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Pereira AP, Antunes P, Peixe L, Freitas AR, Novais C. Current insights into the effects of cationic biocides exposure on Enterococcus spp. Front Microbiol 2024; 15:1392018. [PMID: 39006755 PMCID: PMC11242571 DOI: 10.3389/fmicb.2024.1392018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
Cationic biocides (CBs), such as quaternary ammonium compounds and biguanides, are critical for controlling the spread of bacterial pathogens like Enterococcus spp., a leading cause of multidrug-resistant healthcare-associated infections. The widespread use of CBs in recent decades has prompted concerns about the potential emergence of Enterococcus spp. populations exhibiting resistance to both biocides and antibiotics. Such concerns arise from their frequent exposure to subinhibitory concentrations of CBs in clinical, food chain and diverse environmental settings. This comprehensive narrative review aimed to explore the complexity of the Enterococcus' response to CBs and of their possible evolution toward resistance. To that end, CBs' activity against diverse Enterococcus spp. collections, the prevalence and roles of genes associated with decreased susceptibility to CBs, and the potential for co- and cross-resistance between CBs and antibiotics are reviewed. Significant methodological and knowledge gaps are identified, highlighting areas that future studies should address to enhance our comprehension of the impact of exposure to CBs on Enterococcus spp. populations' epidemiology. This knowledge is essential for developing effective One Health strategies that ensure the continued efficacy of these critical agents in safeguarding Public Health.
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Affiliation(s)
- Ana P Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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2
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Baig MIR, Kadu P, Bawane P, Nakhate KT, Yele S, Ojha S, Goyal SN. Mechanisms of emerging resistance associated with non-antibiotic antimicrobial agents: a state-of-the-art review. J Antibiot (Tokyo) 2023; 76:629-641. [PMID: 37605076 DOI: 10.1038/s41429-023-00649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/23/2023]
Abstract
Although the development of resistance by microorganisms to antimicrobial drugs has been recognized as a global public health concern, the contribution of various non-antibiotic antimicrobial agents to the development of antimicrobial resistance (AMR) remains largely neglected. The present review discusses various chemical substances and factors other than typical antibiotics, such as preservatives, disinfectants, biocides, heavy metals and improper chemical sterilization that contribute to the development of AMR. Furthermore, it encompasses the mechanisms like co-resistance and co-selection, horizontal gene transfer, changes in the composition and permeability of cell membrane, efflux pumps, transposons, biofilm formation and enzymatic degradation of antimicrobial chemicals which underlie the development of resistance to various non-antibiotic antimicrobial agents. In addition, the review addresses the resistance-associated changes that develops in microorganisms due to these agents, which ultimately contribute to the development of resistance to antibiotics. In order to prevent the indiscriminate use of chemical substances and create novel therapeutic agents to halt resistance development, a more holistic scientific approach might provide diversified views on crucial factors contributing to the persistence and spread of AMR. The review illustrates the common and less explored mechanisms contributing directly or indirectly to the development of AMR by non-antimicrobial agents that are commonly used.
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Affiliation(s)
- Mirza Ilyas Rahim Baig
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, Maharashtra, 400056, India
| | - Pramod Kadu
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, Maharashtra, 400056, India.
| | - Pradip Bawane
- Department of Pharmacognosy, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, 424001, India
| | - Kartik T Nakhate
- Department of Pharmacology, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, 424001, India
| | - Santosh Yele
- Department of Pharmacognosy, SVKM's NMIMS, School of Pharmacy & Technology Management, Hyderabad, 509301, India
| | - Shreesh Ojha
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Sameer N Goyal
- Department of Pharmacology, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, 424001, India
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James C, James SJ, Onarinde BA, Dixon RA, Williams N. A Critical Review of AMR Risks Arising as a Consequence of Using Biocides and Certain Metals in Food Animal Production. Antibiotics (Basel) 2023; 12:1569. [PMID: 37998771 PMCID: PMC10668721 DOI: 10.3390/antibiotics12111569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
The focus of this review was to assess what evidence exists on whether, and to what extent, the use of biocides (disinfectants and sanitizers) and certain metals (used in feed and other uses) in animal production (both land and aquatic) leads to the development and spread of AMR within the food chain. A comprehensive literature search identified 3434 publications, which after screening were reduced to 154 relevant publications from which some data were extracted to address the focus of the review. The review has shown that there is some evidence that biocides and metals used in food animal production may have an impact on the development of AMR. There is clear evidence that metals used in food animal production will persist, accumulate, and may impact on the development of AMR in primary animal and food production environments for many years. There is less evidence on the persistence and impact of biocides. There is also particularly little, if any, data on the impact of biocides/metal use in aquaculture on AMR. Although it is recognized that AMR from food animal production is a risk to human health there is not sufficient evidence to undertake an assessment of the impact of biocide or metal use on this risk and further focused in-field studies are needed provide the evidence required.
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Affiliation(s)
- Christian James
- Formerly Food Refrigeration & Process Engineering Research Centre (FRPERC), Grimsby Institute, Nuns Corner, Grimsby DN34 5BQ, UK;
- National Centre for Food Manufacturing (NCFM), University of Lincoln, South Lincolnshire Food Enterprise Zone, Peppermint Way, Holbeach PE12 7FJ, UK;
| | - Stephen J. James
- Formerly Food Refrigeration & Process Engineering Research Centre (FRPERC), Grimsby Institute, Nuns Corner, Grimsby DN34 5BQ, UK;
- National Centre for Food Manufacturing (NCFM), University of Lincoln, South Lincolnshire Food Enterprise Zone, Peppermint Way, Holbeach PE12 7FJ, UK;
| | - Bukola A. Onarinde
- National Centre for Food Manufacturing (NCFM), University of Lincoln, South Lincolnshire Food Enterprise Zone, Peppermint Way, Holbeach PE12 7FJ, UK;
| | - Ronald A. Dixon
- School of Life and Environmental Sciences, University of Lincoln, Lincoln LN6 7DL, UK;
| | - Nicola Williams
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK;
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Pereira AP, Antunes P, Bierge P, Willems RJL, Corander J, Coque TM, Pich OQ, Peixe L, Freitas AR, Novais C. Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions. Microbiol Spectr 2023; 11:e0232423. [PMID: 37737589 PMCID: PMC10581157 DOI: 10.1128/spectrum.02324-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/24/2023] [Indexed: 09/23/2023] Open
Abstract
Quaternary ammonium compounds (QACs) have been extensively used in the community, healthcare facilities, and food chain, in concentrations between 20 and 30,000 mg/L. Enterococcus faecalis and Enterococcus faecium are ubiquitous in these settings and are recognized as nosocomial pathogens worldwide, but QACs' activity against strains from diverse epidemiological and genomic backgrounds remained largely unexplored. We evaluated the role of Enterococcus isolates from different sources, years, and clonal lineages as hosts of QACs tolerance genes and their susceptibility to QACs in optimal, single-stress and cross-stress growth conditions. Only 1% of the Enterococcus isolates included in this study and 0.5% of publicly available Enterococcus genomes carried qacA/B, qacC, qacG, qacJ, qacZ, qrg, bcrABC or oqxAB genes, shared with >60 species of Bacillota, Pseudomonadota, Actinomycetota, or Spirochaetota. These genes were generally found within close proximity of antibiotics and/or metals resistance genes. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) of benzalkonium chloride (BC) and didecyldimethylammonium chloride ranged between 0.5 and 4 mg/L (microdilution: 37°C/20 h/pH = 7/aerobiosis) for 210 E. faecalis and E. faecium isolates (two isolates carrying qacZ). Modified growth conditions (e.g., 22°C/pH = 5) increased MICBC/MBCBC (maximum of eightfold and MBCBC = 16 mg/L) and changed bacterial growth kinetics under BC toward later stationary phases in both species, including in isolates without QACs tolerance genes. In conclusion, Enterococcus are susceptible to in-use QACs concentrations and rarely carry QACs tolerance genes. However, their potential gene exchange with different microbiota, the decreased susceptibility to QACs under specific environmental conditions, and the presence of subinhibitory QACs concentrations in various settings may contribute to the selection of particular strains and, thus, require a One Health strategy to maintain QACs effectiveness. IMPORTANCE Despite the increasing use of quaternary ammonium compounds (QACs), the susceptibility of pathogens to these antimicrobials remains largely unknown. Enterococcus faecium and Enterococcus faecalis are susceptible to in-use QACs concentrations and are not main hosts of QACs tolerance genes but participate in gene transfer pathways with diverse bacterial taxa exposed to these biocides. Moreover, QACs tolerance genes often share the same genetic contexts with antibiotics and/or metals resistance genes, raising concerns about potential co-selection events. E. faecium and E. faecalis showed increased tolerance to benzalkonium chloride under specific environmental conditions (22°C, pH = 5), suggesting that strains might be selected in settings where they occur along with subinhibitory QACs concentrations. Transcriptomic studies investigating the cellular mechanisms of Enterococcus adaptation to QACs tolerance, along with longitudinal metadata analysis of tolerant populations dynamics under the influence of diverse environmental factors, are essential and should be prioritized within a One Health strategy.
