201
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Bello-Ortí B, Howell KJ, Tucker AW, Maskell DJ, Aragon V. Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection. Vet Res 2015; 46:102. [PMID: 26395877 PMCID: PMC4580352 DOI: 10.1186/s13567-015-0225-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/21/2015] [Indexed: 01/08/2023] Open
Abstract
Haemophilus parasuis is a common inhabitant of the upper respiratory tract of pigs, and the causative agent of Glässer’s disease. This disease is characterized by polyserositis and arthritis, produced by the severe inflammation caused by the systemic spread of the bacterium. After an initial colonization of the upper respiratory tract, H. parasuis enters the lung during the early stages of pig infection. In order to study gene expression at this location, we sequenced the ex vivo and in vivo H. parasuis Nagasaki transcriptome in the lung using a metatranscriptomic approach. Comparison of gene expression under these conditions with that found in conventional plate culture showed generally reduced expression of genes associated with anabolic and catabolic pathways, coupled with up-regulation of membrane-related genes involved in carbon acquisition, iron binding and pathogenesis. Some of the up-regulated membrane genes, including ABC transporters, virulence-associated autotransporters (vtaAs) and several hypothetical proteins, were only present in virulent H. parasuis strains, highlighting their significance as markers of disease potential. Finally, the analysis also revealed the presence of numerous antisense transcripts with possible roles in gene regulation. In summary, this data sheds some light on the scarcely studied in vivo transcriptome of H. parasuis, revealing nutritional virulence as an adaptive strategy for host survival, besides induction of classical virulence factors.
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Affiliation(s)
- Bernardo Bello-Ortí
- Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain.
| | - Kate J Howell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Virginia Aragon
- Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Cerdanyola del Vallès, Spain.
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202
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The ocean as a global reservoir of antibiotic resistance genes. Appl Environ Microbiol 2015; 81:7593-9. [PMID: 26296734 DOI: 10.1128/aem.00736-15] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 08/20/2015] [Indexed: 11/20/2022] Open
Abstract
Recent studies of natural environments have revealed vast genetic reservoirs of antibiotic resistance (AR) genes. Soil bacteria and human pathogens share AR genes, and AR genes have been discovered in a variety of habitats. However, there is little knowledge about the presence and diversity of AR genes in marine environments and which organisms host AR genes. To address this, we identified the diversity of genes conferring resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine in diverse marine environments using functional metagenomics (the cloning and screening of random DNA fragments). Marine environments were host to a diversity of AR-conferring genes. Antibiotic-resistant clones were found at all sites, with 28% of the genes identified as known AR genes (encoding beta-lactamases, bicyclomycin resistance pumps, etc.). However, the majority of AR genes were not previously classified as such but had products similar to proteins such as transport pumps, oxidoreductases, and hydrolases. Furthermore, 44% of the genes conferring antibiotic resistance were found in abundant marine taxa (e.g., Pelagibacter, Prochlorococcus, and Vibrio). Therefore, we uncovered a previously unknown diversity of genes that conferred an AR phenotype among marine environments, which makes the ocean a global reservoir of both clinically relevant and potentially novel AR genes.
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203
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Youenou B, Favre-Bonté S, Bodilis J, Brothier E, Dubost A, Muller D, Nazaret S. Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles. Genome Biol Evol 2015; 7:2484-505. [PMID: 26276674 PMCID: PMC4607518 DOI: 10.1093/gbe/evv161] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain's phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance-nodulation-division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.
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Affiliation(s)
- Benjamin Youenou
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sabine Favre-Bonté
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Josselin Bodilis
- EA4312 Laboratoire de Microbiologie Signaux et Microenvironnement, Université de Rouen, Mont-Saint-Aignan, France
| | - Elisabeth Brothier
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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204
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Di Cesare A, Eckert EM, Teruggi A, Fontaneto D, Bertoni R, Callieri C, Corno G. Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake. Mol Ecol 2015; 24:3888-900. [DOI: 10.1111/mec.13293] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Andrea Di Cesare
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
| | - Ester M. Eckert
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
| | - Alessia Teruggi
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
| | - Diego Fontaneto
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
| | - Roberto Bertoni
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
| | - Cristiana Callieri
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
| | - Gianluca Corno
- Microbial Ecology Group; National Research Council - Institute of Ecosystem Study (CNR-ISE); Largo Tonolli 50 28922 Verbania Italy
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205
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A function of SmeDEF, the major quinolone resistance determinant of Stenotrophomonas maltophilia, is the colonization of plant roots. Appl Environ Microbiol 2015; 80:4559-65. [PMID: 24837376 DOI: 10.1128/aem.01058-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Quinolones are synthetic antibiotics, and the main cause of resistance to these antimicrobials is mutation of the genes encoding their targets. However, in contrast to the case for other organisms, such mutations have not been found in quinolone-resistant Stenotrophomonas maltophilia isolates, in which overproduction of the SmeDEF efflux pump is a major cause of quinolone resistance. SmeDEF is chromosomally encoded and highly conserved in all studied S. maltophilia strains; it is an ancient element that evolved over millions of years in this species. It thus seems unlikely that its main function would be resistance to quinolones, a family of synthetic antibiotics not present in natural environments until the last few decades. Expression of SmeDEF is tightly controlled by the transcriptional repressor SmeT. Our work shows that plant-produced flavonoids can bind to SmeT, releasing it from smeDEF and smeT operators. Antibiotics extruded by SmeDEF do not impede the binding of SmeT to DNA. The fact that plant-produced flavonoids specifically induce smeDEF expression indicates that they are bona fide effectors regulating expression of this resistance determinant. Expression of efflux pumps is usually downregulated unless their activity is needed. Since smeDEF expression is triggered by plant-produced flavonoids, we reasoned that this efflux pump may have a role in the colonization of plants by S. maltophilia. Our results showed that, indeed, deletion of smeE impairs S. maltophilia colonization of plant roots. Altogether, our results indicate that quinolone resistance is a recent function of SmeDEF and that colonization of plant roots is likely one original function of this efflux pump.
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206
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Das S, Pettersson BMF, Behra PRK, Ramesh M, Dasgupta S, Bhattacharya A, Kirsebom LA. Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics. Genome Biol Evol 2015; 7:1871-86. [PMID: 26079817 PMCID: PMC4524478 DOI: 10.1093/gbe/evv111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.
