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Denk-Lobnig M, Wood KB. Antibiotic resistance in bacterial communities. Curr Opin Microbiol 2023; 74:102306. [PMID: 37054512 PMCID: PMC10527032 DOI: 10.1016/j.mib.2023.102306] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 03/06/2023] [Indexed: 04/15/2023]
Abstract
Bacteria are single-celled organisms, but the survival of microbial communities relies on complex dynamics at the molecular, cellular, and ecosystem scales. Antibiotic resistance, in particular, is not just a property of individual bacteria or even single-strain populations, but depends heavily on the community context. Collective community dynamics can lead to counterintuitive eco-evolutionary effects like survival of less resistant bacterial populations, slowing of resistance evolution, or population collapse, yet these surprising behaviors are often captured by simple mathematical models. In this review, we highlight recent progress - in many cases, advances driven by elegant combinations of quantitative experiments and theoretical models - in understanding how interactions between bacteria and with the environment affect antibiotic resistance, from single-species populations to multispecies communities embedded in an ecosystem.
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Affiliation(s)
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, United States.
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2
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Newton DP, Ho PY, Huang KC. Modulation of antibiotic effects on microbial communities by resource competition. Nat Commun 2023; 14:2398. [PMID: 37100773 PMCID: PMC10133249 DOI: 10.1038/s41467-023-37895-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 04/28/2023] Open
Abstract
Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigate community responses to species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such as bacteriophages. Our analyses highlight the complex dependence of species coexistence that can arise from the interplay of resource competition and antibiotic activity, independent of other biological mechanisms. In particular, we identify resource competition structures that cause richness to depend on the order of sequential application of antibiotics (non-transitivity), and the emergence of synergistic and antagonistic effects under simultaneous application of multiple antibiotics (non-additivity). These complex behaviors can be prevalent, especially when generalist consumers are targeted. Communities can be prone to either synergism or antagonism, but typically not both, and antagonism is more common. Furthermore, we identify a striking overlap in competition structures that lead to non-transitivity during antibiotic sequences and those that lead to non-additivity during antibiotic combination. In sum, our results establish a broadly applicable framework for predicting microbial community dynamics under deleterious perturbations.
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Affiliation(s)
- Daniel P Newton
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Po-Yi Ho
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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Hu X, Fu Y, Shi H, Xu W, Shen C, Hu B, Ma L, Lou L. Neglected resistance risks: Cooperative resistance of antibiotic resistant bacteria influenced by primary soil components. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128229. [PMID: 35074748 DOI: 10.1016/j.jhazmat.2022.128229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Various antibiotic resistant bacteria (ARB) can thrive in soil and resist such environmental pressures as antibiotics through cooperative resistance, thereby promoting ARB retention and antibiotic resistance genes transmission. However, there has been finite knowledge in regard to the mechanisms and potential ecological risks of cooperative resistance in soil microbiome. In this study, soil minerals and organic matters were designed to treat a mixture of two Escherichia coli strains with different antibiotic resistance (E. coli DH5α/pUC19 and E. coli XL2-Blue) to determine how soil components affected cooperative resistance, and Luria-Bertani plates containing two antibiotics were used to observe dual-drug resistant bacteria (DRB) developed via cooperative resistance. Results showed quartz, humic acid, and biochar promoted E. coli XL2-Blue with high fitness costs, whereas kaolin, montmorillonite, and soot inhibited both strains. Using fluorescence microscope and PCR, it was speculated DRB could resist the antibiotic pressure via E. coli XL2-Blue coating E. coli DH5α/pUC19. E. coli DH5α/pUC19 dominated cooperative resistance. Correlation analysis and scanning electron microscope images indicated soil components influenced cooperative resistance. Biochar promoted cooperative resistance by increasing intracellular reactive oxygen species, thereby reducing the dominant strain concentration required for DRB development. Kaolin inhibited cooperative resistance the most, followed by soot and montmorillonite.
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Affiliation(s)
- Xinyi Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Yulong Fu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Hongyu Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Weijian Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China
| | - Liping Ma
- School of Ecological and Environmental Sciences, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai 200062, People's Republic of China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China.