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Affiliation(s)
- Ana P. Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Paula Bierge
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Sabadell, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Teresa M. Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Oscar Q. Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Sabadell, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Luisa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL., Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - from the ESCMID Study Group on Food- and Water-borne Infections (EFWISG)
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA), Universitat Autònoma de Barcelona, Sabadell, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL., Gandra, Portugal
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Paul SS, Rama Rao SV, Hegde N, Williams NJ, Chatterjee RN, Raju MVLN, Reddy GN, Kumar V, Phani Kumar PS, Mallick S, Gargi M. Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes. Front Microbiol 2022; 13:905050. [PMID: 35783415 PMCID: PMC9244563 DOI: 10.3389/fmicb.2022.905050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial growth promoters (AGPs) are commonly used in broiler production. There is a huge societal concern around their use and their contribution to the proliferation of antimicrobial resistance (AMR) in food-producing animals and dissemination to humans or the environment. However, there is a paucity of comprehensive experimental data on their impact on poultry production and the AMR resistome. Here, we investigated the effect of five antimicrobial growth promoters (virginiamycin, chlortetracycline, bacitracin methyl disalicylate, lincomycin, and tylosin) used in the commercial broiler production in the Indian subcontinent and in the different parts of the world for three consecutive production cycles on performance variables and also the impact on gut bacteria, bacteriophage, and resistome profile using culture-independent approaches. There was no significant effect of AGPs on the cumulative growth or feed efficiency parameters at the end of the production cycles and cumulative mortality rates were also similar across groups. Many antibiotic resistance genes (ARGs) were ubiquitous in the chicken gut irrespective of AGP supplementation. In total, 62 ARGs from 15 antimicrobial classes were detected. Supplementation of AGPs influenced the selection of several classes of ARGs; however, this was not correlated necessarily with genes relevant to the AGP drug class; some AGPs favored the selection of ARGs related to antimicrobials not structurally related to the AGP. AGPs did not impact the gut bacterial community structure, including alpha or beta diversity significantly, with only 16-20 operational taxonomic units (OTUs) of bacteria being altered significantly. However, several AGPs significantly reduced the population density of some of the potential pathogenic genera of bacteria, such as Escherichia coli. Chlortetracycline increased the abundance of Escherichia phage, whereas other AGPs did not influence the abundance of bacteriophage significantly. Considering the evidence that AGPs used in poultry production can select for resistance to more than one class of antimicrobial resistance, and the fact that their effect on performance is not significant, their use needs to be reduced and there is a need to monitor the spread of ARGs in broiler chicken farms.
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Affiliation(s)
- Shyam Sundar Paul
- Poultry Nutrition Lab, ICAR-Directorate of Poultry Research, Poultry Nutrition, Indian Council of Agricultural Research, Hyderabad, India
| | - Savaram Venkata Rama Rao
- Poultry Nutrition Lab, ICAR-Directorate of Poultry Research, Poultry Nutrition, Indian Council of Agricultural Research, Hyderabad, India
| | - Nagendra Hegde
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Nicola J. Williams
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rudra Nath Chatterjee
- Director’s Lab, ICAR-Directorate of Poultry Research, Poultry Nutrition, Indian Council of Agricultural Research, Hyderabad, India
| | | | - Godumagadda Narender Reddy
- Poultry Nutrition Lab, ICAR-Directorate of Poultry Research, Poultry Nutrition, Indian Council of Agricultural Research, Hyderabad, India
| | - Vikas Kumar
- Poultry Nutrition Lab, ICAR-Directorate of Poultry Research, Poultry Nutrition, Indian Council of Agricultural Research, Hyderabad, India
| | - Prakki Santosh Phani Kumar
- Poultry Nutrition Lab, ICAR-Directorate of Poultry Research, Poultry Nutrition, Indian Council of Agricultural Research, Hyderabad, India
| | - Sathi Mallick
- National Institute of Animal Biotechnology, Hyderabad, India
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Brooks L, Narvekar U, McDonald A, Mullany P. Prevalence of antibiotic resistance genes in the oral cavity and mobile genetic elements that disseminate antimicrobial resistance: A systematic review. Mol Oral Microbiol 2022; 37:133-153. [DOI: 10.1111/omi.12375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Laura Brooks
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
| | - Unnati Narvekar
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
| | - Ailbhe McDonald
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
| | - Peter Mullany
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
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8
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Tansirichaiya S, Winje E, Wigand J, Al-Haroni M. Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome. BMC Oral Health 2022; 22:210. [PMID: 35624467 PMCID: PMC9137128 DOI: 10.1186/s12903-022-02209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
The human oral cavity is one of the hotspots harboring multiple mobile genetic elements (MGEs), which are segments of DNA that can move either within bacterial genomes or between bacterial cells that can facilitate the spreading of genetic materials, including antimicrobial resistance genes. It is, therefore, important to investigate genes associated with the MGEs as they have a high probability of dissemination within the bacterial population under selective pressure from human activities. As one-third of oral bacteria are not yet culturable in the laboratory condition, therefore, in this work, it is aimed to detect and identify the genetic contexts of MGEs in the oral cavity through an inverse PCR (IPCR)-based approach on the oral metagenomic. The human oral metagenome was extracted from saliva samples collected from healthy individuals in Tromsø, Norway. The extracted DNA was partially digested with the HindIII restriction enzyme and self-circularized by ligation. DNA primers targeting each MGE were designed to amplify outwards from the MGEs and used for the IPCR on the circularized DNA products. The IPCR amplicons were cloned into a pCR-XL-2-TOP vector, screened, and sequenced. Out of 40 IPCR amplicons, we confirmed and verified the genetic contexts of 11 samples amplified with primers targeting integron gene cassettes (GCs), IS431 composite transposons, and Tn916 conjugative transposons (tet(M) and xis-int). Novel integron GCs, MGEs, and variants of Tn916 conjugative transposons were identified, which is the first report using the IPCR technique to detect the genetic contexts of MGEs in the oral metagenomic DNA.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway
| | - Endre Winje
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Johannes Wigand
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, 9037, Tromsø, Norway.
- Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.
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9
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Wang H, Su X, Su J, Zhu Y, Ding K. Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau. J Environ Sci (China) 2022; 111:442-451. [PMID: 34949372 DOI: 10.1016/j.jes.2021.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 06/14/2023]
Abstract
With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.
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Affiliation(s)
- Hang Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming 650224, China; National Plateau Wetlands Research Center, Southwest Forestry University, Kunming 650224, China
| | - Xiaoxuan Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yongguan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Ding
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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10
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Fritsky IO, Sirenko VY, Shova S, Kucheriv OI, Gural'skiy IA. Crystal structure of 9-aminoacridinium chloride N, N-dimethylformamide monosolvate. Acta Crystallogr E Crystallogr Commun 2021; 77:1303-1306. [PMID: 34925903 PMCID: PMC8647755 DOI: 10.1107/s2056989021011816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022]
Abstract
9-Aminoacridinium chloride N,N-dimethylformamide monosolvate, C13H11N2
+Cl−·C3H7NO, crystallizes in the monoclinic space group P21/c. The salt was crystallized from N,N-dimethylformamide. The asymmetric unit consists of two C13H11N2
+Cl− formula units. The 9-aminoacridinium (9-AA) molecules are protonated with the proton on the N atom of the central ring. This N atom is connected to an N,N-dimethylformamide molecule by a hydrogen bond. The H atoms of the amino groups create short contacts with two chloride ions. The 9-AA cations in adjacent layers are oriented in an antiparallel manner. The molecules are linked via a network of multidirectional π–π interactions between the 9-AA rings, and the whole lattice is additionally stabilized by electrostatic interactions between ions.
