1
|
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 2024:10.1038/s44320-024-00046-5. [PMID: 38877321 DOI: 10.1038/s44320-024-00046-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
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.
| |
Collapse
|
2
|
Luo N, Lu J, Şimşek E, Silver A, Yao Y, Ouyang X, West SA, You L. The collapse of cooperation during range expansion of Pseudomonas aeruginosa. Nat Microbiol 2024; 9:1220-1230. [PMID: 38443483 PMCID: PMC7615952 DOI: 10.1038/s41564-024-01627-8] [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: 08/12/2022] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
Cooperation is commonly believed to be favourable in spatially structured environments, as these systems promote genetic relatedness that reduces the likelihood of exploitation by cheaters. Here we show that a Pseudomonas aeruginosa population that exhibited cooperative swarming was invaded by cheaters when subjected to experimental evolution through cycles of range expansion on solid media, but not in well-mixed liquid cultures. Our results suggest that cooperation is disfavoured in a more structured environment, which is the opposite of the prevailing view. We show that spatial expansion of the population prolongs cooperative swarming, which was vulnerable to cheating. Our findings reveal a mechanism by which spatial structures can suppress cooperation through modulation of the quantitative traits of cooperation, a process that leads to population divergence towards distinct colonization strategies.
Collapse
Affiliation(s)
- Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emrah Şimşek
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Anita Silver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yi Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Xiaoyi Ouyang
- School of Physics, Peking University, Beijing, China
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, UK
| | - 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.
| |
Collapse
|
3
|
Stevanovic M, Teuber Carvalho JP, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures. Phys Biol 2024; 21:036002. [PMID: 38412523 PMCID: PMC10988634 DOI: 10.1088/1478-3975/ad2d64] [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: 09/14/2023] [Revised: 01/25/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
Abstract
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistancetetoperon inE. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.
Collapse
Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - João Pedro Teuber Carvalho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| |
Collapse
|
4
|
Van Goethem MW, Marasco R, Hong P, Daffonchio D. The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms. Microb Biotechnol 2024; 17:e14430. [PMID: 38465465 PMCID: PMC10926060 DOI: 10.1111/1751-7915.14430] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
In the relentless battle for human health, the proliferation of antibiotic-resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening 'antibiotic discovery void'. With nearly 80% of our current antibiotics originating from natural or semi-synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so-called 'microbial oases of interactions'. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever-evolving microbial 'arms race' is constantly in place. Such a continuous cycle of adaptation and counter-adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a 'missing piece of the puzzle' in our fight against antibiotic resistance.
Collapse
Affiliation(s)
- Marc W. Van Goethem
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Pei‐Ying Hong
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Water Desalination and Reuse CenterBiological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| |
Collapse
|
5
|
Zhao X, Ruelens P, Farr AD, de Visser JAGM, Baraban L. Population dynamics of cross-protection against β-lactam antibiotics in droplet microreactors. Front Microbiol 2023; 14:1294790. [PMID: 38192289 PMCID: PMC10773670 DOI: 10.3389/fmicb.2023.1294790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Bacterial strains that are resistant to antibiotics may protect not only themselves, but also sensitive bacteria nearby if resistance involves antibiotic degradation. Such cross-protection poses a challenge to effective antibiotic therapy by enhancing the long-term survival of bacterial infections, however, the current understanding is limited. Methods In this study, we utilize an automated nanoliter droplet analyzer to study the interactions between Escherichia coli strains expressing a β-lactamase (resistant) and those not expressing it (sensitive) when exposed to the β-lactam antibiotic cefotaxime (CTX), with the aim to define criteria contributing to cross-protection. Results We observed a cross-protection window of CTX concentrations for the sensitive strain, extending up to approximately 100 times its minimal inhibitory concentration (MIC). Through both microscopy and enzyme activity analyses, we demonstrate that bacterial filaments, triggered by antibiotic stress, contribute to cross-protection. Discussion The antibiotic concentration window for cross-protection depends on the difference in β-lactamase activity between co-cultured strains: larger differences shift the 'cross-protection window' toward higher CTX concentrations. Our findings highlight the dependence of opportunities for cross-protection on the relative resistance levels of the strains involved and suggest a possible specific role for filamentation.
Collapse
Affiliation(s)
- Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
| | - Philip Ruelens
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
| | - Andrew D. Farr
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
| |
Collapse
|
6
|
Hervin V, Roy V, Agrofoglio LA. Antibiotics and Antibiotic Resistance-Mur Ligases as an Antibacterial Target. Molecules 2023; 28:8076. [PMID: 38138566 PMCID: PMC10745416 DOI: 10.3390/molecules28248076] [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: 07/29/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of Multidrug Resistance (MDR) strains of bacteria has accelerated the search for new antibacterials. The specific bacterial peptidoglycan biosynthetic pathway represents opportunities for the development of novel antibacterial agents. Among the enzymes involved, Mur ligases, described herein, and especially the amide ligases MurC-F are key targets for the discovery of multi-inhibitors, as they share common active sites and structural features.
Collapse
Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| | - Luigi A. Agrofoglio
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| |
Collapse
|
7
|
Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
Collapse
Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| |
Collapse
|
8
|
Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals (Basel) 2023; 16:1615. [PMID: 38004480 PMCID: PMC10675245 DOI: 10.3390/ph16111615] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.
Collapse
Affiliation(s)
- Ghazala Muteeb
- Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11437, Saudi Arabia;
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates;
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman 346, United Arab Emirates
| | - Mohammad Aatif
- Department of Public Health, College of Applied Medical Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| |
Collapse
|
9
|
Hernández-Navarro L, Asker M, Rucklidge AM, Mobilia M. Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance. J R Soc Interface 2023; 20:20230393. [PMID: 37907094 PMCID: PMC10618063 DOI: 10.1098/rsif.2023.0393] [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: 07/10/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behaviour leading to the coexistence of resistant and sensitive cells in large populations and static environments. This picture is, however, greatly altered by the fluctuations arising in volatile environments, in which microbial communities commonly evolve. Here, we study the eco-evolutionary dynamics of a population consisting of an antimicrobial-resistant strain and microbes sensitive to antimicrobial drugs in a time-fluctuating environment, modelled by a carrying capacity randomly switching between states of abundance and scarcity. We assume that antimicrobial resistance (AMR) is a shared public good when the number of resistant cells exceeds a certain threshold. Eco-evolutionary dynamics is thus characterised by demographic noise (birth and death events) coupled to environmental fluctuations which can cause population bottlenecks. By combining analytical and computational means, we determine the environmental conditions for the long-lived coexistence and fixation of both strains, and characterise a fluctuation-driven AMR eradication mechanism, where resistant microbes experience bottlenecks leading to extinction. We also discuss the possible applications of our findings to laboratory-controlled experiments.
Collapse
Affiliation(s)
- Lluís Hernández-Navarro
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Matthew Asker
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Alastair M. Rucklidge
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Mauro Mobilia
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
10
|
Cartagena AJ, Taylor KL, Smith JT, Manson AL, Pierce VM, Earl AM, Bhattacharyya RP. The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541813. [PMID: 37292717 PMCID: PMC10245868 DOI: 10.1101/2023.05.23.541813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Carbapenem-resistant Enterobacterales (CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveillance, infection control, and patient care. We investigated how resistance mechanisms influence the carbapenem inoculum effect (IE), a phenomenon where inoculum size affects antimicrobial susceptibility testing (AST). We demonstrated that seven different carbapenemases impart a meropenem IE in Escherichia coli. Across 110 clinical CRE isolates, the carbapenem IE strictly depended on resistance mechanism: all carbapenemase-producing CRE (CP-CRE) exhibited a strong IE, whereas porin-deficient CRE displayed none. Concerningly, 50% and 24% of CP-CRE isolates changed susceptibility classification to meropenem and ertapenem, respectively, across the allowable inoculum range in clinical guidelines. The meropenem IE, and the ratio of ertapenem to meropenem minimal inhibitory concentration (MIC) at standard inoculum, reliably identified CP-CRE. Understanding how resistance mechanisms affect AST could improve diagnosis and guide therapies for CRE infections.
