093/molbev/msx052] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli. The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC. Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage. However, the evolutionary or functional significance of this high frequency resistance genotype is not fully understood. By combining experimental data and mathematical modeling, we addressed the reasons for the predominance of this specific genotype. The experimental data were used to model trajectories of mutational resistance evolution under different conditions of drug exposure and population bottlenecks. We identified the order in which specific mutations are selected in the clinical genotype, showed that the high frequency genotype could be selected over a range of drug selective pressures, and was strongly influenced by the relative fitness of alternative mutations and factors affecting mutation supply. Our data map for the first time the fitness landscape that constrains the evolutionary trajectories taken during the development of clinical resistance to ciprofloxacin and explain the predominance of the most frequently selected genotype. This study provides strong support for the use of in vitro competition assays as a tool to trace evolutionary trajectories, not only in the antibiotic resistance field.
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Affiliation(s)
- Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Franziska Pietsch
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Angelica Tegehall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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283
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Ge B, Domesle KJ, Yang Q, Young SR, Rice-Trujillo CL, Bodeis Jones SM, Gaines SA, Keller MW, Li X, Piñeiro SA, Whitney BM, Harbottle HC, Gilbert JM. Effects of low concentrations of erythromycin, penicillin, and virginiamycin on bacterial resistance development in vitro. Sci Rep 2017; 7:11017. [PMID: 28887450 PMCID: PMC5591201 DOI: 10.1038/s41598-017-09593-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/26/2017] [Indexed: 12/20/2022] Open
Abstract
Distillers grains are co-products of the corn ethanol industry widely used in animal feed. We examined the effects of erythromycin, penicillin, and virginiamycin at low concentrations reflective of those detected in distillers grains on bacterial resistance selection. At 0.1 µg/ml erythromycin, macrolide-resistant mutants were induced in one Campylobacter coli and one Enterococcus faecium strain, while these strains plus three additional C. coli, one additional E. faecium, and one C. jejuni also developed resistance when exposed to 0.25 µg/ml erythromycin. At 0.5 µg/ml erythromycin, a total of eight strains (four Campylobacter and four Enterococcus) obtained macrolide-resistant mutants, including two strains from each genus that were not selected at lower erythromycin concentrations. For penicillin, three of five E. faecium strains but none of five Enterococcus faecalis strains consistently developed resistance at all three selection concentrations. Virginiamycin at two M1:S1 ratios did not induce resistance development in four out of five E. faecium strains; however, increased resistance was observed in the fifth one under 0.25 and 0.5 µg/ml virginiamycin selections. Although not yet tested in vivo, these findings suggest a potential risk of stimulating bacterial resistance development in the animal gut when distillers grains containing certain antibiotic residues are used in animal feed.
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Affiliation(s)
- Beilei Ge
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA.
| | - Kelly J Domesle
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA
| | - Qianru Yang
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA
| | - Shenia R Young
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA
| | - Crystal L Rice-Trujillo
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA
| | - Sonya M Bodeis Jones
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA
| | - Stuart A Gaines
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology, Laurel, Maryland, 20708, USA
| | - Marla W Keller
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Surveillance and Compliance, Division of Animal Feeds, Rockville, Maryland, 20855, USA
| | - Xin Li
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Surveillance and Compliance, Division of Animal Feeds, Rockville, Maryland, 20855, USA
| | - Silvia A Piñeiro
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of New Animal Drug Evaluation, Division of Human Food Safety, Rockville, Maryland, 20855, USA
| | - Brooke M Whitney
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of New Animal Drug Evaluation, Division of Human Food Safety, Rockville, Maryland, 20855, USA
| | - Heather C Harbottle
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of New Animal Drug Evaluation, Division of Human Food Safety, Rockville, Maryland, 20855, USA
| | - Jeffrey M Gilbert
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of New Animal Drug Evaluation, Division of Human Food Safety, Rockville, Maryland, 20855, USA
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284
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Affiliation(s)
- Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
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285
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Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M. Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. Sci Rep 2017; 7:10392. [PMID: 28871175 PMCID: PMC5583386 DOI: 10.1038/s41598-017-10876-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.