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11
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Zhao W, Hong H, Yin J, Wu B, Zhao F, Zhang XX. Recovery of gut microbiota in mice exposed to tetracycline hydrochloride and their correlation with host metabolism. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1620-1631. [PMID: 33280056 DOI: 10.1007/s10646-020-02319-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Antibiotics can disturb the gut microbial community and host metabolism. However, their recovery after antibiotics exposure needs to be characterized, and the correlation between gut microbiota and host metabolism remains unclear. In this study, mice were exposed to 0.5, 1.5 and 10 g/L tetracycline hydrochloride (TET) for 2 weeks, then recovered without TET for another 2 weeks. The results showed that 2-week TET exposure changed microbial community and functions in the mouse gut, and increased abundance of antibiotic resistance genes (ARGs), especially in the 10 g/L TET group. After a 2-week recovery, these changes could only be recovered to the control level in the 0.5 g/L TET exposure group, except for ARGs. Besides gut microbiota, TET exposure also changed metabolic profiles in mouse urine. The 2-week recovery significantly reduced changes in metabolic profiles. Some altered metabolites were found to have a very high correlation with gut microbial community and functions, indicating that TET exposure might induce certain changes in urinary metabolic profiles by altering the gut microbiota. The results from this study suggest that the influences of low-level TET exposure are reversible, except for ARGs, which should be paid more attention. During the application of TET, their dosage should be effectively considered and controlled.
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Affiliation(s)
- Wei Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Hanlu Hong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Jinbao Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Fuzheng Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
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12
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Huang L, Ahmed S, Gu Y, Huang J, An B, Wu C, Zhou Y, Cheng G. The Effects of Natural Products and Environmental Conditions on Antimicrobial Resistance. Molecules 2021; 26:molecules26144277. [PMID: 34299552 PMCID: PMC8303546 DOI: 10.3390/molecules26144277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/11/2022] Open
Abstract
Due to the extensive application of antibiotics in medical and farming practices, the continued diversification and development of antimicrobial resistance (AMR) has attracted serious public concern. With the emergence of AMR and the failure to treat bacterial infections, it has led to an increased interest in searching for novel antibacterial substances such as natural antimicrobial substances, including microbial volatile compounds (MVCs), plant-derived compounds, and antimicrobial peptides. However, increasing observations have revealed that AMR is associated not only with the use of antibacterial substances but also with tolerance to heavy metals existing in nature and being used in agriculture practice. Additionally, bacteria respond to environmental stresses, e.g., nutrients, oxidative stress, envelope stress, by employing various adaptive strategies that contribute to the development of AMR and the survival of bacteria. Therefore, we need to elucidate thoroughly the factors and conditions affecting AMR to take comprehensive measures to control the development of AMR.
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Affiliation(s)
- Lulu Huang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China; (L.H.); (Y.G.); (J.H.); (B.A.); (C.W.)
| | - Saeed Ahmed
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan;
| | - Yufeng Gu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China; (L.H.); (Y.G.); (J.H.); (B.A.); (C.W.)
| | - Junhong Huang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China; (L.H.); (Y.G.); (J.H.); (B.A.); (C.W.)
| | - Boyu An
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China; (L.H.); (Y.G.); (J.H.); (B.A.); (C.W.)
| | - Cuirong Wu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China; (L.H.); (Y.G.); (J.H.); (B.A.); (C.W.)
| | - Yujie Zhou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China; (L.H.); (Y.G.); (J.H.); (B.A.); (C.W.)
- Correspondence:
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13
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Wang C, Hu R, Strong PJ, Zhuang W, Huang W, Luo Z, Yan Q, He Z, Shu L. Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124985. [PMID: 33421848 DOI: 10.1016/j.jhazmat.2020.124985] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Plants roots are colonised by soil bacteria that are known to be the reservoir of antibiotic resistance genes (ARGs). ARGs can transfer between these microorganisms and pathogens, but to what extent these ARGs and pathogens disseminate from soil into plant is poorly understood. Here, we examined a high-resolution resistome profile along the soil-root continuum of mangrove saplings using amplicon and metagenomic sequencing. Data revealed that 91.4% of total ARGs were shared across four root-associated compartments (endosphere, episphere, rhizosphere and unplanted soil). Rather than compartment-selective dynamics of microbiota, the resistome was disseminated in a continuous fashion along the soil-root continuum. Such dissemination was independent of underlying root-associated bacterial and fungal microbiota, but might be facilitated by a multiplicity of mobile genetic elements. As the multiple-drug resistant pathogens, Vibrio vulnificus, pathogenic Escherichia coli and Klebsiella pneumoniae consistently predominated across four compartments, indicating the potential dissemination of antibiotic pathogens along the soil-root continuum. Through deciphering the profile and dynamics of the root-associated resistome and pathogens, our study identified the soil-root continuum as an interconnected sink through which certain ARGs and pathogens can flow from soil into the plant.
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Affiliation(s)
- Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology, GPO Box 2432, 2 George St, Brisbane QLD 4001, Australia
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China.
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14
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Lunde TM, Hjerde E, Al-Haroni M. Prevalence, diversity and transferability of the Tn 916-Tn 1545 family ICE in oral streptococci. J Oral Microbiol 2021; 13:1896874. [PMID: 33796228 PMCID: PMC7971310 DOI: 10.1080/20002297.2021.1896874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: The Tn916-Tn1545 family of Integrative Conjugative Elements (ICE) are mobile genetic elements (MGEs) that play a role in the spread of antibiotic resistance genes. The Tn916 harbors the tetracycline resistance gene tet(M) and it has been reported in various bacterial species. The increase in the levels of tetracycline resistance among oral streptococci is of great concern primarily due to the abundance of these species in the oral cavity and their ability to act as reservoirs for antibiotic resistance genes.Methods: In the current study, we screened 100 Norwegian clinical oral streptococcal isolates for the presence and diversity of the Tn916-Tn1545 family. In addition, we investigated the transferability the elements, and the associated transfer frequencies.Results: We observed that 21 isolates harboured the Tn916-Tn1545 family and that two of these elements were the novel Tn6815 and Tn6816. The most prevalent member of the Tn916 -Tn1545 family observed in the Norwegian clinical oral streptococcal isolates was the wild type Tn916.Conclusion: The detection of other members of this family of ICE and varying transfer frequencies suggests high versatility of the Tn916 element in oral streptococci in Norway.
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Affiliation(s)
- Tracy Munthali Lunde
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø
| | - Erik Hjerde
- bCenter for Bioinformatics, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø
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15
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Tansirichaiya S, Moyo SJ, Al-Haroni M, Roberts AP. Capture of a novel, antibiotic resistance encoding, mobile genetic element from Escherichia coli using a new entrapment vector. J Appl Microbiol 2020; 130:832-842. [PMID: 32881179 DOI: 10.1111/jam.14837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
Abstract
AIMS Antimicrobial resistance genes (ARGs) are often associated with mobile genetic elements (MGEs), which facilitate their movement within and between bacterial populations. Detection of mobility is therefore important to understand the dynamics of MGE dissemination and their associated genes, especially in resistant clinical isolates that often have multiple ARGs associated with MGEs. Therefore, this study aimed to develop an entrapment vector to capture active MGEs and ARGs in clinical isolates of Escherichia coli. METHODS AND RESULTS We engineered an entrapment vector, called pBACpAK, to capture MGEs in clinical E. coli isolates. It contains a cI-tetA positive selection cartridge in which the cI gene encodes a repressor that inhibits the expression of tetA. Therefore, any disruption of cI, for example, by insertion of a MGE, will allow tetA to be expressed and result in a selectable tetracycline-resistant phenotype. The pBACpAK was introduced into clinical E. coli isolates and grown on tetracycline-containing agar to select for clones with the insertion of MGEs into the entrapment vector. Several insertion sequences were detected within pBACpAK, including IS26, IS903B and ISSbo1. A novel translocatable unit (TU), containing IS26 and dfrA8 was also captured, and dfrA8 was shown to confer trimethoprim resistance when it was cloned into E. coli DH5α. CONCLUSIONS The entrapment vector, pBACpAK was developed and shown to be able to capture MGEs and their associated ARGs from clinical E. coli isolates. We have captured, for the first time, a TU encoding antibiotic resistance. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first time that a TU and associated resistance gene has been captured from clinical E. coli isolates using an entrapment vector. The pBACpAK has the potential to be used not only as a tool to capture MGEs in clinical E. coli isolates, but also to study dynamics, frequency and potentiators of mobility for MGEs.
