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McBee RM, Lucht M, Mukhitov N, Richardson M, Srinivasan T, Meng D, Chen H, Kaufman A, Reitman M, Munck C, Schaak D, Voigt C, Wang HH. Engineering living and regenerative fungal-bacterial biocomposite structures. Nat Mater 2022; 21:471-478. [PMID: 34857911 DOI: 10.1038/s41563-021-01123-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Engineered living materials could have the capacity to self-repair and self-replicate, sense local and distant disturbances in their environment, and respond with functionalities for reporting, actuation or remediation. However, few engineered living materials are capable of both responsivity and use in macroscopic structures. Here we describe the development, characterization and engineering of a fungal-bacterial biocomposite grown on lignocellulosic feedstocks that can form mouldable, foldable and regenerative living structures. We have developed strategies to make human-scale biocomposite structures using mould-based and origami-inspired growth and assembly paradigms. Microbiome profiling of the biocomposite over multiple generations enabled the identification of a dominant bacterial component, Pantoea agglomerans, which was further isolated and developed into a new chassis. We introduced engineered P. agglomerans into native feedstocks to yield living blocks with new biosynthetic and sensing-reporting capabilities. Bioprospecting the native microbiota to develop engineerable chassis constitutes an important strategy to facilitate the development of living biomaterials with new properties and functionalities.
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Affiliation(s)
- Ross M McBee
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Nikita Mukhitov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Miles Richardson
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Tarun Srinivasan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Dechuan Meng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haorong Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Kaufman
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Christian Munck
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Christopher Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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Dehem A, Mazieres J, Chour A, Guisier F, Ferreira M, Boussageon M, Girard N, Moro-Sibilot D, Cadranel J, Zalcman G, Ricordel C, Wislez M, Munck C, Poulet CH, Gauvain C, Descarpentries C, Wasielewski E, Cortot A, Baldacci S. 1341P NRAS mutated non-small cell lung cancer (NSCLC) patients: Characteristics and outcomes. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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3
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Ellabaan MMH, Munck C, Porse A, Imamovic L, Sommer MOA. Forecasting the dissemination of antibiotic resistance genes across bacterial genomes. Nat Commun 2021; 12:2435. [PMID: 33893312 PMCID: PMC8065159 DOI: 10.1038/s41467-021-22757-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/19/2021] [Indexed: 01/22/2023] Open
Abstract
Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination.
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Affiliation(s)
- Mostafa M H Ellabaan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Porse
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lejla Imamovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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4
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Munck C, Sheth RU, Cuaresma E, Weidler J, Stump SL, Zachariah P, Chong DH, Uhlemann AC, Abrams JA, Wang HH, Freedberg DE. The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study. Crit Care 2020; 24:404. [PMID: 32646458 PMCID: PMC7350675 DOI: 10.1186/s13054-020-03061-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The need for early antibiotics in the intensive care unit (ICU) is often balanced against the goal of antibiotic stewardship. Long-course antibiotics increase the burden of antimicrobial resistance within colonizing gut bacteria, but the dynamics of this process are not fully understood. We sought to determine how short-course antibiotics affect the antimicrobial resistance phenotype and genotype of colonizing gut bacteria in the ICU by performing a prospective cohort study with assessments of resistance at ICU admission and exactly 72 h later. METHODS Deep rectal swabs were performed on 48 adults at the time of ICU admission and exactly 72 h later, including patients who did and did not receive antibiotics. To determine resistance phenotype, rectal swabs were cultured for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). In addition, Gram-negative bacterial isolates were cultured against relevant antibiotics. To determine resistance genotype, quantitative PCR (qPCR) was performed from rectal swabs for 87 established resistance genes. Within-individual changes in antimicrobial resistance were calculated based on culture and qPCR results and correlated with exposure to relevant antibiotics (e.g., did β-lactam antibiotic exposure associate with a detectable change in β-lactam resistance over this 72-h period?). RESULTS Of 48 ICU patients, 41 (85%) received antibiotics. Overall, there was no increase in the antimicrobial resistance profile of colonizing gut bacteria during the 72-h study period. There was also no increase in antimicrobial resistance after stratification by receipt of antibiotics (i.e., no detectable increase in β-lactam, vancomycin, or macrolide resistance regardless of whether patients received those same antibiotics). This was true for both culture and PCR. Antimicrobial resistance pattern at ICU admission strongly predicted resistance pattern after 72 h. CONCLUSIONS Short-course ICU antibiotics made little detectable difference in the antimicrobial resistance pattern of colonizing gut bacteria over 72 h in the ICU. This provides an improved understanding of the dynamics of antimicrobial resistance in the ICU and some reassurance that short-course antibiotics may not adversely impact the stewardship goal of reducing antimicrobial resistance.
