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Ma HR, Xu HZ, Kim K, Anderson DJ, You L. Private benefit of β-lactamase dictates selection dynamics of combination antibiotic treatment. Nat Commun 2024; 15:8337. [PMID: 39333122 PMCID: PMC11436977 DOI: 10.1038/s41467-024-52711-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 09/19/2024] [Indexed: 09/29/2024] Open
Abstract
β-lactam antibiotics have been prescribed for most bacterial infections since their discovery. However, resistance to β-lactams, mediated by β-lactamase (Bla) enzymes such as extended spectrum β-lactamases (ESBLs), has become widespread. Bla inhibitors can restore the efficacy of β-lactams against resistant bacteria, an approach which preserves existing antibiotics despite declining industry investment. However, the effects of combination treatment on selection for β-lactam resistance are not well understood. Bla production confers both private benefits for resistant cells and public benefits which faster-growing sensitive cells can also exploit. These benefits may be differentially impacted by Bla inhibitors, leading to non-intuitive selection dynamics. In this study, we demonstrate strain-to-strain variation in effective combination doses, with complex growth dynamics in mixed populations. Using modeling, we derive a criterion for the selection outcome of combination treatment, dependent on the burden and effective private benefit of Bla production. We then use engineered strains and natural isolates to show that strong private benefits of Bla are associated with increased selection for resistance. Finally, we demonstrate that this parameter can be coarsely estimated using high-throughput phenotyping of clonal populations. Our analysis shows that quantifying the phenotypic responses of bacteria to combination treatment can facilitate resistance-minimizing optimization of treatment.
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Affiliation(s)
- Helena R Ma
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
| | - Helen Z Xu
- Department of Biology, Duke University, Durham, NC, USA
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
| | - Deverick J Anderson
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University School of Medicine, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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2
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Şimşek E, Kim K, Lu J, Silver A, Luo N, Lee CT, You L. A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Mol Syst Biol 2024; 20:880-897. [PMID: 38877321 PMCID: PMC11297297 DOI: 10.1038/s44320-024-00046-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/16/2024] Open
Abstract
Bacteria in nature often form surface-attached communities that initially comprise distinct subpopulations, or patches. For pathogens, these patches can form at infection sites, persist during antibiotic treatment, and develop into mature biofilms. Evidence suggests that patches can emerge due to heterogeneity in the growth environment and bacterial seeding, as well as cell-cell signaling. However, it is unclear how these factors contribute to patch formation and how patch formation might affect bacterial survival and evolution. Here, we demonstrate that a 'rich-get-richer' mechanism drives patch formation in bacteria exhibiting collective survival (CS) during antibiotic treatment. Modeling predicts that the seeding heterogeneity of these bacteria is amplified by local CS and global resource competition, leading to patch formation. Increasing the dose of a non-eradicating antibiotic treatment increases the degree of patchiness. Experimentally, we first demonstrated the mechanism using engineered Escherichia coli and then demonstrated its applicability to a pathogen, Pseudomonas aeruginosa. We further showed that the formation of P. aeruginosa patches promoted the evolution of antibiotic resistance. Our work provides new insights into population dynamics and resistance evolution during surface-attached bacterial growth.
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Affiliation(s)
- Emrah Şimşek
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Anita Silver
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Charlotte T Lee
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27708, USA.
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3
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Le Quellec L, Aristov A, Gutiérrez Ramos S, Amselem G, Bos J, Baharoglu Z, Mazel D, Baroud CN. Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations. PLoS One 2024; 19:e0303630. [PMID: 39088440 PMCID: PMC11293721 DOI: 10.1371/journal.pone.0303630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/30/2024] [Indexed: 08/03/2024] Open
Abstract
The emergence of new resistant bacterial strains is a worldwide challenge. A resistant bacterial population can emerge from a single cell that acquires resistance or persistence. Hence, new ways of tackling the mechanism of antibiotic response, such as single cell studies are required. It is necessary to see what happens at the single cell level, in order to understand what happens at the population level. To date, linking the heterogeneity of single-cell susceptibility to the population-scale response to antibiotics remains challenging due to the trade-offs between the resolution and the field of view. Here we present a platform that measures the ability of individual E. coli cells to form small colonies at different ciprofloxacin concentrations, by using anchored microfluidic drops and an image and data analysis pipelines. The microfluidic results are benchmarked against classical microbiology measurements of antibiotic susceptibility, showing an agreement between the pooled microfluidic chip and replated bulk measurements. Further, the experimental likelihood of a single cell to form a colony is used to provide a probabilistic antibiotic susceptibility curve. In addition to the probabilistic viewpoint, the microfluidic format enables the characterization of morphological features over time for a large number of individual cells. This pipeline can be used to compare the response of different bacterial strains to antibiotics with different action mechanisms.