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Affiliation(s)
- S Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.,Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - S J Moyo
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - M Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.,Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway
| | - A P Roberts
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
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16
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Meng L, Wang J, Li X, Cui F. Insight into effect of high-level cephalexin on fate and driver mechanism of antibiotics resistance genes in antibiotic wastewater treatment system. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110739. [PMID: 32505047 DOI: 10.1016/j.ecoenv.2020.110739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
In the study, antibiotic resistance genes (ARGs) were examined in wastewater and sludge samples to explore the effect of cephalexin (CFX) on the spreading and removal of ARGs in the Expanded Granular Sludge Bed (EGSB) reactor treating antibiotics wastewater. The result showed that the addition of CFX in the wastewater affected the removal amount of β-lactam ARGs and other types ARGs. Besides, the addition of CFX in the wastewater had no obviously effect on total concentration of targeted ARGs in the sludge, but it was related to the accumulation of some typical ARGs. Based on gene cassette array libraries analysis, the diversity of gene cassettes carried by intI1 gene was increased by the addition of CFX in the wastewater. Furthermore, the co-occurrence patterns between ARGs and bacterial genus were also investigated. The results showed the CFX in the wastewater not only affected the number of potential host bacteria of ARGs, but also changed the types of potential host bacteria of ARGs. The correlation analysis of ARG in influent, effluent and sludge showed that, for blaCTX-M, sul2, qnrS and AmpC genes, their removal amount in EGSB reactor treating antibiotic wastewater system might be enhanced by reducing their concentration in the sludge.
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Affiliation(s)
- Lingwei Meng
- School of Civil Engineering and Architecture, Northeast Electric Power University, Jilin, 132012, China.
| | - Jichao Wang
- School of Civil Engineering and Architecture, Northeast Electric Power University, Jilin, 132012, China
| | - Xiangkun Li
- School of Civil and Transportation, Hebei University of Technology, Tianjin, 300401, China
| | - Fengguo Cui
- School of Civil Engineering and Architecture, Northeast Electric Power University, Jilin, 132012, China
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17
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The impact of metal pipe materials, corrosion products, and corrosion inhibitors on antibiotic resistance in drinking water distribution systems. Appl Microbiol Biotechnol 2020; 104:7673-7688. [DOI: 10.1007/s00253-020-10777-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 02/07/2023]
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18
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Detection of a Novel, and Likely Ancestral, Tn 916-Like Element from a Human Saliva Metagenomic Library. Genes (Basel) 2020; 11:genes11050548. [PMID: 32422869 PMCID: PMC7288454 DOI: 10.3390/genes11050548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 01/22/2023] Open
Abstract
Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.
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19
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Turner ME, Huynh K, Carney OV, Gross D, Carroll RK, Ahn SJ, Rice KC. Genomic instability of TnSMU2 contributes to Streptococcus mutans biofilm development and competence in a cidB mutant. Microbiologyopen 2019; 8:e934. [PMID: 31599128 PMCID: PMC6925190 DOI: 10.1002/mbo3.934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023] Open
Abstract
Streptococcus mutans is a key pathogenic bacterium in the oral cavity and a primary contributor to dental caries. The S. mutans Cid/Lrg system likely contributes to tolerating stresses encountered in this environment as cid and/or lrg mutants exhibit altered oxidative stress sensitivity, genetic competence, and biofilm phenotypes. It was recently noted that the cidB mutant had two stable colony morphologies: a “rough” phenotype (similar to wild type) and a “smooth” phenotype. In our previously published work, the cidB rough mutant exhibited increased sensitivity to oxidative stress, and RNAseq identified widespread transcriptomic changes in central carbon metabolism and oxidative stress response genes. In this current report, we conducted Illumina‐based genome resequencing of wild type, cidB rough, and cidB smooth mutants and compared their resistance to oxidative and acid stress, biofilm formation, and competence phenotypes. Both cidB mutants exhibited comparable aerobic growth inhibition on agar plates, during planktonic growth, and in the presence of 1 mM hydrogen peroxide. The cidB smooth mutant displayed a significant competence defect in BHI, which was rescuable by synthetic CSP. Both cidB mutants also displayed reduced XIP‐mediated competence, although this reduction was more pronounced in the cidB smooth mutant. Anaerobic biofilms of the cidB smooth mutant displayed increased propidium iodide staining, but corresponding biofilm CFU data suggest this phenotype is due to cell damage and not increased cell death. The cidB rough anaerobic biofilms showed altered structure relative to wild type (reduced biomass and average thickness) which correlated with decreased CFU counts. Sequencing data revealed that the cidB smooth mutant has a unique “loss of read coverage” of ~78 kb of DNA, corresponding to the genomic island TnSMU2 and genes flanking its 3′ end. It is therefore likely that the unique biofilm and competence phenotypes of the cidB smooth mutant are related to its genomic changes in this region.
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Affiliation(s)
- Matthew E Turner
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Khanh Huynh
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - O'neshia V Carney
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Dennis Gross
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, OH, USA
| | - Sang-Joon Ahn
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Kelly C Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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20
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Lunde TM, Roberts AP, Al-Haroni M. Determination of copy number and circularization ratio of Tn 916-Tn 1545 family of conjugative transposons in oral streptococci by droplet digital PCR. J Oral Microbiol 2018; 11:1552060. [PMID: 30598735 PMCID: PMC6292373 DOI: 10.1080/20002297.2018.1552060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 11/09/2022] Open
Abstract
Background: Tn916 and Tn1545 are paradigms of a large family of related, broad host range, conjugative transposons that are widely distributed in bacteria and contribute to the spread of antibiotic resistance genes (ARGs). Variation in the copy number (CN) of Tn916-Tn1545 elements and the circularization ratio (CR) may play an important role in propagation of ARGs carried by these elements. Objectives and Design: In this study, the CN and CR of Tn916-Tn1545 elements in oral streptococci were determined using droplet digital PCR (ddPCR). In addition, we investigated the influence of tetracycline on the CR of Tn916-Tn1545 elements. Results: The ddPCR assay designed in this study is a reliable way to rapidly determine CN and CR of Tn916-Tn1545 elements. Conclusions: Our data also suggest that Tn916-Tn1545 elements are generally stable without selective pressure in the clinical oral Streptococcus strains investigated in this study.
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Affiliation(s)
- Tracy Munthali Lunde
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Adam P Roberts
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
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21
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Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes. Microb Drug Resist 2018; 24:105-112. [DOI: 10.1089/mdr.2017.0105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Guo X, Pang W, Dou C, Yin D. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors. CHEMOSPHERE 2017; 175:21-27. [PMID: 28211331 DOI: 10.1016/j.chemosphere.2017.01.134] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures.
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Affiliation(s)
- Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Weihai Pang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Chunling Dou
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Muziasari WI, Pitkänen LK, Sørum H, Stedtfeld RD, Tiedje JM, Virta M. The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms. Front Microbiol 2017; 7:2137. [PMID: 28111573 PMCID: PMC5216021 DOI: 10.3389/fmicb.2016.02137] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022] Open
Abstract
Our previous studies showed that particular antibiotic resistance genes (ARGs) were enriched locally in sediments below fish farms in the Northern Baltic Sea, Finland, even when the selection pressure from antibiotics was negligible. We assumed that a constant influx of farmed fish feces could be the plausible source of the ARGs enriched in the farm sediments. In the present study, we analyzed the composition of the antibiotic resistome from the intestinal contents of 20 fish from the Baltic Sea farms. We used a high-throughput method, WaferGen qPCR array with 364 primer sets to detect and quantify ARGs, mobile genetic elements (MGE), and the 16S rRNA gene. Despite a considerably wide selection of qPCR primer sets, only 28 genes were detected in the intestinal contents. The detected genes were ARGs encoding resistance to sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(32), tetM, tetO, tetW], aminoglycoside (aadA1, aadA2), chloramphenicol (catA1), and efflux-pumps resistance genes (emrB, matA, mefA, msrA). The detected genes also included class 1 integron-associated genes (intI1, qacEΔ1) and transposases (tnpA). Importantly, most of the detected genes were the same genes enriched in the farm sediments. This preliminary study suggests that feces from farmed fish contribute to the ARG enrichment in farm sediments despite the lack of contemporaneous antibiotic treatments at the farms. We observed that the intestinal contents of individual farmed fish had their own resistome compositions. Our result also showed that the total relative abundances of transposases and tet genes were significantly correlated (p = 0.001, R2 = 0.71). In addition, we analyzed the mucosal skin and gill filament resistomes of the farmed fish but only one multidrug-efflux resistance gene (emrB) was detected. To our knowledge, this is the first study reporting the resistome of farmed fish using a culture-independent method. Determining the possible sources of ARGs, especially mobilized ARGs, is essential for controlling the occurrence and spread of ARGs at fish farming facilities and for lowering the risk of ARG spread from the farms to surrounding environments.