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Affiliation(s)
- Christian Munck
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA.
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Edward Cuaresma
- Department of Medicine, Columbia University Irving Medical Center, New York, USA
| | - Jessica Weidler
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Stephania L Stump
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Philip Zachariah
- Division of Pediatric Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - David H Chong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA.
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Porse A, Schou TS, Munck C, Ellabaan MMH, Sommer MOA. Biochemical mechanisms determine the functional compatibility of heterologous genes. Nat Commun 2018; 9:522. [PMID: 29410400 PMCID: PMC5802803 DOI: 10.1038/s41467-018-02944-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/09/2018] [Indexed: 11/28/2022] Open
Abstract
Elucidating the factors governing the functional compatibility of horizontally transferred genes is important to understand bacterial evolution, including the emergence and spread of antibiotic resistance, and to successfully engineer biological systems. In silico efforts and work using single-gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast to previous work, we find that GC content, codon usage, and mRNA-folding energy are of minor importance for the compatibility of mechanistically diverse gene products at moderate expression. Instead, we identify the phylogenetic origin, and the dependence of a resistance mechanism on host physiology, as major factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance. Sequence composition is thought to be a major factor governing the functionality of horizontally transferred genes. In contrast, Porse et al. show that phylogenetic origin, and the type of resistance mechanism, are major factors affecting the functionality of horizontally transferred antibiotic resistance genes.
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Affiliation(s)
- Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Thea S Schou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Christian Munck
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
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6
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Gumpert H, Kubicek-Sutherland JZ, Porse A, Karami N, Munck C, Linkevicius M, Adlerberth I, Wold AE, Andersson DI, Sommer MOA. Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment. Front Microbiol 2017; 8:1852. [PMID: 29018426 PMCID: PMC5622998 DOI: 10.3389/fmicb.2017.01852] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics. Using whole genome sequencing, we observed large genomic deletions, bacteriophage infections, as well as the loss and acquisition of plasmids in these lineages during their colonization of the human gut. In particular, we captured the exchange of multidrug resistance genes, and identified a clinically relevant conjugative plasmid mediating the transfer. This resistant transconjugant lineage was maintained for months, demonstrating that antibiotic resistance genes can disseminate and persist in the gut microbiome; even in absence of antibiotic selection. Furthermore, through in vivo competition assays, we suggest that the resistant transconjugant can persist through a fitness advantage in the mouse gut in spite of a fitness cost in vitro. Our findings highlight the dynamic nature of the human gut microbiota and provide the first genomic description of antibiotic resistance gene transfer between bacteria in the unperturbed human gut. These results exemplify that conjugative plasmids, harboring resistance determinants, can transfer and persists in the gut in the absence of antibiotic treatment.