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Affiliation(s)
- Lena Le Quellec
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Andrey Aristov
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
| | - Salomé Gutiérrez Ramos
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Gabriel Amselem
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Julia Bos
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Bacterial Genome Plasticity Unit, Paris, France
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Bacterial Genome Plasticity Unit, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Bacterial Genome Plasticity Unit, Paris, France
| | - Charles N. Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris, France
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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4
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Qiu M, Fu M, Zhang Z, Fu S, Yuan C. Assessing the ecological risk of croplands in loess drylands by combining environmental disturbance with ecosystem vulnerability. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119231. [PMID: 37804628 DOI: 10.1016/j.jenvman.2023.119231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
Agroecosystems suffer various ecological risks due to the intensive production of crops. However, comprehensive assessments of cropland ecological risks remain limited. This study developed an assessment method for cropland ecological risks by combining environmental disturbance with ecosystem vulnerability. Environmental disturbance reflects stresses caused by risk sources in an environment, while ecosystem vulnerability is the susceptibility of an ecosystem to adverse disturbances and its capacity to cope and adapt. The proposed method is conducive to understanding the complex exposure-response relationship between croplands and environmental stresses. Cropland ecological risk was evaluated by conducting a case study on a loess dryland region in Shaanxi. The hot spots and driving factors of risk were explored using spatial autocorrelation and quantile regression methods, respectively. Results show that overall cropland ecological risk is at medium low level. Risk hot spots are concentrated in the north of the loess dryland. Ecosystem vulnerability exerts greater effect on the distribution of hot spots than environmental disturbance in the study area. Road density (RDD), river density, and soil organic matter exert the most important effects on cropland ecological risk. Moreover, the same driving factor exhibits various effects on cropland ecological risk in different risk level areas. RDD, slope, precipitation, elevation, fertilizer application rate, gross domestic product, and distance to town center have greater effects on risk in regions with high cropland ecological risk than in regions with low cropland ecological risk. The findings of this study must be considered in formulating targeted policies for controlling cropland ecological risk in loess drylands to realize sustainable crop production.
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Affiliation(s)
- Menglong Qiu
- Center for Land Resource Research in Northwest China, Shaanxi Normal University, Xi'an, 710119, China
| | - Mengyu Fu
- Center for Land Resource Research in Northwest China, Shaanxi Normal University, Xi'an, 710119, China
| | - Zhiwei Zhang
- Anqiu Bureau of Agriculture and Rural Affairs, Weifang, 262100, China
| | - Shaowu Fu
- Center for Land Resource Research in Northwest China, Shaanxi Normal University, Xi'an, 710119, China
| | - Chengcheng Yuan
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China.
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5
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Thorogood R, Mustonen V, Aleixo A, Aphalo PJ, Asiegbu FO, Cabeza M, Cairns J, Candolin U, Cardoso P, Eronen JT, Hällfors M, Hovatta I, Juslén A, Kovalchuk A, Kulmuni J, Kuula L, Mäkipää R, Ovaskainen O, Pesonen AK, Primmer CR, Saastamoinen M, Schulman AH, Schulman L, Strona G, Vanhatalo J. Understanding and applying biological resilience, from genes to ecosystems. NPJ BIODIVERSITY 2023; 2:16. [PMID: 39242840 PMCID: PMC11332022 DOI: 10.1038/s44185-023-00022-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/07/2023] [Indexed: 09/09/2024]
Abstract
The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.
