1
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Stauffer PE, Brinkley J, Jacobson DA, Quaranta V, Tyson DR. Purinergic Ca 2+ Signaling as a Novel Mechanism of Drug Tolerance in BRAF-Mutant Melanoma. Cancers (Basel) 2024; 16:2426. [PMID: 39001489 PMCID: PMC11240618 DOI: 10.3390/cancers16132426] [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: 05/30/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Drug tolerance is a major cause of relapse after cancer treatment. Despite intensive efforts, its molecular basis remains poorly understood, hampering actionable intervention. We report a previously unrecognized signaling mechanism supporting drug tolerance in BRAF-mutant melanoma treated with BRAF inhibitors that could be of general relevance to other cancers. Its key features are cell-intrinsic intracellular Ca2+ signaling initiated by P2X7 receptors (purinergic ligand-gated cation channels) and an enhanced ability for these Ca2+ signals to reactivate ERK1/2 in the drug-tolerant state. Extracellular ATP, virtually ubiquitous in living systems, is the ligand that can initiate Ca2+ spikes via P2X7 channels. ATP is abundant in the tumor microenvironment and is released by dying cells, ironically implicating treatment-initiated cancer cell death as a source of trophic stimuli that leads to ERK reactivation and drug tolerance. Such a mechanism immediately offers an explanation of the inevitable relapse after BRAFi treatment in BRAF-mutant melanoma and points to actionable strategies to overcome it.
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Affiliation(s)
- Philip E. Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jordon Brinkley
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - David A. Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Vito Quaranta
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Darren R. Tyson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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2
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Li H, Hong L, Szymczak W, Orner E, Garber AI, Cooper VS, Chen W, De A, Tang JX, Mani S. Protocol for isolating single species of bacteria with swarming ability from human feces. STAR Protoc 2024; 5:102961. [PMID: 38573864 PMCID: PMC10999858 DOI: 10.1016/j.xpro.2024.102961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Understanding the specific movements of bacteria isolated from human feces can serve as a novel diagnostic and therapeutic tool for inflammatory bowel disease. Here, we present a protocol for a microbial swarming assay and to isolate the bacteria responsible for swarming activity. We describe steps for identifying bacteria using MALDI-TOF mass spectrometry and whole-genome sequencing. We then detail procedures for validating findings by observing the same swarming phenotype upon reperforming the swarming assay. For complete details on the use and execution of this protocol, please refer to De et al.1.
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Affiliation(s)
- Hao Li
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lilli Hong
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wendy Szymczak
- Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Orner
- Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Weijie Chen
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Intelligent Medicine Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Arpan De
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay X Tang
- Brown University, Physics Department, Providence, RI 02912, USA
| | - Sridhar Mani
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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3
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Şimşek E, Kim K, Lu J, Silver A, Luo N, Lee CT, You L. A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Mol Syst Biol 2024:10.1038/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.
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Affiliation(s)
- Emrah Şimşek
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Anita Silver
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
| | - Nan Luo
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Charlotte T Lee
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Center for Quantitative Biodesign, Duke University, Durham, NC, 27708, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27708, USA.
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4
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Rolon ML, Voloshchuk O, Bartlett KV, LaBorde LF, Kovac J. Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride. Biofilm 2024; 7:100177. [PMID: 38304489 PMCID: PMC10832383 DOI: 10.1016/j.bioflm.2024.100177] [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: 11/07/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Listeria monocytogenes may survive and persist in food processing environments due to formation of complex multi-species biofilms of environmental microbiota that co-exists in these environments. This study aimed to determine the effect of selected environmental microbiota on biofilm formation and tolerance of L. monocytogenes to benzalkonium chloride in formed biofilms. The studied microbiota included bacterial families previously shown to co-occur with L. monocytogenes in tree fruit packing facilities, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae. Biofilm formation ability and the effect of formed biofilms on the tolerance of L. monocytogenes to benzalkonium chloride was measured in single- and multi-family assemblages. Biofilms were grown statically on polystyrene pegs submerged in a R2A broth. Biofilm formation was quantified using a crystal violet assay, spread-plating, confocal laser scanning microscopy, and its composition was assessed using amplicon sequencing. The concentration of L. monocytogenes in biofilms was determined using the most probable number method. Biofilms were exposed to the sanitizer benzalkonium chloride, and the death kinetics of L. monocytogenes were quantified using a most probable number method. A total of 8, 8, 6, and 3 strains of Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, respectively, were isolated from the environmental microbiota of tree fruit packing facilities and were used in this study. Biofilms formed by Pseudomonadaceae, Xanthomonadaceae, and all multi-family assemblages had significantly higher concentration of bacteria, as well as L. monocytogenes, compared to biofilms formed by L. monocytogenes alone. Furthermore, multi-family assemblage biofilms increased the tolerance of L. monocytogenes to benzalkonium chloride compared to L. monocytogenes mono-species biofilms and planktonic multi-family assemblages. These findings suggest that L. monocytogenes control strategies should focus not only on assessing the efficacy of sanitizers against L. monocytogenes, but also against biofilm-forming microorganisms that reside in the food processing built environment, such as Pseudomonadaceae or Xanthomonadaceae.
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Affiliation(s)
- M. Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Olena Voloshchuk
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Katelyn V. Bartlett
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Luke F. LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
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5
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Zhu J, Xie R, Gao R, Zhao Y, Yodsanit N, Zhu M, Burger JC, Ye M, Tong Y, Gong S. Multimodal nanoimmunotherapy engages neutrophils to eliminate Staphylococcus aureus infections. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01648-8. [PMID: 38632494 DOI: 10.1038/s41565-024-01648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
The increasing prevalence of antimicrobial resistance in Staphylococcus aureus necessitates alternative therapeutic approaches. Neutrophils play a crucial role in the fight against S. aureus but suffer from deficiencies in function leading to increased infection. Here we report a nanoparticle-mediated immunotherapy aimed at potentiating neutrophils to eliminate S. aureus. The nanoparticles consist of naftifine, haemoglobin (Hb) and a red blood cell membrane coating. Naftifine disrupts staphyloxanthin biosynthesis, Hb reduces bacterial hydrogen sulfide levels and the red blood cell membrane modifies bacterial lipid composition. Collectively, the nanoparticles can sensitize S. aureus to host oxidant killing. Furthermore, in the infectious microenvironment, Hb triggers lipid peroxidation in S. aureus, promoting neutrophil chemotaxis. Oxygen supplied by Hb can also significantly enhance the bactericidal capability of the recruited neutrophils by restoring neutrophil respiratory burst via hypoxia relief. This multimodal nanoimmunotherapy demonstrates excellent therapeutic efficacy in treating antimicrobial-resistant S. aureus persisters, biofilms and S. aureus-induced infection in mice.