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Affiliation(s)
- Sarbashis Das
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | | | | | - Malavika Ramesh
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Sweden
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207
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Kappell AD, DeNies MS, Ahuja NH, Ledeboer NA, Newton RJ, Hristova KR. Detection of multi-drug resistant Escherichia coli in the urban waterways of Milwaukee, WI. Front Microbiol 2015; 6:336. [PMID: 25972844 PMCID: PMC4413672 DOI: 10.3389/fmicb.2015.00336] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/05/2015] [Indexed: 11/13/2022] Open
Abstract
Urban waterways represent a natural reservoir of antibiotic resistance which may provide a source of transferable genetic elements to human commensal bacteria and pathogens. The objective of this study was to evaluate antibiotic resistance of Escherichia coli isolated from the urban waterways of Milwaukee, WI compared to those from Milwaukee sewage and a clinical setting in Milwaukee. Antibiotics covering 10 different families were utilized to determine the phenotypic antibiotic resistance for all 259 E. coli isolates. All obtained isolates were determined to be multi-drug resistant. The E. coli isolates were also screened for the presence of the genetic determinants of resistance including ermB (macrolide resistance), tet(M) (tetracycline resistance), and β-lactamases (bla OXA, bla SHV, and bla PSE). E. coli from urban waterways showed a greater incidence of antibiotic resistance to 8 of 17 antibiotics tested compared to human derived sources. These E. coli isolates also demonstrated a greater incidence of resistance to higher numbers of antibiotics compared to the human derived isolates. The urban waterways demonstrated a greater abundance of isolates with co-occurrence of antibiotic resistance than human derived sources. When screened for five different antibiotic resistance genes conferring macrolide, tetracycline, and β-lactam resistance, clinical E. coli isolates were more likely to harbor ermB and bla OXA than isolates from urban waterway. These results indicate that Milwaukee's urban waterways may select or allow for a greater incidence of multiple antibiotic resistance organisms and likely harbor a different antibiotic resistance gene pool than clinical sources. The implications of this study are significant to understanding the presence of resistance in urban freshwater environments by supporting the idea that sediment from urban waterways serves as a reservoir of antibiotic resistance.
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Affiliation(s)
- Anthony D Kappell
- Department of Biological Sciences, Marquette University Milwaukee, WI, USA
| | - Maxwell S DeNies
- Department of Biological Sciences, Marquette University Milwaukee, WI, USA
| | - Neha H Ahuja
- Department of Biological Sciences, Marquette University Milwaukee, WI, USA
| | - Nathan A Ledeboer
- Department of Pathology, Medical College of Wisconsin Milwaukee, WI, USA ; Dynacare Laboratories, Milwaukee WI, USA
| | - Ryan J Newton
- School of Freshwater Sciences, Great Lakes WATER Institute, University of Wisconsin-Milwaukee Milwaukee, WI, USA
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208
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Venter H, Mowla R, Ohene-Agyei T, Ma S. RND-type drug efflux pumps from Gram-negative bacteria: molecular mechanism and inhibition. Front Microbiol 2015; 6:377. [PMID: 25972857 PMCID: PMC4412071 DOI: 10.3389/fmicb.2015.00377] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/12/2015] [Indexed: 11/13/2022] Open
Abstract
Drug efflux protein complexes confer multidrug resistance on bacteria by transporting a wide spectrum of structurally diverse antibiotics. Moreover, organisms can only acquire resistance in the presence of an active efflux pump. The substrate range of drug efflux pumps is not limited to antibiotics, but it also includes toxins, dyes, detergents, lipids, and molecules involved in quorum sensing; hence efflux pumps are also associated with virulence and biofilm formation. Inhibitors of efflux pumps are therefore attractive compounds to reverse multidrug resistance and to prevent the development of resistance in clinically relevant bacterial pathogens. Recent successes on the structure determination and functional analysis of the AcrB and MexB components of the AcrAB-TolC and MexAB-OprM drug efflux systems as well as the structure of the fully assembled, functional triparted AcrAB-TolC complex significantly contributed to our understanding of the mechanism of substrate transport and the options for inhibition of efflux. These data, combined with the well-developed methodologies for measuring efflux pump inhibition, could allow the rational design, and subsequent experimental verification of potential efflux pump inhibitors (EPIs). In this review we will explore how the available biochemical and structural information can be translated into the discovery and development of new compounds that could reverse drug resistance in Gram-negative pathogens. The current literature on EPIs will also be analyzed and the reasons why no compounds have yet progressed into clinical use will be explored.
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Affiliation(s)
- Henrietta Venter
- School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia Adelaide, SA, Australia
| | - Rumana Mowla
- School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia Adelaide, SA, Australia
| | | | - Shutao Ma
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University Jinan, China
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209
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Li XZ, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev 2015; 28:337-418. [PMID: 25788514 PMCID: PMC4402952 DOI: 10.1128/cmr.00117-14] [Citation(s) in RCA: 899] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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210
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Berg G, Martinez JL. Friends or foes: can we make a distinction between beneficial and harmful strains of the Stenotrophomonas maltophilia complex? Front Microbiol 2015; 6:241. [PMID: 25873912 PMCID: PMC4379930 DOI: 10.3389/fmicb.2015.00241] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 03/12/2015] [Indexed: 11/21/2022] Open
Abstract
Stenotrophomonas maltophilia is an emerging multi-drug-resistant global opportunistic pathogen of environmental, mainly plant-associated origin. It is also used as a biocontrol or stress protecting agent for crops in sustainable agricultural as well as in bioremediation strategies. In order to establish effective protocols to distinguish harmless from harmful strains, our discussion must take into consideration the current data available surrounding the ecology, evolution and pathogenicity of the species complex. The mutation rate was identified as one of several possible criteria for strain plasticity, but it is currently impossible to distinguish beneficial from harmful S. maltophilia strains. This may compromise the possibility of the release and application for environmental biotechnology of this bacterial species. The close relative S. rhizophila, which can be clearly differentiated from S. maltophilia, provides a harmless alternative for biotechnological applications without human health risks. This is mainly because it is unable to growth at the human body temperature, 37∘C due to the absence of heat shock genes and a potentially temperature-regulated suicide mechanism.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz Austria
| | - Jose L Martinez
- Centro Nacional de Biotecnologia - Consejo Superior de Investigaciones Científicas, Madrid Spain
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211
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Early gene expression in Pseudomonas fluorescens exposed to a polymetallic solution. Cell Biol Toxicol 2015; 31:39-81. [DOI: 10.1007/s10565-015-9294-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/23/2015] [Indexed: 11/27/2022]
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212
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McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015; 4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.
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Affiliation(s)
- Jason E. McDermott
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul Bruillard
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | | | - Luke Gosink
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | - Stephen R. Lindemann
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
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213
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McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Res 2015; 4:60. [PMID: 26913187 PMCID: PMC4743146 DOI: 10.12688/f1000research.6200.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 03/26/2024] Open
Abstract
There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.