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Affiliation(s)
- Windi I Muziasari
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Leena K Pitkänen
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
| | - Henning Sørum
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences Oslo, Norway
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Center for Microbial Ecology, Michigan State University Michigan, MI, USA
| | - James M Tiedje
- Department of Civil and Environmental Engineering, Center for Microbial Ecology, Michigan State University Michigan, MI, USA
| | - Marko Virta
- Department of Food and Environmental Sciences, University of Helsinki Helsinki, Finland
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Tansirichaiya S, Mullany P, Roberts AP. PCR-based detection of composite transposons and translocatable units from oral metagenomic DNA. FEMS Microbiol Lett 2016; 363:fnw195. [PMID: 27521260 PMCID: PMC5024762 DOI: 10.1093/femsle/fnw195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 12/29/2022] Open
Abstract
A composite transposon is a mobile genetic element consisting of two insertion sequences (ISs) flanking a segment of cargo DNA often containing antibiotic resistance (AR) genes. Composite transposons can move as a discreet unit. There have been recently several reports on a novel mechanism of movement of an IS26-based composite transposon through the formation of a translocatable unit (TU), carrying the internal DNA segment of a composite transposon and one copy of a flanking IS. In this study, we determined the presence of composite transposons and TUs in human oral metagenomic DNA using PCR primers from common IS elements. Analysis of resulting amplicons showed four different IS1216 composite transposons and one IS257 composite transposon in our metagenomic sample. As our PCR strategy would also detect TUs, PCR was carried out to detect circular TUs predicted to originate from these composite transposons. We confirmed the presence of two novel TUs, one containing an experimentally proven antiseptic resistance gene and another containing a putative universal stress response protein (UspA) encoding gene. This is the first report of a PCR strategy to amplify the DNA segment on composite transposons and TUs in metagenomic DNA. This can be used to identify AR genes associated with a variety of mobile genetic elements from metagenomes. Using a PCR approach, we have detected composite transposons and TUs directly from human oral metagenomic DNA.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbial Diseases, University College London, Eastman Dental Institute, 256 Gray's Inn Road, London WC1×8LD, UK
| | - Peter Mullany
- Department of Microbial Diseases, University College London, Eastman Dental Institute, 256 Gray's Inn Road, London WC1×8LD, UK
| | - Adam P Roberts
- Department of Microbial Diseases, University College London, Eastman Dental Institute, 256 Gray's Inn Road, London WC1×8LD, UK
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Abstract
Antibiotic resistance is considered one of the greatest threats to global public health. Resistance is often conferred by the presence of antibiotic resistance genes (ARGs), which are readily found in the oral microbiome. In-depth genetic analyses of the oral microbiome through metagenomic techniques reveal a broad distribution of ARGs (including novel ARGs) in individuals not recently exposed to antibiotics, including humans in isolated indigenous populations. This has resulted in a paradigm shift from focusing on the carriage of antibiotic resistance in pathogenic bacteria to a broader concept of an oral resistome, which includes all resistance genes in the microbiome. Metagenomics is beginning to demonstrate the role of the oral resistome and horizontal gene transfer within and between commensals in the absence of selective pressure, such as an antibiotic. At the chairside, metagenomic data reinforce our need to adhere to current antibiotic guidelines to minimize the spread of resistance, as such data reveal the extent of ARGs without exposure to antimicrobials and the ecologic changes created in the oral microbiome by even a single dose of antibiotics. The aim of this review is to discuss the role of metagenomics in the investigation of the oral resistome, including the transmission of antibiotic resistance in the oral microbiome. Future perspectives, including clinical implications of the findings from metagenomic investigations of oral ARGs, are also considered.
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Xu L, Ouyang W, Qian Y, Su C, Su J, Chen H. High-throughput profiling of antibiotic resistance genes in drinking water treatment plants and distribution systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 213:119-126. [PMID: 26890482 DOI: 10.1016/j.envpol.2016.02.013] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/03/2016] [Accepted: 02/04/2016] [Indexed: 05/04/2023]
Abstract
Antibiotic resistance genes (ARGs) are present in surface water and often cannot be completely eliminated by drinking water treatment plants (DWTPs). Improper elimination of the ARG-harboring microorganisms contaminates the water supply and would lead to animal and human disease. Therefore, it is of utmost importance to determine the most effective ways by which DWTPs can eliminate ARGs. Here, we tested water samples from two DWTPs and distribution systems and detected the presence of 285 ARGs, 8 transposases, and intI-1 by utilizing high-throughput qPCR. The prevalence of ARGs differed in the two DWTPs, one of which employed conventional water treatments while the other had advanced treatment processes. The relative abundance of ARGs increased significantly after the treatment with biological activated carbon (BAC), raising the number of detected ARGs from 76 to 150. Furthermore, the final chlorination step enhanced the relative abundance of ARGs in the finished water generated from both DWTPs. The total enrichment of ARGs varied from 6.4-to 109.2-fold in tap water compared to finished water, among which beta-lactam resistance genes displayed the highest enrichment. Six transposase genes were detected in tap water samples, with the transposase gene TnpA-04 showing the greatest enrichment (up to 124.9-fold). We observed significant positive correlations between ARGs and mobile genetic elements (MGEs) during the distribution systems, indicating that transposases and intI-1 may contribute to antibiotic resistance in drinking water. To our knowledge, this is the first study to investigate the diversity and abundance of ARGs in drinking water treatment systems utilizing high-throughput qPCR techniques in China.
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Affiliation(s)
- Like Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiying Ouyang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyun Qian
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chao Su
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Yin J, Zhang XX, Wu B, Xian Q. Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:2125-2132. [PMID: 26423395 DOI: 10.1007/s10646-015-1540-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge.
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Affiliation(s)
- Jinbao Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China.
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China
| | - Qiming Xian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China.
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Co-Selection of Resistance to Antibiotics, Biocides and Heavy Metals, and Its Relevance to Foodborne Pathogens. Antibiotics (Basel) 2015; 4:567-604. [PMID: 27025641 PMCID: PMC4790313 DOI: 10.3390/antibiotics4040567] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 02/07/2023] Open
Abstract
Concerns have been raised in recent years regarding co-selection for antibiotic resistance among bacteria exposed to biocides used as disinfectants, antiseptics and preservatives, and to heavy metals (particularly copper and zinc) used as growth promoters and therapeutic agents for some livestock species. There is indeed experimental and observational evidence that exposure to these non-antibiotic antimicrobial agents can induce or select for bacterial adaptations that result in decreased susceptibility to one or more antibiotics. This may occur via cellular mechanisms that are protective across multiple classes of antimicrobial agents or by selection of genetic determinants for resistance to non-antibiotic agents that are linked to genes for antibiotic resistance. There may also be relevant effects of these antimicrobial agents on bacterial community structure and via non-specific mechanisms such as mobilization of genetic elements or mutagenesis. Notably, some co-selective adaptations have adverse effects on fitness in the absence of a continued selective pressure. The present review examines the evidence for the significance of these phenomena, particularly in respect of bacterial zoonotic agents that commonly occur in livestock and that may be transmitted, directly or via the food chain, to human populations.
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29
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Quaternary ammonium disinfectants: microbial adaptation, degradation and ecology. Curr Opin Biotechnol 2015; 33:296-304. [DOI: 10.1016/j.copbio.2015.03.018] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 03/22/2015] [Accepted: 03/26/2015] [Indexed: 11/18/2022]
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30
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Vandecandelaere I, Coenye T. Microbial composition and antibiotic resistance of biofilms recovered from endotracheal tubes of mechanically ventilated patients. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 830:137-55. [PMID: 25366226 DOI: 10.1007/978-3-319-11038-7_9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In critically ill patients, breathing is impaired and mechanical ventilation, using an endotracheal tube (ET) connected to a ventilator, is necessary. Although mechanical ventilation is a life-saving procedure, it is not without risk. Because of several reasons, a biofilm often forms at the distal end of the ET and this biofilm is a persistent source of bacteria which can infect the lungs, causing ventilator-associated pneumonia (VAP). There is a link between the microbial flora of ET biofilms and the microorganisms involved in the onset of VAP. Culture dependent and independent techniques were already used to identify the microbial flora of ET biofilms and also, the antibiotic resistance of microorganisms obtained from ET biofilms was determined. The ESKAPE pathogens play a dominant role in the onset of VAP and these organisms were frequently identified in ET biofilms. Also, antibiotic resistant microorganisms were frequently present in ET biofilms. Members of the normal oral flora were also identified in ET biofilms but it is thought that these organisms initiate ET biofilm formation and are not directly involved in the development of VAP.