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Affiliation(s)
- Lina Amlinger
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mirthe Hoekzema
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Magnus Lundgren
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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286
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Lupan I, Carpa R, Oltean A, Kelemen BS, Popescu O. Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania. Microbes Environ 2017; 32:219-225. [PMID: 28781345 PMCID: PMC5606691 DOI: 10.1264/jsme2.me17016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county. The resistance to sulfamethoxazole and tetracycline and some of their representative resistance genes: sul1, tet(O), and tet(W) were assessed in this study. The results obtained showed that bacteria resistant to sulphonamides were more abundant than those resistant to tetracycline. The concentration of bacteria with antibiotic resistance changed after the treatment, namely, bacteria resistant to sulfamethoxazole. The removal of all bacteria and antibiotic-resistant bacteria was 98–99% and the degree of removal of bacteria resistant to tetracycline was higher than the bacteria resistant to sulfamethoxazole compared to total bacteria. The wastewater treatment plant not only contributed to elevating ARG concentrations, it also enhanced the possibility of horizontal gene transfer (HGT) by increasing the abundance of the intI1 gene. Even though the treatment process reduced the concentration of bacteria by two orders of magnitude, the wastewater treatment plant in Cluj-Napoca contributed to an increase in antibiotic-resistant bacteria concentrations up to 10 km downstream of its discharge in Someşul Mic river.
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Affiliation(s)
- Iulia Lupan
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Rahela Carpa
- Babeş Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology
| | - Andreea Oltean
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Beatrice Simona Kelemen
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Octavian Popescu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
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287
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Sommer MOA, Munck C, Toft-Kehler RV, Andersson DI. Prediction of antibiotic resistance: time for a new preclinical paradigm? Nat Rev Microbiol 2017; 15:689-696. [DOI: 10.1038/nrmicro.2017.75] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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288
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Lind PA, Arvidsson L, Berg OG, Andersson DI. Variation in Mutational Robustness between Different Proteins and the Predictability of Fitness Effects. Mol Biol Evol 2017; 34:408-418. [PMID: 28025272 DOI: 10.1093/molbev/msw239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Random mutations in genes from disparate protein classes may have different distributions of fitness effects (DFEs) depending on different structural, functional, and evolutionary constraints. We measured the fitness effects of 156 single mutations in the genes encoding AraC (transcription factor), AraD (enzyme), and AraE (transporter) used for bacterial growth on l-arabinose. Despite their different molecular functions these genes all had bimodal DFEs with most mutations either being neutral or strongly deleterious, providing a general expectation for the DFE. This contrasts with the unimodal DFEs previously obtained for ribosomal protein genes where most mutations were slightly deleterious. Based on theoretical considerations, we suggest that the 33-fold higher average mutational robustness of ribosomal proteins is due to stronger selection for reduced costs of translational and transcriptional errors. Whereas the large majority of synonymous mutations were deleterious for ribosomal proteins genes, no fitness effects could be detected for the AraCDE genes. Four mutations in AraC and AraE increased fitness, suggesting that slightly advantageous mutations make up a significant fraction of the DFE, but that they often escape detection due to the limited sensitivity of commonly used fitness assays. We show that the fitness effects of amino acid substitutions can be predicted based on evolutionary conservation, but those weakly deleterious mutations are less reliably detected. This suggests that large-effect mutations and the fraction of highly deleterious mutations can be computationally predicted, but that experiments are required to characterize the DFE close to neutrality, where many mutations ultimately fixed in a population will occur.
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Affiliation(s)
- Peter A Lind
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Lars Arvidsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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289
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Antimicrobial resistance and its association with tolerance to heavy metals in agriculture production. Food Microbiol 2017; 64:23-32. [DOI: 10.1016/j.fm.2016.12.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 11/20/2022]
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290
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Bioremediation of Mercury by Vibrio fluvialis Screened from Industrial Effluents. BIOMED RESEARCH INTERNATIONAL 2017. [PMID: 28626761 PMCID: PMC5463146 DOI: 10.1155/2017/6509648] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Thirty-one mercury-resistant bacterial strains were isolated from the effluent discharge sites of the SIPCOT industrial area. Among them, only one strain (CASKS5) was selected for further investigation due to its high minimum inhibitory concentration of mercury and low antibiotic susceptibility. In accordance with 16S ribosomal RNA gene sequences, the strain CASKS5 was identified as Vibrio fluvialis. The mercury-removal capacity of V. fluvialis was analyzed at four different concentrations (100, 150, 200, and 250 μg/ml). Efficient bioremediation was observed at a level of 250 μg/ml with the removal of 60% of mercury ions. The interesting outcome of this study was that the strain V. fluvialis had a high bioremediation efficiency but had a low antibiotic resistance. Hence, V. fluvialis could be successfully used as a strain for the ecofriendly removal of mercury.
