1
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Sarangi A, Singh SP, Das BS, Rajput S, Fatima S, Bhattacharya D. Mycobacterial biofilms: A therapeutic target against bacterial persistence and generation of antibiotic resistance. Heliyon 2024; 10:e32003. [PMID: 38882302 PMCID: PMC11176842 DOI: 10.1016/j.heliyon.2024.e32003] [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: 01/22/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Mycobacterium tuberculosis (M. tb) is the causative agent of Tuberculosis, one of the deadliest infectious diseases. According to the WHO Report 2023, in 2022, approximately 10.6 million people got infected with TB, and 1.6 million died. It has multiple antibiotics for treatment, but the major drawback of anti-tuberculosis therapy (ATT) is, its prolonged treatment duration. The major contributors to the lengthy treatment period are mycobacterial persistence and drug tolerance. Persistent M. tb is phenotypically drug tolerant and metabolically slow down which makes it difficult to be eliminated during ATT. These persisting bacteria are a huge reservoir of impending disease, waiting to get reactivated upon the onset of an immune compromising state. Directly Observed Treatment Short-course, although effective against replicating bacteria; fails to eliminate the drug-tolerant persisters making TB still the second-highest killer globally. There are different mechanisms for the development of drug-tolerant mycobacterial populations being investigated. Recently, the role of biofilms in the survival and host-evasion mechanism of persisters has come to light. Therefore, it is crucial to understand the mechanism of adaptation, survival and attainment of drug tolerance by persisting M. tb-populations, in order to design better immune responses and therapeutics for the effective elimination of these bacteria by reducing the duration of treatment and also circumvent the generation of drug-resistance to achieve the goal of global eradication of TB. This review summarizes the drug-tolerance mechanism and biofilms' role in providing a niche to dormant-M.tb. We also discuss methods of targeting biofilms to achieve sterile eradication of the mycobacteria and prevent its reactivation by achieving adequate immune responses.
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Affiliation(s)
- Ashirbad Sarangi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Shashi Prakash Singh
- Vaccine and Gene Therapy Institute (VGTI) Oregon National Primate Research Centre (ONPRC) Oregon Health and Science University (OHSU) Beaverton, Oregon, USA
| | - Bhabani Shankar Das
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Sristi Rajput
- Departmental of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Samreen Fatima
- UMass Chan Medical School, University of Massachusetts, Worcester, MA, USA
| | - Debapriya Bhattacharya
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
- Departmental of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
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2
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Qiu X, Wang B, Ren S, Liu X, Wang Y. Regulation of quorum sensing for the manipulation of conjugative transfer of antibiotic resistance genes in wastewater treatment system. WATER RESEARCH 2024; 253:121222. [PMID: 38335841 DOI: 10.1016/j.watres.2024.121222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/29/2023] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
The emergence and transmission of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation has become a significant worldwide public health threat. Biofilms are widely recognized as the primary reservoirs for ARGs, providing favorable conditions for horizontal gene transfer. Quorum sensing (QS) plays a critical role in bacterial biofilm formation, which further influences the spread of bacterial resistance. In this study, we examined the effects of vanillin, a QS inhibitor (QSI), at subinhibitory concentrations (sub-MICs) ranging from 0 - 0.1 g/L, on the transfer of ARGs between Escherichia coli and Pseudomonas aeruginosa. Our findings indicated that vanillin at sub-MICs inhibited the conjugative transfer frequency of the RP4 plasmid. This inhibition was supported by the downregulation of plasmid transfer genes. The suppression of conjugation can mainly be attributed to the inhibition of biofilm formation, the synthesis of extracellular polymeric substances (EPS), and the secretion of virulence factors, all of which are regulated by the bacterial QS system. On the other hand, the levels of ROS and cell membrane permeability were not primary explanations for this phenomenon. Furthermore, vanillin also reduced the conjugative transfer frequency of ARGs in wastewater effluent, providing a potential approach to alleviate bacterial resistance in water environments. These findings underscore the regulatory role of QSI in controlling ARGs transfer and have significant implications for manipulating the dissemination of bacterial resistance in the environment.