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Affiliation(s)
- Heidi Gumpert
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.,Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | | | - Andreas Porse
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Marius Linkevicius
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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7
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Sommer MOA, Munck C, Toft-Kehler RV, Andersson DI. Prediction of antibiotic resistance: time for a new preclinical paradigm? Nat Rev Microbiol 2017; 15:689-696. [DOI: 10.1038/nrmicro.2017.75] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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8
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Jiang X, Ellabaan MMH, Charusanti P, Munck C, Blin K, Tong Y, Weber T, Sommer MOA, Lee SY. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat Commun 2017; 8:15784. [PMID: 28589945 PMCID: PMC5467266 DOI: 10.1038/ncomms15784] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/27/2017] [Indexed: 12/25/2022] Open
Abstract
It has been hypothesized that some antibiotic resistance genes (ARGs) found in pathogenic bacteria derive from antibiotic-producing actinobacteria. Here we provide bioinformatic and experimental evidence supporting this hypothesis. We identify genes in proteobacteria, including some pathogens, that appear to be closely related to actinobacterial ARGs known to confer resistance against clinically important antibiotics. Furthermore, we identify two potential examples of recent horizontal transfer of actinobacterial ARGs to proteobacterial pathogens. Based on this bioinformatic evidence, we propose and experimentally test a 'carry-back' mechanism for the transfer, involving conjugative transfer of a carrier sequence from proteobacteria to actinobacteria, recombination of the carrier sequence with the actinobacterial ARG, followed by natural transformation of proteobacteria with the carrier-sandwiched ARG. Our results support the existence of ancient and, possibly, recent transfers of ARGs from antibiotic-producing actinobacteria to proteobacteria, and provide evidence for a defined mechanism.
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Affiliation(s)
- Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Mostafa M. Hashim Ellabaan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Morten O. A. Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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9
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Hickman RA, Munck C, Sommer MOA. Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs. Front Microbiol 2017; 8:893. [PMID: 28596757 PMCID: PMC5442168 DOI: 10.3389/fmicb.2017.00893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/03/2017] [Indexed: 12/18/2022] Open
Abstract
Understanding the evolutionary processes that lead to antibiotic resistance can help to achieve better treatment strategies. Yet, little is known about the dynamics of the resistance alleles during adaptation. Here, we use population sequencing to monitor genetic changes in putative resistance loci at several time-points during adaptive evolution experiments involving five different antibiotic conditions. We monitor the mutational spectra in lineages evolved to be resistant to single antibiotics [amikacin (AMK), chloramphenicol (CHL), and ciprofloxacin (CIP)], as well as antibiotic combinations (AMK + CHL and CHL + CIP). We find that lineages evolved to antibiotic combinations exhibit different resistance allele dynamics compared with those of single-drug evolved lineages, especially for a drug pair with reciprocal collateral sensitivity. During adaptation, we observed interfering, superimposing and fixation allele dynamics. To further understand the selective forces driving specific allele dynamics, a subset of mutations were introduced into the ancestral wild type enabling differentiation between clonal interference and negative epistasis.
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Affiliation(s)
- Rachel A Hickman
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
| | - Christian Munck
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
| | - Morten O A Sommer
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
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10
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Jahn LJ, Munck C, Ellabaan MMH, Sommer MOA. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes. Front Microbiol 2017; 8:816. [PMID: 28553265 PMCID: PMC5425606 DOI: 10.3389/fmicb.2017.00816] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 12/01/2022] Open
Abstract
Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution. However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes are simpler to implement and therefore allow higher throughput. The specific regimen of adaptive evolution may have a profound impact on the adapted cell state. Indeed, substantial effects of the selection regime on the resulting geno- and phenotypes have been reported in the literature. In this study we compare the geno- and phenotypes of Escherichia coli after evolution to Amikacin, Piperacillin, and Tetracycline under four different selection regimes. Interestingly, key mutations that confer antibiotic resistance as well as phenotypic changes like collateral sensitivity and cross-resistance emerge independently of the selection regime. Yet, lineages that underwent evolution under mild selection displayed a growth advantage independently of the acquired level of antibiotic resistance compared to lineages adapted under maximal selection in a drug gradient. Our data suggests that even though different selection regimens result in subtle genotypic and phenotypic differences key adaptations appear independently of the selection regime.