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Affiliation(s)
- Jingcheng Zhu
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ruosen Xie
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ruixuan Gao
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yi Zhao
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Nisakorn Yodsanit
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Min Zhu
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacobus C Burger
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Mingzhou Ye
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yao Tong
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Shaoqin Gong
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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6
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Stauffer PE, Brinkley J, Jacobson D, Quaranta V, Tyson DR. Purinergic Ca 2+ signaling as a novel mechanism of drug tolerance in BRAF mutant melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565532. [PMID: 37961267 PMCID: PMC10635130 DOI: 10.1101/2023.11.03.565532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Drug tolerance is a major cause of relapse after cancer treatment. In spite of intensive efforts1-9, its molecular basis remains poorly understood, hampering actionable intervention. We report a previously unrecognized signaling mechanism supporting drug tolerance in BRAF-mutant melanoma treated with BRAF inhibitors that could be of general relevance to other cancers. Its key features are cell-intrinsic intracellular Ca2+ signaling initiated by P2X7 receptors (purinergic ligand-gated cation channels), and an enhanced ability for these Ca2+ signals to reactivate ERK1/2 in the drug-tolerant state. Extracellular ATP, virtually ubiquitous in living systems, is the ligand that can initiate Ca2+ spikes via P2X7 channels. ATP is abundant in the tumor microenvironment and is released by dying cells, ironically implicating treatment-initiated cancer cell death as a source of trophic stimuli that leads to ERK reactivation and drug tolerance. Such a mechanism immediately offers an explanation of the inevitable relapse after BRAFi treatment in BRAF-mutant melanoma, and points to actionable strategies to overcome it.
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Affiliation(s)
- Philip E Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - Jordon Brinkley
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - David Jacobson
- Departments of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - Vito Quaranta
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - Darren R Tyson
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
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7
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Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes 2024; 16:2296603. [PMID: 38149632 PMCID: PMC10761165 DOI: 10.1080/19490976.2023.2296603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023] Open
Abstract
The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.
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Affiliation(s)
- Shuang Wang
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lingyi Mu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
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8
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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.
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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
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9
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Zhang C, Kong Y, Xiang Q, Ma Y, Guo Q. Bacterial memory in antibiotic resistance evolution and nanotechnology in evolutionary biology. iScience 2023; 26:107433. [PMID: 37575196 PMCID: PMC10415926 DOI: 10.1016/j.isci.2023.107433] [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: 08/15/2023] Open
Abstract
Bacterial memory refers to the phenomenon in which past experiences influence current behaviors in response to changing environments. It serves as a crucial process that enables adaptation and evolution. We first summarize the state-of-art approaches regarding history-dependent behaviors that impact growth dynamics and underlying mechanisms. Then, the phenotypic and genotypic origins of memory and how encoded memory modulates drug tolerance/resistance are reviewed. We also provide a summary of possible memory effects induced by antimicrobial nanoparticles. The regulatory networks and genetic underpinnings responsible for memory building partially overlap with nanoparticle and drug exposures, which may raise concerns about the impact of nanotechnology on adaptation. Finally, we provide a perspective on the use of nanotechnology to harness bacterial memory based on its unique mode of actions on information processing and transmission in bacteria. Exploring bacterial memory mechanisms provides valuable insights into acclimation, evolution, and the potential applications of nanotechnology in harnessing memory.
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Affiliation(s)
- Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yan Kong
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingxin Xiang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yayun Ma
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Quanyi Guo
- School of Environment, Beijing Normal University, Beijing 100875, China
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10
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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.
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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.
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11
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Zhang Y, Cai Y, Chen Z. Community-specific diffusion characteristics determine resistance of biofilms to oxidative stress. SCIENCE ADVANCES 2023; 9:eade2610. [PMID: 36961890 DOI: 10.1126/sciadv.ade2610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Biofilms are multicellular communities with a spatial structure. Different from single-cell scale diffusion in planktonic systems, the diffusion distance becomes the dimension of multicellular clusters in a biofilm. Such differences in diffusion behavior affect the tolerance and response to exogenous stress. Here, we found that at the same doses of exogenous hydrogen peroxide (H2O2), planktonic Escherichia coli were completely killed within two hours, whereas the biofilm resumed growth in six hours by building a catalase barrier to block H2O2 penetration, despite the growth burden. Unexpectedly, when we changed the carbon source from glucose to glycerol, H2O2 instantly counterintuitively boosted biofilm growth due to supplemental oxygen, which was the growth-limiting factor. We further demonstrated that the energy metabolism modes determined the growth-limiting factor, which then determined the two patterns of biofilms resistances to H2O2.
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Affiliation(s)
- Yuzhen Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yumin Cai
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhaoyuan Chen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315020, China
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12
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [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: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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13
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Khan M, Ma K, Wan I, Willcox MD. Ciprofloxacin resistance and tolerance of Pseudomonas aeruginosa ocular isolates. Cont Lens Anterior Eye 2023; 46:101819. [PMID: 36732125 DOI: 10.1016/j.clae.2023.101819] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 12/18/2022] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
PURPOSE Tolerance to antibiotics may occur due to changes in bacterial growth patterns and can be a precursor to development of resistance. However, there is a lack of information on the ability of ocular bacteria isolates to develop tolerance. This paper explores the tolerance to 8 different antibiotics of 61 microbial keratitis isolates of Pseudomonas aeruginosa from Australia and India using the MBC/MIC ratio, with tolerance defined by a ratio ≥ 32, and tolerance to ciprofloxacin by an agar diffusion assay. METHODS Antibiotics used were ciprofloxacin, levofloxacin, gentamicin, tobramycin, piperacillin, imipenem, ceftazidime and polymyxin B. Isolates were sourced from microbial keratitis infections in Australia and India. Minimum bactericidal and minimum inhibitory concentration (MBC and MIC) were obtained using broth microdilution and compared to breakpoints from the Clinical Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) to determine bacterial susceptibility. Tolerance was assessed as MBC/MIC ≥ 32. An alternative method for tolerance detection (TD) was assessed with 13P. aeruginosa sensitive isolates by agar disk diffusion assay of ciprofloxacin followed by application of glucose to the agar and observation of re-growth of colonies. RESULTS Thirty-three isolates were resistant to imipenem, 20 to ciprofloxacin, 14 to tobramycin and piperacillin, 12 to levofloxacin and ceftazidime, 8 to gentamicin, and 5 to polymyxin B. The percentage of strains resistant to levofloxacin (7 vs 30 %; p = 0.023), gentamicin (0 vs 24 %; p = 0.005) and tobramycin (4 vs 33 %; p = 0.004) was significantly greater in isolates from India.On average, strains from India exhibited notably greater MIC and MBC values compared to strains obtained from Australia. Out of 61 isolates, none displayed an MBC/MIC ratio ≥ 32. However, three sensitive isolates had low tolerance, nine had medium tolerance and one had high tolerance to ciprofloxacin with the TDtest. CONCLUSIONS This study used two methods to determine whether P. aeruginosa strains could show tolerance to antibiotics. Using the MBC/MIC criteria no strain was considered tolerant to any of the eight antibiotics used. When 13 strains were tested for tolerance against ciprofloxacin, the most commonly used monotherapy for keratitis, one had high tolerance and nine had medium tolerance. This demonstrates the capacity of P. aeruginosa to develop tolerance which may result in therapeutic failures if inappropriate dosing regimens are used to treat keratitis.