Collapse
Affiliation(s)
| | - Kyra L. Taylor
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua T. Smith
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Virginia M. Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Pathology and Clinical Laboratories, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Roby P. Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| |
Collapse
|
11
|
Stevanovic M, Carvalho JPT, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance to metabolism explains emergence of heterogeneity during drug exposures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558994. [PMID: 37790326 PMCID: PMC10542528 DOI: 10.1101/2023.09.22.558994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistance tet operon in E. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.
Collapse
Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - João Pedro Teuber Carvalho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| |
Collapse
|
12
|
Shamim A, Ansari MJ, Aodah A, Iqbal M, Aqil M, Mirza MA, Iqbal Z, Ali A. QbD-Engineered Development and Validation of a RP-HPLC Method for Simultaneous Estimation of Rutin and Ciprofloxacin HCl in Bilosomal Nanoformulation. ACS OMEGA 2023; 8:21618-21627. [PMID: 37360463 PMCID: PMC10286274 DOI: 10.1021/acsomega.3c00956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
In the given study, a new reverse-phase high-performance liquid chromatography (RP-HPLC) method has been reported for the simultaneous estimation of ciprofloxacin hydrochloride (CPX) and rutin (RUT) using quality by design (QbD) approach. The analysis was carried out by applying the Box-Behnken design having fewer design points and less experimental runs. It relates between factors and responses and gives statistically significant values, along with enhancing the quality of the analysis. CPX and RUT were separated on the Kromasil C18 column (4.6 × 150 mm, 5 μm) using an isocratic mobile phase combination of phosphoric acid buffer (pH 3.0) and acetonitrile with the ratio of 87:13% v/v at a flow rate of 1.0 mL/min. CPX and RUT were detected at their respective wavelengths of 278 and 368 nm using a photodiode array detector. The developed method was validated according to guideline ICH Q2 R (1). The validation parameters taken were linearity, system suitability, accuracy, precision, robustness, sensitivity, and solution stability which were in the acceptable range. The findings suggest that the developed RP-HPLC method can be successfully applied to analyze novel CPX-RUT-loaded bilosomal nanoformulation prepared by thin-film hydration technique.
Collapse
Affiliation(s)
- Athar Shamim
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Javed Ansari
- Department
of Pharmaceutics, College of Pharmacy, Prince
Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Alhussain Aodah
- Department
of Pharmaceutics, College of Pharmacy, Prince
Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muzaffar Iqbal
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451,Saudi Arabia
| | - Mohd. Aqil
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mohd. Aamir Mirza
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Zeenat Iqbal
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Asgar Ali
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| |
Collapse
|
13
|
González-Reguero D, Robas-Mora M, Fernández-Pastrana VM, Probanza-Lobo A, Jiménez-Gómez PA. Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB. BIOLOGY 2023; 12:801. [PMID: 37372086 DOI: 10.3390/biology12060801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.
Collapse
Affiliation(s)
- Daniel González-Reguero
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Marina Robas-Mora
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Vanesa M Fernández-Pastrana
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Agustín Probanza-Lobo
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| | - Pedro Antonio Jiménez-Gómez
- Department of Pharmaceutical Science and Health, San Pablo University, CEU Universities, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain
| |
Collapse
|
14
|
Fang P, Elena AX, Kunath MA, Berendonk TU, Klümper U. Reduced selection for antibiotic resistance in community context is maintained despite pressure by additional antibiotics. ISME COMMUNICATIONS 2023; 3:52. [PMID: 37258727 PMCID: PMC10232432 DOI: 10.1038/s43705-023-00262-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Selection for antibiotic resistance at very low antibiotic concentrations has been demonstrated for individual antibiotics in single species experiments. Furthermore, selection in these focal strains is reduced when taking place in complex microbial community context. However, in the environment, bacteria are rarely exposed to single, but rather complex mixtures of selective agents. Here, we explored how the presence of a second selective agent affects selection dynamics between isogenic pairs of focal E. coli strains, differing exclusively in a single resistance determinant, in the absence and presence of a model wastewater community across a gradient of antibiotics. An additional antibiotic that exclusively affects the model wastewater community, but to which the focal strains are resistant to, was chosen as the second selective agent. This allowed exploring how inhibition alters the community's ability to reduce selection. In the presence of the community, the selection coefficient at specific antibiotic concentrations was consistently decreased compared to the absence of the community. While pressure through the second antibiotic significantly decreased the activity and diversity of the community, its ability to reduce selection was consistently maintained at levels comparable to those recorded in absence of the second antibiotic. This indicates that the observed effects of community context on selection dynamics are rather based on competitive or protective effects between the focal strains and a small proportion of bacteria within the community, than on general competition for nutrients. These findings have implications for our understanding of the evolution and selection for multi-drug resistant strains.
Collapse
Affiliation(s)
- Peiju Fang
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Alan Xavier Elena
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Maxi Antonia Kunath
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Thomas U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Uli Klümper
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany.
| |
Collapse
|
15
|
França A. The Role of Coagulase-Negative Staphylococci Biofilms on Late-Onset Sepsis: Current Challenges and Emerging Diagnostics and Therapies. Antibiotics (Basel) 2023; 12:antibiotics12030554. [PMID: 36978421 PMCID: PMC10044083 DOI: 10.3390/antibiotics12030554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Infections are one of the most significant complications of neonates, especially those born preterm, with sepsis as one of the principal causes of mortality. Coagulase-negative staphylococci (CoNS), a group of staphylococcal species that naturally inhabit healthy human skin and mucosa, are the most common cause of late-onset sepsis, especially in preterms. One of the risk factors for the development of CoNS infections is the presence of implanted biomedical devices, which are frequently used for medications and/or nutrient delivery, as they serve as a scaffold for biofilm formation. The major concerns related to CoNS infections have to do with the increasing resistance to multiple antibiotics observed among this bacterial group and biofilm cells’ increased tolerance to antibiotics. As such, the treatment of CoNS biofilm-associated infections with antibiotics is increasingly challenging and considering that antibiotics remain the primary form of treatment, this issue will likely persist in upcoming years. For that reason, the development of innovative and efficient therapeutic measures is of utmost importance. This narrative review assesses the current challenges and emerging diagnostic tools and therapies for the treatment of CoNS biofilm-associated infections, with a special focus on late-onset sepsis.
Collapse
Affiliation(s)
- Angela França
- Centre of Biological Engineering, LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, Braga and Guimarães, Portugal
| |
Collapse
|
16
|
Adenaya A, Berger M, Brinkhoff T, Ribas-Ribas M, Wurl O. Usage of antibiotics in aquaculture and the impact on coastal waters. MARINE POLLUTION BULLETIN 2023; 188:114645. [PMID: 36724669 DOI: 10.1016/j.marpolbul.2023.114645] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.