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Affiliation(s)
- Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Christian Munck
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
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11
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Soltana WB, Munck C, Baert G, Mordon S, Betrouni N. Real-time light dosimetry for intra-cavity photodynamic therapy. Photodiagnosis Photodyn Ther 2017. [DOI: 10.1016/j.pdpdt.2017.01.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Munck C, Betrouni N, Mordon S. Illumination profile characterization of a light applicator. Photodiagnosis Photodyn Ther 2017. [DOI: 10.1016/j.pdpdt.2017.01.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Large conjugative plasmids are important drivers of bacterial evolution and contribute significantly to the dissemination of antibiotic resistance. Although plasmid borne multidrug resistance is recognized as one of the main challenges in modern medicine, the adaptive forces shaping the evolution of these plasmids within pathogenic hosts are poorly understood. Here we study plasmid–host adaptations following transfer of a 73 kb conjugative multidrug resistance plasmid to naïve clinical isolates of Klebsiella pneumoniae and Escherichia coli. We use experimental evolution, mathematical modelling and population sequencing to show that the long-term persistence and molecular integrity of the plasmid is highly influenced by multiple factors within a 25 kb plasmid region constituting a host-dependent burden. In the E. coli hosts investigated here, improved plasmid stability readily evolves via IS26 mediated deletions of costly regions from the plasmid backbone, effectively expanding the host-range of the plasmid. Although these adaptations were also beneficial to plasmid persistence in a naïve K. pneumoniae host, they were never observed in this species, indicating that differential evolvability can limit opportunities of plasmid adaptation. While insertion sequences are well known to supply plasmids with adaptive traits, our findings suggest that they also play an important role in plasmid evolution by maintaining the plasticity necessary to alleviate plasmid–host constrains. Further, the observed evolutionary strategy consistently followed by all evolved E. coli lineages exposes a trade-off between horizontal and vertical transmission that may ultimately limit the dissemination potential of clinical multidrug resistance plasmids in these hosts.
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Affiliation(s)
- Andreas Porse
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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14
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Munck C, Helby J, Westergaard CG, Porsbjerg C, Backer V, Hansen LH. Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients. PLoS One 2016; 11:e0158622. [PMID: 27391160 PMCID: PMC4938234 DOI: 10.1371/journal.pone.0158622] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/20/2016] [Indexed: 02/03/2023] Open
Abstract
Asthma is a common disease causing cough, wheezing and shortness of breath. It has been shown that the lung microbiota in asthma patients is different from the lung microbiota in healthy controls suggesting that a connection between asthma and the lung microbiome exists. Individuals with asthma who are also tobacco smokers experience more severe asthma symptoms and smoking cessation is associated with improved asthma control. In the present study we investigated if smoking cessation in asthma patients is associated with a change in the bacterial community in the lungs, examined using induced sputum. We found that while tobacco smokers with asthma have a greater bacterial diversity in the induced sputum compared to non-smoking healthy controls, smoking cessation does not lead to a change in the microbial diversity.
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Affiliation(s)
- Christian Munck
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, Hørsholm, Denmark
- * E-mail: (CM); (LHH)
| | - Jens Helby
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | | | - Celeste Porsbjerg
- Respiratory Research Unit, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Vibeke Backer
- Respiratory Research Unit, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Lars H. Hansen
- Aarhus University, Department of Environmental Science, Roskilde, Denmark
- * E-mail: (CM); (LHH)
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15
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Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehár J, Sommer MOA. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis. PLoS One 2016; 11:e0147651. [PMID: 26821252 PMCID: PMC4731467 DOI: 10.1371/journal.pone.0147651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 01/06/2016] [Indexed: 01/09/2023] Open
Abstract
Flux balance analysis (FBA) is an increasingly useful approach for modeling the behavior of metabolic systems. However, standard FBA modeling of genetic knockouts cannot predict drug combination synergies observed between serial metabolic targets, even though such synergies give rise to some of the most widely used antibiotic treatments. Here we extend FBA modeling to simulate responses to chemical inhibitors at varying concentrations, by diverting enzymatic flux to a waste reaction. This flux diversion yields very similar qualitative predictions to prior methods for single target activity. However, we find very different predictions for combinations, where flux diversion, which mimics the kinetics of competitive metabolic inhibitors, can explain serial target synergies between metabolic enzyme inhibitors that we confirmed in Escherichia coli cultures. FBA flux diversion opens the possibility for more accurate genome-scale predictions of drug synergies, which can be used to suggest treatments for infections and other diseases.