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Affiliation(s)
- Jason E. McDermott
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul Bruillard
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | | | - Luke Gosink
- National Security Divisions, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
| | - Stephen R. Lindemann
- Biological Sciences, Pacific Northwest National Laboratory, Washington, WA, 99352, USA
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214
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Ioannidis A, Magana M, Bologa CG, Oprea TI, Paulsen IT, Tegos GP. Defining the microbial effluxome in the content of the host-microbiome interaction. Front Pharmacol 2015; 6:31. [PMID: 25745401 PMCID: PMC4333769 DOI: 10.3389/fphar.2015.00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anastasios Ioannidis
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese Sparta, Greece ; Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital Athens, Greece
| | - Maria Magana
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese Sparta, Greece
| | - Cristian G Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center Albuquerque, NM, USA
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center Albuquerque, NM, USA ; Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark Lyngby, Denmark
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University NSW, Australia
| | - George P Tegos
- Torrey Pines Institute for Molecular Studies, Port St. Lucie FL, USA ; Department of Dermatology, Harvard Medical School Boston, MA, USA ; Wellman Center for Photomedicine, Massachusetts General Hospital Boston MA, USA
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215
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Ruer S, Pinotsis N, Steadman D, Waksman G, Remaut H. Virulence-targeted Antibacterials: Concept, Promise, and Susceptibility to Resistance Mechanisms. Chem Biol Drug Des 2015; 86:379-99. [DOI: 10.1111/cbdd.12517] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/23/2014] [Accepted: 01/06/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Ségolène Ruer
- Structural and Molecular Microbiology; Structural Biology Research Center; VIB; Pleinlaan 2 Brussels 1050 Belgium
- Structural Biology Brussels; Vrije Universiteit Brussel; Pleinlaan 2 Brussels 1050 Belgium
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology (ISMB); UCL and Birkbeck College; London WC1E 7HX UK
| | - David Steadman
- Wolfson Institute for Biomedical Research (WIBR); UCL; London WC1E 6BT UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology (ISMB); UCL and Birkbeck College; London WC1E 7HX UK
| | - Han Remaut
- Structural and Molecular Microbiology; Structural Biology Research Center; VIB; Pleinlaan 2 Brussels 1050 Belgium
- Structural Biology Brussels; Vrije Universiteit Brussel; Pleinlaan 2 Brussels 1050 Belgium
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216
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Identification and characterization of a serious multidrug resistant Stenotrophomonas maltophilia strain in China. BIOMED RESEARCH INTERNATIONAL 2015; 2015:580240. [PMID: 25654114 PMCID: PMC4310304 DOI: 10.1155/2015/580240] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/01/2014] [Indexed: 11/17/2022]
Abstract
An S. maltophilia strain named WJ66 was isolated from a patient; WJ66 showed resistance to more antibiotics than the other S. maltophilia strains. This bacteraemia is resistant to sulphonamides, or fluoroquinolones, while the representative strain of S. maltophilia, K279a, is sensitive to both. To explore drug resistance determinants of this strain, the draft genome sequence of WJ66 was determined and compared to other S. maltophilia sequences. Genome sequencing and genome-wide evolutionary analysis revealed that WJ66 was highly homologous with the strain K279a, but strain WJ66 contained additional antibiotic resistance genes. Further analysis confirmed that strain WJ66 contained an amino acid substitution (Q83L) in fluoroquinolone target GyrA and carried a class 1 integron, with an aadA2 gene in the resistance gene cassette. Homology analysis from the pathogen-host interaction database showed that strain WJ66 lacks raxST and raxA, which is consistent with K279a. Comparative genomic analyses revealed that subtle nucleotide differences contribute to various significant phenotypes in close genetic relationship strains.
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217
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Martinez JL. General principles of antibiotic resistance in bacteria. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 11:33-9. [PMID: 24847651 DOI: 10.1016/j.ddtec.2014.02.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Given the impact of antibiotic resistance on human health, its study is of great interest from a clinical view- point. In addition, antibiotic resistance is one of the few examples of evolution that can be studied in real time. Knowing the general principles involved in the acquisition of antibiotic resistance is therefore of interest to clinicians, evolutionary biologists and ecologists. The origin of antibiotic resistance genes now possessed by human pathogens can be traced back to environmental microorganisms. Consequently, a full understanding of the evolution of antibiotic resistance requires the study of natural environments as well as clinical ecosystems. Updated information on the evolutionary mechanisms behind resistance, indicates that ecological connectivity, founder effect and fitness costs are important bottle- necks that modulate the transfer of resistance from environmental microorganisms to pathogens.
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218
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Nesme J, Simonet P. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ Microbiol 2014; 17:913-30. [DOI: 10.1111/1462-2920.12631] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Joseph Nesme
- Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue Ecully 69134 France
| | - Pascal Simonet
- Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue Ecully 69134 France
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219
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Abstract
Metagenomic studies have shown that antibiotic resistance genes are ubiquitous in the environment, which has led to the suggestion that there is a high risk that these genes will spread to bacteria that cause human infections. If this is true, estimating the real risk of dissemination of resistance genes from environmental reservoirs to human pathogens is therefore very difficult. In this Opinion article, we analyse the current definitions of antibiotic resistance and antibiotic resistance genes, and we describe the bottlenecks that affect the transfer of antibiotic resistance genes to human pathogens. We propose rules for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections.
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220
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López M, Barbosa B, Gato E, Bou G, Tomás M. Patents on antivirulence therapies. World J Pharmacol 2014; 3:97-109. [DOI: 10.5497/wjp.v3.i4.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 10/02/2014] [Accepted: 11/10/2014] [Indexed: 02/06/2023] Open
Abstract
Antivirulence therapy inhibits bacterial virulence factors, thus preventing the development of infection without affecting bacterial growth. The development of new antibiotics is complicated by the increasing incidence of antibiotic resistance in pathogenic bacteria. Antivirulence therapy is a promising alternative to traditional antibiotic therapy for the treatment of infectious disease, either alone or in combination with antibiotic treatment. In this review, we consider patents concerning inhibition of several bacterial virulence factors: adhesion/colonization, secretion systems, cellular signalling systems and antimicrobial resistance mechanisms. Finally, we emphasize the importance of analyzing new targets and/or molecules in this field and of considering possible resistance mechanisms.
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221
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Liu M, Ding R, Zhang Y, Gao Y, Tian Z, Zhang T, Yang M. Abundance and distribution of Macrolide-Lincosamide-Streptogramin resistance genes in an anaerobic-aerobic system treating spiramycin production wastewater. WATER RESEARCH 2014; 63:33-41. [PMID: 24973730 DOI: 10.1016/j.watres.2014.05.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 06/03/2023]
Abstract
The behaviors of the Macrolide-Lincosamide-Streptogramin (MLS) resistance genes were investigated in an anaerobic-aerobic pilot-scale system treating spiramycin (SPM) production wastewater. After screening fifteen typical MLS resistance genes with different mechanisms using conventional PCR, eight detected genes were determined by quantitative PCR, together with three mobile elements. Aerobic sludge in the pilot system exhibited a total relative abundance of MLS resistance genes (per 16S rRNA gene) 2.5 logs higher than those in control samples collected from sewage and inosine wastewater treatment systems (P < 0.05), implying the presence of SPM could induce the production of MLS resistance genes. However, the total relative gene abundance in anaerobic sludge (4.3 × 10(-1)) was lower than that in aerobic sludge (3.7 × 10(0)) despite of the higher SPM level in anaerobic reactor, showing the advantage of anaerobic treatment in reducing the production of MLS resistance genes. The rRNA methylase genes (erm(B), erm(F), erm(X)) were the most abundant in the aerobic sludge (5.3 × 10(-1)-1.7 × 10(0)), followed by esterase gene ere(A) (1.3 × 10(-1)) and phosphorylase gene mph(B) (5.7 × 10(-2)). In anaerobic sludge, erm(B), erm(F), ere(A), and msr(D) were the major ones (1.2 × 10(-2)-3.2 × 10(-1)). These MLS resistance genes (except for msr(D)) were positively correlated with Class 1 integron (r(2) = 0.74-0.93, P < 0.05), implying the significance of horizontal transfer in their proliferation.