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Affiliation(s)
- Xiao Qiu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Bingjie Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Shaojie Ren
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaoli Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Yunkun Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China.
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3
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Redman RM, Maughan TD, Smith CB, Crossno PF, Granger DL. Development of multidrug-resistant Mycobacterium tuberculosis in the biofilm of a peritoneal-venous shunt. IDCases 2023; 32:e01801. [PMID: 37250376 PMCID: PMC10209681 DOI: 10.1016/j.idcr.2023.e01801] [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: 04/04/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
A patient with ascites received a peritoneal-venous shunt for presumed cirrhosis, however surgical specimens grew Mycobacterium tuberculosis (MTb) sensitive to all anti-tuberculous drugs. Directly-Observed-Therapy (DOT) led to improvement followed by relapse with multidrug resistant MTb (MDRTB). We discuss pathways for selection of MDRTB within mycobacterial biofilm. This case illustrates the potential for development of MDRTB in patients with long-term indwelling catheters. We emphasize catheter removal and if not possible continuing follow-up for symptoms and signs of relapse.
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Affiliation(s)
- Romany M. Redman
- Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, UT 84145, USA
| | - Timothy D. Maughan
- Infectious Diseases Clinic, Providence Sacred Heart Hospital, 101 West 8th Avenue, Spokane, WA 99204, USA
| | - Charles B. Smith
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, UT 84132, USA
- Veterans Affairs Medical Center, 500 Foothill Drive, Salt Lake City, UT 84145, USA
| | - Peter F. Crossno
- Division of Pulmonary Medicine, Department of Medicine, Intermountain Healthcare, 5121 Cottonwood Street, Murray, UT 84107, USA
| | - Donald L. Granger
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, UT 84132, USA
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4
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Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol 2023; 8:695-710. [PMID: 36823286 PMCID: PMC10066036 DOI: 10.1038/s41564-023-01333-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.
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Affiliation(s)
- Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lexi A Serpa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ben J Braunecker
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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5
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Boopathi S, Ramasamy S, Haridevamuthu B, Murugan R, Veerabadhran M, Jia AQ, Arockiaraj J. Intercellular communication and social behaviors in mycobacteria. Front Microbiol 2022; 13:943278. [PMID: 36177463 PMCID: PMC9514802 DOI: 10.3389/fmicb.2022.943278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.
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Affiliation(s)
- Seenivasan Boopathi
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Subbiah Ramasamy
- Department of Biochemistry, Cardiac Metabolic Disease Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Raghul Murugan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Maruthanayagam Veerabadhran
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- *Correspondence: Ai-Qun Jia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
- Jesu Arockiaraj ;
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6
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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7
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Sadiq FA, Hansen MF, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhang H. Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature. FEMS Microbiol Rev 2022; 46:6595875. [PMID: 35640890 DOI: 10.1093/femsre/fuac024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.
