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Crofts TS, Gasparrini AJ, Dantas G. Next-generation approaches to understand and combat the antibiotic resistome. Nat Rev Microbiol 2017; 15:422-434. [PMID: 28392565 DOI: 10.1038/nrmicro.2017.28] [Citation(s) in RCA: 309] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities. As the study of antibiotic resistance advances, it is important to incorporate this comprehensive approach to better inform global antibiotic resistance surveillance and antibiotic development. It is increasingly becoming apparent that although not all resistance genes are likely to geographically and phylogenetically disseminate, the threat presented by those that are is serious and warrants an interdisciplinary research focus. In this Review, we highlight seminal work in the resistome field, discuss recent advances in the studies of resistomes, and propose a resistome paradigm that can pave the way for the improved proactive identification and mitigation of emerging antibiotic resistance threats.
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Affiliation(s)
- Terence S Crofts
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA
| | - Andrew J Gasparrini
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine.,Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA
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Meadow JF, Altrichter AE, Bateman AC, Stenson J, Brown GZ, Green JL, Bohannan BJM. Humans differ in their personal microbial cloud. PeerJ 2015; 3:e1258. [PMID: 26417541 PMCID: PMC4582947 DOI: 10.7717/peerj.1258] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/02/2015] [Indexed: 12/26/2022] Open
Abstract
Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.
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Affiliation(s)
- James F Meadow
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR , USA
| | - Adam E Altrichter
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR , USA
| | - Ashley C Bateman
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR , USA
| | - Jason Stenson
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Architecture, Energy Studies in Buildings Laboratory, University of Oregon , Eugene, OR , USA
| | - G Z Brown
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Architecture, Energy Studies in Buildings Laboratory, University of Oregon , Eugene, OR , USA
| | - Jessica L Green
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR , USA ; Santa Fe Institute , Santa Fe, NM , USA
| | - Brendan J M Bohannan
- Biology and the Built Environment Center, University of Oregon , Eugene, OR , USA ; Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR , USA
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Milshteyn A, Schneider JS, Brady SF. Mining the metabiome: identifying novel natural products from microbial communities. CHEMISTRY & BIOLOGY 2014; 21:1211-23. [PMID: 25237864 PMCID: PMC4171686 DOI: 10.1016/j.chembiol.2014.08.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022]
Abstract
Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.
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Affiliation(s)
- Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jessica S Schneider
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Abstract
This review focuses on the era of antibiosis that led to a better understanding of bacterial morphology, in particular the cell wall component peptidoglycan. This is an effort to take readers on a tour de force from the concept of antibiosis, to the serendipity of antibiotics, evolution of beta-lactam development, and the molecular biology of antibiotic resistance. These areas of research have culminated in a deeper understanding of microbiology, particularly in the area of bacterial cell wall synthesis and recycling. In spite of this knowledge, which has enabled design of new even more effective therapeutics to combat bacterial infection and has provided new research tools, antibiotic resistance remains a worldwide health care problem.
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Affiliation(s)
- Kok-Fai Kong
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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Linden B. Basic Blue Skies Research in the UK: Are we losing out? JOURNAL OF BIOMEDICAL DISCOVERY AND COLLABORATION 2008; 3:3. [PMID: 18312612 PMCID: PMC2292148 DOI: 10.1186/1747-5333-3-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 02/29/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND The term blue skies research implies a freedom to carry out flexible, curiosity-driven research that leads to outcomes not envisaged at the outset. This research often challenges accepted thinking and introduces new fields of study. Science policy in the UK has given growing support for short-term goal-oriented scientific research projects, with pressure being applied on researchers to demonstrate the future application of their work. These policies carry the risk of restricting freedom, curbing research direction, and stifling rather than stimulating the creativity needed for scientific discovery. METHODS This study tracks the tortuous routes that led to three major discoveries in cardiology. It then investigates the constraints in current research, and opportunities that may be lost with existing funding processes, by interviewing selected scientists and fund providers for their views on curiosity-driven research and the freedom needed to allow science to flourish. The transcripts were analysed using a grounded theory approach to gather recurrent themes from the interviews. RESULTS The results from these interviews suggest that scientists often cannot predict the future applications of research. Constraints such as lack of scientific freedom, and a narrow focus on relevance and accountability were believed to stifle the discovery process. Although it was acknowledged that some research projects do need a clear and measurable framework, the interviewees saw a need for inquisitive, blue skies research to be managed in a different way. They provided examples of situations where money allocated to 'safe' funding was used for more innovative research. CONCLUSION This sample of key UK scientists and grant providers acknowledge the importance of basic blue skies research. Yet the current evaluation process often requires that scientists predict their likely findings and estimate short-term impact, which does not permit freedom of research direction. There is a vital need for prominent scientists and for universities to help the media, the public, and policy makers to understand the importance of innovative thought along with the need for scientists to have the freedom to challenge accepted thinking. Encouraging an avenue for blue skies research could have immense influence over future scientific discoveries.
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