Collapse
Affiliation(s)
- Adenike Adenaya
- Center for Marine Sensors, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Wilhelmshaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Mariana Ribas-Ribas
- Center for Marine Sensors, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Wilhelmshaven, Germany
| | - Oliver Wurl
- Center for Marine Sensors, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Wilhelmshaven, Germany.
| |
Collapse
|
17
|
AtbFinder Diagnostic Test System Improves Optimal Selection of Antibiotic Therapy in Persons with Cystic Fibrosis. J Clin Microbiol 2023; 61:e0155822. [PMID: 36602344 PMCID: PMC9879114 DOI: 10.1128/jcm.01558-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cystic fibrosis (CF) is characterized by mutations of CFTR that lead to increased viscous secretions, bacterial colonization, and recurrent infections. Chronic Pseudomonas aeruginosa infection in persons with CF is associated with progressive and accelerated lung function decline despite aggressive antibiotic treatment. We report the management of respiratory infections in persons with CF with antibiotic therapy that was based on the recommendations of AtbFinder, a novel, rapid, culture-based diagnostic test system that employs a novel paradigm of antibiotic selection. AtbFinder mimics bacterial interactions with antibiotics at concentrations that can be achieved in affected tissues or organs and models conditions of interbacterial interactions within polymicrobial biofilms. This open-label, single-arm, investigator-initiated clinical study was designed to identify the efficacy of antibiotics selected using AtbFinder in persons with CF. Microbiological and clinical parameters were assessed following the change of antibiotic therapy to antibiotics selected with AtbFinder between January 2016 and December 2018 and retrospectively compared with clinical data collected between January 2013 and December 2015. We enrolled 35 persons with CF (33 with chronic P. aeruginosa colonization). Antibiotics selected using AtbFinder resulted in clearance of P. aeruginosa in 81.8% of subsequent cultures, decreased pulmonary exacerbations from 1.21 per patient per annum to 0, and an increase in predicted percent predicted forced expiratory volume in 1 s up to 28.4% from baseline. The number of systemic antibiotic courses used in patients after switching to the AtbFinder-selected therapy was reduced from 355 to 178. These findings describe the superiority of antibiotic regimens selected with AtbFinder compared with routine antimicrobial susceptibility testing.
Collapse
|
18
|
Pakkulnan R, Thonglao N, Chareonsudjai S. DNase I and chitosan enhance efficacy of ceftazidime to eradicate Burkholderia pseudomallei biofilm cells. Sci Rep 2023; 13:1059. [PMID: 36658182 PMCID: PMC9852466 DOI: 10.1038/s41598-023-27790-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Biofilm-associated Burkholderia pseudomallei infection contributes to antibiotic resistance and relapse of melioidosis. Burkholderia pseudomallei biofilm matrix contains extracellular DNA (eDNA) that is crucial for biofilm establishment. However, the contribution of eDNA to antibiotic resistance by B. pseudomallei remains unclear. In this study, we first demonstrated in vitro that DNase I with the administration of ceftazidime (CAZ) at 24 h considerably inhibited the 2-day biofilm formation and reduced the number of viable biofilm cells of clinical B. pseudomallei isolates compared to biofilm treated with CAZ alone. A 3-4 log reduction in numbers of viable cells embedded in the 2-day biofilm was observed when CAZ was combined with DNase I. Confocal laser-scanning microscope visualization emphasized the competence of DNase I followed by CAZ supplementation to significantly limit B. pseudomallei biofilm development and to eradicate viable embedded B. pseudomallei biofilm cells. Furthermore, DNase I supplemented with chitosan (CS) linked with CAZ (CS/CAZ) significantly eradicated shedding planktonic and biofilm cells. These findings indicated that DNase I effectively degraded eDNA leading to biofilm inhibition and dispersion, subsequently allowing CAZ and CS/CAZ to eradicate both shedding planktonic and embedded biofilm cells. These findings provide efficient strategies to interrupt biofilm formation and improve antibiotic susceptibility of biofilm-associated infections.
Collapse
Affiliation(s)
- Rattiyaphorn Pakkulnan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nuttaya Thonglao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sorujsiri Chareonsudjai
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand. .,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
| |
Collapse
|
19
|
Tetz GV, Kardava KM, Vecherkovskaya MF, Tsifansky MD, Tetz VV. Treatment of chronic relapsing urinary tract infection with antibiotics selected by AtbFinder. Urol Case Rep 2022; 46:102312. [PMID: 36619660 PMCID: PMC9817160 DOI: 10.1016/j.eucr.2022.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 12/29/2022] Open
Abstract
We report the case of a 46-year-old patient who, after renal cancer surgery, developed a recurrent urinary tract infection that lasted for more than 2 years. Despite repeated antibiotic courses, including broad-spectrum drugs chosen using conventional antibiotic susceptibility testing, multiple reinfections followed. The patient was successfully treated once antibiotics were selected with AtbFinder. Unlike routine antimicrobial susceptibility methods, which select antibiotics effective only against a "lead bacterial pathogen," AtbFinder identifies antibiotics that target the mixture of bacteria at the infection site. This case demonstrates the ability of AtbFinder to successfully select antibiotics for the treatment of relapsing urinary tract infections.
Collapse
Affiliation(s)
- George V. Tetz
- Human Microbiology Institute, New York, NY, USA,Corresponding author. 101 Avenue of the Americas, New York, NY, 10013, USA.
| | | | | | - Michael D. Tsifansky
- Department of Pediatrics, George Washington University (GWU), Washington, DC, USA,Divisions of Cardiac Critical Care Medicine and Pulmonary, Children's National Hospital, Washington, DC, USA
| | | |
Collapse
|
20
|
Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection. Microorganisms 2022; 10:microorganisms10122383. [PMID: 36557636 PMCID: PMC9781420 DOI: 10.3390/microorganisms10122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches.
Collapse
|
21
|
Reding C. Predicting the re-distribution of antibiotic molecules caused by inter-species interactions in microbial communities. ISME COMMUNICATIONS 2022; 2:110. [PMID: 37938684 PMCID: PMC9723709 DOI: 10.1038/s43705-022-00186-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2023]
Abstract
Microbes associate in nature forming complex communities, but they are often studied in purified form. Here I show that neighbouring species enforce the re-distribution of carbon and antimicrobial molecules, predictably changing drug efficacy with respect to standard laboratory assays. A simple mathematical model, validated experimentally using pairwise competition assays, suggests that differences in drug sensitivity between the competing species causes the re-distribution of drug molecules without affecting carbon uptake. The re-distribution of drug is even when species have similar drug sensitivity, reducing drug efficacy. But when their sensitivities differ the re-distribution is uneven: The most sensitive species accumulates more drug molecules, increasing efficacy against it. Drug efficacy tests relying on samples with multiple species are considered unreliable and unpredictable, but study demonstrates that efficacy in these cases can be qualitatively predicted. It also suggests that living in communities can be beneficial even when all species compete for a single carbon source, as the relationship between cell density and drug required to inhibit their growth may be more complex than previously thought.
Collapse
Affiliation(s)
- Carlos Reding
- Department of Biosciences, University of Exeter, EX4 4QD, Exeter, UK.
