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Chen X, Zhu N, Yang G, Guo X, Sun S, Leng F, Wang Y. Role of cspA on the Preparation of Escherichia coli Competent Cells by Calcium Chloride Method. J Basic Microbiol 2024; 64:e2400113. [PMID: 38924123 DOI: 10.1002/jobm.202400113] [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: 02/28/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
One of the fundamental techniques in genetic engineering is the creation of Escherichia coli competent cells using the CaCl2 method. However, little is known about the mechanism of E. coli competence formation. We have previously found that the cspA gene may play an indispensable role in the preparation of E. coli DH5α competent cells through multiomics analysis. In the present study, the cellular localization, physicochemical properties, and function of the protein expressed by the cspA gene were analyzed. To investigate the role of the cspA gene in E. coli transformation, cspA-deficient mutant was constructed by red homologous recombination. The growth, transformation efficiency, and cell morphology of the cspA-deficient strain and E. coli were compared. It was found that there were no noticeable differences in growth and morphology between E. coli and the cspA-deficient strain cultured at 37°C, but the mutant exhibited increased transformation efficiencies compared to E. coli DH5α for plasmids pUC19, pET-32a, and p1304, with enhancements of 2.23, 2.24, and 3.46 times, respectively. It was proved that cspA gene is an important negative regulatory gene in the CaCl2 preparation of competent cells.
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Affiliation(s)
- Xiaona Chen
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Ning Zhu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Guangrui Yang
- Gansu Zhongshang Food Quality Test and Detection Co. Ltd., Lanzhou, China
- Gansu Business Science and Technology Institute Co. Ltd., Lanzhou, China
| | - Xiaopeng Guo
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Shangchen Sun
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
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2
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Tran NN, Morrisette T, Jorgensen SCJ, Orench-Benvenutti JM, Kebriaei R. Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections. Pharmacotherapy 2023; 43:816-832. [PMID: 37133439 DOI: 10.1002/phar.2806] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 05/04/2023]
Abstract
Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for the enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies, and reported alternatives are discussed.
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Affiliation(s)
- Nikki N Tran
- Department of Pharmacy, The Ohio State University Wexner Medical Center - The James Cancer Hospital and Solove Research Institute, Columbus, Ohio, USA
| | - Taylor Morrisette
- Department of Clinical Pharmacy and Outcomes Sciences, Medical University of South Carolina College of Pharmacy, Charleston, South Carolina, USA
- Department of Pharmacy Services, Medical University of South Carolina Shawn Jenkins Children's Hospital, Charleston, South Carolina, USA
| | - Sarah C J Jorgensen
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - José M Orench-Benvenutti
- P3 Research Laboratory, Division of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Razieh Kebriaei
- P3 Research Laboratory, Division of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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3
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Ontiveros VJ, Capitán JA, Casamayor EO, Alonso D. Colonization-persistence trade-offs in natural bacterial communities. Proc Biol Sci 2023; 290:20230709. [PMID: 37403500 PMCID: PMC10320335 DOI: 10.1098/rspb.2023.0709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Fitness equalizing mechanisms, such as trade-offs, are recognized as one of the main factors promoting species coexistence in community ecology. However, they have rarely been explored in microbial communities. Although microbial communities are highly diverse, the coexistence of their multiple taxa is largely attributed to niche differences and high dispersal rates, following the principle 'everything is everywhere, but the environment selects'. We use a dynamical stochastic model based on the theory of island biogeography to study highly diverse bacterial communities over time across three different systems (soils, alpine lakes and shallow saline lakes). Assuming fitness equalization mechanisms, here we newly analytically derive colonization-persistence trade-offs, and report a signal of such trade-offs in natural bacterial communities. Moreover, we show that different subsets of species in the community drive this trade-off. Rare taxa, which are occasional and more likely to follow independent colonization/extinction dynamics, drive this trade-off in the aquatic communities, while the core sub-community did it in the soils. We conclude that equalizing mechanisms may be more important than previously recognized in bacterial communities. Our work also emphasizes the fundamental value of dynamical models for understanding temporal patterns and processes in highly diverse communities.
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Affiliation(s)
- Vicente J. Ontiveros
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
| | - José A. Capitán
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
- Complex Systems Group. Department of Applied Mathematics, Universidad Politécnica de Madrid. Av. Juan de Herrera, 6. E-28040 Madrid, Spain
| | - Emilio O. Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
| | - David Alonso
- Theoretical and Computational Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
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4
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Guidotti-Takeuchi M, Melo RTD, Ribeiro LNDM, Dumont CF, Ribeiro RAC, Brum BDA, de Amorim Junior TLIF, Rossi DA. Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap. Antibiotics (Basel) 2023; 12:1127. [PMID: 37508224 PMCID: PMC10376302 DOI: 10.3390/antibiotics12071127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the blaTEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.
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Affiliation(s)
- Micaela Guidotti-Takeuchi
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | - Roberta Torres de Melo
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Carolyne Ferreira Dumont
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Bárbara de Araújo Brum
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Daise Aparecida Rossi
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
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Calderón-Franco D, van Loosdrecht MCM, Abeel T, Weissbrodt DG. Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01834-z. [PMID: 37156983 DOI: 10.1007/s10482-023-01834-z] [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: 02/24/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L-1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L-1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.
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Affiliation(s)
| | | | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
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6
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Xiao R, Huang D, Du L, Song B, Yin L, Chen Y, Gao L, Li R, Huang H, Zeng G. Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161855. [PMID: 36708845 DOI: 10.1016/j.scitotenv.2023.161855] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.
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Affiliation(s)
- Ruihao Xiao
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
| | - Li Du
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lingshi Yin
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Yashi Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Lan Gao
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Ruijin Li
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Hai Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, Hunan 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China.
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7
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Bethke JH, Ma HR, Tsoi R, Cheng L, Xiao M, You L. Vertical and horizontal gene transfer tradeoffs direct plasmid fitness. Mol Syst Biol 2022; 19:e11300. [PMID: 36573357 PMCID: PMC9912019 DOI: 10.15252/msb.202211300] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
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Affiliation(s)
- Jonathan H Bethke
- Department of Molecular Genetics and MicrobiologyDuke UniversityNCDurhamUSA
| | - Helena R Ma
- Department of Biomedical EngineeringDuke UniversityNCDurhamUSA,Center for Quantitative BiodesignDuke UniversityNCDurhamUSA
| | - Ryan Tsoi
- Department of Biomedical EngineeringDuke UniversityNCDurhamUSA
| | - Li Cheng
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI‐ShenzhenShenzhenChina,School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
| | - Minfeng Xiao
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI‐ShenzhenShenzhenChina
| | - Lingchong You
- Department of Molecular Genetics and MicrobiologyDuke UniversityNCDurhamUSA,Department of Biomedical EngineeringDuke UniversityNCDurhamUSA,Center for Quantitative BiodesignDuke UniversityNCDurhamUSA,School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
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8
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Pillay S, Calderón-Franco D, Urhan A, Abeel T. Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings. Front Microbiol 2022; 13:1066995. [PMID: 36532424 PMCID: PMC9755710 DOI: 10.3389/fmicb.2022.1066995] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.
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Affiliation(s)
- Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | | | - Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
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9
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Hernández-Beltrán JCR, San Millán A, Fuentes-Hernández A, Peña-Miller R. Mathematical Models of Plasmid Population Dynamics. Front Microbiol 2021; 12:606396. [PMID: 34803935 PMCID: PMC8600371 DOI: 10.3389/fmicb.2021.606396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.
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Affiliation(s)
| | | | | | - Rafael Peña-Miller
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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