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Affiliation(s)
- Rose Thorogood
- HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Ville Mustonen
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Faculty of Science, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - Alexandre Aleixo
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Pedro J Aphalo
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Fred O Asiegbu
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mar Cabeza
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- HELSUS Helsinki Institute of Sustainability Science, University of Helsinki, Helsinki, Finland
| | - Johannes Cairns
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
| | - Ulrika Candolin
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pedro Cardoso
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- CE3C - Centre for Ecology, Evolution and Environmental Changes, CHANGE-Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Jussi T Eronen
- HELSUS Helsinki Institute of Sustainability Science, University of Helsinki, Helsinki, Finland
- Research Programme in Ecosystems and Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- BIOS Research Unit, Helsinki, Finland
| | - Maria Hällfors
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Syke Finnish Environment Institute, Helsinki, Finland
| | - Iiris Hovatta
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Neuroscience Center, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - Aino Juslén
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Syke Finnish Environment Institute, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
- Onego Bio Ltd, Helsinki, Finland
| | - Jonna Kulmuni
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Liisa Kuula
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Raisa Mäkipää
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Otso Ovaskainen
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anu-Katriina Pesonen
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Craig R Primmer
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
| | - Marjo Saastamoinen
- HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alan H Schulman
- Institute of Biotechnology, HiLIFE Helsinki Institute for Life Science, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Leif Schulman
- LUOMUS Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Syke Finnish Environment Institute, Helsinki, Finland
| | - Giovanni Strona
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- European Commission, Joint Research Centre, Directorate D - Sustainable Resources, Ispra, Italy
| | - Jarno Vanhatalo
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Centre for Ecological Change, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
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6
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Hudson CJ, Agostini S, Wada S, Hall-Spencer JM, Connell SD, Harvey BP. Ocean acidification increases the impact of typhoons on algal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161269. [PMID: 36587658 DOI: 10.1016/j.scitotenv.2022.161269] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Long-term environmental change, sudden pulses of extreme perturbation, or a combination of both can trigger regime shifts by changing the processes and feedbacks which determine community assembly, structure, and function, altering the state of ecosystems. Our understanding of the mechanisms that stabilise against regime shifts or lock communities into altered states is limited, yet also critical to anticipating future states, preventing regime shifts, and reversing unwanted state change. Ocean acidification contributes to the restructuring and simplification of algal systems, however the mechanisms through which this occurs and whether additional drivers are involved requires further study. Using monthly surveys over three years at a shallow-water volcanic seep we examined how the composition of algal communities change seasonally and following periods of significant physical disturbance by typhoons at three levels of ocean acidification (equivalent to means of contemporary ∼350 and future ∼500 and 900 μatm pCO2). Sites exposed to acidification were increasingly monopolised by structurally simple, fast-growing turf algae, and were clearly different to structurally complex macrophyte-dominated reference sites. The distinct contemporary and acidified community states were stabilised and maintained at their respective sites by different mechanisms following seasonal typhoon disturbance. Macroalgal-dominated sites were resistant to typhoon damage. In contrast, significant losses of algal biomass represented a near total ecosystem reset by typhoons for the turf-dominated communities at the elevated pCO2 sites (i.e. negligible resistance). A combination of disturbance and subsequent turf recovery maintained the same simplified state between years (elevated CO2 levels promote turf growth following algal removal, inhibiting macroalgal recruitment). Thus, ocean acidification may promote shifts in algal systems towards degraded ecosystem states, and short-term disturbances which reset successional trajectories may 'lock-in' these alternative states of low structural and functional diversity.
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Affiliation(s)
- Callum J Hudson
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth PL4 8AA, UK; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Shigeki Wada
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Jason M Hall-Spencer
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth PL4 8AA, UK; Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Sean D Connell
- Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Ben P Harvey
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan.
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7
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Sheets MB, Tague N, Dunlop MJ. An optogenetic toolkit for light-inducible antibiotic resistance. Nat Commun 2023; 14:1034. [PMID: 36823420 PMCID: PMC9950086 DOI: 10.1038/s41467-023-36670-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Antibiotics are a key control mechanism for synthetic biology and microbiology. Resistance genes are used to select desired cells and regulate bacterial populations, however their use to-date has been largely static. Precise spatiotemporal control of antibiotic resistance could enable a wide variety of applications that require dynamic control of susceptibility and survival. Here, we use light-inducible Cre recombinase to activate expression of drug resistance genes in Escherichia coli. We demonstrate light-activated resistance to four antibiotics: carbenicillin, kanamycin, chloramphenicol, and tetracycline. Cells exposed to blue light survive in the presence of lethal antibiotic concentrations, while those kept in the dark do not. To optimize resistance induction, we vary promoter, ribosome binding site, and enzyme variant strength using chromosome and plasmid-based constructs. We then link inducible resistance to expression of a heterologous fatty acid enzyme to increase production of octanoic acid. These optogenetic resistance tools pave the way for spatiotemporal control of cell survival.
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Affiliation(s)
- Michael B Sheets
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Nathan Tague
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Biological Design Center, Boston University, Boston, MA, 02215, USA.
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8
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Li W, Wang J, Li C, Zong Z, Zhao J, Gao H, Liu D. Achieving Ultrasensitive Chromogenic Probes for Rapid, Direct Detection of Carbapenemase-Producing Bacteria in Sputum. JACS AU 2023; 3:227-238. [PMID: 36711106 PMCID: PMC9875220 DOI: 10.1021/jacsau.2c00607] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
Carbapenemase-producing bacteria (CPB) stand as the most dangerous "superbugs" in the clinic. Rapid point-of-care (POC) detection of CPB in clinical samples is key to timely and effective infection management. We herein report the first ultrasensitive chromogenic probe that allows direct POC detection of CPB in clinical sputum samples at a sample-to-result time of less than 15 min. This chromogenic probe is modularly designed by conjugating the carbapenem core with a benzene derivative bearing an electronegativity-tunable substituent. Unexpectedly high sensitivity was achieved simply by choosing strong electron-withdrawing substituents, such as -N+(CH3)3, without resorting to complex molecular design. Through integrating the probes with a portable paper chip, 24 out of 80 clinical sputum samples from sepsis patients with lung infections were quickly diagnosed as CPB-positive, exhibiting 100% clinical sensitivity and specificity. This low-cost paper chip assay can be readily performed on-site, breaking through the dilemma of rapid CPB detection, especially in resource-limited settings.