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94304, USA.
| |
Collapse
|
22
|
The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies. Antibiotics (Basel) 2022; 11:antibiotics11091215. [PMID: 36139994 PMCID: PMC9495013 DOI: 10.3390/antibiotics11091215] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 12/26/2022] Open
Abstract
Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics according to the antibacterial mechanism of antibiotics, involving the mutation of drug target, secreting hydrolase, and discharging antibiotics out of cells through an efflux pump, etc. In recent years, bacteria are found to constantly evolve new resistance mechanisms to antibiotics, including target protective protein, changes in cell morphology, and so on, endowing them with multiple defense systems against antibiotics, leading to the emergence of multi-drug resistant (MDR) bacteria and the unavailability of drugs in clinics. Correspondingly, researchers attempt to uncover the mystery of bacterial resistance to develop more convenient and effective antibacterial strategies. Although traditional antibiotics still play a significant role in the treatment of diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy in the MDR bacteria. Therefore, highly effective antibacterial compounds, such as phage therapy and CRISPER-Cas precision therapy, are gaining an increasing amount of attention, and are considered to be the treatments with the moist potential with regard to resistance against MDR in the future. In this review, nine identified drug resistance mechanisms are summarized, which enhance the retention rate of bacteria under the action of antibiotics and promote the distribution of drug-resistant bacteria (DRB) in the population. Afterwards, three kinds of potential antibacterial methods are introduced, in which new antibacterial compounds exhibit broad application prospects with different action mechanisms, the phage therapy has been successfully applied to infectious diseases caused by super bacteria, and the CRISPER-Cas precision therapy as a new technology can edit drug-resistant genes in pathogenic bacteria at the gene level, with high accuracy and flexibility. These antibacterial methods will provide more options for clinical treatment, and will greatly alleviate the current drug-resistant crisis.
Collapse
|
23
|
Lee DH, Cha JH, Kim DW, Lee K, Kim YS, Oh HY, Cho YH, Cha CJ. Colistin-degrading proteases confer collective resistance to microbial communities during polymicrobial infections. MICROBIOME 2022; 10:129. [PMID: 35982474 PMCID: PMC9389796 DOI: 10.1186/s40168-022-01315-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The increasing prevalence of resistance against the last-resort antibiotic colistin is a significant threat to global public health. Here, we discovered a novel colistin resistance mechanism via enzymatic inactivation of the drug and proposed its clinical importance in microbial communities during polymicrobial infections. RESULTS A bacterial strain of the Gram-negative opportunistic pathogen Stenotrophomonas maltophilia capable of degrading colistin and exhibiting a high-level colistin resistance was isolated from the soil environment. A colistin-degrading protease (Cdp) was identified in this strain, and its contribution to colistin resistance was demonstrated by growth inhibition experiments using knock-out (Δcdp) and complemented (Δcdp::cdp) mutants. Coculture and coinfection experiments revealed that S. maltophilia carrying the cdp gene could inactivate colistin and protect otherwise susceptible Pseudomonas aeruginosa, which may seriously affect the clinical efficacy of the drug for the treatment of cystic fibrosis patients with polymicrobial infection. CONCLUSIONS Our results suggest that Cdp should be recognized as a colistin resistance determinant that confers collective resistance at the microbial community level. Our study will provide vital information for successful clinical outcomes during the treatment of complex polymicrobial infections, particularly including S. maltophilia and other colistin-susceptible Gram-negative pathogens such as P. aeruginosa. Video abstract.
Collapse
Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
- Division of Life Sciences, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Hyo-Young Oh
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, 13488, Republic of Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, 13488, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea.
| |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Jagir R. Hussan
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, NZ
- * E-mail:
| | - 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
| |
Collapse
|
25
|
Sadiq FA, Hansen MF, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhang H. Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature. FEMS Microbiol Rev 2022; 46:6595875. [PMID: 35640890 DOI: 10.1093/femsre/fuac024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.
Collapse
Affiliation(s)
- Faizan Ahmed Sadiq
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Private Bag, 11222, Palmerston North, New Zealand
| | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
26
|
Houtz JL, Taff CC, Vitousek MN. Gut Microbiome as a Mediator of Stress Resilience: A Reactive Scope Model Framework. Integr Comp Biol 2022; 62:41-57. [PMID: 35544275 DOI: 10.1093/icb/icac030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stress resilience is defined as the ability to rebound to a homeostatic state after exposure to a perturbation. Organisms modulate various physiological mediators to respond to unpredictable changes in their environment. The gut microbiome is a key example of a physiological mediator that coordinates a myriad of host functions including counteracting stressors. Here, we highlight the gut microbiome as a mediator of host stress resilience in the framework of the reactive scope model. The reactive scope model integrates physiological mediators with unpredictable environmental changes to predict how animals respond to stressors. We provide examples of how the gut microbiome responds to stressors within the four ranges of the reactive scope model (i.e., predictive homeostasis, reactive homeostasis, homeostatic overload, and homeostatic failure). We identify measurable metrics of the gut microbiome that could be used to infer the degree to which the host is experiencing chronic stress, including microbial diversity, flexibility, and gene richness. The goal of this perspective piece is to highlight the underutilized potential of measuring the gut microbiome as a mediator of stress resilience in wild animal hosts.
Collapse
Affiliation(s)
- Jennifer L Houtz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Conor C Taff
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Maren N Vitousek
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Ndukwe ARN, Wiedbrauk S, Boase NRB, Fairfull-Smith KE. Strategies to improve the potency of oxazolidinones towards bacterial biofilms. Chem Asian J 2022; 17:e202200201. [PMID: 35352479 PMCID: PMC9321984 DOI: 10.1002/asia.202200201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Biofilms are part of the natural lifecycle of bacteria and are known to cause chronic infections that are difficult to treat. Most antibiotics are developed and tested against bacteria in the planktonic state and are ineffective against bacterial biofilms. The oxazolidinones, including the last resort drug linezolid, are one of the main classes of synthetic antibiotics progressed to clinical use in the last 50 years. They have a unique mechanism of action and only develop low levels of resistance in the clinical setting. With the aim of providing insight into strategies to design more potent antibiotic compounds with activity against bacterial biofilms, we review the biofilm activity of clinically approved oxazolidinones and report on structural modifications to oxazolidinones and their delivery systems which lead to enhanced anti‐biofilm activity.
Collapse
Affiliation(s)
- Audrey R N Ndukwe
- Queensland University of Technology - QUT: Queensland University of Technology, Faculty of Science, AUSTRALIA
| | - Sandra Wiedbrauk
- Queensland University of Technology - QUT: Queensland University of Technology, Faculty of Science, AUSTRALIA
| | - Nathan R B Boase
- Queensland University of Technology - QUT: Queensland University of Technology, Faculty of Science, AUSTRALIA
| | - Kathryn E Fairfull-Smith
- Queensland University of Technology Faculty of Science, Centre for Materials Science, 2 George St, 4001, Brisbane, AUSTRALIA
| |
Collapse
|
29
|
Inter-species interactions alter antibiotic efficacy in bacterial communities. THE ISME JOURNAL 2022; 16:812-821. [PMID: 34628478 PMCID: PMC8857223 DOI: 10.1038/s41396-021-01130-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/14/2022]
Abstract
The efficacy of antibiotic treatments targeting polymicrobial communities is not well predicted by conventional in vitro susceptibility testing based on determining minimum inhibitory concentration (MIC) in monocultures. One reason for this is that inter-species interactions can alter the community members' susceptibility to antibiotics. Here we quantify, and identify mechanisms for, community-modulated changes of efficacy for clinically relevant antibiotics against the pathogen Pseudomonas aeruginosa in model cystic fibrosis (CF) lung communities derived from clinical samples. We demonstrate that multi-drug resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to otherwise sensitive P. aeruginosa. Exposure protection to imipenem was provided by chromosomally encoded metallo-β-lactamase that detoxified the environment; protection was dependent upon S. maltophilia cell density and was provided by S. maltophilia strains isolated from CF sputum, increasing the MIC of P. aeruginosa by up to 16-fold. In contrast, the presence of S. maltophilia provided no protection against meropenem, another routinely used carbapenem. Mathematical ordinary differential equation modelling shows that the level of exposure protection provided against different carbapenems can be explained by differences in antibiotic efficacy and inactivation rate. Together, these findings reveal that exploitation of pre-occurring antimicrobial resistance, and inter-specific competition, can have large impacts on pathogen antibiotic susceptibility, highlighting the importance of microbial ecology for designing successful antibiotic treatments for multispecies communities.