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Affiliation(s)
- Miaomiao Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.
| | - Ran Ding
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.
| | - Yingxin Gao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.
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222
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Ohene-Agyei T, Mowla R, Rahman T, Venter H. Phytochemicals increase the antibacterial activity of antibiotics by acting on a drug efflux pump. Microbiologyopen 2014; 3:885-96. [PMID: 25224951 PMCID: PMC4263512 DOI: 10.1002/mbo3.212] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/01/2014] [Accepted: 08/01/2014] [Indexed: 12/18/2022] Open
Abstract
Drug efflux pumps confer resistance upon bacteria to a wide range of antibiotics from various classes. The expression of efflux pumps are also implicated in virulence and biofilm formation. Moreover, organisms can only acquire resistance in the presence of active drug efflux pumps. Therefore, efflux pump inhibitors (EPIs) are attractive compounds to reverse multidrug resistance and to prevent the development of resistance in clinically relevant bacterial pathogens. We investigated the potential of pure compounds isolated from plants to act as EPIs. In silico screening was used to predict the bioactivity of plant compounds and to compare that with the known EPI, phe-arg-β-naphthylamide (PAβN). Subsequently, promising products have been tested for their ability to inhibit efflux. Plumbagin nordihydroguaretic acid (NDGA) and to a lesser degree shikonin, acted as sensitizers of drug-resistant bacteria to currently used antibiotics and were able to inhibit the efflux pump-mediated removal of substrate from cells. We demonstrated the feasibility of in silico screening to identify compounds that potentiate the action of antibiotics against drug-resistant strains and which might be potentially useful lead compounds for an EPI discovery program.
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Affiliation(s)
- Thelma Ohene-Agyei
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, United Kingdom
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223
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The TetR-type MfsR protein of the integrative and conjugative element (ICE) ICEclc controls both a putative efflux system and initiation of ICE transfer. J Bacteriol 2014; 196:3971-9. [PMID: 25182498 DOI: 10.1128/jb.02129-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR.
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224
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Rossi F, Rizzotti L, Felis GE, Torriani S. Horizontal gene transfer among microorganisms in food: Current knowledge and future perspectives. Food Microbiol 2014; 42:232-43. [DOI: 10.1016/j.fm.2014.04.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/10/2014] [Indexed: 01/01/2023]
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225
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Marmulla R, Harder J. Microbial monoterpene transformations-a review. Front Microbiol 2014; 5:346. [PMID: 25076942 PMCID: PMC4097962 DOI: 10.3389/fmicb.2014.00346] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/21/2014] [Indexed: 11/17/2022] Open
Abstract
Isoprene and monoterpenes constitute a significant fraction of new plant biomass. Emission rates into the atmosphere alone are estimated to be over 500 Tg per year. These natural hydrocarbons are mineralized annually in similar quantities. In the atmosphere, abiotic photochemical processes cause lifetimes of minutes to hours. Microorganisms encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and on plants, in the soil and in aquatic habitats. Below toxic concentrations, the compounds can serve as carbon and energy source for aerobic and anaerobic microorganisms. Besides these catabolic reactions, transformations may occur as part of detoxification processes. Initial transformations of monoterpenes involve the introduction of functional groups, oxidation reactions, and molecular rearrangements catalyzed by various enzymes. Pseudomonas and Rhodococcus strains and members of the genera Castellaniella and Thauera have become model organisms for the elucidation of biochemical pathways. We review here the enzymes and their genes together with microorganisms known for a monoterpene metabolism, with a strong focus on microorganisms that are taxonomically validly described and currently available from culture collections. Metagenomes of microbiomes with a monoterpene-rich diet confirmed the ecological relevance of monoterpene metabolism and raised concerns on the quality of our insights based on the limited biochemical knowledge.
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Affiliation(s)
- Robert Marmulla
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
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226
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Fajardo A, Hernando-Amado S, Oliver A, Ball G, Filloux A, Martinez JL. Characterization of a novel Zn2+-dependent intrinsic imipenemase from Pseudomonas aeruginosa. J Antimicrob Chemother 2014; 69:2972-8. [DOI: 10.1093/jac/dku267] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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227
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Allen HK. Antibiotic resistance gene discovery in food-producing animals. Curr Opin Microbiol 2014; 19:25-29. [PMID: 24994584 DOI: 10.1016/j.mib.2014.06.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/28/2014] [Accepted: 06/07/2014] [Indexed: 12/14/2022]
Abstract
Numerous environmental reservoirs contribute to the widespread antibiotic resistance problem in human pathogens. One environmental reservoir of particular importance is the intestinal bacteria of food-producing animals. In this review I examine recent discoveries of antibiotic resistance genes in agricultural animals. Two types of antibiotic resistance gene discoveries will be discussed: the use of classic microbiological and molecular techniques, such as culturing and PCR, to identify known genes not previously reported in animals; and the application of high-throughput technologies, such as metagenomics, to identify novel genes and gene transfer mechanisms. These discoveries confirm that antibiotics should be limited to prudent uses.
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Affiliation(s)
- Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
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228
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Gibello A, Díaz de Alba P, Blanco MM, Machuca J, Cutuli MT, Rodríguez-Martínez JM. Lactococcus garvieae carries a chromosomally encoded pentapeptide repeat protein that confers reduced susceptibility to quinolones in Escherichia coli producing a cytotoxic effect. Res Microbiol 2014; 165:590-9. [PMID: 24965125 DOI: 10.1016/j.resmic.2014.05.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/09/2014] [Accepted: 05/13/2014] [Indexed: 01/09/2023]
Abstract
This study characterises a chromosomal gene of Lactococcus garvieae encoding a pentapeptide repeat protein designated as LgaQnr. This gene has been implicated in reduced susceptibility to quinolones in this bacterium, which is of relevance to both veterinary and human medicine. All of the L. garvieae isolates analysed were positive for the lgaqnr gene. The expression of lgaqnr in Escherichia coli reduced the susceptibility to quinolones, producing an adverse effect. The reduced susceptibility to ciprofloxacin was 16-fold in E. coli ATCC 25922 and 32-fold in E. coli DH10B, compared to the control strains. The minimum inhibitory concentration of nalidixic acid was also increased 4 or 5-fold. The effect of the expression of lgaqnr in E. coli was investigated by electron microscopy and was observed to affect the structure of the cell and the inner membrane of the recombinant cells.