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Affiliation(s)
- Wenshuai Li
- State
Key Laboratory of Medicinal Chemical Biology, Research Center for
Analytical Sciences, and Tianjin Key Laboratory of Molecular Recognition
and Biosensing, Frontiers Science Center for New Organic Matter, College
of Chemistry, Nankai University, Tianjin300071, China
| | - Jingjing Wang
- Department
of Intensive Care Unit, Key Laboratory for Critical Care Medicine
of the Ministry of Health, Emergency Medicine Research Institute,
Tianjin First Center Hospital, School of Medicine, Nankai University, Tianjin300071, China
| | - Chen Li
- College
of Arts and Sciences, Shanxi Agricultural
University, Taigu030801, China
| | - Zhiyou Zong
- State
Key Laboratory of Medicinal Chemical Biology, Research Center for
Analytical Sciences, and Tianjin Key Laboratory of Molecular Recognition
and Biosensing, Frontiers Science Center for New Organic Matter, College
of Chemistry, Nankai University, Tianjin300071, China
| | - Jinzhong Zhao
- College
of Arts and Sciences, Shanxi Agricultural
University, Taigu030801, China
| | - Hongmei Gao
- Department
of Intensive Care Unit, Key Laboratory for Critical Care Medicine
of the Ministry of Health, Emergency Medicine Research Institute,
Tianjin First Center Hospital, School of Medicine, Nankai University, Tianjin300071, China
| | - Dingbin Liu
- State
Key Laboratory of Medicinal Chemical Biology, Research Center for
Analytical Sciences, and Tianjin Key Laboratory of Molecular Recognition
and Biosensing, Frontiers Science Center for New Organic Matter, College
of Chemistry, Nankai University, Tianjin300071, China
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9
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Sharma U, Rawat D, Mukherjee P, Farooqi F, Mishra V, Sharma RS. Ecological life strategies of microbes in response to antibiotics as a driving factor in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158791. [PMID: 36108841 DOI: 10.1016/j.scitotenv.2022.158791] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.
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Affiliation(s)
- Udita Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Deepak Rawat
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Department of Environmental Studies, Janki Devi Memorial College, University of Delhi, Delhi 110060, India
| | - Paromita Mukherjee
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Furqan Farooqi
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Vandana Mishra
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Centre for Interdisciplinary Studies on Mountain & Hill Environment (CISMHE), University of Delhi, Delhi 110007, India.
| | - Radhey Shyam Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi 110007, India.
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10
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Liu X, Fan D, Feng X, Zheng Y, Wegner SV, Liu M, Chen F, Zeng W. Breaching Bacterial Biofilm Barriers: Efficient Combinatorial Theranostics for Multidrug-Resistant Bacterial Biofilms with a Novel Penetration-Enhanced AIEgen Probe. ACS APPLIED MATERIALS & INTERFACES 2022; 14:41671-41683. [PMID: 36083296 DOI: 10.1021/acsami.2c07378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The formation of microbial biofilms is acknowledged as a major virulence factor in a range of persistent local infections. Failures to remove biofilms with antibiotics foster the emergence of antibiotic-resistant bacteria and result in chronic infections. As a result, the construction of effective biofilm-inhibiting and biofilm-eradicating chemicals is urgently required. Herein, we designed a water-soluble probe APDIS for membrane-active fluorescence and broad-spectrum antimicrobial actions, particularly against methicillin-resistant Staphylococcus aureus (MRSA), which shows multidrug resistance. In vitro and in vivo experiments demonstrate its high antibacterial effects comparable to vancomycin. Furthermore, it inhibits biofilm formation by effectively killing planktonic bacteria at low inhibitory concentrations, without toxicity to mammalian cells. More importantly, this probe can efficiently penetrate through biofilm barriers and exterminate bacteria that are enclosed within biofilms and startle existing biofilms. In the mouse model of implant-related biofilm infections, this probe exhibits strong antibiofilm activity against MRSA biofilms, thus providing a novel theranostic strategy to disrupt biofilms in vivo effectively. Our results indicate that this probe has the potential to be used for the development of a combinatorial theranostic platform with synergistic enhanced effects for the treatment of multidrug-resistant bacterial infections and antibiofilm medications.