Collapse
|
30
|
Haenni M, Dagot C, Chesneau O, Bibbal D, Labanowski J, Vialette M, Bouchard D, Martin-Laurent F, Calsat L, Nazaret S, Petit F, Pourcher AM, Togola A, Bachelot M, Topp E, Hocquet D. Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes. ENVIRONMENT INTERNATIONAL 2022; 159:107047. [PMID: 34923370 DOI: 10.1016/j.envint.2021.107047] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.
Collapse
Affiliation(s)
- Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES (French Agency for Food, Environmental and Occupational Health & Safety) - Université de Lyon, Lyon, France
| | - Christophe Dagot
- Université of Limoges, RESINFIT, UMR INSERM 1092, CHU, F-87000 Limoges, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Microbiology Department, Institut Pasteur, Paris, France
| | - Delphine Bibbal
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Jérôme Labanowski
- Université de Poitiers, UMR CNRS 7285 IC2MP, ENSI Poitiers, Poitiers, France
| | | | - Damien Bouchard
- National Agency for Veterinary Medicinal Products, ANSES, Fougères, France
| | | | - Louisiane Calsat
- Risk Assessment Department (DER), ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Maisons-Alfort, France
| | - Sylvie Nazaret
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Fabienne Petit
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie Université Rouen, France; Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris F-75005, France
| | | | | | - Morgane Bachelot
- ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Maisons-Alfort, France
| | - Edward Topp
- Agriculture and Agri-Food Canada, and University of Western Ontario, London, ON, Canada
| | - Didier Hocquet
- UMR Chronoenvironnement CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France; Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.
| |
Collapse
|
31
|
La Fortezza M, Velicer GJ. Social selection within aggregative multicellular development drives morphological evolution. Proc Biol Sci 2021; 288:20211522. [PMID: 34814750 PMCID: PMC8611335 DOI: 10.1098/rspb.2021.1522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/02/2021] [Indexed: 12/17/2022] Open
Abstract
Aggregative multicellular development is a social process involving complex forms of cooperation among unicellular organisms. In some aggregative systems, development culminates in the construction of spore-packed fruiting bodies and often unfolds within genetically and behaviourally diverse conspecific cellular environments. Here, we use the bacterium Myxococcus xanthus to test whether the character of the cellular environment during aggregative development shapes its morphological evolution. We manipulated the cellular composition of Myxococcus development in an experiment in which evolving populations initiated from a single ancestor repeatedly co-developed with one of several non-evolving partners-a cooperator, three cheaters and three antagonists. Fruiting body morphology was found to diversify not only as a function of partner genotype but more broadly as a function of partner social character, with antagonistic partners selecting for greater fruiting body formation than cheaters or the cooperator. Yet even small degrees of genetic divergence between distinct cheater partners sufficed to drive treatment-level morphological divergence. Co-developmental partners also determined the magnitude and dynamics of stochastic morphological diversification and subsequent convergence. In summary, we find that even just a few genetic differences affecting developmental and social features can greatly impact morphological evolution of multicellular bodies and experimentally demonstrate that microbial warfare can promote cooperation.
Collapse
Affiliation(s)
- Marco La Fortezza
- Institute for Integrative Biology, ETH Zürich, Zürich 8092, Switzerland
| | | |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Josyula A, Parikh KS, Pitha I, Ensign LM. Engineering biomaterials to prevent post-operative infection and fibrosis. Drug Deliv Transl Res 2021; 11:1675-1688. [PMID: 33710589 PMCID: PMC8238864 DOI: 10.1007/s13346-021-00955-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/19/2022]
Abstract
Implantable biomaterials are essential surgical devices, extending and improving the quality of life of millions of people globally. Advances in materials science, manufacturing, and in our understanding of the biological response to medical device implantation over several decades have resulted in improved safety and functionality of biomaterials. However, post-operative infection and immune responses remain significant challenges that interfere with biomaterial functionality and host healing processes. The objectives of this review is to provide an overview of the biology of post-operative infection and the physiological response to implanted biomaterials and to discuss emerging strategies utilizing local drug delivery and surface modification to improve the long-term safety and efficacy of biomaterials.
Collapse
Affiliation(s)
- Aditya Josyula
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kunal S Parikh
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Center for Bioengineering Innovation and Design, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ian Pitha
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Laura M Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, 21287, USA.
- Departments Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| |
Collapse
|
34
|
Causes and consequences of pattern diversification in a spatially self-organizing microbial community. THE ISME JOURNAL 2021; 15:2415-2426. [PMID: 33664433 PMCID: PMC8319339 DOI: 10.1038/s41396-021-00942-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 01/31/2023]
Abstract
Surface-attached microbial communities constitute a vast amount of life on our planet. They contribute to all major biogeochemical cycles, provide essential services to our society and environment, and have important effects on human health and disease. They typically consist of different interacting genotypes that arrange themselves non-randomly across space (referred to hereafter as spatial self-organization). While spatial self-organization is important for the functioning, ecology, and evolution of these communities, the underlying determinants of spatial self-organization remain unclear. Here, we performed a combination of experiments, statistical modeling, and mathematical simulations with a synthetic cross-feeding microbial community consisting of two isogenic strains. We found that two different patterns of spatial self-organization emerged at the same length and time scales, thus demonstrating pattern diversification. This pattern diversification was not caused by initial environmental heterogeneity or by genetic heterogeneity within populations. Instead, it was caused by nongenetic heterogeneity within populations, and we provide evidence that the source of this nongenetic heterogeneity is local differences in the initial spatial positionings of individuals. We further demonstrate that the different patterns exhibit different community-level properties; namely, they have different expansion speeds. Together, our results demonstrate that pattern diversification can emerge in the absence of initial environmental heterogeneity or genetic heterogeneity within populations and can affect community-level properties, thus providing novel insights into the causes and consequences of microbial spatial self-organization.
Collapse
|
35
|
Neto I, Domínguez-Martín EM, Ntungwe E, Reis CP, Pesic M, Faustino C, Rijo P. Dehydroabietic Acid Microencapsulation Potential as Biofilm-Mediated Infections Treatment. Pharmaceutics 2021; 13:pharmaceutics13060825. [PMID: 34199531 PMCID: PMC8229915 DOI: 10.3390/pharmaceutics13060825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 11/30/2022] Open
Abstract
The antimicrobial activity of dehydroabietic acid (DHA) for its use as an antibiofilm agent was tested in this work. DHA was assayed against a collection of Gram-positive, Gram-negative sensitive and resistant bacteria and yeasts through the minimum inhibitory concentration (MIC), MIC with Bioburden challenge, minimum bactericidal concentration (MBC), minimum biofilm inhibitory concentration (MBIC), MBIC with Bioburden challenge and growth curve studies. Toxicological studies (Artemia salina, sulforhodamine B (SRB) assay) were done to assess if the compound had antimicrobial and not cytotoxic properties. Furthermore, microencapsulation and stability studies were carried out to evaluate the chemical behavior and stability of DHA. On MIC results, Gram-positive bacteria Staphylococcus aureus ATCC 1228 and Mycobacterium smegmatis ATCC 607 presented a high efficiency (7.81 µg/mL), while on Gram-negative bacteria the highest MIC value of 125 µg/mL was obtained by all Klebsiella pneumoniae strains and Escherichia coli isolate strain HSM 303. Bioburden challenge showed that MIC, MBIC and percentage biofilm inhibition (BI) values suffered alterations, therefore, having higher concentrations. MBIC values demonstrated that DHA has a higher efficiency against S. aureus ATCC 43866 with a percentage of BI of 75.13 ± 0.82% at 0.49 µg/mL. Growth curve kinetic profiles of DHA against S. aureus ATCC 25923 were observed to be bacteriostatic. DHA-alginate beads had a average size of 2.37 ± 0.20 and 2.31 ± 0.17 × 103 µm2 with an encapsulation efficiency (EE%) around 99.49 ± 0.05%, a protection percentage (PP%) of 60.00 ± 0.05% in the gastric environment and a protection efficiency (PE%) around 88.12 ± 0.05% against UV light. In toxicological studies DHA has shown IC50 of 19.59 ± 7.40 µg/mL and a LC50 of 21.71 ± 2.18%. The obtained results indicate that DHA is a promising antimicrobial candidate against a wide range of bacteria and biofilm formation that must be further explored.