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Affiliation(s)
- Alicia Gibello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - Paula Díaz de Alba
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Sevilla, Spain.
| | - M Mar Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | - Jesus Machuca
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Virgen de la Macarena, 41007 Sevilla, Spain.
| | - M Teresa Cutuli
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
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229
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AraC/XylS family stress response regulators Rob, SoxS, PliA, and OpiA in the fire blight pathogen Erwinia amylovora. J Bacteriol 2014; 196:3098-110. [PMID: 24936054 DOI: 10.1128/jb.01838-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional regulators of the AraC/XylS family have been associated with multidrug resistance, organic solvent tolerance, oxidative stress, and virulence in clinically relevant enterobacteria. In the present study, we identified four homologous AraC/XylS regulators, Rob, SoxS, PliA, and OpiA, from the fire blight pathogen Erwinia amylovora Ea1189. Previous studies have shown that the regulators MarA, Rob, and SoxS from Escherichia coli mediate multiple-antibiotic resistance, primarily by upregulating the AcrAB-TolC efflux system. However, none of the four AraC/XylS regulators from E. amylovora was able to induce a multidrug resistance phenotype in the plant pathogen. Overexpression of rob led to a 2-fold increased expression of the acrA gene. However, the rob-overexpressing strain showed increased resistance to only a limited number of antibiotics. Furthermore, Rob was able to induce tolerance to organic solvents in E. amylovora by mechanisms other than efflux. We demonstrated that SoxS from E. amylovora is involved in superoxide resistance. A soxS-deficient mutant of Ea1189 was not able to grow on agar plates supplemented with the superoxide-generating agent paraquat. Furthermore, expression of soxS was induced by redox cycling agents. We identified two novel members of the AraC/XylS family in E. amylovora. PliA was highly upregulated during the early infection phase in apple rootstock and immature pear fruits. Multiple compounds were able to induce the expression of pliA, including apple leaf extracts, phenolic compounds, redox cycling agents, heavy metals, and decanoate. OpiA was shown to play a role in the regulation of osmotic and alkaline pH stress responses.
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230
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Sun J, Deng Z, Yan A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun 2014; 453:254-67. [PMID: 24878531 DOI: 10.1016/j.bbrc.2014.05.090] [Citation(s) in RCA: 432] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023]
Abstract
Multidrug resistance (MDR) refers to the capability of bacterial pathogens to withstand lethal doses of structurally diverse drugs which are capable of eradicating non-resistant strains. MDR has been identified as a major threat to the public health of human being by the World Health Organization (WHO). Among the four general mechanisms that cause antibiotic resistance including target alteration, drug inactivation, decreased permeability and increased efflux, drug extrusion by the multidrug efflux pumps serves as an important mechanism of MDR. Efflux pumps not only can expel a broad range of antibiotics owing to their poly-substrate specificity, but also drive the acquisition of additional resistance mechanisms by lowering intracellular antibiotic concentration and promoting mutation accumulation. Over-expression of multidrug efflux pumps have been increasingly found to be associated with clinically relevant drug resistance. On the other hand, accumulating evidence has suggested that efflux pumps also have physiological functions in bacteria and their expression is subject tight regulation in response to various of environmental and physiological signals. A comprehensive understanding of the mechanisms of drug extrusion, and regulation and physiological functions of efflux pumps is essential for the development of anti-resistance interventions. In this review, we summarize the development of these research areas in the recent decades and present the pharmacological exploitation of efflux pump inhibitors as a promising anti-drug resistance intervention.
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Affiliation(s)
- Jingjing Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Ziqing Deng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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231
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Arioli S, Guglielmetti S, Amalfitano S, Viti C, Marchi E, Decorosi F, Giovannetti L, Mora D. Characterization of tetA-like gene encoding for a major facilitator superfamily efflux pump in Streptococcus thermophilus. FEMS Microbiol Lett 2014; 355:61-70. [PMID: 24766488 DOI: 10.1111/1574-6968.12449] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/07/2014] [Accepted: 04/22/2014] [Indexed: 11/26/2022] Open
Abstract
Efflux pumps are membrane proteins involved in the active extrusion of a wide range of structurally dissimilar substrates from cells. A multidrug efflux pump named TetA belonging to the major facilitator superfamily (MFS) of transporters was identified in the Streptococcus thermophilus DSM 20617(T) genome. The tetA-like gene was found in the genomes of a number of S. thermophilus strains sequenced to date and in Streptococcus macedonicus ACA-DC 198, suggesting a possible horizontal gene transfer event between these two Streptococcus species, which are both adapted to the milk environment. Flow cytometry (single-cell) analysis revealed bistable TetA activity in the S. thermophilus population, and tetA-like gene over-expression resulted in a reduced susceptibility to ethidium bromide, tetracycline, and other toxic compounds even when the efflux pump was over-expressed in a strain naturally lacking tetA-like gene.
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Affiliation(s)
- Stefania Arioli
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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232
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Abstract
The emergence and spread of antibiotic resistance among human pathogens is a relevant problem for human health and one of the few evolution processes amenable to experimental studies. In the present review, we discuss some basic aspects of antibiotic resistance, including mechanisms of resistance, origin of resistance genes, and bottlenecks that modulate the acquisition and spread of antibiotic resistance among human pathogens. In addition, we analyse several parameters that modulate the evolution landscape of antibiotic resistance. Learning why some resistance mechanisms emerge but do not evolve after a first burst, whereas others can spread over the entire world very rapidly, mimicking a chain reaction, is important for predicting the evolution, and relevance for human health, of a given mechanism of resistance. Because of this, we propose that the emergence and spread of antibiotic resistance can only be understood in a multi-parameter space. Measuring the effect on antibiotic resistance of parameters such as contact rates, transfer rates, integration rates, replication rates, diversification rates, and selection rates, for different genes and organisms, growing under different conditions in distinct ecosystems, will allow for a better prediction of antibiotic resistance and possibilities of focused interventions.
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Affiliation(s)
- José Luis Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) and CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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233
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Metabolic compensation of fitness costs associated with overexpression of the multidrug efflux pump MexEF-OprN in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2014; 58:3904-13. [PMID: 24777101 DOI: 10.1128/aac.00121-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The acquisition of antibiotic resistance has been associated with a possible nonspecific, metabolic burden that is reflected in decreased fitness among resistant bacteria. We have recently demonstrated that overexpression of the MexEF-OprN multidrug efflux pump does not produce a metabolic burden when measured by classical competitions tests but rather leads to a number of changes in the organism's physiology. One of these changes is the untimely activation of the nitrate respiratory chain under aerobic conditions. MexEF-OprN is a proton/substrate antiporter. Overexpression of this element should result in a constant influx of protons, which may lead to cytoplasmic acidification. Acidification was not observed in aerobiosis, a situation in which the MexEF-overproducing mutant increases oxygen consumption. This enhanced oxygen uptake serves to eliminate intracellular proton accumulation, preventing the cytoplasmic acidification that was observed exclusively under anaerobic conditions, a situation in which the fitness of the MexEF-OprN-overproducing mutant decreases. Finally, we determined that the early activation of the nitrate respiratory chain under aerobic conditions plays a role in preventing a deleterious effect associated with the overexpression of MexEF-OprN. Our results show that metabolic rewiring may assist in overcoming the potential fitness cost associated with the acquisition of antibiotic resistance. Furthermore, the capability to metabolically compensate for this effect is habitat dependent, as demonstrated by our results under anaerobic conditions. The development of drugs that prevent metabolic compensation of fitness costs may help to reduce the persistence and dissemination of antibiotic resistance.