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Affiliation(s)
- Xiaohui Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410078, P. R. China
| | - Duoyang Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410078, P. R. China
| | - Xueping Feng
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha 410078, P. R. China
| | - Yanjun Zheng
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Meihui Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410078, P. R. China
| | - Fei Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410078, P. R. China
| | - Wenbin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410078, P. R. China
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11
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Hussan JR, Irwin SG, Mathews B, Swift S, Williams DL, Cornish J. Optimal dose of lactoferrin reduces the resilience of in vitro Staphylococcus aureus colonies. PLoS One 2022; 17:e0273088. [PMID: 35960734 PMCID: PMC9374217 DOI: 10.1371/journal.pone.0273088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/02/2022] [Indexed: 11/19/2022] Open
Abstract
The rise in antibiotic resistance has stimulated research into adjuvants that can improve the efficacy of broad-spectrum antibiotics. Lactoferrin is a candidate adjuvant; it is a multifunctional iron-binding protein with antimicrobial properties. It is known to show dose-dependent antimicrobial activity against Staphylococcus aureus through iron sequestration and repression of β-lactamase expression. However, S. aureus can extract iron from lactoferrin through siderophores for their growth, which confounds the resolution of lactoferrin's method of action. We measured the minimum inhibitory concentration (MIC) for a range of lactoferrin/ β-lactam antibiotic dose combinations and observed that at low doses (< 0.39 μM), lactoferrin contributes to increased S. aureus growth, but at higher doses (> 6.25 μM), iron-depleted native lactoferrin reduced bacterial growth and reduced the MIC of the β-lactam-antibiotic cefazolin. This differential behaviour points to a bacterial population response to the lactoferrin/ β-lactam dose combination. Here, with the aid of a mathematical model, we show that lactoferrin stratifies the bacterial population, and the resulting population heterogeneity is at the basis of the dose dependent response seen. Further, lactoferrin disables a sub-population from β-lactam-induced production of β-lactamase, which when sufficiently large reduces the population's ability to recover after being treated by an antibiotic. Our analysis shows that an optimal dose of lactoferrin acts as a suitable adjuvant to eliminate S. aureus colonies using β-lactams, but sub-inhibitory doses of lactoferrin reduces the efficacy of β-lactams.
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Affiliation(s)
- Jagir R. Hussan
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Stuart G. Irwin
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Brya Mathews
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
| | - Dustin L. Williams
- Department of Microbiology and Immunology, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Jillian Cornish
- Department of Medicine, University of Auckland, Auckland, NZ
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12
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Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight. Nat Commun 2022; 13:3363. [PMID: 35690608 PMCID: PMC9188569 DOI: 10.1038/s41467-022-31033-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2022] [Indexed: 12/19/2022] Open
Abstract
Small-scale, low-cost bioreactors provide exquisite control of environmental parameters of microbial cultures over long durations. Their use is gaining popularity in quantitative systems and synthetic biology. However, existing setups are limited in their measurement capabilities. Here, we present ReacSight, a strategy to enhance bioreactor arrays for automated measurements and reactive experiment control. ReacSight leverages low-cost pipetting robots for sample collection, handling and loading, and provides a flexible instrument control architecture. We showcase ReacSight capabilities on three applications in yeast. First, we demonstrate real-time optogenetic control of gene expression. Second, we explore the impact of nutrient scarcity on fitness and cellular stress using competition assays. Third, we perform dynamic control of the composition of a two-strain consortium. We combine custom or chi.bio reactors with automated cytometry. To further illustrate ReacSight's genericity, we use it to enhance plate-readers with pipetting capabilities and perform repeated antibiotic treatments on a bacterial clinical isolate.
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13
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Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics. Proc Natl Acad Sci U S A 2022; 119:e2116954119. [PMID: 35394868 PMCID: PMC9169654 DOI: 10.1073/pnas.2116954119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAntibiotic exposure stands among the most used interventions to drive microbial communities away from undesired states. How the ecology of microbial communities shapes their recovery-e.g., posttreatment shifts toward Clostridioides difficile infections in the gut-after antibiotic exposure is poorly understood. We study community response to antibiotics using a model community that can reach two alternative states. Guided by theory, our experiments show that microbial growth following antibiotic exposure can counteract antibiotic susceptibility in driving transitions between alternative community states. This makes it possible to reverse the outcome of antibiotic exposure through modifying growth dynamics, including cooperative growth, of community members. Our research highlights the relevance of simple ecological models to better understand the long-term effects of antibiotic treatment.