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Affiliation(s)
- Mahjabeen Khan
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Karen Ma
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ingrid Wan
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mark Dp Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales 2052, Australia
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14
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Antidepressants can induce mutation and enhance persistence toward multiple antibiotics. Proc Natl Acad Sci U S A 2023; 120:e2208344120. [PMID: 36689653 PMCID: PMC9945972 DOI: 10.1073/pnas.2208344120] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Antibiotic resistance is an urgent threat to global health. Antidepressants are consumed in large quantities, with a similar pharmaceutical market share (4.8%) to antibiotics (5%). While antibiotics are acknowledged as the major driver of increasing antibiotic resistance, little attention is paid to the contribution of antidepressants in this process. Here, we demonstrate that antidepressants at clinically relevant concentrations induce resistance to multiple antibiotics, even following short periods of exposure. Antibiotic persistence was also enhanced. Phenotypic and genotypic analyses revealed the enhanced production of reactive oxygen species following exposure to antidepressants was directly associated with increased resistance. An enhanced stress signature response and stimulation of efflux pump expression were also associated with increased resistance and persistence. Mathematical modeling also predicted that antidepressants would accelerate the emergence of antibiotic-resistant bacteria, and persister cells would help to maintain the resistance. Overall, our findings highlight the antibiotic resistance risk caused by antidepressants.
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15
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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.
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16
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Sun C, Hu J, Wu L, Xia Q, Jiao F. Construction of a Novel Visible-Light-Driven Z-Scheme NiAl-LDH Modified (BiO) 2CO 3 Heterostructure for Enhanced Photocatalytic Degradation Antibiotics Performance in Natural Water Bodies. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c03700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chun Sun
- School of Chemistry and Chemical Engineering, Central South University, Changsha410083, China
| | - Jun Hu
- School of Chemistry and Chemical Engineering, Central South University, Changsha410083, China
| | - Lixu Wu
- School of Chemistry and Chemical Engineering, Central South University, Changsha410083, China
| | - Qinglin Xia
- School of Physics and Electronics, Central South University, Changsha410083, China
| | - Feipeng Jiao
- School of Chemistry and Chemical Engineering, Central South University, Changsha410083, China
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17
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Diaz-Tang G, Meneses EM, Patel K, Mirkin S, García-Diéguez L, Pajon C, Barraza I, Patel V, Ghali H, Tracey AP, Blanar CA, Lopatkin AJ, Smith RP. Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics. SCIENCE ADVANCES 2022; 8:eadd0924. [PMID: 36516248 PMCID: PMC9750144 DOI: 10.1126/sciadv.add0924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/11/2022] [Indexed: 06/10/2023]
Abstract
Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.
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Affiliation(s)
- Gabriela Diaz-Tang
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Estefania Marin Meneses
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Kavish Patel
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Sophia Mirkin
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Laura García-Diéguez
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Camryn Pajon
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Ivana Barraza
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Vijay Patel
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Helana Ghali
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Angelica P. Tracey
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Christopher A. Blanar
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Allison J. Lopatkin
- Department of Biology, Barnard College, Columbia University, New York, NY10025, USA
- Data Science Institute, Columbia University, New York, NY10025, USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY10025, USA
| | - Robert P. Smith
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
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18
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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.
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19
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Zhang Y, Cai Y, Zeng L, Liu P, Ma LZ, Liu J. A Microfluidic Approach for Quantitative Study of Spatial Heterogeneity in Bacterial Biofilms. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202200047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yuzhen Zhang
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences Beijing 100084 China
| | - Yumin Cai
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
| | - Lingbin Zeng
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
| | - Peng Liu
- Department of Biomedical Engineering School of Medicine Tsinghua University Beijing 100084 China
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Jintao Liu
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences Beijing 100084 China
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20
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Sarian FD, Ando K, Tsurumi S, Miyashita R, Ute K, Ohama T. Evaluation of the Growth-Inhibitory Spectrum of Three Types of Cyanoacrylate Nanoparticles on Gram-Positive and Gram-Negative Bacteria. MEMBRANES 2022; 12:782. [PMID: 36005697 PMCID: PMC9414559 DOI: 10.3390/membranes12080782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The development of novel effective antibacterial agents is crucial due to increasing antibiotic resistance in various bacteria. Poly (alkyl cyanoacrylate) nanoparticles (PACA-NPs) are promising novel antibacterial agents as they have shown antibacterial activity against several Gram-positive and Gram-negative bacteria. However, the antibacterial mechanism remains unclear. Here, we compared the antibacterial efficacy of ethyl cyanoacrylate nanoparticles (ECA-NPs), isobutyl cyanoacrylate NPs (iBCA-NPs), and ethoxyethyl cyanoacrylate NPs (EECA-NPs) using five Gram-positive and five Gram-negative bacteria. Among these resin nanoparticles, ECA-NPs showed the highest growth inhibitory effect against all the examined bacterial species, and this effect was higher against Gram-positive bacteria than Gram-negative. While iBCA-NP could inhibit the cell growth only in two Gram-positive bacteria, i.e., Bacillus subtilis and Staphylococcus aureus, it had negligible inhibitory effect against all five Gram-negative bacteria examined. Irrespective of the differences in growth inhibition induced by these three NPs, N-acetyl-L-cysteine (NAC), a well-known reactive oxygen species (ROS) scavenger, efficiently restored growth in all the bacterial strains to that similar to untreated cells. This strongly suggests that the exposure to NPs generates ROS, which mainly induces cell growth inhibition irrespective of the difference in bacterial species and cyanoacrylate NPs used.
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Affiliation(s)
- Fean Davisunjaya Sarian
- School of Environmental Science and Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami 782-8502, Japan
| | - Kazuki Ando
- School of Environmental Science and Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami 782-8502, Japan
| | - Shota Tsurumi
- School of Environmental Science and Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami 782-8502, Japan
| | - Ryohei Miyashita
- Department of Applied Chemistry, Tokushima University, 2-1 Minami-Josanjima, Tokushima 770-8506, Japan
| | - Koichi Ute
- Department of Applied Chemistry, Tokushima University, 2-1 Minami-Josanjima, Tokushima 770-8506, Japan
| | - Takeshi Ohama
- School of Environmental Science and Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami 782-8502, Japan
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21
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Antimicrobial tolerance and its role in the development of resistance: Lessons from enterococci. Adv Microb Physiol 2022; 81:25-65. [PMID: 36167442 DOI: 10.1016/bs.ampbs.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria have developed resistance against every antimicrobial in clinical use at an alarming rate. There is a critical need for more effective use of antimicrobials to both extend their shelf life and prevent resistance from arising. Significantly, antimicrobial tolerance, i.e., the ability to survive but not proliferate during antimicrobial exposure, has been shown to precede the development of bona fide antimicrobial resistance (AMR), sparking a renewed and rapidly increasing interest in this field. As a consequence, problematic infections for the first time are now being investigated for antimicrobial tolerance, with increasing reports demonstrating in-host evolution of antimicrobial tolerance. Tolerance has been identified in a wide array of bacterial species to all bactericidal antimicrobials. Of particular interest are enterococci, which contain the opportunistic bacterial pathogens Enterococcus faecalis and Enterococcus faecium. Enterococci are one of the leading causes of hospital-acquired infection and possess intrinsic tolerance to a number of antimicrobial classes. Persistence of these infections in the clinic is of growing concern, particularly for the immunocompromised. Here, we review current known mechanisms of antimicrobial tolerance, and include an in-depth analysis of those identified in enterococci with implications for both the development and prevention of AMR.