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Affiliation(s)
- Ilse Vandecandelaere
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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31
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Kirchner M, Mafura M, Hunt T, Abu-Oun M, Nunez-Garcia J, Hu Y, Weile J, Coates A, Card R, Anjum MF. Antimicrobial resistance characteristics and fitness of Gram-negative fecal bacteria from volunteers treated with minocycline or amoxicillin. Front Microbiol 2014; 5:722. [PMID: 25566232 PMCID: PMC4269195 DOI: 10.3389/fmicb.2014.00722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/02/2014] [Indexed: 11/13/2022] Open
Abstract
A yearlong study was performed to examine the effect of antibiotic administration on the bacterial gut flora. Gram-negative facultative anaerobic bacteria were recovered from the feces of healthy adult volunteers administered amoxicillin, minocycline or placebo, and changes determined in antimicrobial resistance (AMR) gene carriage. Seventy percent of the 1039 facultative anaerobic isolates recovered were identified by MALDI-TOF as Escherichia coli. A microarray used to determine virulence and resistance gene carriage demonstrated that AMR genes were widespread in all administration groups, with the most common resistance genes being blaTEM, dfr, strB, tet(A), and tet(B). Following amoxicillin administration, an increase in the proportion of amoxicillin resistant E. coli and a three-fold increase in the levels of blaTEM gene carriage was observed, an effect not observed in the other two treatment groups. Detection of virulence genes, including stx1A, indicated not all E. coli were innocuous commensals. Approximately 150 E. coli collected from 6 participants were selected for pulse field gel electrophoresis (PFGE), and a subset used for characterisation of plasmids and Phenotypic Microarrays (PM). PFGE indicated some E. coli clones had persisted in volunteers for up to 1 year, while others were transient. Although there were no unique characteristics associated with plasmids from persistent or transient isolates, PM assays showed transient isolates had greater adaptability to a range of antiseptic biocides and tetracycline; characteristics which were lost in some, but not all persistent isolates. This study indicates healthy individuals carry bacteria harboring resistance to a variety of antibiotics and biocides in their intestinal tract. Antibiotic administration can have a temporary effect of selecting bacteria, showing co-resistance to multiple antibiotics, some of which can persist within the gut for up to 1 year.
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Affiliation(s)
- Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Muriel Mafura
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Theresa Hunt
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Manal Abu-Oun
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Javier Nunez-Garcia
- Specialist Scientific Services Department, Animal and Plant Health Agency Addlestone, UK
| | - Yanmin Hu
- Department of Medical Microbiology, Institute of Infection and Immunity, St. George's University of London London, UK
| | - Jan Weile
- Institute for Laboratory and Transfusion Medicine at the Heart and Diabetes Centre NRW, University Hospital of the Ruhr University Bochum, Germany
| | - Anthony Coates
- Department of Medical Microbiology, Institute of Infection and Immunity, St. George's University of London London, UK
| | - Roderick Card
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
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Santoro F, Vianna ME, Roberts AP. Variation on a theme; an overview of the Tn916/Tn1545 family of mobile genetic elements in the oral and nasopharyngeal streptococci. Front Microbiol 2014; 5:535. [PMID: 25368607 PMCID: PMC4202715 DOI: 10.3389/fmicb.2014.00535] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/25/2014] [Indexed: 11/17/2022] Open
Abstract
The oral and nasopharyngeal streptococci are a major part of the normal microbiota in humans. Most human associated streptococci are considered commensals, however, a small number of them are pathogenic, causing a wide range of diseases including oral infections such as dental caries and periodontitis and diseases at other body sites including sinusitis and endocarditis, and in the case of Streptococcus pneumoniae, meningitis. Both phenotypic and sequence based studies have shown that the human associated streptococci from the mouth and nasopharynx harbor a large number of antibiotic resistance genes and these are often located on mobile genetic elements (MGEs) known as conjugative transposons or integrative and conjugative elements of the Tn916/Tn1545 family. These MGEs are responsible for the spread of the resistance genes between streptococci and also between streptococci and other bacteria. In this review we describe the resistances conferred by, and the genetic variations between the many different Tn916-like elements found in recent studies of oral and nasopharyngeal streptococci and show that Tn916-like elements are important mediators of antibiotic resistance genes within this genus. We will also discuss the role of the oral environment and how this is conducive to the transfer of these elements and discuss the contribution of both transformation and conjugation on the transfer and evolution of these elements in different streptococci.
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Affiliation(s)
- Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of SienaSiena, Italy
| | - Morgana E. Vianna
- Unit of Endodontology, UCL Eastman Dental Institute, University College LondonLondon, UK
| | - Adam P. Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College LondonLondon, UK
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Roberts AP, Kreth J. The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome. Front Cell Infect Microbiol 2014; 4:124. [PMID: 25250243 PMCID: PMC4157583 DOI: 10.3389/fcimb.2014.00124] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/19/2014] [Indexed: 02/06/2023] Open
Abstract
The oral microbiome is composed of a multitude of different species of bacteria, each capable of occupying one or more of the many different niches found within the human oral cavity. This community exhibits many types of complex interactions which enable it to colonize and rapidly respond to changes in the environment in which they live. One of these interactions is the transfer, or acquisition, of DNA within this environment, either from co-resident bacterial species or from exogenous sources. Horizontal gene transfer in the oral cavity gives some of the resident bacteria the opportunity to sample a truly enormous metagenome affording them considerable adaptive potential which may be key to survival in such a varying environment. In this review the underlying mechanisms of HGT are discussed in relation to the oral microbiome with numerous examples described where the direct acquisition of exogenous DNA has contributed to the fitness of the bacterial host within the human oral cavity.
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Affiliation(s)
- Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London London, UK
| | - Jens Kreth
- Department of Microbiology and Immunology, College of Medicine, University of Oklahoma Health Sciences Center Oklahoma City, OK, USA
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34
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Synthesis and structural characterization of a cocrystal salt containing acriflavine and 3,5-dinitrobenzoic acid. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.02.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Ciric L, Brouwer MSM, Mullany P, Roberts AP. Minocycline resistance in an oral Streptococcus infantis isolate is encoded by tet(S) on a novel small, low copy number plasmid. FEMS Microbiol Lett 2014; 353:106-15. [PMID: 24605990 PMCID: PMC4237122 DOI: 10.1111/1574-6968.12410] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 11/29/2022] Open
Abstract
We have determined the genetic basis of minocycline resistance in a strain of Streptococcus infantis isolated from a healthy human oral cavity. We demonstrate that tet(S), identical to tet(S) found on the enterococcal conjugative transposon Tn6000, is responsible for the observed resistance. The gene is located on a small, low copy number plasmid and is flanked by IS1216 elements. The tet(S) gene is capable of excising from the plasmid together with one of the IS1216 elements. The plasmid contains a putative toxin/antitoxin system related to relBE. Deletion of the toxin, relE, did not result in plasmid instability but did increase the fitness of the mutant compared to the wild-type strain.
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Affiliation(s)
- Lena Ciric
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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36
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Seier-Petersen MA, Jasni A, Aarestrup FM, Vigre H, Mullany P, Roberts AP, Agersø Y. Effect of subinhibitory concentrations of four commonly used biocides on the conjugative transfer of Tn916 in Bacillus subtilis. J Antimicrob Chemother 2013; 69:343-8. [PMID: 24092655 PMCID: PMC3886932 DOI: 10.1093/jac/dkt370] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objectives Large amounts of biocides are used to reduce and control bacterial growth in the healthcare sector, food production and agriculture. This work explores the effect of subinhibitory concentrations of four commonly used biocides (ethanol, hydrogen peroxide, chlorhexidine digluconate and sodium hypochlorite) on the conjugative transposition of the mobile genetic element Tn916. Methods Conjugation assays were carried out between Bacillus subtilis strains. The donor containing Tn916 was pre-exposed to subinhibitory concentrations of each biocide for a defined length of time, which was determined by an analysis of the transcriptional response of the promoter upstream of tet(M) using β-glucuronidase reporter assays. Results Ethanol significantly (P = 0.01) increased the transfer of Tn916 by 5-fold, whereas hydrogen peroxide, chlorhexidine digluconate and sodium hypochlorite did not significantly affect the transfer frequency. Conclusions These results suggest that exposure to subinhibitory concentrations of ethanol may induce the transfer of Tn916-like elements and any resistance genes they contain.