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14
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Drug-dependent growth curve reshaping reveals mechanisms of antifungal resistance in Saccharomyces cerevisiae. Commun Biol 2022; 5:292. [PMID: 35361876 PMCID: PMC8971432 DOI: 10.1038/s42003-022-03228-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 03/07/2022] [Indexed: 11/15/2022] Open
Abstract
Microbial drug resistance is an emerging global challenge. Current drug resistance assays tend to be simplistic, ignoring complexities of resistance manifestations and mechanisms, such as multicellularity. Here, we characterize multicellular and molecular sources of drug resistance upon deleting the AMN1 gene responsible for clumping multicellularity in a budding yeast strain, causing it to become unicellular. Computational analysis of growth curve changes upon drug treatment indicates that the unicellular strain is more sensitive to four common antifungals. Quantitative models uncover entwined multicellular and molecular processes underlying these differences in sensitivity and suggest AMN1 as an antifungal target in clumping pathogenic yeasts. Similar experimental and mathematical modeling pipelines could reveal multicellular and molecular drug resistance mechanisms, leading to more effective treatments against various microbial infections and possibly even cancers. Combined growth curve experiments and quantitative modeling reveal antifungal responses of planktonic yeast, providing a future framework to examine antimicrobial drug resistance.
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15
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Sunilkumar CR, Stephen-Victor E, Naripogu KB, Samanth Kumar J, Nuthan BR, Marulasiddaswamy KM, Kini KR, Geetha N. Differential Multi-cellularity Is Required for the Adaptation for Bacillus licheniformis to Withstand Heavy Metals Toxicity. Indian J Microbiol 2021; 61:524-529. [PMID: 34744208 DOI: 10.1007/s12088-021-00958-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/14/2021] [Indexed: 12/28/2022] Open
Abstract
Bacillus licheniformis is a multi-metal tolerant bacteria, isolated from the paddy rhizospheric soil sample. Upon the multiple metal toxicity, B. licheniformis altered their phenotypic/morphogenesis. Here we examined the effects of cadmium (Cd2+), chromium (Cr2+), and mercury (Hg2+) on the morphogenesis of B. licheniformis in comparison to control. We found that the ability of bacteria to grow effectively in presence of cadmium and chromium comes at a cost of acquiring cell density-driven mobility and reformation of filamentous to donut shape respectively. In particular, when bacteria grown on mercury it showed the bacteriostatic strategy to resist mercury. Furthermore, the findings suggest a large variation in the production of exo-polysaccharides (EPS) and suggest the possible role of EPS in gaining resistance to cadmium and chromium. Together this study identifies previously unknown characteristics of B. licheniformis to participate in bioremediation and provides the first evidence on positive effects of bacterial morphogenesis and the involvement of EPS in bacteria to resisting metal toxicity.
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Affiliation(s)
- Channarayapatna-Ramesh Sunilkumar
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Research Institute for Interdisciplinary Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530 Japan.,Laboratory of Microbial Metabolism and Stress Response, Department of Biotechnology, SDM and MMK College for Women, Mysuru, India
| | - Emmanuel Stephen-Victor
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Kishore Babu Naripogu
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Research Institute for Interdisciplinary Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530 Japan
| | - J Samanth Kumar
- Department of Studies in Biotechnology, Manasagangotri, University of Mysore, Mysuru, India
| | - Bettadapura Rameshgowda Nuthan
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysuru, India
| | - K M Marulasiddaswamy
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Studies in Biotechnology, Manasagangotri, University of Mysore, Mysuru, India
| | | | - Nagaraja Geetha
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Studies in Biotechnology, Manasagangotri, University of Mysore, Mysuru, India
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16
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Sharma A, Wood KB. Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress. THE ISME JOURNAL 2021; 15:3019-3033. [PMID: 33953363 PMCID: PMC8443724 DOI: 10.1038/s41396-021-00982-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 02/01/2023]
Abstract
Antibiotic resistance in microbial communities reflects a combination of processes operating at different scales. In this work, we investigate the spatiotemporal dynamics of bacterial colonies comprised of drug-resistant and drug-sensitive cells undergoing range expansion under antibiotic stress. Using the opportunistic pathogen Enterococcus faecalis with plasmid-encoded β-lactamase, we track colony expansion dynamics and visualize spatial patterns in fluorescently labeled populations exposed to antibiotics. We find that the radial expansion rate of mixed communities is approximately constant over a wide range of drug concentrations and initial population compositions. Imaging of the final populations shows that resistance to ampicillin is cooperative, with sensitive cells surviving in the presence of resistant cells at otherwise lethal concentrations. The populations exhibit a diverse range of spatial segregation patterns that depend on drug concentration and initial conditions. Mathematical models indicate that the observed dynamics are consistent with global cooperation, despite the fact that β-lactamase remains cell-associated. Experiments confirm that resistant colonies provide a protective effect to sensitive cells on length scales multiple times the size of a single colony, and populations seeded with (on average) no more than a single resistant cell can produce mixed communities in the presence of the drug. While biophysical models of drug degradation suggest that individual resistant cells offer only short-range protection to neighboring cells, we show that long-range protection may arise from synergistic effects of multiple resistant cells, providing surprisingly large protection zones even at small population fractions.