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291
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Poole K. At the Nexus of Antibiotics and Metals: The Impact of Cu and Zn on Antibiotic Activity and Resistance. Trends Microbiol 2017; 25:820-832. [PMID: 28526548 DOI: 10.1016/j.tim.2017.04.010] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 12/14/2022]
Abstract
Environmental influences on antibiotic activity and resistance can wreak havoc with in vivo antibiotic efficacy and, ultimately, antimicrobial chemotherapy. In nature, bacteria encounter a variety of metal ions, particularly copper (Cu) and zinc (Zn), as contaminants in soil and water, as feed additives in agriculture, as clinically-used antimicrobials, and as components of human antibacterial responses. Importantly, there is a growing body of evidence for Cu/Zn driving antibiotic resistance development in metal-exposed bacteria, owing to metal selection of genetic elements harbouring both metal and antibiotic resistance genes, and metal recruitment of antibiotic resistance mechanisms. Many classes of antibiotics also form complexes with metal cations, including Cu and Zn, and this can hinder (or enhance) antibiotic activity. This review highlights the ways in which Cu/Zn influence antibiotic resistance development and antibiotic activity, and in so doing impact in vivo antibiotic efficacy.
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Affiliation(s)
- Keith Poole
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada, K7L 3N6.
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292
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Östman M, Lindberg RH, Fick J, Björn E, Tysklind M. Screening of biocides, metals and antibiotics in Swedish sewage sludge and wastewater. WATER RESEARCH 2017; 115:318-328. [PMID: 28288311 DOI: 10.1016/j.watres.2017.03.011] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/04/2017] [Accepted: 03/04/2017] [Indexed: 06/06/2023]
Abstract
Incoming sewage water, treated effluent and digested sludge were collected from 11 Swedish sewage treatment plants (STPs) on 3 different days. Analytical protocols were established for a large number of compounds (47) with antimicrobial properties and the collected samples were then screened for the presence of these selected substances. Liquid chromatography tandem mass spectrometry (LC-MS/MS) and inductively coupled plasma mass spectrometry (ICP-MS) were used to analyse the samples. Thirty organic compounds and 10 metals were detected above their respective detection limit. Quaternary ammonium compounds were the most abundant substances in the particulate phases with levels up to 370 μg/g and benzotriazoles were the most common in the aqueous phases with levels up to 24 μg/L. Several compounds with no, or very limited, previously reported data were detected in this study, including chlorhexidine, hexadecylpyridinium chloride and 10-benzalkonium chloride. Some of these were both frequently detected (>60% detection frequency) and found in high levels (up to 19 μg/g d.w. sludge). This study gives a comprehensive overview of the presence in Swedish STPs of a number of antimicrobial substances, providing crucial information in designing relevant studies on potential microbial co- and cross resistance development between antibiotics, biocides, and metals in the sewage system.
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Affiliation(s)
- Marcus Östman
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden.
| | | | - Jerker Fick
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
| | - Mats Tysklind
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
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293
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Hall JPJ, Brockhurst MA, Dytham C, Harrison E. The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories? Plasmid 2017; 91:90-95. [PMID: 28461121 DOI: 10.1016/j.plasmid.2017.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 11/16/2022]
Abstract
Conjugative plasmids are widespread and play an important role in bacterial evolution by accelerating adaptation through horizontal gene transfer. However, explaining the long-term stability of plasmids remains challenging because segregational loss and the costs of plasmid carriage should drive the loss of plasmids though purifying selection. Theoretical and experimental studies suggest two key evolutionary routes to plasmid stability: First, the evolution of high conjugation rates would allow plasmids to survive through horizontal transmission as infectious agents, and second, compensatory evolution to ameliorate the cost of plasmid carriage can weaken purifying selection against plasmids. How these two evolutionary strategies for plasmid stability interact is unclear. Here, we summarise the literature on the evolution of plasmid stability and then use individual based modelling to investigate the evolutionary interplay between the evolution of plasmid conjugation rate and cost amelioration. We find that, individually, both strategies promote plasmid stability, and that they act together to increase the likelihood of plasmid survival. However, due to the inherent costs of increasing conjugation rate, particularly where conjugation is unlikely to be successful, our model predicts that amelioration is the more likely long-term solution to evolving stable bacteria-plasmid associations. Our model therefore suggests that bacteria-plasmid relationships should evolve towards lower plasmid costs that may forestall the evolution of highly conjugative, 'infectious' plasmids.