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Affiliation(s)
- Andrew S. Krueger
- Boston University, 44 Cummington St, Boston, MA, United States of America
| | - Christian Munck
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Hørsholm, Denmark
| | - Gautam Dantas
- Center for Genome Science & Systems Biology, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - James Galagan
- Boston University, 44 Cummington St, Boston, MA, United States of America
- Broad Institute, Cambridge Center, Cambridge, Massachusetts, United States of America
| | - Joseph Lehár
- Boston University, 44 Cummington St, Boston, MA, United States of America
- * E-mail: (JL); (MOAS)
| | - Morten O. A. Sommer
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Hørsholm, Denmark
- * E-mail: (JL); (MOAS)
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Fry S, Mallart A, Lamblin C, Wallaert B, Munck C. Prévalence des troubles du sommeil chez des patients suivis pour une pneumopathie infiltrante diffuse fibrosante. Rev Mal Respir 2016. [DOI: 10.1016/j.rmr.2015.10.686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MOA. Limited dissemination of the wastewater treatment plant core resistome. Nat Commun 2015; 6:8452. [PMID: 26419330 PMCID: PMC4598724 DOI: 10.1038/ncomms9452] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/21/2015] [Indexed: 01/28/2023] Open
Abstract
Horizontal gene transfer is a major contributor to the evolution of bacterial genomes and can facilitate the dissemination of antibiotic resistance genes between environmental reservoirs and potential pathogens. Wastewater treatment plants (WWTPs) are believed to play a central role in the dissemination of antibiotic resistance genes. However, the contribution of the dominant members of the WWTP resistome to resistance in human pathogens remains poorly understood. Here we use a combination of metagenomic functional selections and comprehensive metagenomic sequencing to uncover the dominant genes of the WWTP resistome. We find that this core resistome is unique to the WWTP environment, with <10% of the resistance genes found outside the WWTP environment. Our data highlight that, despite an abundance of functional resistance genes within WWTPs, only few genes are found in other environments, suggesting that the overall dissemination of the WWTP resistome is comparable to that of the soil resistome.
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Affiliation(s)
- Christian Munck
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, DK-2970 Hørsholm, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Amar Telke
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Mostafa Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, DK-2970 Hørsholm, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, DK-2970 Hørsholm, Denmark
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Munck C, Mordon S, Scherpereel A, Porte H, Dhalluin X, Betrouni N. Dosimetry optimization of intrapleural photodynamic therapy for malignant pleural mesothelioma. Photodiagnosis Photodyn Ther 2015. [DOI: 10.1016/j.pdpdt.2015.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Munck C, Gumpert HK, Wallin AIN, Wang HH, Sommer MOA. Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci Transl Med 2015; 6:262ra156. [PMID: 25391482 DOI: 10.1126/scitranslmed.3009940] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Resistance arises quickly during chemotherapeutic selection and is particularly problematic during long-term treatment regimens such as those for tuberculosis, HIV infections, or cancer. Although drug combination therapy reduces the evolution of drug resistance, drug pairs vary in their ability to do so. Thus, predictive models are needed to rationally design resistance-limiting therapeutic regimens. Using adaptive evolution, we studied the resistance response of the common pathogen Escherichia coli to 5 different single antibiotics and all 10 different antibiotic drug pairs. By analyzing the genomes of all evolved E. coli lineages, we identified the mutational events that drive the differences in drug resistance levels and found that the degree of resistance development against drug combinations can be understood in terms of collateral sensitivity and resistance that occurred during adaptation to the component drugs. Then, using engineered E. coli strains, we confirmed that drug resistance mutations that imposed collateral sensitivity were suppressed in a drug pair growth environment. These results provide a framework for rationally selecting drug combinations that limit resistance evolution.