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Affiliation(s)
- Anupama Sharma
- Department of Biophysics, University of Michigan, Ann Arbor, USA
- Department of Mathematics, BITS Pilani K K Birla Goa Campus, Goa, India
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, Ann Arbor, USA.
- Department of Physics, University of Michigan, Ann Arbor, USA.
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17
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Liao H, Bai Y, Liu C, Wen C, Yang Q, Chen Z, Banerjee S, Zhou S, Friman VP. Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage. Environ Microbiol 2021; 23:7483-7496. [PMID: 34259375 DOI: 10.1111/1462-2920.15672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 11/27/2022]
Abstract
Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yudan Bai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chang Wen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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18
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Abstract
Nucleotide metabolism plays a central role in bacterial physiology, producing the nucleic acids necessary for DNA replication and RNA transcription. Recent studies demonstrate that nucleotide metabolism also proactively contributes to antibiotic-induced lethality in bacterial pathogens and that disruptions to nucleotide metabolism contributes to antibiotic treatment failure in the clinic. As antimicrobial resistance continues to grow unchecked, new approaches are needed to study the molecular mechanisms responsible for antibiotic efficacy. Here we review emerging technologies poised to transform understanding into why antibiotics may fail in the clinic. We discuss how these technologies led to the discovery that nucleotide metabolism regulates antibiotic drug responses and why these are relevant to human infections. We highlight opportunities for how studies into nucleotide metabolism may enhance understanding of antibiotic failure mechanisms.
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Affiliation(s)
- Allison J Lopatkin
- Department of Biology, Barnard College, New York, NY, United States.,Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States.,Data Science Institute, Columbia University, New York, NY, United States
| | - Jason H Yang
- Ruy V. Lourenço Center for Emerging and Re-emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, United States.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
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19
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Zwanzig M. The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling. Comput Struct Biotechnol J 2020; 19:586-599. [PMID: 33510864 PMCID: PMC7807137 DOI: 10.1016/j.csbj.2020.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 12/27/2022] Open
Abstract
Many antibiotic resistance genes are associated with plasmids. The ecological success of these mobile genetic elements within microbial communities depends on varying mechanisms to secure their own propagation, not only on environmental selection. Among the most important are the cost of plasmids and their ability to be transferred to new hosts through mechanisms such as conjugation. These are regulated by dynamic control systems of the conjugation machinery and genetic adaptations that plasmid-host pairs can acquire in coevolution. However, in complex communities, these processes and mechanisms are subject to a variety of interactions with other bacterial species and other plasmid types. This article summarizes basic plasmid properties and ecological principles particularly important for understanding the persistence of plasmid-coded antibiotic resistance in aquatic environments. Through selected examples, it further introduces to the features of different types of simulation models such as systems of ordinary differential equations and individual-based models, which are considered to be important tools to understand these complex systems. This ecological perspective aims to improve the way we study and understand the dynamics, diversity and persistence of plasmids and associated antibiotic resistance genes.
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Affiliation(s)
- Martin Zwanzig
- Faculty of Environmental Sciences, Technische Universität Dresden, Pienner Str. 8, D-01737 Tharandt, Germany
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20
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Lee CY, Cheu RK, Lemke MM, Gustin AT, France MT, Hampel B, Thurman AR, Doncel GF, Ravel J, Klatt NR, Arnold KB. Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. Nat Commun 2020; 11:6147. [PMID: 33262350 PMCID: PMC7708644 DOI: 10.1038/s41467-020-19880-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Bacterial vaginosis is a condition associated with adverse reproductive outcomes and characterized by a shift from a Lactobacillus-dominant vaginal microbiota to a polymicrobial microbiota, consistently colonized by strains of Gardnerella vaginalis. Metronidazole is the first-line treatment; however, treatment failure and recurrence rates remain high. To understand complex interactions between Gardnerella vaginalis and Lactobacillus involved in efficacy, here we develop an ordinary differential equation model that predicts bacterial growth as a function of metronidazole uptake, sensitivity, and metabolism. The model shows that a critical factor in efficacy is Lactobacillus sequestration of metronidazole, and efficacy decreases when the relative abundance of Lactobacillus is higher pre-treatment. We validate results in Gardnerella and Lactobacillus co-cultures, and in two clinical cohorts, finding women with recurrence have significantly higher pre-treatment levels of Lactobacillus relative to bacterial vaginosis-associated bacteria. Overall results provide mechanistic insight into how personalized differences in microbial communities influence vaginal antibiotic efficacy.