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Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Calvin Dytham
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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294
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Millar JA, Raghavan R. Accumulation and expression of multiple antibiotic resistance genes in Arcobacter cryaerophilus that thrives in sewage. PeerJ 2017; 5:e3269. [PMID: 28462059 PMCID: PMC5407278 DOI: 10.7717/peerj.3269] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/03/2017] [Indexed: 01/10/2023] Open
Abstract
We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also determined that a majority of ARGs was being expressed in sewage, suggestive of trace levels of antibiotics or other stresses that could act as a selective force that amplifies multidrug resistant bacteria in municipal sewage. Because all bacteria are not eliminated even after several rounds of wastewater treatment, ARGs in sewage could affect public health due to their potential to contaminate environmental water.
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Affiliation(s)
- Jess A Millar
- Biology Department, Portland State University, Portland, OR, United States
| | - Rahul Raghavan
- Biology Department, Portland State University, Portland, OR, United States
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295
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Abstract
Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding.
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296
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Baquero F, Valenzuela AS, Ripoll A, Turrientes MC, Morales E, Rodriguez-Baños M, Bustamante M, Vrijheid M, López-Espinosa MJ, Llop S, Marina LS, Jiménez-Zabala A, Moreno Bofarull A, Cantón R, Sunyer J, Coque TM, Baquero F. PHENOTYPIC COPPER RESISTANCE IN AEROBIC INTESTINAL BACTERIA FROM CHILDREN WITH DIFFERENT LEVELS OF COPPER-EXPOSURE. ACTA ACUST UNITED AC 2017. [DOI: 10.15436/2378-6841.17.1219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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297
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Stanborough T, Fegan N, Powell SM, Tamplin M, Chandry PS. Insight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium. Appl Environ Microbiol 2017; 83:e02786-16. [PMID: 27986732 PMCID: PMC5311415 DOI: 10.1128/aem.02786-16] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/14/2016] [Indexed: 01/16/2023] Open
Abstract
Brochothrix thermosphacta is a dominant but poorly studied meat spoilage organism. It is a close relative of the foodborne pathogen Listeria monocytogenes, and Brochothrix constitutes the second genus in the Listeriaceae family. Here, the genomes of 12 B. thermosphacta strains were sequenced, assembled into draft genomes, characterized, and compared with the genomes of Brochothrix campestris and L. monocytogenes Phenotypic properties including biogenic amine production and antibiotic and heavy metal susceptibilities were tested. Comparative genomic analyses revealed a high degree of similarity among the B. thermosphacta strains, with bacteriophage genes constituting a significant proportion of the accessory genome. Genes for the production of the malodorous compounds acetate, acetoin, butanediol, and fatty acids were found, as were stress response regulatory genes, which likely play important roles in the spoilage process. Amino acid decarboxylases were not identified in the genomes, and phenotypic testing confirmed their absence. Orthologs of Listeria virulence proteins involved in virulence regulation, intracellular survival, and surface protein anchoring were found; however, key virulence genes were absent. Analysis of antibiotic susceptibility showed that strains were sensitive to the four tested antibiotics, except for one tetracycline-resistant isolate with plasmid-mediated tetracycline resistance genes. Strains tolerated higher levels of copper and cobalt than of cadmium although not at concentrations high enough to categorize the strains as being resistant. This study provides insight into the Brochothrix genome, links previous phenotypic data and data provided here to the gene inventory, and identifies genes that may contribute to the persistence of this organism in the food chain.IMPORTANCE Despite increasing knowledge and advances in food preservation techniques, microbial spoilage of foods causes substantial losses, with negative social and economic consequences. To better control the contamination and microbial spoilage of foods, fundamental knowledge of the biology of key spoilage bacteria is crucial. As a common meat spoilage organism, B. thermosphacta contributes substantially to spoilage-associated losses. Nonetheless, this organism and particularly its genome remain largely unstudied. This study contributes to improving our knowledge of the Brochothrix genus. Spoilage-relevant pathways and genes that may play a role in the survival of this organism in a food processing environment were identified, linking previous phenotypic data and data provided here to the gene inventory of Brochothrix and establishing parallels to and differences from the closely related foodborne pathogen L. monocytogenes.