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22
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Liu Y, Fang D, Yang K, Xu T, Su C, Li R, Xiao X, Wang Z. Sodium dehydroacetate confers broad antibiotic tolerance by remodeling bacterial metabolism. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128645. [PMID: 35299107 DOI: 10.1016/j.jhazmat.2022.128645] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic tolerance has been a growing crisis that is seriously threatening global public health. However, little is known about the exogenous factors capable of triggering the development of antibiotic tolerance, particularly in vivo. Here we uncovered that an previously approved food additive termed sodium dehydroacetate (DHA-S) supplementation remarkably impaired the activity of bactericidal antibiotics against various bacterial pathogens. Mechanistic studies indicated that DHA-S induced glyoxylate shunt and reduced bacterial cellular respiration by inhibiting the enzymatic activity of α-ketoglutarate dehydrogenase (α-KGDH). Furthermore, DHA-S mitigated oxidative stress imposed by bactericidal antibiotics and enhanced the function of multidrug efflux pumps. These actions worked together to induce bacterial tolerance to antibiotic killing. Interestingly, the addition of five exogenous amino acids, particularly cysteine and proline, effectively reversed antibiotic tolerance elicited by DHA-S both in vitro and in mouse models of infection. Taken together, these findings advance our understanding of the potential risks of DHA-S in the treatment of bacterial infections, and shed new insights into the relationships between antibiotic tolerance and bacterial metabolism.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China.
| | - Dan Fang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Kangni Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Tianqi Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Chengrui Su
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xia Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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23
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Mizrahi A, Chat L, Danjean M, Mory C, Nguyen Van JC, de Ponfilly GP, Caméléna F, Le Monnier A, Bercot B, Birgy A, Jacquier H, Pilmis B. Inoculum effect of Enterobacterales co-expressing OXA-48 and CTX-M on the susceptibility to ceftazidime/avibactam and meropenem. Eur J Clin Microbiol Infect Dis 2022; 41:853-858. [PMID: 35322329 DOI: 10.1007/s10096-022-04430-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/09/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND The treatment of infections caused by OXA-48/CTX-M-coproducing Enterobacterales may be based on new beta-lactam/beta-lactamase inhibitors, such as ceftazidime/avibactam (CZA), or on high dose of meropenem (MER). However, bacterial density at the infection site may vary widely, and the inoculum effect of such antimicrobial strategies has never been specifically investigated. To determine if CZA or MER susceptibilities are impacted by high inocula of Enterobacterales co-expressing both enzymes: OXA-48 like and CTX-M. METHODS Determination of an inoculum effect was performed with a standard inoculum of 108 CFU/mL (0.5 McFarland) as recommended by EUCAST guidelines and compared to a twofold increase as well as a tenfold increase (1 McFarland and 5 McFarland respectively). RESULTS Thirty-nine isolates of ceftazidime-resistant Enterobacterales were included of which 27 (70%) co-expressed OXA-48 + CTX-M-15, 6 (15%) OXA-48 + CTX-M-14, and 6 (15%) OXA-181 + CTX-M-15. The susceptibility to the CZA combination was preserved whatever the inoculum used. Regarding MER, 24 (61.5%) of the isolates were susceptible to MER with the standard inoculum, 19 (48.7%) with a twofold increase, and only 15 (38.5%) with a tenfold increase. CONCLUSION We showed that in vitro inoculum effect was observed with meropenem but not with CZA for OXA-48- combined with CTX-M-producing Enterobacterales.
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Affiliation(s)
- A Mizrahi
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, 185 rue Raymond Losserand, 75014, Paris, France.
- UMR 1319, Institut Micalis, Université Paris-Saclay, INRAeChâtenay Malabry, AgroParisTech, France.
| | - L Chat
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, 185 rue Raymond Losserand, 75014, Paris, France
| | - M Danjean
- Service de Microbiologie Clinique, Hôpital Universitaire Robert Debré, Paris, France
| | - C Mory
- Plateforme de Dosages Des Anti-Infectieux, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - J C Nguyen Van
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, 185 rue Raymond Losserand, 75014, Paris, France
| | - G Péan de Ponfilly
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, 185 rue Raymond Losserand, 75014, Paris, France
- UMR 1319, Institut Micalis, Université Paris-Saclay, INRAeChâtenay Malabry, AgroParisTech, France
| | - F Caméléna
- Service de Bactériologie, AP-HP Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal Site Saint Louis, Paris, France
- UMR1137, IAME, Université de Paris, INSERM, Paris, France
| | - A Le Monnier
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, 185 rue Raymond Losserand, 75014, Paris, France
- UMR 1319, Institut Micalis, Université Paris-Saclay, INRAeChâtenay Malabry, AgroParisTech, France
| | - B Bercot
- Service de Bactériologie, AP-HP Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal Site Saint Louis, Paris, France
- UMR1137, IAME, Université de Paris, INSERM, Paris, France
| | - A Birgy
- Service de Microbiologie Clinique, Hôpital Universitaire Robert Debré, Paris, France
- UMR1137, IAME, Université de Paris, INSERM, Paris, France
| | - H Jacquier
- Service de Bactériologie, AP-HP Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal Site Saint Louis, Paris, France
- UMR1137, IAME, Université de Paris, INSERM, Paris, France
| | - B Pilmis
- UMR1137, IAME, Université de Paris, INSERM, Paris, France
- Équipe Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
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Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nat Commun 2022; 13:2296. [PMID: 35484157 PMCID: PMC9051133 DOI: 10.1038/s41467-022-29919-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and timescales shaping this resistome remain elusive. Using an antibiotic cocktail administered to a murine model along with a longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire antimicrobial resistance genes (ARGs) after a single antibiotic course. While most of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Enterobacteriaceae, Enterococcaceae, and Lactobacillaceae families acquire resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotics in the corresponding metagenome-assembled genomes (MAGs) and trace their origins within each genome. Here we show that, while mobile genetic elements (MGEs), including bacteriophages and plasmids, contribute to the spread of ARGs, integrons represent key factors mediating AMR in the antibiotic-treated mice. Our findings suggest that a single course of antibiotics alone may act as the selective sweep driving ARG acquisition and incidence in gut commensals over a single mammalian lifespan. Antimicrobial resistance represents an ongoing silent pandemic. Here, de Nies et al. show that a single antibiotic treatment leads to resistance in bacteria such as Akkermansia muciniphila and that integrons play a key role in mediating this resistance.
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25
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Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics. Proc Natl Acad Sci U S A 2022; 119:e2116954119. [PMID: 35394868 PMCID: PMC9169654 DOI: 10.1073/pnas.2116954119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAntibiotic exposure stands among the most used interventions to drive microbial communities away from undesired states. How the ecology of microbial communities shapes their recovery-e.g., posttreatment shifts toward Clostridioides difficile infections in the gut-after antibiotic exposure is poorly understood. We study community response to antibiotics using a model community that can reach two alternative states. Guided by theory, our experiments show that microbial growth following antibiotic exposure can counteract antibiotic susceptibility in driving transitions between alternative community states. This makes it possible to reverse the outcome of antibiotic exposure through modifying growth dynamics, including cooperative growth, of community members. Our research highlights the relevance of simple ecological models to better understand the long-term effects of antibiotic treatment.