Collapse
Affiliation(s)
- Iris Neto
- CBIOS-Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (I.N.); (E.M.D.-M.); (E.N.)
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal;
| | - Eva María Domínguez-Martín
- CBIOS-Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (I.N.); (E.M.D.-M.); (E.N.)
- Pharmacology Area (Pharmacognosy Laboratory), New Antitumor Compounds: Toxic Action on Leukemia Cells Research Group. Ctra. A2, Department of Biomedical Sciences, Faculty of Pharmacy, Km 33.100—Campus Universitario, University of Alcalá de Henares, Alcalá de Henares, 28805 Madrid, Spain
| | - Epole Ntungwe
- CBIOS-Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (I.N.); (E.M.D.-M.); (E.N.)
- Pharmacology Area (Pharmacognosy Laboratory), New Antitumor Compounds: Toxic Action on Leukemia Cells Research Group. Ctra. A2, Department of Biomedical Sciences, Faculty of Pharmacy, Km 33.100—Campus Universitario, University of Alcalá de Henares, Alcalá de Henares, 28805 Madrid, Spain
| | - Catarina P. Reis
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal;
| | - Milica Pesic
- Institute for Biological Research “Sinisa Stankovic”-National Institute of Republic of Serbia, University of Belgrade 142, 11060 Belgrade, Serbia;
| | - Célia Faustino
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal;
- Correspondence: (C.F.); (P.R.)
| | - Patrícia Rijo
- CBIOS-Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (I.N.); (E.M.D.-M.); (E.N.)
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal;
- Correspondence: (C.F.); (P.R.)
| |
Collapse
|
36
|
Ecology and evolution of antimicrobial resistance in bacterial communities. THE ISME JOURNAL 2021; 15:939-948. [PMID: 33219299 PMCID: PMC8115348 DOI: 10.1038/s41396-020-00832-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
Accumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by the presence of other interacting microbes. These interactions are not typically accounted for when determining pathogen sensitivity to antibiotics. In this perspective, we argue that resistance and evolutionary responses to antibiotic treatments should not be considered only a trait of an individual bacteria species but also an emergent property of the microbial community in which pathogens are embedded. We outline how interspecies interactions can affect the responses of individual species and communities to antibiotic treatment, and how these responses could affect the strength of selection, potentially changing the trajectory of resistance evolution. Finally, we identify key areas of future research which will allow for a more complete understanding of antibiotic resistance in bacterial communities. We emphasise that acknowledging the ecological context, i.e. the interactions that occur between pathogens and within communities, could help the development of more efficient and effective antibiotic treatments.
Collapse
|
37
|
Oliveira VDC, Steixner S, Nascimento CD, Pagnano VO, Silva-Lovato CH, Paranhos HDFO, Wilflingseder D, Coraça-Huber D, Watanabe E. Expression of virulence factors by Pseudomonas aeruginosa biofilm after bacteriophage infection. Microb Pathog 2021; 154:104834. [PMID: 33691179 DOI: 10.1016/j.micpath.2021.104834] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
The use of bacteriophages for the treatment of bacterial infections has been extensively studied. Nonetheless, the stress response regarding bacteriophage infection and the expression of virulence factors of Pseudomonas aeruginosa after phage infection is poorly discussed. In this study, we evaluated biofilm formation capacity and expression of virulence factors of P. aeruginosa after bacteriophage infection. Biofilm growth rates, biofilm morphology, pyocyanin production and elastase activity were evaluated after 2, 8, 24 and 48 h of co-cultivation with bacteriophages that was recently characterized and showed to be infective towards clinical isolates. In parallel, quantitative real-time polymerase chain reactions were carried out to verify the expression of virulence-related genes. Bacteriophages promoted substantial changes in P. aeruginosa biofilm growth at early co-culture time. In addition, at 8 h, we observed that some cultures developed filaments. Although bacteriophages did not alter both pyocyanin and protease activity, changes on the expression level of genes related to virulence factors were detected. Usually, lasI, pslA, lasB and phzH genes were upregulated after 2 and 48 h of co-culture. These results highlight the need for extensive investigation of pathways and molecules involved in phage infection, since the transcriptional changes would suggest a response activation by P. aeruginosa.
Collapse
Affiliation(s)
- Viviane de Cássia Oliveira
- Human Exposome and Infectious Diseases Network - HEID, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil; Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Stephan Steixner
- Research Laboratory for Biofilms and Implant Associated Infections (BIOFILM LAB), Department of Orthopedic Surgery, Experimental Orthopedics, Medical University of Innsbruck, Innsbruck, Austria
| | - Cássio do Nascimento
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Valéria Oliveira Pagnano
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cláudia Helena Silva-Lovato
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Helena de Freitas Oliveira Paranhos
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Débora Coraça-Huber
- Research Laboratory for Biofilms and Implant Associated Infections (BIOFILM LAB), Department of Orthopedic Surgery, Experimental Orthopedics, Medical University of Innsbruck, Innsbruck, Austria
| | - Evandro Watanabe
- Human Exposome and Infectious Diseases Network - HEID, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil; Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
38
|
Zimmermann M, Patil KR, Typas A, Maier L. Towards a mechanistic understanding of reciprocal drug-microbiome interactions. Mol Syst Biol 2021; 17:e10116. [PMID: 33734582 PMCID: PMC7970330 DOI: 10.15252/msb.202010116] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Broad-spectrum antibiotics target multiple gram-positive and gram-negative bacteria, and can collaterally damage the gut microbiota. Yet, our knowledge of the extent of damage, the antibiotic activity spectra, and the resistance mechanisms of gut microbes is sparse. This limits our ability to mitigate microbiome-facilitated spread of antibiotic resistance. In addition to antibiotics, non-antibiotic drugs affect the human microbiome, as shown by metagenomics as well as in vitro studies. Microbiome-drug interactions are bidirectional, as microbes can also modulate drugs. Chemical modifications of antibiotics mostly function as antimicrobial resistance mechanisms, while metabolism of non-antibiotics can also change the drugs' pharmacodynamic, pharmacokinetic, and toxic properties. Recent studies have started to unravel the extensive capacity of gut microbes to metabolize drugs, the mechanisms, and the relevance of such events for drug treatment. These findings raise the question whether and to which degree these reciprocal drug-microbiome interactions will differ across individuals, and how to take them into account in drug discovery and precision medicine. This review describes recent developments in the field and discusses future study areas that will benefit from systems biology approaches to better understand the mechanistic role of the human gut microbiota in drug actions.