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Affiliation(s)
- Faizan Ahmed Sadiq
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Private Bag, 11222, Palmerston North, New Zealand
| | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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8
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Chen B, Han J, Dai H, Jia P. Biocide-tolerance and antibiotic-resistance in community environments and risk of direct transfers to humans: Unintended consequences of community-wide surface disinfecting during COVID-19? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 283:117074. [PMID: 33848900 PMCID: PMC8019131 DOI: 10.1016/j.envpol.2021.117074] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/09/2021] [Accepted: 03/30/2021] [Indexed: 05/17/2023]
Abstract
During the current pandemic, chemical disinfectants are ubiquitously and routinely used in community environments, especially on common touch surfaces in public settings, as a means of controlling the virus spread. An underappreciated risk in current regulatory guidelines and scholarly discussions, however, is that the persisting input of chemical disinfectants can exacerbate the growth of biocide-tolerant and antibiotic-resistant bacteria on those surfaces and allow their direct transfers to humans. For COVID-19, the most commonly used disinfecting agents are quaternary ammonium compounds, hydrogen peroxide, sodium hypochlorite, and ethanol, which account for two-thirds of the active ingredients in current EPA-approved disinfectant products for the novel coronavirus. Tolerance to each of these compounds, which can be either intrinsic or acquired, has been observed on various bacterial pathogens. Of those, mutations and horizontal gene transfer, upregulation of efflux pumps, membrane alteration, and biofilm formation are the common mechanisms conferring biocide tolerance in bacteria. Further, the linkage between disinfectant use and antibiotic resistance was suggested in laboratory and real-life settings. Evidence showed that substantial bacterial transfers to hands could effectuate from short contacts with surrounding surfaces and further from fingers to lips. While current literature on disinfectant-induced antimicrobial resistance predominantly focuses on municipal wastes and the natural environments, in reality the community and public settings are most severely impacted by intensive and regular chemical disinfecting during COVID-19 and, due to their proximity to humans, biocide-tolerant and antibiotic-resistant bacteria emerged in these environments may pose risks of direct transfers to humans, particularly in densely populated urban communities. Here we highlight these risk factors by reviewing the most pertinent and up-to-date evidence, and provide several feasible strategies to mitigate these risks in the scenario of a prolonging pandemic.
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Affiliation(s)
- Bo Chen
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China; Department of Environmental Science and Engineering, College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, PR China
| | - Jie Han
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China.
| | - Han Dai
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Puqi Jia
- Department of Environmental Science and Engineering, College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, PR China
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9
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Abstract
Current models of horizontal gene transfer (HGT) in mycobacteria are based on “distributive conjugal transfer” (DCT), an HGT type described in the fast-growing, saprophytic model organism Mycobacterium smegmatis, which creates genome mosaicism in resulting strains and depends on an ESX-1 type VII secretion system. In contrast, only few data on interstrain DNA transfer are available for tuberculosis-causing mycobacteria, for which chromosomal DNA transfer between two Mycobacterium canettii strains was reported, a process which, however, was not observed for Mycobacterium tuberculosis strains. Here, we have studied a wide range of human- and animal-adapted members of the Mycobacterium tuberculosis complex (MTBC) using an optimized filter-based mating assay together with three selected strains of M. canettii that acted as DNA recipients. Unlike in previous approaches, we obtained a high yield of thousands of recombinants containing transferred chromosomal DNA fragments from various MTBC donor strains, as confirmed by whole-genome sequence analysis of 38 randomly selected clones. While the genome organizations of the obtained recombinants showed mosaicisms of donor DNA fragments randomly integrated into a recipient genome backbone, reminiscent of those described as being the result of ESX-1-mediated DCT in M. smegmatis, we observed similar transfer efficiencies when ESX-1-deficient donor and/or recipient mutants were used, arguing that in tubercle bacilli, HGT is an ESX-1-independent process. These findings provide new insights into the genetic events driving the pathoevolution of M. tuberculosis and radically change our perception of HGT in mycobacteria, particularly for those species that show recombinogenic population structures despite the natural absence of ESX-1 secretion systems.
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10
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Niño-Padilla EI, Velazquez C, Garibay-Escobar A. Mycobacterial biofilms as players in human infections: a review. BIOFOULING 2021; 37:410-432. [PMID: 34024206 DOI: 10.1080/08927014.2021.1925886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/18/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
The role of biofilms in pathogenicity and treatment strategies is often neglected in mycobacterial infections. In recent years, the emergence of nontuberculous mycobacterial infections has necessitated the development of novel prophylactic strategies and elucidation of the mechanisms underlying the establishment of chronic infections. More importantly, the question arises whether members of the Mycobacterium tuberculosis complex can form biofilms and contribute to latent tuberculosis and drug resistance because of the long-lasting and recalcitrant nature of its infections. This review discusses some of the molecular mechanisms by which biofilms could play a role in infection or pathological events in humans.