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26
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Yu C, Armengaud J, Blaustein RA, Chen K, Ye Z, Xu F, Gaillard JC, Qin Z, Fu Y, Hartmann EM, Shen C. Antibiotic tolerance and degradation capacity of the organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9 T. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127712. [PMID: 34865898 DOI: 10.1016/j.jhazmat.2021.127712] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/14/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Antibiotics are ubiquitous in soil due to natural ecological competition, as well as emerging contaminants due to anthropogenic inputs. Under environmental factors like antibiotic stress, some bacteria, including those that degrade environmental pollutants, can enter a dormant state as a survival strategy, thereby limiting their metabolic activity and function. Dormancy has a critical influence on the degradative activity of bacteria, dramatically decreasing the rate at which they transform organic pollutants. To better understand this phenomenon in environmental pollutant-degrading bacteria, we investigated dormancy transitions induced with norfloxacin in Rhodococcus biphenylivorans TG9T using next-generation proteomics, proteogenomics, and additional experiments. Our results suggest that exposure to norfloxacin inhibited DNA replication, which led to damage to the cell. Dormant cells then likely triggered DNA repair, particularly homologous recombination, for continued survival. The results also indicated that substrate transport (ATP-binding cassette transporter), ATP production, and the tricarboxylic acid (TCA) cycle were repressed during dormancy, and degradation of organic pollutants was down-regulated. Given the widespread phenomenon of dormancy among bacteria involved in pollutant removal systems, this study improves our understanding of possible implications of antibiotic survival strategies on biotransformation of mixtures containing antibiotics as well as other organics.
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Affiliation(s)
- Chungui Yu
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France
| | - Ryan Andrew Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Kezhen Chen
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Zhe Ye
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Fengjun Xu
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France
| | - Zhihui Qin
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Yulong Fu
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Erica Marie Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
| | - Chaofeng Shen
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China.
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27
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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.
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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.
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28
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Wet-dry cycles protect surface-colonizing bacteria from major antibiotic classes. THE ISME JOURNAL 2022; 16:91-100. [PMID: 34253853 PMCID: PMC8692528 DOI: 10.1038/s41396-021-01051-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
Diverse antibiotic compounds are abundant in microbial habitats undergoing recurrent wet-dry cycles, such as soil, root and leaf surfaces, and the built environment. These antibiotics play a central role in microbial warfare and competition, thus affecting population dynamics and the composition of natural microbial communities. Yet, the impact of wet-dry cycles on bacterial response to antibiotics has been scarcely explored. Using the bacterium E. coli as a model organism, we show through a combination of experiments and computational modeling, that wet-dry cycles protect bacteria from beta-lactams. This is due to the combined effect of several mechanisms including tolerance induced by high salt concentrations and slow cell-growth, which are inherently associated with microscopic surface wetness-a hydration state typical to 'dry' periods. Moreover, we find evidence for a cross-protection effect, where lethal doses of antibiotic considerably increase bacterial survival during the dry periods. This work focuses on beta-lactams, yet similar protection was observed for additional major antibiotic classes. Our findings shed new light on how we understand bacterial response to antibiotics, with broad implications for population dynamics, interspecies interactions, and the evolution of antibiotic resistance in vast terrestrial microbial habitats.
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29
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Apreja M, Sharma A, Balda S, Kataria K, Capalash N, Sharma P. Antibiotic residues in environment: antimicrobial resistance development, ecological risks, and bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3355-3371. [PMID: 34773239 DOI: 10.1007/s11356-021-17374-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The overuse of antibiotics and their disposal without processing are leading the environment and its inhabitants towards a serious health emergency. There is abundance of diverse antibiotic resistance genes and bacteria in environment, which demands immediate attention for the effective removal of antibiotics. There are physical and chemical methods for removal, but the generation of toxic byproducts has directed the efforts towards bioremediation for eco-friendly and sustainable elimination of antibiotics from the environment. Various effective and reliable bioremediation approaches have been used, but still antibiotic residues pose a major global threat. Recent developments in molecular and synthetic biology might offer better solution for engineering of microbe-metabolite biodevices and development of novel strains endowed with desirable properties. This review summarizes the impact of antibiotics on environment, mechanisms of resistance development, and different bioremediation approaches.
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Affiliation(s)
- Mansi Apreja
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
| | - Aarjoo Sharma
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
| | - Sanjeev Balda
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
| | - Kirti Kataria
- Department of Microbiology, Panjab University, Chandigarh, 160014, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, 160014, India.
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30
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Seregina TA, Lobanov KV, Shakulov RS, Mironov AS. Enhancement of the Bactericidal Effect of Antibiotics by Inhibition of Enzymes Involved in Production of Hydrogen Sulfide in Bacteria. Mol Biol 2022; 56:638-648. [PMID: 36217334 PMCID: PMC9534473 DOI: 10.1134/s0026893322050120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 11/23/2022]
Abstract
Counteraction of the origin and distribution of multidrug-resistant pathogens responsible for intra-hospital infections is a worldwide issue in medicine. In this brief review, we discuss the results of our recent investigations, which argue that many antibiotics, along with inactivation of their traditional biochemical targets, can induce oxidative stress (ROS production), thus resulting in increased bactericidal efficiency. As we previously showed, hydrogen sulfide, which is produced in the cells of different pathogens protects them not only against oxidative stress but also against bactericidal antibiotics. Next, we clarified the interplay of oxidative stress, cysteine metabolism, and hydrogen sulfide production. Finally, demonstrated that small molecules, which inhibit a bacterial enzyme involved in hydrogen sulfide production, potentiate bactericidal antibiotics including quinolones, beta-lactams, and aminoglycosides against bacterial pathogens in in vitro and in mouse models of infection. These inhibitors also suppress bacterial tolerance to antibiotics by disrupting the biofilm formation and substantially reducing the number of persister bacteria, which survive the antibiotic treatment. We hypothesise that agents which limit hydrogen sulfide biosynthesis are effective tools to counteract the origin and distribution of multidrug-resistant pathogens.
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Affiliation(s)
- T. A. Seregina
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, 119991 Moscow, Russia
| | - K. V. Lobanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, 119991 Moscow, Russia
| | - R. S. Shakulov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, 119991 Moscow, Russia
| | - A. S. Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, 119991 Moscow, Russia
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31
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Abstract
In the struggle with antibiotic resistance, we are losing. There is now a serious threat of moving into a postantibiotic world. High levels of resistance, in terms of both frequency and strength, have evolved against all clinically approved antibiotics worldwide. The usable life span of new clinically approved antibiotics is typically less than a decade before resistance reaches frequencies so high as to require only guarded usage. However, microbes have produced antibiotics for millennia without resistance becoming an existential issue. If resistance is the inevitable consequence of antibiotic usage, as has been the human experience, why has it not become an issue for microbes as well, especially since resistance genes are as prevalent in nature as the genes responsible for antibiotic production? Here, we ask how antibiotics can exist given the almost ubiquitous presence of resistance genes in the very microbes that have produced and used antibiotics since before humans walked the planet. We find that the context of both production and usage of antibiotics by microbes may be key to understanding how resistance is managed over time, with antibiotic synthesis and resistance existing in a paired relationship, much like a cipher and key, that impacts microbial community assembly. Finally, we put forward the cohesive, ecologically based "secret society" hypothesis to explain the longevity of antibiotics in nature.