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Affiliation(s)
- Tamsyn Stanborough
- CSIRO Agriculture and Food, Werribee, Victoria, Australia
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Narelle Fegan
- CSIRO Agriculture and Food, Werribee, Victoria, Australia
| | - Shane M Powell
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Mark Tamplin
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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298
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Colombi E, Straub C, Künzel S, Templeton MD, McCann HC, Rainey PB. Evolution of copper resistance in the kiwifruit pathogenPseudomonas syringaepv.actinidiaethrough acquisition of integrative conjugative elements and plasmids. Environ Microbiol 2017; 19:819-832. [DOI: 10.1111/1462-2920.13662] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/02/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Elena Colombi
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
| | - Christina Straub
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology; Plön Germany
| | - Matthew D. Templeton
- Plant and Food Research; Auckland New Zealand
- School of Biological Sciences; University of Auckland; Auckland New Zealand
| | - Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
- South China Botanical Institute; Chinese Academy of Sciences; Guangzhou China
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University; Auckland New Zealand
- Max Planck Institute for Evolutionary Biology; Plön Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris-Tech), PSL Research University; Paris France
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299
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Hu HW, Wang JT, Li J, Shi XZ, Ma YB, Chen D, He JZ. Long-Term Nickel Contamination Increases the Occurrence of Antibiotic Resistance Genes in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:790-800. [PMID: 27977160 DOI: 10.1021/acs.est.6b03383] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heavy metal contamination is assumed to be a selection pressure on antibiotic resistance, but to our knowledge, evidence of the heavy metal-induced changes of antibiotic resistance is lacking on a long-term basis. Using quantitative PCR array and Illumina sequencing, we investigated the changes of a wide spectrum of soil antibiotic resistance genes (ARGs) following 4-5 year nickel exposure (0-800 mg kg-1) in two long-term experimental sites. A total of 149 unique ARGs were detected, with multidrug and β-lactam resistance as the most prevailing ARG types. The frequencies and abundance of ARGs tended to increase along the gradient of increasing nickel concentrations, with the highest values recorded in the treatments amended with 400 mg nickel kg-1 soil. The abundance of mobile genetic elements (MGEs) was significantly associated with ARGs, suggesting that nickel exposure might enhance the potential for horizontal transfer of ARGs. Network analysis demonstrated significant associations between ARGs and MGEs, with the integrase intI1 gene having the most frequent interactions with other co-occurring ARGs. The changes of ARGs were mainly driven by nickel bioavailability and MGEs as revealed by structural equation models. Taken together, long-term nickel exposure significantly increased the diversity, abundance, and horizontal transfer potential of soil ARGs.
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Affiliation(s)
- Hang-Wei Hu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
| | - Jing Li
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
| | - Xiu-Zhen Shi
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Yi-Bing Ma
- National Soil Fertility and Fertilizer Effects Long-term Monitoring Network, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences , Beijing 100081, China
| | - Deli Chen
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
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300
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Cairns J, Frickel J, Jalasvuori M, Hiltunen T, Becks L. Genomic evolution of bacterial populations under coselection by antibiotics and phage. Mol Ecol 2017; 26:1848-1859. [DOI: 10.1111/mec.13950] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/06/2016] [Accepted: 11/28/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Johannes Cairns
- Department of Food and Environmental Sciences / Microbiology and Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Jens Frickel
- Department of Evolutionary Ecology / Community Dynamics Group; Max Planck Institute for Evolutionary Biology; August Thienemann Street 2 24306 Plön Germany
| | - Matti Jalasvuori
- Department of Biological and Environmental Science / Centre of Excellence in Biological Interactions; University of Jyväskylä; P.O. Box 35 Jyväskylä 40014 Finland
| | - Teppo Hiltunen
- Department of Food and Environmental Sciences / Microbiology and Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Lutz Becks
- Department of Evolutionary Ecology / Community Dynamics Group; Max Planck Institute for Evolutionary Biology; August Thienemann Street 2 24306 Plön Germany
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