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Affiliation(s)
- M A Seier-Petersen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Bertsch D, Uruty A, Anderegg J, Lacroix C, Perreten V, Meile L. Tn6198, a novel transposon containing the trimethoprim resistance gene dfrG embedded into a Tn916 element in Listeria monocytogenes. J Antimicrob Chemother 2013; 68:986-91. [DOI: 10.1093/jac/dks531] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Trzybiński D, Sikorski A. Solvent-bridged frameworks of hydrogen bonds in crystals of 9-aminoacridinium halides. CrystEngComm 2013. [DOI: 10.1039/c3ce41027g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shi P, Jia S, Zhang XX, Zhang T, Cheng S, Li A. Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water. WATER RESEARCH 2013; 47:111-20. [PMID: 23084468 DOI: 10.1016/j.watres.2012.09.046] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/03/2012] [Accepted: 09/22/2012] [Indexed: 05/21/2023]
Abstract
This study aimed to investigate the chlorination effects on microbial antibiotic resistance in a drinking water treatment plant. Biochemical identification, 16S rRNA gene cloning and metagenomic analysis consistently indicated that Proteobacteria were the main antibiotic resistant bacteria (ARB) dominating in the drinking water and chlorine disinfection greatly affected microbial community structure. After chlorination, higher proportion of the surviving bacteria was resistant to chloramphenicol, trimethoprim and cephalothin. Quantitative real-time PCRs revealed that sulI had the highest abundance among the antibiotic resistance genes (ARGs) detected in the drinking water, followed by tetA and tetG. Chlorination caused enrichment of ampC, aphA2, bla(TEM-1), tetA, tetG, ermA and ermB, but sulI was considerably removed (p < 0.05). Metagenomic analysis confirmed that drinking water chlorination could concentrate various ARGs, as well as of plasmids, insertion sequences and integrons involved in horizontal transfer of the ARGs. Water pipeline transportation tended to reduce the abundance of most ARGs, but various ARB and ARGs were still present in the tap water, which deserves more public health concerns. The results highlighted prevalence of ARB and ARGs in chlorinated drinking water and this study might be technologically useful for detecting the ARGs in water environments.
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Affiliation(s)
- Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046, China
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Aminian M, Nabatchian F, Vaisi-Raygani A, Torabi M. Mechanism of Coomassie Brilliant Blue G-250 binding to cetyltrimethylammonium bromide: an interference with the Bradford assay. Anal Biochem 2012; 434:287-91. [PMID: 23219565 DOI: 10.1016/j.ab.2012.11.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 11/25/2022]
Abstract
The Bradford protein assay is a popular method because of its rapidity, sensitivity, and relative specificity. This method is subject to some interference by nonprotein compounds. In this study, we describe the interference of cetyltrimethylammonium bromide (CTAB) with the Bradford assay. This interference is based on the interaction of Coomassie Brilliant Blue G-250 (CBB) with this cationic detergent. This study suggests that both electrostatic and hydrophobic interactions are involved in the interaction of CTAB and CBB. The anionic and neutral forms of CBB bind to CTAB by electrostatic attraction, which accelerates hydrophobic interactions of these CBB forms and the hydrophobic tail of CTAB. Consequently, the hydrophobic regions of the dominant free cationic form of CBB dye compete for the tail of CTAB with two other forms of the dye and gradually displace the primary hydrophobic interactions and rearrange the primary CBB-CTAB complex. This interaction of CTAB and CBB dye produces a primary 650-nm-absorbing complex that then gradually rearranges to a complex that shows an absorbance shoulder at 800-950 nm. This study conclusively shows a strong response of CBB to CTAB that causes a time-dependent and nearly additive interference with the Bradford assay. This study also may promote an application of CBB for CTAB quantification.
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Affiliation(s)
- Mahdi Aminian
- Department of Clinical Biochemistry, School of Medicine, Tehran, Iran.
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Katharios-Lanwermeyer S, Rakic-Martinez M, Elhanafi D, Ratani S, Tiedje JM, Kathariou S. Coselection of cadmium and benzalkonium chloride resistance in conjugative transfers from nonpathogenic Listeria spp. to other Listeriae. Appl Environ Microbiol 2012; 78:7549-56. [PMID: 22904051 PMCID: PMC3485730 DOI: 10.1128/aem.02245-12] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/09/2012] [Indexed: 11/20/2022] Open
Abstract
Resistance to the quaternary ammonium disinfectant benzalkonium chloride (BC) may be an important contributor to the ability of Listeria spp. to persist in the processing plant environment. Although a plasmid-borne disinfectant resistance cassette (bcrABC) has been identified in Listeria monocytogenes, horizontal transfer of these genes has not been characterized. Nonpathogenic Listeria spp. such as L. innocua and L. welshimeri are more common than L. monocytogenes in food processing environments and may contribute to the dissemination of disinfectant resistance genes in listeriae, including L. monocytogenes. In this study, we investigated conjugative transfer of resistance to BC and to cadmium from nonpathogenic Listeria spp. to other nonpathogenic listeriae, as well as to L. monocytogenes. BC-resistant L. welshimeri and L. innocua harboring bcrABC, along with the cadmium resistance determinant cadA2, were able to transfer resistance to other nonpathogenic listeriae as well as to L. monocytogenes of diverse serotypes, including strains from the 2011 cantaloupe outbreak. Transfer among nonpathogenic Listeria spp. was noticeably higher at 25°C than at 37°C, whereas acquisition of resistance by L. monocytogenes was equally efficient at 25 and 37°C. When the nonpathogenic donors were resistant to both BC and cadmium, acquisition of cadmium resistance was an effective surrogate for transfer of resistance to BC, suggesting coselection between these resistance attributes. The results suggest that nonpathogenic Listeria spp. may behave as reservoirs for disinfectant and heavy metal resistance genes for other listeriae, including the pathogenic species L. monocytogenes.
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Affiliation(s)
| | | | - D. Elhanafi
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina, USA
| | - S. Ratani
- Department of Food, Bioprocessing, and Nutrition Sciences
| | - J. M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - S. Kathariou
- Department of Food, Bioprocessing, and Nutrition Sciences
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Bryant J, Chewapreecha C, Bentley SD. Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences. Future Microbiol 2012; 7:1283-1296. [PMID: 23075447 PMCID: PMC3996552 DOI: 10.2217/fmb.12.108] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Evolution of bacterial pathogen populations has been detected in a variety of ways including phenotypic tests, such as metabolic activity, reaction to antisera and drug resistance and genotypic tests that measure variation in chromosome structure, repetitive loci and individual gene sequences. While informative, these methods only capture a small subset of the total variation and, therefore, have limited resolution. Advances in sequencing technologies have made it feasible to capture whole-genome sequence variation for each sample under study, providing the potential to detect all changes at all positions in the genome from single nucleotide changes to large-scale insertions and deletions. In this review, we focus on recent work that has applied this powerful new approach and summarize some of the advances that this has brought in our understanding of the details of how bacterial pathogens evolve.
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Affiliation(s)
- Josephine Bryant
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Claire Chewapreecha
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
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Amábile-Cuevas CF. Antibiotic resistance: from Darwin to Lederberg to Keynes. Microb Drug Resist 2012; 19:73-87. [PMID: 23046150 DOI: 10.1089/mdr.2012.0115] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The emergence and spread of antibiotic-resistant bacteria reflects both, a gradual, completely Darwinian evolution, which mostly yields slight decreases in antibiotic susceptibility, along with phenotypes that are not precisely characterized as "resistance"; and sudden changes, from full susceptibility to full resistance, which are driven by a vast array of horizontal gene transfer mechanisms. Antibiotics select for more than just antibiotic resistance (i.e., increased virulence and enhanced gene exchange abilities); and many non-antibiotic agents or conditions select for or maintain antibiotic resistance traits as a result of a complex network of underlying and often overlapping mechanisms. Thus, the development of new antibiotics and thoughtful, integrated anti-infective strategies is needed to address the immediate and long-term threat of antibiotic resistance. Since the biology of resistance is complex, these new drugs and strategies will not come from free-market forces, or from "incentives" for pharmaceutical companies.