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Affiliation(s)
- Fabrizio Spagnolo
- Biology Department, Queens College of The City University of New York, Flushing, New York, USA
| | - Monica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College, The City University of New York, Bayside, New York, USA
| | - John J. Dennehy
- Biology Department, Queens College of The City University of New York, Flushing, New York, USA
- The Graduate Center of The City University of New York, New York, New York, USA
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32
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Kapoor A, Rajput JK. Staudinger k
etene–imine
[2+2] cycloaddition of novel azomethines to synthesize biologically active azetidinone derivatives and their in vitro antimicrobial studies. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Atul Kapoor
- Department of Chemistry Dr. B.R Ambedkar National Institute of Technology Jalandhar India
| | - Jaspreet Kaur Rajput
- Department of Chemistry Dr. B.R Ambedkar National Institute of Technology Jalandhar India
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33
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Sharma A, Wood KB. Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress. THE ISME JOURNAL 2021; 15:3019-3033. [PMID: 33953363 PMCID: PMC8443724 DOI: 10.1038/s41396-021-00982-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 02/01/2023]
Abstract
Antibiotic resistance in microbial communities reflects a combination of processes operating at different scales. In this work, we investigate the spatiotemporal dynamics of bacterial colonies comprised of drug-resistant and drug-sensitive cells undergoing range expansion under antibiotic stress. Using the opportunistic pathogen Enterococcus faecalis with plasmid-encoded β-lactamase, we track colony expansion dynamics and visualize spatial patterns in fluorescently labeled populations exposed to antibiotics. We find that the radial expansion rate of mixed communities is approximately constant over a wide range of drug concentrations and initial population compositions. Imaging of the final populations shows that resistance to ampicillin is cooperative, with sensitive cells surviving in the presence of resistant cells at otherwise lethal concentrations. The populations exhibit a diverse range of spatial segregation patterns that depend on drug concentration and initial conditions. Mathematical models indicate that the observed dynamics are consistent with global cooperation, despite the fact that β-lactamase remains cell-associated. Experiments confirm that resistant colonies provide a protective effect to sensitive cells on length scales multiple times the size of a single colony, and populations seeded with (on average) no more than a single resistant cell can produce mixed communities in the presence of the drug. While biophysical models of drug degradation suggest that individual resistant cells offer only short-range protection to neighboring cells, we show that long-range protection may arise from synergistic effects of multiple resistant cells, providing surprisingly large protection zones even at small population fractions.
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Affiliation(s)
- Anupama Sharma
- Department of Biophysics, University of Michigan, Ann Arbor, USA
- Department of Mathematics, BITS Pilani K K Birla Goa Campus, Goa, India
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, Ann Arbor, USA.
- Department of Physics, University of Michigan, Ann Arbor, USA.
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34
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Hou L, Wang H, Chen Q, Su JQ, Gad M, Li J, Mulla SI, Yu CP, Hu A. Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126083. [PMID: 34000699 DOI: 10.1016/j.jhazmat.2021.126083] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingfu Chen
- Yundang Lake Management Center, Xiamen, Fujian 361004, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Mahmoud Gad
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sikandar I Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Biochemistry, School of Applied Sciences, Reva University, Bangalore 560064, India
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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35
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Qin K, Zhao Q, Yu H, Xia X, Li J, He S, Wei L, An T. A review of bismuth-based photocatalysts for antibiotic degradation: Insight into the photocatalytic degradation performance, pathways and relevant mechanisms. ENVIRONMENTAL RESEARCH 2021; 199:111360. [PMID: 34022231 DOI: 10.1016/j.envres.2021.111360] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/06/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
The intensive production and utilization of antibiotics worldwide has inevitably led to releases of very large amounts of these medicines into the environment, and numerous strategies have recently been developed to eliminate antibiotic pollution. Therefore, bismuth-based photocatalysts have attracted much attention due to their high adsorption of visible light and low production cost. This review summarizes the performance, degradation pathways and relevant mechanisms of typical antibiotics during bismuth-based photocatalytic degradation. First, the band gap and redox ability of the bismuth-based catalysts and modified materials (such as morphology, structure mediation, heterojunction construction and element doping) were compared and evaluated. Second, the performance and potential mechanisms of bismuth oxides, bismuth sulfides, bismuth oxyhalides and bismuth-based metal oxides for antibiotic removal were investigated. Third, we analysed the effect of co-existing interfering substances in a real water matrix on the photocatalytic ability, as well as the coupling processes for degradation enhancement. In the last section, current difficulties and future perspectives on photocatalytic degradation for antibiotic elimination by bismuth-based catalysts are summarized. Generally, modified bismuth-based compounds showed better performance than single-component photocatalysts during photocatalytic degradation for most antibiotics, in which h+ played a predominant role among all the related reactive oxygen species. Moreover, the crystal structures and morphologies of bismuth-based catalysts seriously affected their practical efficiencies.
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Affiliation(s)
- Kena Qin
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Qingliang Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Hang Yu
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xinhui Xia
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jianju Li
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Shufei He
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Liangliang Wei
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Taicheng An
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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36
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Gjini E, Wood KB. Price equation captures the role of drug interactions and collateral effects in the evolution of multidrug resistance. eLife 2021; 10:e64851. [PMID: 34289932 PMCID: PMC8331190 DOI: 10.7554/elife.64851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/08/2021] [Indexed: 01/03/2023] Open
Abstract
Bacterial adaptation to antibiotic combinations depends on the joint inhibitory effects of the two drugs (drug interaction [DI]) and how resistance to one drug impacts resistance to the other (collateral effects [CE]). Here we model these evolutionary dynamics on two-dimensional phenotype spaces that leverage scaling relations between the drug-response surfaces of drug-sensitive (ancestral) and drug-resistant (mutant) populations. We show that evolved resistance to the component drugs - and in turn, the adaptation of growth rate - is governed by a Price equation whose covariance terms encode geometric features of both the two-drug-response surface (DI) in ancestral cells and the correlations between resistance levels to those drugs (CE). Within this framework, mean evolutionary trajectories reduce to a type of weighted gradient dynamics, with the drug interaction dictating the shape of the underlying landscape and the collateral effects constraining the motion on those landscapes. We also demonstrate how constraints on available mutational pathways can be incorporated into the framework, adding a third key driver of evolution. Our results clarify the complex relationship between drug interactions and collateral effects in multidrug environments and illustrate how specific dosage combinations can shift the weighting of these two effects, leading to different and temporally explicit selective outcomes.