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Spatial structure impacts adaptive therapy by shaping intra-tumoral competition. COMMUNICATIONS MEDICINE 2022; 2:46. [PMID: 35603284 PMCID: PMC9053239 DOI: 10.1038/s43856-022-00110-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/28/2022] [Indexed: 02/07/2023] Open
Abstract
Background Adaptive therapy aims to tackle cancer drug resistance by leveraging resource competition between drug-sensitive and resistant cells. Here, we present a theoretical study of intra-tumoral competition during adaptive therapy, to investigate under which circumstances it will be superior to aggressive treatment. Methods We develop and analyse a simple, 2-D, on-lattice, agent-based tumour model in which cells are classified as fully drug-sensitive or resistant. Subsequently, we compare this model to its corresponding non-spatial ordinary differential equation model, and fit it to longitudinal prostate-specific antigen data from 65 prostate cancer patients undergoing intermittent androgen deprivation therapy following biochemical recurrence. Results Leveraging the individual-based nature of our model, we explicitly demonstrate competitive suppression of resistance during adaptive therapy, and examine how different factors, such as the initial resistance fraction or resistance costs, alter competition. This not only corroborates our theoretical understanding of adaptive therapy, but also reveals that competition of resistant cells with each other may play a more important role in adaptive therapy in solid tumours than was previously thought. To conclude, we present two case studies, which demonstrate the implications of our work for: (i) mathematical modelling of adaptive therapy, and (ii) the intra-tumoral dynamics in prostate cancer patients during intermittent androgen deprivation treatment, a precursor of adaptive therapy. Conclusion Our work shows that the tumour’s spatial architecture is an important factor in adaptive therapy and provides insights into how adaptive therapy leverages both inter- and intra-specific competition to control resistance. Cancer therapy traditionally focuses on maximising tumour cell kill with the aim of achieving a cure, but such aggressive treatment can open up space for drug-resistant cells to grow. In contrast, adaptive therapy aims to leverage competition between drug-sensitive and resistant cells by adjusting treatment to maintain the tumour at a tolerable size, whilst preserving drug-sensitive cells. This approach is being tested in trials but is not yet widely used as deeper understanding of cell-cell competition is required. Here, we used a mathematical model to investigate how strongly, and with whom, resistant cells compete during continuous and adaptive therapy, and applied our insights to hormone therapy in prostate cancer where adaptive therapy has recently been successfully trialed. Our results provide new insights into how adaptive therapy works and show that, by shaping cell competition, the tumour’s spatial architecture is important in determining therapy response. Strobl et al. develop an agent-based spatial model of drug resistance in tumour cells under adaptive therapy. Using this model, they investigate how the tumour’s spatial architecture impacts intratumoural competitive dynamics of drug-sensitive vs. -resistant clones in response to therapy.
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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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Mancuso CP, Lee H, Abreu CI, Gore J, Khalil AS. Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community. eLife 2021; 10:e67175. [PMID: 34477107 PMCID: PMC8460265 DOI: 10.7554/elife.67175] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022] Open
Abstract
Environmental disturbances have long been theorized to play a significant role in shaping the diversity and composition of ecosystems. However, an inability to specify the characteristics of a disturbance experimentally has produced an inconsistent picture of diversity-disturbance relationships (DDRs). Here, using a high-throughput programmable culture system, we subjected a soil-derived bacterial community to dilution disturbance profiles with different intensities (mean dilution rates), applied either constantly or with fluctuations of different frequencies. We observed an unexpected U-shaped relationship between community diversity and disturbance intensity in the absence of fluctuations. Adding fluctuations increased community diversity and erased the U-shape. All our results are well-captured by a Monod consumer resource model, which also explains how U-shaped DDRs emerge via a novel 'niche flip' mechanism. Broadly, our combined experimental and modeling framework demonstrates how distinct features of an environmental disturbance can interact in complex ways to govern ecosystem assembly and offers strategies for reshaping the composition of microbiomes.