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Affiliation(s)
- Christina Y Lee
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ryan K Cheu
- University of Miami Department of Pediatrics, University of Miami, Miami, FL, USA
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Melissa M Lemke
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Andrew T Gustin
- University of Miami Department of Pediatrics, University of Miami, Miami, FL, USA
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Michael T France
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin Hampel
- Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zürich, Switzerland
| | | | | | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nichole R Klatt
- University of Miami Department of Pediatrics, University of Miami, Miami, FL, USA.
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA.
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA.
| | - Kelly B Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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21
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Unchartered waters: the unintended impacts of residual chlorine on water quality and biofilms. NPJ Biofilms Microbiomes 2020; 6:34. [PMID: 32978404 PMCID: PMC7519676 DOI: 10.1038/s41522-020-00144-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/25/2020] [Indexed: 02/08/2023] Open
Abstract
Disinfection residuals in drinking water protect water quality and public heath by limiting planktonic microbial regrowth during distribution. However, we do not consider the consequences and selective pressures of such residuals on the ubiquitous biofilms that persist on the vast internal surface area of drinking water distribution systems. Using a full scale experimental facility, integrated analyses were applied to determine the physical, chemical and biological impacts of different free chlorine regimes on biofilm characteristics (composition, structure and microbiome) and water quality. Unexpectedly, higher free chlorine concentrations resulted in greater water quality degredation, observable as elevated inorganic loading and greater discolouration (a major cause of water quality complaints and a mask for other failures). High-chlorine concentrations also reduced biofilm cell concentrations but selected for a distinct biofilm bacterial community and inorganic composition, presenting unique risks. The results challenge the assumption that a measurable free chlorine residual necessarily assures drinking water safety.
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22
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Hallinen KM, Karslake J, Wood KB. Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations. eLife 2020; 9:e52813. [PMID: 32207406 PMCID: PMC7159880 DOI: 10.7554/elife.52813] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/16/2020] [Indexed: 12/18/2022] Open
Abstract
The molecular underpinnings of antibiotic resistance are increasingly understood, but less is known about how these molecular events influence microbial dynamics on the population scale. Here, we show that the dynamics of E. faecalis communities exposed to antibiotics can be surprisingly rich, revealing scenarios where increasing population size or delaying drug exposure can promote population collapse. Specifically, we demonstrate how density-dependent feedback loops couple population growth and antibiotic efficacy when communities include drug-resistant subpopulations, leading to a wide range of behavior, including population survival, collapse, or one of two qualitatively distinct bistable behaviors where survival is favored in either small or large populations. These dynamics reflect competing density-dependent effects of different subpopulations, with growth of drug-sensitive cells increasing but growth of drug-resistant cells decreasing effective drug inhibition. Finally, we demonstrate how populations receiving immediate drug influx may sometimes thrive, while identical populations exposed to delayed drug influx collapse.
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Affiliation(s)
- Kelsey M Hallinen
- Department of Biophysics, University of MichiganAnn ArborUnited States
| | - Jason Karslake
- Department of Biophysics, University of MichiganAnn ArborUnited States
| | - Kevin B Wood
- Department of Biophysics, University of MichiganAnn ArborUnited States
- Department of Physics, University of MichiganAnn ArborUnited States
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23
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Carvalho G, Forestier C, Mathias JD. Antibiotic resilience: a necessary concept to complement antibiotic resistance? Proc Biol Sci 2019; 286:20192408. [PMID: 31795866 DOI: 10.1098/rspb.2019.2408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Resilience is the capacity of systems to recover their initial state or functions after a disturbance. The concepts of resilience and resistance are complementary in ecology and both represent different aspects of the stability of ecosystems. However, antibiotic resilience is not used in clinical bacteriology whereas antibiotic resistance is a recognized major problem. To join the fields of ecology and clinical bacteriology, we first review the resilience concept from ecology, socio-ecological systems and microbiology where it is widely developed. We then review resilience-related concepts in microbiology, including bacterial tolerance and persistence, phenotypic heterogeneity and collective tolerance and resistance. We discuss how antibiotic resilience could be defined and argue that the use of this concept largely relies on its experimental measure and its clinical relevance. We review indicators in microbiology which could be used to reflect antibiotic resilience and used as valuable indicators to anticipate the capacity of bacteria to recover from antibiotic treatments.
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Affiliation(s)
- Gabriel Carvalho
- Université Clermont Auvergne, Irstea, UR LISC, Centre de Clermont-Ferrand, 9 Avenue Blaise Pascal CS 20085, F-63178, Aubière, France
| | | | - Jean-Denis Mathias
- Université Clermont Auvergne, Irstea, UR LISC, Centre de Clermont-Ferrand, 9 Avenue Blaise Pascal CS 20085, F-63178, Aubière, France
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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