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234
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Rossbach S, Kunze K, Albert S, Zehner S, Göttfert M. The Sinorhizobium meliloti EmrAB efflux system is regulated by flavonoids through a TetR-like regulator (EmrR). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:379-387. [PMID: 24224534 DOI: 10.1094/mpmi-09-13-0282-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The divergently oriented Sinorhizobium meliloti emrAB (SMc03168 and SMc03167) and emrR (SMc03169) genes are predicted to encode an efflux system of the major facilitator superfamily and a TetR-like transcriptional regulator, respectively. The transcription of the emrA gene was found to be inducible by flavonoids, including luteolin and apigenin, which are known inducers of the nodulation genes in S. meliloti. Interestingly, quercetin, which does not induce nodulation genes, was also a potent inducer of emrA, indicating that NodD is not directly involved in regulation of emrA. The likely regulator of emrAB is EmrR, which binds to palindrome-like sequences in the intergenic region. Several modifications of the palindromes, including an increase of the spacing between the two half sites, prevented binding of EmrR. Binding was also impaired by the presence of luteolin. Mutations in emrA had no obvious effect on symbiosis. This was in contrast to the emrR mutant, which exhibited a symbiotic deficiency with Medicago sativa. Conserved binding sites for TetR-like regulators within the intergenic regions between the emrAB and emrR genes were identified in many symbiotic and pathogenic members of the order Rhizobiales.
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235
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Schlatter DC, Kinkel LL. Global biogeography ofStreptomycesantibiotic inhibition, resistance, and resource use. FEMS Microbiol Ecol 2014; 88:386-97. [DOI: 10.1111/1574-6941.12307] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/10/2014] [Accepted: 02/13/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; Saint Paul MN USA
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236
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García-León G, Salgado F, Oliveros JC, Sánchez MB, Martínez JL. Interplay between intrinsic and acquired resistance to quinolones in Stenotrophomonas maltophilia. Environ Microbiol 2014; 16:1282-96. [PMID: 24447641 DOI: 10.1111/1462-2920.12408] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/14/2014] [Indexed: 01/26/2023]
Abstract
To analyse whether the mutation-driven resistance-acquisition potential of a given bacterium might be a function of its intrinsic resistome, quinolones were used as selective agents and Stenotrophomonas maltophilia was chosen as a bacterial model. S. maltophilia has two elements - SmQnr and SmeDEF - that are important in intrinsic resistance to quinolones. Using a battery of mutants in which either or both of these elements had been removed, the apparent mutation frequency for quinolone resistance and the phenotype of the selected mutants were found to be related to the intrinsic resistome and also depended on the concentration of the selector. Most mutants had phenotypes compatible with the overexpression of multidrug efflux pump(s); SmeDEF overexpression was the most common cause of quinolone resistance. Whole genome sequencing showed that mutations of the SmeRv regulator, which result in the overexpression of the efflux pump SmeVWX, are the cause of quinolone resistance in mutants not overexpressing SmeDEF. These results indicate that the development of mutation-driven antibiotic resistance is highly dependent on the intrinsic resistome, which, at least for synthetic antibiotics such as quinolones, did not develop as a response to the presence of antibiotics in the natural ecosystems in which S. maltophilia evolved.
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Affiliation(s)
- Guillermo García-León
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, Madrid, 28049, Spain
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237
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Effects of Chlorophyll-Derived Efflux Pump Inhibitor Pheophorbide a and Pyropheophorbide a on Growth and Macrolide Antibiotic Resistance of Indicator and Anaerobic Swine Manure Bacteria. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/185068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Natural plant compounds, such as the chlorophyll a catabolites pheophorbide a (php) and pyropheophorbide a (pyp), are potentially active in the gastrointestinal tracts and manure of livestock as antimicrobial resistance-modifying agents through inhibition of bacterial efflux pumps. To investigate whether php, a known efflux pump inhibitor, and pyp influence bacterial resistance, we determined their long-term effects on the MICs of erythromycin for reference strains of clinically relevant indicator bacteria with macrolide or multidrug resistance efflux pumps. Pyp reduced the final MIC endpoint for Staphylococcus (S.) aureus and Escherichia (E.) coli by up to 1536 and 1024 μg erythromycin mL−1 or 1.4- and 1.2-fold, respectively. Estimation of growth parameters of S. aureus revealed that pyp exerted an intrinsic inhibitory effect under anaerobic conditions and was synergistically active, thereby potentiating the effect of erythromycin and partially reversing high-level erythromycin resistance. Anaerobe colony counts of total and erythromycin-resistant bacteria from stored swine manure samples tended to be lower in the presence of pyp. Tylosin, php, and pyp were not detectable by HPLC in the manure or medium. This is the first study showing that pyp affects growth and the level of sensitivity to erythromycin of S. aureus, E. coli, and anaerobic manure bacteria.
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238
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Identification of Genes Required for Soil Survival in Burkholderia thailandensis by Transposon-Directed Insertion Site Sequencing. Curr Microbiol 2014; 68:693-701. [DOI: 10.1007/s00284-014-0526-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 11/23/2013] [Indexed: 01/19/2023]
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239
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Mardanova AM, Bogomol’naya LM, Romanova YD, Sharipova MR. Efflux systems in Serratia marcescens. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714010093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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240
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241
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Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. ISME JOURNAL 2013; 8:249-56. [PMID: 24152720 DOI: 10.1038/ismej.2013.175] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 11/08/2022]
Abstract
Soil bacteria produce a diverse array of antibiotics, yet our understanding of the specific roles of antibiotics in the ecological and evolutionary dynamics of microbial interactions in natural habitats remains limited. Here, we show a significant role for antibiotics in mediating antagonistic interactions and nutrient competition among locally coexisting Streptomycete populations from soil. We found that antibiotic inhibition is significantly more intense among sympatric than allopatric Streptomycete populations, indicating local selection for inhibitory phenotypes. For sympatric but not allopatric populations, antibiotic inhibition is significantly positively correlated with niche overlap, indicating that inhibition is targeted toward bacteria that pose the greatest competitive threat. Our results support the hypothesis that antibiotics serve as weapons in mediating local microbial interactions in soil and suggest that coevolutionary niche displacement may reduce the likelihood of an antibiotic arms race. Further insight into the diverse roles of antibiotics in microbial ecology and evolution has significant implications for understanding the persistence of antibiotic inhibitory and resistance phenotypes in environmental microbes, optimizing antibiotic drug discovery and developing strategies for managing microbial coevolutionary dynamics to enhance inhibitory phenotypes.