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Affiliation(s)
- Christian Munck
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Heidi K Gumpert
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Annika I Nilsson Wallin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Morten O A Sommer
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
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Rodriguez de Evgrafov M, Gumpert H, Munck C, Thomsen TT, Sommer MOA. Collateral Resistance and Sensitivity Modulate Evolution of High-Level Resistance to Drug Combination Treatment in Staphylococcus aureus. Mol Biol Evol 2015; 32:1175-85. [PMID: 25618457 DOI: 10.1093/molbev/msv006] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
As drug-resistant pathogens continue to emerge, combination therapy will increasingly be relied upon to treat infections and to help combat further development of multidrug resistance. At present a dichotomy exists between clinical practice, which favors therapeutically synergistic combinations, and the scientific model emerging from in vitro experimental work, which maintains that this interaction provides greater selective pressure toward resistance development than other interaction types. We sought to extend the current paradigm, based on work below or near minimum inhibitory concentration levels, to reflect drug concentrations more likely to be encountered during treatment. We performed a series of adaptive evolution experiments using Staphylococcus aureus. Interestingly, no relationship between drug interaction type and resistance evolution was found as resistance increased significantly beyond wild-type levels. All drug combinations, irrespective of interaction types, effectively limited resistance evolution compared with monotreatment. Cross-resistance and collateral sensitivity were found to be important factors in the extent of resistance evolution toward a combination. Comparative genomic analyses revealed that resistance to drug combinations was mediated largely by mutations in the same genes as single-drug-evolved lineages highlighting the importance of the component drugs in determining the rate of resistance evolution. Results of this work suggest that the mechanisms of resistance to constituent drugs should be the focus of future resistance evolution work.
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Affiliation(s)
| | - Heidi Gumpert
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Munck
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Thomas T Thomsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten O A Sommer
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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Westergaard CG, Munck C, Helby J, Porsbjerg C, Hansen LH, Backer V. Predictors of neutrophilic airway inflammation in young smokers with asthma. J Asthma 2014; 51:341-7. [PMID: 24404796 DOI: 10.3109/02770903.2014.880718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
INTRODUCTION Asthma is one of the most widespread chronic diseases worldwide. In spite of numerous detrimental effects on asthma, smoking is common among asthma patients. These smoking-induced aggravations of asthma may be attributed to changes in airway inflammation, which is characterized by a higher degree of neutrophilic inflammation than in non-smokers. A state of neutrophilic inflammation may lead to increased steroid resistance and an accelerated loss of lung function owing to tissue destruction. The aim of this study was to elucidate predictors of neutrophilic inflammation in young asthmatic smokers not on steroid treatment, including analysis of tobacco history and bacterial colonization. METHODS In a cross-sectional study, 52 steroid-free, current smokers with asthma were examined with induced sputum, fractional exhaled nitric oxide (FeNO), lung function, ACQ6 score, mannitol and methacholine challenge. A sample from the sputum induction was taken for bacterial analysis using 16S gene PCR technique and sequencing. RESULTS Using one-way analysis of variance and binary and linear regression models, only age and ACQ6 score were found to be significant predictors for airway neutrophilia. The investigation also included analysis for effect of pack years, current tobacco consumption, body mass index, lung function, FeNO; methacholine and mannitol responsiveness, atopy, gender, asthma history and presence of bacteria. The most common potentially pathogenic bacteria found were Streptococcus spp., Haemophilus spp. and Mycoplasma spp. CONCLUSION In this study, no tobacco-related predictors of airway neutrophilia were found, indicating that in the younger years of asthma patients who smoke, the amount of tobacco smoked in life does not influence the degree of neutrophilia. Conversely, for asthmatic smokers, neutrophilia may be induced when a certain threshold of tobacco consumption is reached.