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Affiliation(s)
- Christopher P Mancuso
- Department of Biomedical Engineering and Biological Design Center, Boston UniversityBostonUnited States
| | - Hyunseok Lee
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Clare I Abreu
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Jeff Gore
- Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston UniversityBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
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Gjini E, Wood KB. Price equation captures the role of drug interactions and collateral effects in the evolution of multidrug resistance. eLife 2021; 10:e64851. [PMID: 34289932 PMCID: PMC8331190 DOI: 10.7554/elife.64851] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/08/2021] [Indexed: 01/03/2023] Open
Abstract
Bacterial adaptation to antibiotic combinations depends on the joint inhibitory effects of the two drugs (drug interaction [DI]) and how resistance to one drug impacts resistance to the other (collateral effects [CE]). Here we model these evolutionary dynamics on two-dimensional phenotype spaces that leverage scaling relations between the drug-response surfaces of drug-sensitive (ancestral) and drug-resistant (mutant) populations. We show that evolved resistance to the component drugs - and in turn, the adaptation of growth rate - is governed by a Price equation whose covariance terms encode geometric features of both the two-drug-response surface (DI) in ancestral cells and the correlations between resistance levels to those drugs (CE). Within this framework, mean evolutionary trajectories reduce to a type of weighted gradient dynamics, with the drug interaction dictating the shape of the underlying landscape and the collateral effects constraining the motion on those landscapes. We also demonstrate how constraints on available mutational pathways can be incorporated into the framework, adding a third key driver of evolution. Our results clarify the complex relationship between drug interactions and collateral effects in multidrug environments and illustrate how specific dosage combinations can shift the weighting of these two effects, leading to different and temporally explicit selective outcomes.
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Affiliation(s)
- Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Tecnico, University of Lisbon, PortugalLisbonPortugal
| | - Kevin B Wood
- Departments of Biophysics and Physics, University of MichiganAnn ArborUnited States
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Dawan J, Ahn J. Assessment of cooperative antibiotic resistance of Salmonella Typhimurium within heterogeneous population. Microb Pathog 2021; 157:104973. [PMID: 34029657 DOI: 10.1016/j.micpath.2021.104973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022]
Abstract
This study was designed to investigate the cooperative resistance in the mixed culture of antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium. Strains of S. Typhimurium ATCC 19585 (STS) and clinically isolated antibiotic-resistant S. Typhimurium CCARM 8009 (STR) grown in single and mixture with 1 × MIC ceftriaxone (CEF) were used to determine the viability, β-lactamase activity, and gene expression. The MIC50 values of STR to CEF was increased by more than 5-fold with increasing inoculum densities from 102 to 107 CFU/mL. STS was resistant to 1 × MIC CEF in the mixed culture of STS and STR, showing the more than 108 CFU/mL after 20 h of incubation at 37 °C. The highest β-lactamase activity was 18 μmol/min/mL in the mixed culture, corresponding to the highest relative expression of β-lactamase-related genes (blaTEM). These results shed new light on the cooperative resistance of antibiotic-sensitive bacteria within a heterogeneous population including β-lactamase-producing bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea.
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9
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Using ecological coexistence theory to understand antibiotic resistance and microbial competition. Nat Ecol Evol 2021; 5:431-441. [PMID: 33526890 DOI: 10.1038/s41559-020-01385-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/11/2020] [Indexed: 01/30/2023]
Abstract
Tackling antibiotic resistance necessitates deep understanding of how resource competition within and between species modulates the fitness of resistant microbes. Recent advances in ecological coexistence theory offer a powerful framework to probe the mechanisms regulating intra- and interspecific competition, but the significance of this body of theory to the problem of antibiotic resistance has been largely overlooked. In this Perspective, we draw on emerging ecological theory to illustrate how changes in resource niche overlap can be equally important as changes in competitive ability for understanding costs of resistance and the persistence of resistant pathogens in microbial communities. We then show how different temporal patterns of resource and antibiotic supply, alongside trade-offs in competitive ability at high and low resource concentrations, can have diametrically opposing consequences for the coexistence and exclusion of resistant and susceptible strains. These insights highlight numerous opportunities for innovative experimental and theoretical research into the ecological dimensions of antibiotic resistance.