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242
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Silva-Rocha R, de Azevedo JSN, Carepo MSP, Lopes de Souza R, Silva A, de Lorenzo V, Schneider MPC. Vestigialization of arsenic resistance phenotypes/genotypes inChromobacterium violaceumstrains thriving in pristine Brazilian sites. BIOCATAL BIOTRANSFOR 2013. [DOI: 10.3109/10242422.2013.843170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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243
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Ballesté-Delpierre C, Solé M, Domènech Ò, Borrell J, Vila J, Fàbrega A. Molecular study of quinolone resistance mechanisms and clonal relationship of Salmonella enterica clinical isolates. Int J Antimicrob Agents 2013; 43:121-5. [PMID: 24139882 DOI: 10.1016/j.ijantimicag.2013.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 11/30/2022]
Abstract
In the last few years, the number of Salmonella enterica strains resistant to nalidixic acid has steadily increased. In a previous study, the quinolone susceptibility phenotype and genotype of 38 S. enterica clinical isolates (19 S. enterica serovar Typhimurium and 19 S. enterica serovar Enteritidis) were determined. Forty-two percent of the isolates showed nalidixic acid resistance associated with a mutation in gyrA together with putative overexpression of efflux pump(s). In this study, mutations in the quinolone resistance-determining region (QRDR) of parE and the regulators of AcrAB (acrR, marRAB, soxRS and ramR) were analysed. Intracellular accumulation of ciprofloxacin and nalidixic acid was determined. Gene expression of the efflux pump components acrB, tolC, acrF and emrB was also assessed. In addition, an epidemiological study of the isolates by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) was performed. No mutations were detected in parE, whereas two amino acid substitutions were found in two susceptible strains in MarR (I84L) and AcrR (N214T) in one strain each, although both were suggested to be polymorphisms. No changes in the gene expression of acrB, tolC, acrF and emrB were detected between nalidixic-acid-resistant and -susceptible strains. Intracellular accumulation was not useful to reveal differences. Epidemiological analysis showed an important clonal relatedness among the S. Enteritidis isolates, whereas major divergence was seen for S. Typhimurium. Altogether, these results suggest the presence of previously undiscovered drug efflux pump(s) and confirm the high clonality of S. Enteritidis and the genetic divergence of S. Typhimurium.
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Affiliation(s)
- Clara Ballesté-Delpierre
- Centre for International Health Research, CRESIB, Hospital Clínic, University of Barcelona, Rosselló 149-153, 1st Floor, 08036 Barcelona, Spain
| | - Mar Solé
- Centre for International Health Research, CRESIB, Hospital Clínic, University of Barcelona, Rosselló 149-153, 1st Floor, 08036 Barcelona, Spain
| | - Òscar Domènech
- Department of Physical Chemistry, School of Pharmacy, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Jordi Borrell
- Department of Physical Chemistry, School of Pharmacy, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Jordi Vila
- Centre for International Health Research, CRESIB, Hospital Clínic, University of Barcelona, Rosselló 149-153, 1st Floor, 08036 Barcelona, Spain; Department of Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Villarroel 170, 08036 Barcelona, Spain.
| | - Anna Fàbrega
- Centre for International Health Research, CRESIB, Hospital Clínic, University of Barcelona, Rosselló 149-153, 1st Floor, 08036 Barcelona, Spain
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244
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Listeria monocytogenes multidrug resistance transporters and cyclic di-AMP, which contribute to type I interferon induction, play a role in cell wall stress. J Bacteriol 2013; 195:5250-61. [PMID: 24056102 DOI: 10.1128/jb.00794-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular bacterial pathogen Listeria monocytogenes activates a robust type I interferon response upon infection. This response is partially dependent on the multidrug resistance (MDR) transporter MdrM and relies on cyclic-di-AMP (c-di-AMP) secretion, yet the functions of MdrM and cyclic-di-AMP that lead to this response are unknown. Here we report that it is not MdrM alone but a cohort of MDR transporters that together contribute to type I interferon induction during infection. In a search for a physiological function of these transporters, we revealed that they play a role in cell wall stress responses. A mutant with deletion of four transporter genes (ΔmdrMTAC) was found to be sensitive to sublethal concentrations of vancomycin due to an inability to produce and shed peptidoglycan under this stress. Remarkably, c-di-AMP is involved in this phenotype, as overexpression of the c-di-AMP phosphodiesterase (PdeA) resulted in increased susceptibility of the ΔmdrMTAC mutant to vancomycin, whereas overexpression of the c-di-AMP diadenylate cyclase (DacA) reduced susceptibility to this drug. These observations suggest a physiological association between c-di-AMP and the MDR transporters and support the model that MDR transporters mediate c-di-AMP secretion to regulate peptidoglycan synthesis in response to cell wall stress.
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245
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Miranda CD, Rojas R, Garrido M, Geisse J, González G. Role of shellfish hatchery as a reservoir of antimicrobial resistant bacteria. MARINE POLLUTION BULLETIN 2013; 74:334-343. [PMID: 23880028 DOI: 10.1016/j.marpolbul.2013.06.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/16/2013] [Accepted: 06/17/2013] [Indexed: 06/02/2023]
Abstract
The main aim of this study was to determine the occurrence of resistant bacteria in florfenicol-treated and untreated scallop larval cultures from a commercial hatchery and to characterize some selected florfenicol-resistant strains. Larval cultures from untreated and treated rearing tanks exhibited percentages of copiotrophic bacteria resistant to florfenicol ranging from 0.03% to 10.67% and 0.49-18.34%, respectively, whereas florfenicol resistance among oligotrophic bacteria varied from 1.44% to 35.50% and 3.62-95.71%, from untreated and treated larvae, respectively. Florfenicol resistant microbiota from reared scallop larvae mainly belonged to the Pseudomonas and Pseudoalteromonas genus and were mainly resistant to florfenicol, chloramphenicol, streptomycin and co-trimoxazole. This is the first study reporting antimicrobial resistant bacteria associated to a shellfish hatchery and the results suggest that a continuous surveillance of antimicrobial resistance even in absence of antibacterial therapy is urgently required to evaluate potential undesirable consequences on the surrounding environments.
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Affiliation(s)
- Claudio D Miranda
- Aquatic Pathobiology Laboratory, Department of Aquaculture, Universidad Católica del Norte, 1281 Larrondo Street, Coquimbo, Chile; Centro de Estudios Avanzados (CEAZA), 1281 Larrondo Street, Coquimbo, Chile.
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246
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Chien CC, Lin BC, Wu CH. Biofilm formation and heavy metal resistance by an environmental Pseudomonas sp. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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247
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Santimano MC, Kowshik M. Altered growth and enzyme expression profile of ZnO nanoparticles exposed non-target environmentally beneficial bacteria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2013; 185:7205-7214. [PMID: 23341058 DOI: 10.1007/s10661-013-3094-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 01/14/2013] [Indexed: 06/01/2023]
Abstract
The extensive production and usage of nanoparticles with ultimate disposal in the environment leads to unintentional exposure of non-target environmentally beneficial bacteria thereby posing a serious threat to the native soil inhabitants. Soil microflora is an important link in the biogeochemical cycling of nutrients, affecting ecosystem functioning and productivity. This study evaluates the effect of one of the widely used nanoparticles, zinc oxide on two predominant soil bacteria, Gram-positive Bacillus subtilis and Gram-negative Pseudomonas aeruginosa with respect to their biocatalytic activities. Growth profiles of these bacteria in the presence of zinc oxide nanoparticles (ZnONPs) at a concentration of 20 ppm exhibited a prolonged lag phase in B. subtilis, whereas no significant effect was observed in the case of P. aeruginosa even at 200 ppm. Interestingly, the enzymatic profile of both the organisms was affected at non-lethal ZnONPs concentrations. The most pronounced effect was on the enzymes associated with amylolytic activity, denitrification and urea degradation wherein total inhibition of activity was noted in B. subtilis. The enzyme activities were lowered in the case of P. aeruginosa. The results presented here reiterate a critical need for exposure assessment and risk characterization of nanomaterial disposal on soil microflora while formalizing waste management strategies.