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Affiliation(s)
- Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Tecnico, University of Lisbon, PortugalLisbonPortugal
| | - Kevin B Wood
- Departments of Biophysics and Physics, University of MichiganAnn ArborUnited States
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37
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Shatalin K, Nuthanakanti A, Kaushik A, Shishov D, Peselis A, Shamovsky I, Pani B, Lechpammer M, Vasilyev N, Shatalina E, Rebatchouk D, Mironov A, Fedichev P, Serganov A, Nudler E. Inhibitors of bacterial H 2S biogenesis targeting antibiotic resistance and tolerance. Science 2021; 372:1169-1175. [PMID: 34112687 PMCID: PMC10723041 DOI: 10.1126/science.abd8377] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics. Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide (H2S)-mediated defense system. We identified cystathionine γ-lyase (CSE) as the primary generator of H2S in two major human pathogens, Staphylococcus aureus and Pseudomonas aeruginosa, and discovered small molecules that inhibit bacterial CSE. These inhibitors potentiate bactericidal antibiotics against both pathogens in vitro and in mouse models of infection. CSE inhibitors also suppress bacterial tolerance, disrupting biofilm formation and substantially reducing the number of persister bacteria that survive antibiotic treatment. Our results establish bacterial H2S as a multifunctional defense factor and CSE as a drug target for versatile antibiotic enhancers.
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Affiliation(s)
- Konstantin Shatalin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Abhishek Kaushik
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bibhusita Pani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mirna Lechpammer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Elena Shatalina
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119991, Russia
| | | | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
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38
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Abstract
The activity of many antibiotics depends on the initial density of cells used in bacterial growth inhibition assays. This phenomenon, termed the inoculum effect, can have important consequences for the therapeutic efficacy of the drugs, because bacterial loads vary by several orders of magnitude in clinically relevant infections. Antimicrobial peptides are a promising class of molecules in the fight against drug-resistant bacteria because they act mainly by perturbing the cell membranes rather than by inhibiting intracellular targets. Here, we report a systematic characterization of the inoculum effect for this class of antibacterial compounds. Minimum inhibitory concentration values were measured for 13 peptides (including all-D enantiomers) and peptidomimetics, covering more than seven orders of magnitude in inoculated cell density. In most cases, the inoculum effect was significant for cell densities above the standard inoculum of 5 × 105 cells/mL, while for lower densities the active concentrations remained essentially constant, with values in the micromolar range. In the case of membrane-active peptides, these data can be rationalized by considering a simple model, taking into account peptide-cell association, and hypothesizing that a threshold number of cell-bound peptide molecules is required in order to cause bacterial killing. The observed effect questions the clinical utility of activity and selectivity determinations performed at a fixed, standardized cell density. A routine evaluation of the dependence of the activity of antimicrobial peptides and peptidomimetics on the inoculum should be considered.
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39
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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.
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40
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Manrique PD, Gnanakaran S. Microscopic Approach to Intrinsic Antibiotic Resistance. J Phys Chem B 2021; 125:3114-3118. [PMID: 33754733 DOI: 10.1021/acs.jpcb.1c00607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emergence of multidrug resistance in Gram-negative pathogens is critically determined by the interplay between efflux pumps activity and low permeation outer membrane. Although phenotypic heterogeneity in isogenic cells is recognized as a key factor of treatment failure, a mathematical framework able to integrate growth dynamics and single-cell heterogeneity in antimicrobial resistance, remains absent. Here we provide such framework that bridges single-cell and colony scales in the context of bacterial survival and efficacy against drugs. Using experimental inputs, our approach produces testable outputs and reveals nontrivial collective effects with key implications for fitness and survival of the colony. This framework provides a mathematical tool to test stress response strategies in organisms that can potentially guide experiments in natural and synthetic cellular systems.
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Affiliation(s)
- Pedro D Manrique
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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41
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Grobas I, Polin M, Asally M. Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms. eLife 2021; 10:62632. [PMID: 33722344 PMCID: PMC7963483 DOI: 10.7554/elife.62632] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/26/2021] [Indexed: 12/23/2022] Open
Abstract
Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.
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Affiliation(s)
- Iago Grobas
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom
| | - Marco Polin
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom.,Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, United Kingdom.,Physics Department, University of Warwick, Coventry, United Kingdom.,Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), C/ Miquel Marqués, Balearic Islands, Spain
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
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42
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Bistable Bacterial Growth Dynamics in the Presence of Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10010087. [PMID: 33477524 PMCID: PMC7831100 DOI: 10.3390/antibiotics10010087] [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: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/22/2022] Open
Abstract
The outcome of an antibiotic treatment on the growth capacity of bacteria is largely dependent on the initial population size (Inoculum Effect). We characterized and built a model of this effect in E. coli cultures using a large variety of antimicrobials, including conventional antibiotics, and for the first time, cationic antimicrobial peptides (CAMPs). Our results show that all classes of antimicrobial drugs induce an inoculum effect, which, as we explain, implies that the dynamic is bistable: For a range of anti-microbial densities, a very small inoculum decays whereas a larger inoculum grows, and the threshold inoculum depends on the drug concentration. We characterized three distinct classes of drug-induced bistable growth dynamics and demonstrate that in rich medium, CAMPs correspond to the simplest class, bacteriostatic antibiotics to the second class, and all other traditional antibiotics to the third, more complex class. These findings provide a unifying universal framework for describing the dynamics of the inoculum effect induced by antimicrobials with inherently different killing mechanisms.
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43
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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.
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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
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44
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Lv R, Shi R, Wu E, Ma C, Guo R, Li J, Ouyang F, Fang Q, Hu L, Sun C, Liu Y, Kang Z, Liu J. Spatial-temporal profiling of antibiotic metabolites using graphite dots-assisted laser desorption ionization mass spectrometry. Talanta 2020; 220:121371. [DOI: 10.1016/j.talanta.2020.121371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022]
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45
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Wang P, Qiao Z, Li X, Wu D, Xie B. Fate of integrons, antibiotic resistance genes and associated microbial community in food waste and its large-scale biotreatment systems. ENVIRONMENT INTERNATIONAL 2020; 144:106013. [PMID: 32771831 DOI: 10.1016/j.envint.2020.106013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/14/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
The prevalence and dissemination of antibiotic resistance genes (ARGs) have been globally gained increasing concerns. However, the fate and spread of ARGs in food waste (FW) and its large-scale biotreatment systems are seldomly understood. Here, we investigated the initial and biologically treated FW in two major FW treatment systems of aerobic fermentation (AF) and anaerobic co-digestion (AcoD) processes. The total relative abundances of integrons and ARGs significantly increased from initial FW to treated FW. Among targeted ARGs, ermB and strB were predominant ARGs, which accounted for 52.58-95.28% of total abundance across all samples. Mantel test indicated that integrons (intl1 and intl2) were positively and significantly correlated with detected ARGs (Mantel test, r = 0.24, p < 0.05), suggesting integrons display significant contributions on driving ARG alteration during FW treatment processes. RDA results indicated that blaOXA, strB and blaTEM were more likely to be proliferated by potential host of Firmicutes (96.55-99.77%) in initial FW, while blaCTX-M and mefA were potentially enriched by Proteobacteria (17.12-49.82%) in AF system and ermB, sul1, aadA and tetQ were possibly enhanced by Bacteroidetes (27.43-43.71%) in AcoD system. Consideration of the higher enriched abundance of total ARGs (66.88 ± 87.34 times) and the used inoculum sludge in AcoD-treated system, the resource utilization of anaerobically digested products should draw our more attentions. These findings would deepen our understanding of prevalence and proliferation of ARGs in FW treatment systems and serve as a foundation for guiding the application of biologically treated FW.