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Warburton PJ, Ciric L, Lerner A, Seville LA, Roberts AP, Mullany P, Allan E. TetAB46, a predicted heterodimeric ABC transporter conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity. J Antimicrob Chemother 2012; 68:17-22. [PMID: 22941900 PMCID: PMC3522447 DOI: 10.1093/jac/dks351] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objectives To identify the genes responsible for tetracycline resistance in a strain of Streptococcus australis isolated from pooled saliva from healthy volunteers in France. S. australis is a viridans Streptococcus, originally isolated from the oral cavity of children in Australia, and subsequently reported in the lungs of cystic fibrosis patients and as a cause of invasive disease in an elderly patient. Methods Agar containing 2 mg/L tetracycline was used for the isolation of tetracycline-resistant organisms. A genomic library in Escherichia coli was used to isolate the tetracycline resistance determinant. In-frame deletions and chromosomal repair were used to confirm function. Antibiotic susceptibility was determined by agar dilution and disc diffusion assay. Results The tetracycline resistance determinant from S. australis FRStet12 was isolated from a genomic library in E. coli and DNA sequencing showed two open reading frames predicted to encode proteins with similarity to multidrug resistance-type ABC transporters. Both genes were required for tetracycline resistance (to both the naturally occurring and semi-synthetic tetracyclines) and they were designated tetAB(46). Conclusions This is the first report of a predicted ABC transporter conferring tetracycline resistance in a member of the oral microbiota.
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Affiliation(s)
- Philip J Warburton
- Research Department of Microbial Diseases, UCL Eastman Dental Institute, 256 Gray's Inn Road, University College London, London WC1X 8LD, UK
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Poza M, Gayoso C, Gómez MJ, Rumbo-Feal S, Tomás M, Aranda J, Fernández A, Bou G. Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing. PLoS One 2012; 7:e44105. [PMID: 22952889 PMCID: PMC3430676 DOI: 10.1371/journal.pone.0044105] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 07/30/2012] [Indexed: 02/01/2023] Open
Abstract
Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.
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Affiliation(s)
- Margarita Poza
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
| | - Carmen Gayoso
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
| | - Manuel J. Gómez
- Sequencing and Bioinformatics Department, Astrobiology Center INTA-CSIC, Madrid, Spain
| | - Soraya Rumbo-Feal
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
| | - María Tomás
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
| | - Jesús Aranda
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
| | - Ana Fernández
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
| | - Germán Bou
- Microbioloy Department, Biomedical Research Institute-University Hospital, A Coruña, Spain
- * E-mail:
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Tello A, Austin B, Telfer TC. Selective pressure of antibiotic pollution on bacteria of importance to public health. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:1100-6. [PMID: 22571927 PMCID: PMC3440082 DOI: 10.1289/ehp.1104650] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 04/16/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND Many bacteria of clinical importance survive and may grow in different environments. Antibiotic pollution may exert on them a selective pressure leading to an increase in the prevalence of resistance. OBJECTIVES In this study we sought to determine whether environmental concentrations of antibiotics and concentrations representing action limits used in environmental risk assessment may exert a selective pressure on clinically relevant bacteria in the environment. METHODS We used bacterial inhibition as an assessment end point to link antibiotic selective pressures to the prevalence of resistance in bacterial populations. Species sensitivity distributions were derived for three antibiotics by fitting log-logistic models to end points calculated from minimum inhibitory concentration (MIC) distributions based on worldwide data collated by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). To place bacteria represented in these distributions in a broader context, we performed a brief phylogenetic analysis. The potentially affected fraction of bacterial genera at measured environmental concentrations of antibiotics and environmental risk assessment action limits was used as a proxy for antibiotic selective pressure. Measured environmental concentrations and environmental risk assessment action limits were also directly compared to wild-type cut-off values. RESULTS The potentially affected fraction of bacterial genera estimated based on antibiotic concentrations measured in water environments is ≤ 7%. We estimated that measured environmental concentrations in river sediments, swine feces lagoons, liquid manure, and farmed soil inhibit wild-type populations in up to 60%, 92%, 100%, and 30% of bacterial genera, respectively. At concentrations used as action limits in environmental risk assessment, erythromycin and ciprofloxacin were estimated to inhibit wild-type populations in up to 25% and 76% of bacterial genera. CONCLUSIONS Measured environmental concentrations of antibiotics, as well as concentrations representing environmental risk assessment action limits, are high enough to exert a selective pressure on clinically relevant bacteria that may lead to an increase in the prevalence of resistance.
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Affiliation(s)
- Alfredo Tello
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.
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Corver J, Bakker D, Brouwer MSM, Harmanus C, Hensgens MP, Roberts AP, Lipman LJA, Kuijper EJ, van Leeuwen HC. Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164. BMC Microbiol 2012; 12:130. [PMID: 22747711 PMCID: PMC3485107 DOI: 10.1186/1471-2180-12-130] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/25/2012] [Indexed: 11/28/2022] Open
Abstract
Background Clostridium difficile is the main cause of antibiotic associated diarrhea. In the past decade, the number of C. difficile patients has increased dramatically, coinciding with the emergence of two PCR ribotypes 027 and 078. PCR ribotype 078 is also frequently found during C. difficile outbreaks in pigfarms. Previously, the genome of the PCR ribotype 078 strain M120, a human isolate, was described to contain a unique insert of 100 kilobases. Results Analysis of this insert revealed over 90 open reading frames, encoding proteins originating from transposons, phages and plasmids. The insert was shown to be a transposon (Tn6164), as evidenced by the presence of an excised and circularised molecule, containing the ligated 5’and 3’ends of the insert. Transfer of the element could not be shown through filter-mating experiments. Whole genome sequencing of PCR ribotype 078 strain 31618, isolated from a diarrheic piglet, showed that Tn6164 was not present in this strain. To test the prevalence of Tn6164, a collection of 231 Clostridium difficile PCR ribotype 078 isolates from human (n = 173) and porcine (n = 58) origin was tested for the presence of this element by PCR. The transposon was present in 9 human, tetracycline resistant isolates, originating from various countries in Europe, and none of the pig strains. Nine other strains, also tetracycline resistant human isolates, contained half of the transposon, suggesting multiple insertion steps yielding the full Tn6164. Other PCR ribotypes (n = 66) were all negative for the presence of the transposon. Multi locus variable tandem repeat analysis revealed genetic relatedness among transposon containing isolates. Although the element contained several potential antibiotic resistance genes, it did not yield a readily distinguishable phenotype. Conclusions Tn6164 is a newly described transposon, occurring sporadically in C. difficile PCR ribotype 078 strains. Although no transfer of the element could be shown, we hypothesize that the element could serve as a reservoir of antibiotic resistance genes for other bacteria. Further research is needed to investigate the transfer capabilities of the element and to substantiate the possible role of Tn6164 as a source of antibiotic resistance genes for other gut pathogens.
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Affiliation(s)
- Jeroen Corver
- Department of Medical Microbiology, Section Experimental Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
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Ciric L, Ellatif M, Sharma P, Patel R, Song X, Mullany P, Roberts AP. Tn916-like elements from human, oral, commensal streptococci possess a variety of antibiotic and antiseptic resistance genes. Int J Antimicrob Agents 2012; 39:360-1. [DOI: 10.1016/j.ijantimicag.2011.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 01/28/2023]
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Emergence of resistance to antibacterial agents: the role of quaternary ammonium compounds--a critical review. Int J Antimicrob Agents 2012; 39:381-9. [PMID: 22421329 DOI: 10.1016/j.ijantimicag.2012.01.011] [Citation(s) in RCA: 343] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/11/2022]
Abstract
Quaternary ammonium compounds (QACs) are widely distributed in hospitals, industry and cosmetics. Little attention has been focused on the potential impact of QACs on the emergence of antibiotic resistance in patients and the environment. To assess this issue, we conducted a literature review on QAC chemical structure, fields of application, mechanism of action, susceptibility testing, prevalence, and co- or cross-resistance to antibiotics. Special attention was paid to the effects of QACs on microflora; in particular, the issue of the potential of QACs for applying selective pressure on multiple-antibiotic-resistant organisms was raised. It was found that there is a lack of standardised procedures for interpreting susceptibility test results. QACs have different impacts on the minimum inhibitory concentrations of antibacterials depending on the antibacterial compound investigated, the resistance genes involved, the measuring methodology and the interpretative criteria. The unmet needs for adequate detection of reduced susceptibility to QACs and antibiotics include (i) a consensus definition for resistance, (ii) epidemiological cut-off values and (iii) clinical resistance breakpoints. This review advocates the design of international guidelines for QAC use.
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