Collapse
Affiliation(s)
- Michael Zimmermann
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Athanasios Typas
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’University of TübingenTübingenGermany
| |
Collapse
|
39
|
Kranjec C, Morales Angeles D, Torrissen Mårli M, Fernández L, García P, Kjos M, Diep DB. Staphylococcal Biofilms: Challenges and Novel Therapeutic Perspectives. Antibiotics (Basel) 2021; 10:131. [PMID: 33573022 PMCID: PMC7911828 DOI: 10.3390/antibiotics10020131] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococci, like Staphylococcus aureus and S. epidermidis, are common colonizers of the human microbiota. While being harmless in many cases, many virulence factors result in them being opportunistic pathogens and one of the major causes of hospital-acquired infections worldwide. One of these virulence factors is the ability to form biofilms-three-dimensional communities of microorganisms embedded in an extracellular polymeric matrix (EPS). The EPS is composed of polysaccharides, proteins and extracellular DNA, and is finely regulated in response to environmental conditions. This structured environment protects the embedded bacteria from the human immune system and decreases their susceptibility to antimicrobials, making infections caused by staphylococci particularly difficult to treat. With the rise of antibiotic-resistant staphylococci, together with difficulty in removing biofilms, there is a great need for new treatment strategies. The purpose of this review is to provide an overview of our current knowledge of the stages of biofilm development and what difficulties may arise when trying to eradicate staphylococcal biofilms. Furthermore, we look into promising targets and therapeutic methods, including bacteriocins and phage-derived antibiofilm approaches.
Collapse
Affiliation(s)
- Christian Kranjec
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Danae Morales Angeles
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Lucía Fernández
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (L.F.); (P.G.)
- DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Pilar García
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (L.F.); (P.G.)
- DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| |
Collapse
|
40
|
Grobas I, Bazzoli DG, Asally M. Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools. Biochem Soc Trans 2020; 48:2903-2913. [PMID: 33300966 PMCID: PMC7752047 DOI: 10.1042/bst20200972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell-cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.
Collapse
Affiliation(s)
- Iago Grobas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - Dario G. Bazzoli
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, U.K
| | - Munehiro Asally
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K
| |
Collapse
|
41
|
Jabila Mary TR, Kannan RR, Muthamil Iniyan A, Carlton Ranjith WA, Nandhagopal S, Vishwakarma V, Prakash Vincent SG. β-lactamase inhibitory potential of kalafungin from marine Streptomyces in Staphylococcus aureus infected zebrafish. Microbiol Res 2020; 244:126666. [PMID: 33338970 DOI: 10.1016/j.micres.2020.126666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022]
Abstract
β-lactamase inhibitors are potent synergistic drugs to deteriorate the multidrug-resistant bacteria. Here, we report the β-lactamase inhibitory ability of kalafungin isolated from a marine sponge derived Streptomyces sp. SBRK1. The IC50 value of the kalafungin was calculated as 225.37 ± 1.95 μM against β-lactamase. The enzyme kinetic analysis showed the Km value of 3.448 ± 0.7 μM and Vmax value of 215.356 ± 8 μM/min and the inhibition mechanism was identified as uncompetitive type. Along with the antibacterial activity, the cell surface analysis of kalafungin treated Staphylococcus aureus cells revealed destruction of cell membrane in response to β-lactamase inhibition. Molecular docking studies have confirmed the binding property of kalafungin against β-lactamase with two hydrogen bonds. In vivo efficacy studies in the zebrafish model by green fluorescent protein expressing S. aureus infection, survival, safety and behavioral profile were reported. The toxicity and anti-infection revealed that the compound was evidently active and safe to all organs. In conclusion, this is the first report on kalafungin with β- lactamase inhibition and suggests that kalafungin may useful for synergic antibacterial therapy with β-lactam drugs to overcome β-lactamase-based resistance of any bacterial pathogens.
Collapse
Affiliation(s)
- Thankaraj Rajam Jabila Mary
- Infectious Disease Biology Lab, Centre for Molecular and Nanomedical Sciences, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai, 600119, Tamil Nadu, India
| | - Rajaretinam Rajesh Kannan
- Infectious Disease Biology Lab, Centre for Molecular and Nanomedical Sciences, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai, 600119, Tamil Nadu, India.
| | - Appadurai Muthamil Iniyan
- Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari, 629502, Tamil Nadu, India
| | - Wilson Alphonse Carlton Ranjith
- Infectious Disease Biology Lab, Centre for Molecular and Nanomedical Sciences, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai, 600119, Tamil Nadu, India
| | - Soundarapandian Nandhagopal
- Infectious Disease Biology Lab, Centre for Molecular and Nanomedical Sciences, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai, 600119, Tamil Nadu, India
| | - Vinita Vishwakarma
- Infectious Disease Biology Lab, Centre for Molecular and Nanomedical Sciences, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai, 600119, Tamil Nadu, India
| | - Samuel Gnana Prakash Vincent
- Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, Kanyakumari, 629502, Tamil Nadu, India
| |
Collapse
|
42
|
Rezzoagli C, Archetti M, Mignot I, Baumgartner M, Kümmerli R. Combining antibiotics with antivirulence compounds can have synergistic effects and reverse selection for antibiotic resistance in Pseudomonas aeruginosa. PLoS Biol 2020; 18:e3000805. [PMID: 32810152 PMCID: PMC7433856 DOI: 10.1371/journal.pbio.3000805] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/14/2020] [Indexed: 12/28/2022] Open
Abstract
Antibiotics are losing efficacy due to the rapid evolution and spread of resistance. Treatments targeting bacterial virulence factors have been considered as alternatives because they target virulence instead of pathogen viability, and should therefore exert weaker selection for resistance than conventional antibiotics. However, antivirulence treatments rarely clear infections, which compromises their clinical applications. Here, we explore the potential of combining antivirulence drugs with antibiotics against the opportunistic human pathogen Pseudomonas aeruginosa. We combined two antivirulence compounds (gallium, a siderophore quencher, and furanone C-30, a quorum sensing [QS] inhibitor) together with four clinically relevant antibiotics (ciprofloxacin, colistin, meropenem, tobramycin) in 9×9 drug concentration matrices. We found that drug-interaction patterns were concentration dependent, with promising levels of synergies occurring at intermediate drug concentrations for certain drug pairs. We then tested whether antivirulence compounds are potent adjuvants, especially when treating antibiotic resistant (AtbR) clones. We found that the addition of antivirulence compounds to antibiotics could restore growth inhibition for most AtbR clones, and even abrogate or reverse selection for resistance in five drug combination cases. Molecular analyses suggest that selection against resistant clones occurs when resistance mechanisms involve restoration of protein synthesis, but not when efflux pumps are up-regulated. Altogether, our work provides a first systematic analysis of antivirulence-antibiotic combinatorial treatments and suggests that such combinations have the potential to be both effective in treating infections and in limiting the spread of antibiotic resistance.
Collapse
Affiliation(s)
- Chiara Rezzoagli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Martina Archetti
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Ingrid Mignot
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Michael Baumgartner
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
43
|
Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells. Proc Natl Acad Sci U S A 2020; 117:19455-19464. [PMID: 32703812 PMCID: PMC7431077 DOI: 10.1073/pnas.1919672117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of antibiotic resistance poses a critical threat to the efficacy of antibiotic treatments. A resistant bacterial population must originally arise from a single cell that mutates or acquires a resistance gene. This single cell may, by chance, fail to successfully reproduce before it dies, leading to loss of the nascent resistant lineage. Here, we show that antibiotic concentrations that selectively favor resistance are nonetheless sufficient to reduce the chance of outgrowth from a single cell to a very low probability. Our findings suggest that lower antibiotic concentrations than those required to clear a large resistant population may be sufficient to prevent, with high probability, outgrowth of initially rare resistant mutants. A better understanding of how antibiotic exposure impacts the evolution of resistance in bacterial populations is crucial for designing more sustainable treatment strategies. The conventional approach to this question is to measure the range of concentrations over which resistant strain(s) are selectively favored over a sensitive strain. Here, we instead investigate how antibiotic concentration impacts the initial establishment of resistance from single cells, mimicking the clonal expansion of a resistant lineage following mutation or horizontal gene transfer. Using two Pseudomonas aeruginosa strains carrying resistance plasmids, we show that single resistant cells have <5% probability of detectable outgrowth at antibiotic concentrations as low as one-eighth of the resistant strain’s minimum inhibitory concentration (MIC). This low probability of establishment is due to detrimental effects of antibiotics on resistant cells, coupled with the inherently stochastic nature of cell division and death on the single-cell level, which leads to loss of many nascent resistant lineages. Our findings suggest that moderate doses of antibiotics, well below the MIC of resistant strains, may effectively restrict de novo emergence of resistance even though they cannot clear already-large resistant populations.