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Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. Antimicrob Agents Chemother 2020; 65:AAC.01273-20. [PMID: 33106260 PMCID: PMC7927859 DOI: 10.1128/aac.01273-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022] Open
Abstract
As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will be increasingly relied upon to treat infections and to lower the rate of multidrug resistance. The majority of work in this area has investigated how resistance evolution toward a single antibiotic effects a specific organism’s collateral response to a wide variety of antibiotics. The results of these studies have been used to identify networks of drugs which can be used to drive resistance in a particular direction. As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will be increasingly relied upon to treat infections and to lower the rate of multidrug resistance. The majority of work in this area has investigated how resistance evolution toward a single antibiotic effects a specific organism’s collateral response to a wide variety of antibiotics. The results of these studies have been used to identify networks of drugs which can be used to drive resistance in a particular direction. However, little is known about the extent of evolutionary conservation of these responses across species. We sought to address this knowledge gap by performing a systematic resistance evolution study of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) under uniform growth conditions using five clinically relevant antibiotics with diverse modes of action. Evolved lineages were analyzed for collateral effects and the molecular mechanisms behind the observed phenotypes. Fourteen universal cross-resistance and two global collateral sensitivity relationships were found among the lineages. Genomic analyses revealed drug-dependent divergent and conserved evolutionary trajectories among the pathogens. Our findings suggest that collateral responses may be preserved across species. These findings may help extend the contribution of previous collateral network studies in the development of treatment strategies to address the problem of antibiotic resistance.
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Hallinen KM, Guardiola-Flores KA, Wood KB. Fluorescent reporter plasmids for single-cell and bulk-level composition assays in E. faecalis. PLoS One 2020; 15:e0232539. [PMID: 32369497 PMCID: PMC7199960 DOI: 10.1371/journal.pone.0232539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 01/04/2023] Open
Abstract
Fluorescent reporters are an important tool for monitoring dynamics of bacterial populations at the single cell and community level. While there are a large range of reporter constructs available–particularly for common model organisms like E. coli–fewer options exist for other species, including E. faecalis, a gram-positive opportunistic pathogen. To expand the potential toolkit available for E. faecalis, we exchanged the original fluorescent reporter in a previously developed plasmid (pBSU101) with one of eight fluorescent reporters and confirmed that all constructs exhibited detectable fluorescence in single E. faecalis cells and mixed biofilm communities. To identify promising constructs for bulk-level experiments, we then measured the fluorescence spectra from E. faecalis populations in microwell plate (liquid) cultures during different phases of aerobic growth. Cultures showed density- and reporter-specific variations in fluorescent signal, though spectral signatures of all reporters become clear in late-exponential and stationary-phase populations. Based on these results, we identified six pairs of reporters that can be combined with simple spectral unmixing to accurately estimate population composition in 2-strain mixtures at or near stationary phase. This approach offers a simple and scalable method for selection and competition experiments in simple two-species populations under aerobic growth conditions. Finally, we incorporated codon-optimized variants of blue (BFP) and red (RFP) reporters and show that they lead to increased fluorescence in exponentially growing cells. As a whole, the results inform the scope of application of different reporters and identify both single reporters and reporter pairs that are promising for fluorescence-based assays at bulk and single-cell levels in E. faecalis.
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Affiliation(s)
- Kelsey M. Hallinen
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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12
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Marrec L, Bitbol AF. Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial. PLoS Comput Biol 2020; 16:e1007798. [PMID: 32275712 PMCID: PMC7176291 DOI: 10.1371/journal.pcbi.1007798] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/22/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, using a stochastic model that includes variations of both population composition and size, and fully incorporates stochastic population extinctions. We show that fast alternations of presence and absence of antimicrobial are inefficient to eradicate the microbial population and strongly favor the establishment of resistance, unless the antimicrobial increases enough the death rate. We further demonstrate that if the period of alternations is longer than a threshold value, the microbial population goes extinct upon the first addition of antimicrobial, if it is not rescued by resistance. We express the probability that the population is eradicated upon the first addition of antimicrobial, assuming rare mutations. Rescue by resistance can happen either if resistant mutants preexist, or if they appear after antimicrobial is added to the environment. Importantly, the latter case is fully prevented by perfect biostatic antimicrobials that completely stop division of sensitive microorganisms. By contrast, we show that the parameter regime where treatment is efficient is larger for biocidal drugs than for biostatic drugs. This sheds light on the respective merits of different antimicrobial modes of action.
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Affiliation(s)
- Loïc Marrec
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), F-75005 Paris, France
| | - Anne-Florence Bitbol
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), F-75005 Paris, France
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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