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Moore AM, Munck C, Sommer MOA, Dantas G. Functional metagenomic investigations of the human intestinal microbiota. Front Microbiol 2011; 2:188. [PMID: 22022321 PMCID: PMC3195301 DOI: 10.3389/fmicb.2011.00188] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 08/23/2011] [Indexed: 12/15/2022] Open
Abstract
The human intestinal microbiota encode multiple critical functions impacting human health, including metabolism of dietary substrate, prevention of pathogen invasion, immune system modulation, and provision of a reservoir of antibiotic resistance genes accessible to pathogens. The complexity of this microbial community, its recalcitrance to standard cultivation, and the immense diversity of its encoded genes has necessitated the development of novel molecular, microbiological, and genomic tools. Functional metagenomics is one such culture-independent technique, used for decades to study environmental microorganisms, but relatively recently applied to the study of the human commensal microbiota. Metagenomic functional screens characterize the functional capacity of a microbial community, independent of identity to known genes, by subjecting the metagenome to functional assays in a genetically tractable host. Here we highlight recent work applying this technique to study the functional diversity of the intestinal microbiota, and discuss how an approach combining high-throughput sequencing, cultivation, and metagenomic functional screens can improve our understanding of interactions between this complex community and its human host.
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Affiliation(s)
- Aimee M Moore
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine St. Louis, MO, USA
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Abstract
A survey of dental schools in the European Union was carried out for two main reasons. Firstly to promote the exchange of information in respect of curriculum objectives in the different countries and secondly to ascertain the differences in the interpretation of the 1978 EU sectoral directives for dental education and training. Out of 127 schools, only 30 responded, yet the information provided is of considerable importance. It demonstrates wide divergence in the interpretation of the 1978 Directives and methods of assessment of clinical competence. There is a considerable difference throughout Europe in hours devoted to the various subjects included in the Dental Directives. There is little evidence of convergence in methods of assessment or quality assurance. The survey demonstrates the difference in resources, levels of staff, availability of clinical training places, output in research and patient treatments throughout the European Union. The results question the effectiveness of the 1978 Dental Directives in promoting convergence of standards. As there is free movement of dentists throughout the European Union, it is concluded that a different approach may be necessary to ensure that all European Union dental graduates achieve comparable standards in their education and training.
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Affiliation(s)
- D B Shanley
- School of Dental Science, Trinity College, Dublin, Ireland
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Munck C. [History--wear it with honor. Interview by Grethe Kjaergaard]. Sygeplejersken 1992; 92:12-4. [PMID: 1293802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Helm S, Kreiborg S, Barlebo J, Caspersen I, Eriksen JH, Hansen W, Hanusardottir B, Munck C, Perregaard J, Prydso U, Reumert C, Spedtsberg H. [Evaluation of orthodontic treatment in a Danish school population]. Mondo Ortod 1977; 19:100-9. [PMID: 277774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Helm S, Kreiborg S, Barlebo J, Caspersen I, Eriksen JH, Hansen W, Hanusardottir B, Munck C, Perregaard J, Prydsö U, Reumert C, Spedtsberg H. Estimates of orthodontic treatment need in Danish schoolchildren. Community Dent Oral Epidemiol 1975; 3:136-42. [PMID: 1056819 DOI: 10.1111/j.1600-0528.1975.tb00295.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Orthodontic treatment need has been assessed on the basis of complete orthodontic records in a random sample of 293 Danish children aged 13-17 years by a group of postgraduate orthodontic students and by three orthodontists. The estimates of treatment need ranged from 45% to 61%. Interexaminer agreement in pairs was observed in 77%-92% (mean 83%) of the cases. Uniformity in four individual assessments was reached in 69% of the cases: 38% were considered in need of treatment and 31% were considered not to present such need; conversely, 31% gave rise to disagreement. It is argued that, at present, the orthodontist's subjective estimate of treatment need probably constitutes a more realistic approach to the problem of assigning treatment priority than the various indices of malocclusion.
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