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Affiliation(s)
- Panliang Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ziru Qiao
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Xunan Li
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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46
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Salas JR, Jaberi-Douraki M, Wen X, Volkova VV. Mathematical modeling of the 'inoculum effect': six applicable models and the MIC advancement point concept. FEMS Microbiol Lett 2020; 367:5710933. [PMID: 31960902 PMCID: PMC7317156 DOI: 10.1093/femsle/fnaa012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/17/2020] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial treatment regimens against bacterial pathogens are designed using the drug's minimum inhibitory concentration (MIC) measured at a bacterial density of 5.7 log10(colony-forming units (CFU)/mL) in vitro. However, MIC changes with pathogen density, which varies among infectious diseases and during treatment. Incorporating this into treatment design requires realistic mathematical models of the relationships. We compared the MIC–density relationships for Gram-negative Escherichia coli and non-typhoidal Salmonella enterica subsp. enterica and Gram-positive Staphylococcus aureus and Streptococcus pneumonia (for n = 4 drug-susceptible strains per (sub)species and 1–8 log10(CFU/mL) densities), for antimicrobial classes with bactericidal activity against the (sub)species: β-lactams (ceftriaxone and oxacillin), fluoroquinolones (ciprofloxacin), aminoglycosides (gentamicin), glycopeptides (vancomycin) and oxazolidinones (linezolid). Fitting six candidate mathematical models to the log2(MIC) vs. log10(CFU/mL) curves did not identify one model best capturing the relationships across the pathogen–antimicrobial combinations. Gompertz and logistic models (rather than a previously proposed Michaelis–Menten model) fitted best most often. Importantly, the bacterial density after which the MIC sharply increases (an MIC advancement-point density) and that density's intra-(sub)species range evidently depended on the antimicrobial mechanism of action. Capturing these dependencies for the disease–pathogen–antimicrobial combination could help determine the MICs for which bacterial densities are most informative for treatment regimen design.
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Affiliation(s)
- Jessica R Salas
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Majid Jaberi-Douraki
- Department of Mathematics, Kansas State University, Manhattan, KS 66506, USA.,Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA
| | - Xuesong Wen
- Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA.,Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA
| | - Victoriya V Volkova
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA.,Center for Outcomes Research and Epidemiology, Kansas State University, Manhattan, KS 66506, USA
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47
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Rocha-Granados MC, Zenick B, Englander HE, Mok WWK. The social network: Impact of host and microbial interactions on bacterial antibiotic tolerance and persistence. Cell Signal 2020; 75:109750. [PMID: 32846197 DOI: 10.1016/j.cellsig.2020.109750] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/07/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022]
Abstract
Antibiotics have vastly improved our quality of life since their discovery and introduction into modern medicine. Yet, widespread use and misuse have compromised the efficacy of these compounds and put our ability to cure infectious diseases in jeopardy. To defend themselves against antibiotics, bacteria have evolved an arsenal of survival strategies. In addition to acquiring mutations and genetic determinants that confer antibiotic resistance, bacteria can respond to environmental cues and adopt reversible phenotypic changes that transiently enhance their ability to survive adverse conditions, including those brought on by antibiotics. These antibiotic tolerant and persistent bacteria, which are prevalent in biofilms and can survive antimicrobial therapy without inheriting resistance, are thought to underlie treatment failure and infection relapse. At infection sites, bacteria encounter a range of signals originating from host immunity and the local microbiota that can induce transcriptomic and metabolic reprogramming. In this review, we will focus on the impact of host factors and microbial interactions on antibiotic tolerance and persistence. We will also outline current efforts in leveraging the knowledge of host-microbe and microbe-microbe interactions in designing therapies that potentiate antibiotic activity and reduce the burden caused by recurrent infections.
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Affiliation(s)
| | - Blesing Zenick
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, CT, 06032, USA
| | - Hanna E Englander
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, CT, 06032, USA; Department of Physiology & Neurobiology, University of Connecticut, Storrs, CT 06269-3156, United States of America
| | - Wendy W K Mok
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, CT, 06032, USA.
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48
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Ojkic N, Lilja E, Direito S, Dawson A, Allen RJ, Waclaw B. A Roadblock-and-Kill Mechanism of Action Model for the DNA-Targeting Antibiotic Ciprofloxacin. Antimicrob Agents Chemother 2020; 64:e02487-19. [PMID: 32601161 PMCID: PMC7449190 DOI: 10.1128/aac.02487-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/19/2020] [Indexed: 12/19/2022] Open
Abstract
Fluoroquinolones, antibiotics that cause DNA damage by inhibiting DNA topoisomerases, are clinically important, but their mechanism of action is not yet fully understood. In particular, the dynamical response of bacterial cells to fluoroquinolone exposure has hardly been investigated, although the SOS response, triggered by DNA damage, is often thought to play a key role. Here, we investigated the growth inhibition of the bacterium Escherichia coli by the fluoroquinolone ciprofloxacin at low concentrations. We measured the long-term and short-term dynamical response of the growth rate and DNA production rate to ciprofloxacin at both the population and single-cell levels. We show that, despite the molecular complexity of DNA metabolism, a simple roadblock-and-kill model focusing on replication fork blockage and DNA damage by ciprofloxacin-poisoned DNA topoisomerase II (gyrase) quantitatively reproduces long-term growth rates in the presence of ciprofloxacin. The model also predicts dynamical changes in the DNA production rate in wild-type E. coli and in a recombination-deficient mutant following a step-up of ciprofloxacin. Our work highlights that bacterial cells show a delayed growth rate response following fluoroquinolone exposure. Most importantly, our model explains why the response is delayed: it takes many doubling times to fragment the DNA sufficiently to inhibit gene expression. We also show that the dynamical response is controlled by the timescale of DNA replication and gyrase binding/unbinding to the DNA rather than by the SOS response, challenging the accepted view. Our work highlights the importance of including detailed biophysical processes in biochemical-systems models to quantitatively predict the bacterial response to antibiotics.
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Affiliation(s)
- Nikola Ojkic
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Elin Lilja
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Susana Direito
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Angela Dawson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosalind J Allen
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, Edinburgh, United Kingdom
| | - Bartlomiej Waclaw
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, Edinburgh, United Kingdom
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Temporal encoding of bacterial identity and traits in growth dynamics. Proc Natl Acad Sci U S A 2020; 117:20202-20210. [PMID: 32747578 DOI: 10.1073/pnas.2008807117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In biology, it is often critical to determine the identity of an organism and phenotypic traits of interest. Whole-genome sequencing can be useful for this but has limited power for trait prediction. However, we can take advantage of the inherent information content of phenotypes to bypass these limitations. We demonstrate, in clinical and environmental bacterial isolates, that growth dynamics in standardized conditions can differentiate between genotypes, even among strains from the same species. We find that for pairs of isolates, there is little correlation between genetic distance, according to phylogenetic analysis, and phenotypic distance, as determined by growth dynamics. This absence of correlation underscores the challenge in using genomics to infer phenotypes and vice versa. Bypassing this complexity, we show that growth dynamics alone can robustly predict antibiotic responses. These findings are a foundation for a method to identify traits not easily traced to a genetic mechanism.
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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.
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