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Affiliation(s)
- Maria Celisa Santimano
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, KK Birla Goa Campus, Zuarinagar, Goa 403726, India
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248
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Contribution of efflux pumps, porins, and β-lactamases to multidrug resistance in clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 2013; 57:5247-57. [PMID: 23939894 DOI: 10.1128/aac.00730-13] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We investigated the mechanisms of resistance to carbapenems, aminoglycosides, glycylcyclines, tetracyclines, and quinolones in 90 multiresistant clinical strains of Acinetobacter baumannii isolated from two genetically unrelated A. baumannii clones: clone PFGE-ROC-1 (53 strains producing the OXA-58 β-lactamase enzyme and 18 strains with the OXA-24 β-lactamase) and clone PFGE-HUI-1 (19 strains susceptible to carbapenems). We used real-time reverse transcriptase PCR to correlate antimicrobial resistance (MICs) with expression of genes encoding chromosomal β-lactamases (AmpC and OXA-51), porins (OmpA, CarO, Omp33, Dcap-like, OprB, Omp25, OprC, OprD, and OmpW), and proteins integral to six efflux systems (AdeABC, AdeIJK, AdeFGH, CraA, AbeM, and AmvA). Overexpression of the AdeABC system (level of expression relative to that by A. baumannii ATCC 17978, 30- to 45-fold) was significantly associated with resistance to tigecycline, minocycline, and gentamicin and other biological functions. However, hyperexpression of the AdeIJK efflux pump (level of expression relative to that by A. baumannii ATCC 17978, 8- to 10-fold) was significantly associated only with resistance to tigecycline and minocycline (to which the TetB efflux system also contributed). TetB and TetA(39) efflux pumps were detected in clinical strains and were associated with resistance to tetracyclines and doxycycline. The absence of the AdeABC system and the lack of expression of other mechanisms suggest that tigecycline-resistant strains of the PFGE-HUI-1 clone may be associated with a novel resistance-nodulation-cell efflux pump (decreased MICs in the presence of the inhibitor Phe-Arg β-naphthylamide dihydrochloride) and the TetA(39) system.
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249
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Matsuo T, Nakamura K, Kodama T, Mikami T, Hiyoshi H, Tsuchiya T, Ogawa W, Kuroda T. Characterization of all RND-type multidrug efflux transporters in Vibrio parahaemolyticus. Microbiologyopen 2013; 2:725-42. [PMID: 23894076 PMCID: PMC3831635 DOI: 10.1002/mbo3.100] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/21/2013] [Accepted: 05/21/2013] [Indexed: 01/13/2023] Open
Abstract
Resistance nodulation cell division (RND)-type efflux transporters play the main role in intrinsic resistance to various antimicrobial agents in many gram-negative bacteria. Here, we estimated 12 RND-type efflux transporter genes in Vibrio parahaemolyticus. Because VmeAB has already been characterized, we cloned the other 11 RND-type efflux transporter genes and characterized them in Escherichia coli KAM33 cells, a drug hypersusceptible strain. KAM33 expressing either VmeCD, VmeEF, or VmeYZ showed increased minimum inhibitory concentrations (MICs) for several antimicrobial agents. Additional four RND-type transporters were functional as efflux pumps only when co-expressed with VpoC, an outer membrane component in V. parahaemolyticus. Furthermore, VmeCD, VmeEF, and VmeYZ co-expressed with VpoC exhibited a broader substrate specificity and conferred higher resistance than that with TolC of E. coli. Deletion mutants of these transporter genes were constructed in V. parahaemolyticus. TM32 (ΔvmeAB and ΔvmeCD) had significantly decreased MICs for many antimicrobial agents and the number of viable cells after exposure to deoxycholate were markedly reduced. Strains in which 12 operons were all disrupted had very low MICs and much lower fluid accumulation in rabbit ileal loops. These results indicate that resistance nodulation cell division-type efflux transporters contribute not only to intrinsic resistance but also to exerting the virulence of V. parahaemolyticus.
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Affiliation(s)
- Taira Matsuo
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
| | - Koji Nakamura
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
| | - Toshio Kodama
- Pathogenic Microbes Repository Unit, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka UniversityOsaka, Japan
| | - Taro Mikami
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
| | - Hirotaka Hiyoshi
- Laboratory of Genomic Research on Pathogenic Bacteria, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka UniversityOsaka, Japan
| | - Tomofusa Tsuchiya
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
| | - Wakano Ogawa
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
| | - Teruo Kuroda
- Department of Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayama, Japan
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250
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Copper efflux is induced during anaerobic amino acid limitation in Escherichia coli to protect iron-sulfur cluster enzymes and biogenesis. J Bacteriol 2013; 195:4556-68. [PMID: 23893112 DOI: 10.1128/jb.00543-13] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Adaptation to changing environments is essential to bacterial physiology. Here we report a unique role of the copper homeostasis system in adapting Escherichia coli to its host-relevant environment of anaerobiosis coupled with amino acid limitation. We found that expression of the copper/silver efflux pump CusCFBA was significantly upregulated during anaerobic amino acid limitation in E. coli without the supplement of exogenous copper. Inductively coupled plasma mass spectrometry analysis of the total intracellular copper content combined with transcriptional assay of the P(cusC)-lacZ reporter in the presence of specific Cu(I) chelators indicated that anaerobic amino acid limitation led to the accumulation of free Cu(I) in the periplasmic space of E. coli, resulting in Cu(I) toxicity. Cells lacking cusCFBA and another copper transporter, copA, under this condition displayed growth defects and reduced ATP production during fumarate respiration. Ectopic expression of the Fe-S cluster enzyme fumarate reductase (Frd), or supplementation with amino acids whose biosynthesis involves Fe-S cluster enzymes, rescued the poor growth of ΔcusC cells. Yet, Cu(I) treatment did not impair the Frd activity in vitro. Further studies revealed that the alternative Fe-S cluster biogenesis system Suf was induced during the anaerobic amino acid limitation, and ΔcusC enhanced this upregulation, indicating the impairment of the Fe-S cluster assembly machinery and the increased Fe-S cluster demands under this condition. Taken together, we conclude that the copper efflux system CusCFBA is induced during anaerobic amino acid limitation to protect Fe-S cluster enzymes and biogenesis from the endogenously originated Cu(I) toxicity, thus facilitating the physiological adaptation of E. coli.
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