Collapse
|
44
|
Beta-Lactam Sensitive Bacteria Can Acquire ESBL-Resistance via Conjugation after Long-Term Exposure to Lethal Antibiotic Concentration. Antibiotics (Basel) 2020; 9:antibiotics9060296. [PMID: 32498393 PMCID: PMC7345503 DOI: 10.3390/antibiotics9060296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Beta-lactams are commonly used antibiotics that prevent cell-wall biosynthesis. Beta-lactam sensitive bacteria can acquire conjugative resistance elements and hence become resistant even after being exposed to lethal (above minimum inhibitory) antibiotic concentrations. Here we show that neither the length of antibiotic exposure (1 to 16 h) nor the beta-lactam type (penam or cephem) have a major impact on the rescue of sensitive bacteria. We demonstrate that an evolutionary rescue can occur between different clinically relevant bacterial species (Klebsiella pneumoniae and Escherichia coli) by plasmids that are commonly associated with extended-spectrum beta-lactamase (ESBL) positive hospital isolates. As such, it is possible that this resistance dynamic may play a role in failing antibiotic therapies in those cases where resistant bacteria may readily migrate into the proximity of sensitive pathogens. Furthermore, we engineered a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-plasmid to encode a guiding CRISPR-RNA against the migrating ESBL-plasmid. By introducing this plasmid into the sensitive bacterium, the frequency of the evolutionarily rescued bacteria decreased by several orders of magnitude. As such, engineering pathogens during antibiotic treatment may provide ways to prevent ESBL-plasmid dispersal and hence resistance evolution.
Collapse
|
45
|
Baumgartner M, Bayer F, Pfrunder-Cardozo KR, Buckling A, Hall AR. Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples. PLoS Biol 2020; 18:e3000465. [PMID: 32310938 PMCID: PMC7192512 DOI: 10.1371/journal.pbio.3000465] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/30/2020] [Accepted: 04/02/2020] [Indexed: 01/05/2023] Open
Abstract
Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g., via resource competition) but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonisation by focal E. coli but also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic-resistance evolution of individual species.
Collapse
Affiliation(s)
- Michael Baumgartner
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- * E-mail:
| | - Florian Bayer
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Katia R. Pfrunder-Cardozo
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Alex R. Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
46
|
Mei H, Arbeithuber B, Cremona MA, DeGiorgio M, Nekrutenko A. A High-Resolution View of Adaptive Event Dynamics in a Plasmid. Genome Biol Evol 2020; 11:3022-3034. [PMID: 31539047 PMCID: PMC6827461 DOI: 10.1093/gbe/evz197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2019] [Indexed: 11/30/2022] Open
Abstract
Coadaptation between bacterial hosts and plasmids frequently results in adaptive changes restricted exclusively to host genome leaving plasmids unchanged. To better understand this remarkable stability, we transformed naïve Escherichia coli cells with a plasmid carrying an antibiotic-resistance gene and forced them to adapt in a turbidostat environment. We then drew population samples at regular intervals and subjected them to duplex sequencing—a technique specifically designed for identification of low-frequency mutations. Variants at ten sites implicated in plasmid copy number control emerged almost immediately, tracked consistently across the experiment’s time points, and faded below detectable frequencies toward the end. This variation crash coincided with the emergence of mutations on the host chromosome. Mathematical modeling of trajectories for adaptive changes affecting plasmid copy number showed that such mutations cannot readily fix or even reach appreciable frequencies. We conclude that there is a strong selection against alterations of copy number even if it can provide a degree of growth advantage. This incentive is likely rooted in the complex interplay between mutated and wild-type plasmids constrained within a single cell and underscores the importance of understanding of intracellular plasmid variability.
Collapse
Affiliation(s)
- Han Mei
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University
| | | | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University.,Department of Operations and Decision Systems, Université Laval
| | - Michael DeGiorgio
- Department of Biology, The Pennsylvania State University.,Department of Statistics, The Pennsylvania State University.,Institute for CyberScience, The Pennsylvania State University
| | - Anton Nekrutenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Ciccarese D, Zuidema A, Merlo V, Johnson DR. Interaction-dependent effects of surface structure on microbial spatial self-organization. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190246. [PMID: 32200742 DOI: 10.1098/rstb.2019.0246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
Collapse
Affiliation(s)
- Davide Ciccarese
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Anita Zuidema
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Valeria Merlo
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| |
Collapse
|
49
|
Wu F, Tan C. Dead bacterial absorption of antimicrobial peptides underlies collective tolerance. J R Soc Interface 2020; 16:20180701. [PMID: 30958185 DOI: 10.1098/rsif.2018.0701] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The collective tolerance towards antimicrobial peptides (APs) is thought to occur primarily through mechanisms associated with live bacterial cells. In contrast to the focus on live cells, we discover that the LL37 antimicrobial peptide kills a subpopulation of Escherichia coli, forming dead cells that absorb the remaining LL37 from the environment. Combining mathematical modelling with population and single-cell experiments, we show that bacteria absorb LL37 at a timing that coincides with the permeabilization of their cytoplasmic membranes. Furthermore, we show that one bacterial strain can absorb LL37 and protect another strain from killing by LL37. Finally, we demonstrate that the absorption of LL37 by dead bacteria can be reduced using a peptide adjuvant. In contrast to the known collective tolerance mechanisms, we show that the absorption of APs by dead bacteria is a dynamic process that leads to emergent population behaviour.
Collapse
Affiliation(s)
- Fan Wu
- Department of Biomedical Engineering, University of California Davis , Davis, CA 95616 , USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis , Davis, CA 95616 , USA
| |
Collapse
|
50
|
Galera-Laporta L, Garcia-Ojalvo J. Antithetic population response to antibiotics in a polybacterial community. SCIENCE ADVANCES 2020; 6:eaaz5108. [PMID: 32181369 PMCID: PMC7060062 DOI: 10.1126/sciadv.aaz5108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/05/2019] [Indexed: 05/31/2023]
Abstract
Much is known about the effects of antibiotics on isolated bacterial species, but their influence on polybacterial communities is less understood. Here, we study the joint response of a mixed community of nonresistant Bacillus subtilis and Escherichia coli bacteria to moderate concentrations of the β-lactam antibiotic ampicillin. We show that when the two organisms coexist, their population response to the antibiotic is opposite to that in isolation: Whereas in monoculture B. subtilis is tolerant and E. coli is sensitive to ampicillin, in coculture it is E. coli who can proliferate in the presence of the antibiotic, while B. subtilis cannot. This antithetic behavior is predicted by a mathematical model constrained only by the responses of the two species in isolation. Our results thus show that the collective response of mixed bacterial ecosystems to antibiotics can run counter to what single-species potency studies tell us about their efficacy.
Collapse
|