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Affiliation(s)
| | - Carlos Velazquez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
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11
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Tsegaye MM, Chouhan G, Fentie M, Tyagi P, Nand P. Therapeutic Potential of Green Synthesized Metallic Nanoparticles against Staphylococcus aureus. Curr Drug Res Rev 2021; 13:172-183. [PMID: 33634763 DOI: 10.2174/2589977513666210226123920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/08/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The recent treatment challenges posed by the widespread emergence of pathogenic Multidrug-Resistant (MDR) bacterial strains are a cause of huge health troubles worldwide. Infections caused by MDR organisms are associated with longer period of hospitalization, increased mortality, and inflated healthcare costs. Staphylococcus aureus is one of these MDR organisms identified as an urgent threat to human health by the World Health Organization. Infections caused by S. aureus may range from simple cutaneous infestations to life threatening bacteremia. S. aureus infections get easily escalated in severely ill, hospitalized and or immunocompromised patients with incapacitated immune system. Also, in HIV-positive patients S. aureus ranks amongst one of the most common comorbidities where it can further worsen a patient's health condition. At present anti-staphylococcal therapy is reliant typically on chemotherapeutics that are gathering resistance and pose unfavorable side-effects. Thus, newer drugs are required that can bridge these shortcomings and aid effective control against S. aureus. OBJECTIVE In this review, we summarize drug resistance exhibited by S. aureus and lacunae in current anti-staphylococcal therapy, nanoparticles as an alternative therapeutic modality. The focus lays on various green synthesized nanoparticles, their mode of action and application as potent antibacterial compounds against S. aureus. CONCLUSION Use of nanoparticles as anti-bacterial drugs has gained momentum in recent past and green synthesized nanoparticles, which involves microorganisms and plants or their byproducts for synthesis of nanoparticles offer a potent, as well as environment friendly solution in warfare against MDR bacte.
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Affiliation(s)
- Meron Moges Tsegaye
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh. India
| | - Garima Chouhan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh. India
| | - Molla Fentie
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh. India
| | - Priya Tyagi
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh. India
| | - Parma Nand
- School of Engineering and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh. India
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12
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Pereira AC, Ramos B, Reis AC, Cunha MV. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 2020; 8:microorganisms8091380. [PMID: 32916931 PMCID: PMC7563442 DOI: 10.3390/microorganisms8091380] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-500-000 (ext. 22461)
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13
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McLean TC, Lo R, Tschowri N, Hoskisson PA, Al Bassam MM, Hutchings MI, Som NF. Sensing and responding to diverse extracellular signals: an updated analysis of the sensor kinases and response regulators of Streptomyces species. MICROBIOLOGY-SGM 2020; 165:929-952. [PMID: 31334697 DOI: 10.1099/mic.0.000817] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Streptomyces venezuelae is a Gram-positive, filamentous actinomycete with a complex developmental life cycle. Genomic analysis revealed that S. venezuelae encodes a large number of two-component systems (TCSs): these consist of a membrane-bound sensor kinase (SK) and a cognate response regulator (RR). These proteins act together to detect and respond to diverse extracellular signals. Some of these systems have been shown to regulate antimicrobial biosynthesis in Streptomyces species, making them very attractive to researchers. The ability of S. venezuelae to sporulate in both liquid and solid cultures has made it an increasingly popular model organism in which to study these industrially and medically important bacteria. Bioinformatic analysis identified 58 TCS operons in S. venezuelae with an additional 27 orphan SK and 18 orphan RR genes. A broader approach identified 15 of the 58 encoded TCSs to be highly conserved in 93 Streptomyces species for which high-quality and complete genome sequences are available. This review attempts to unify the current work on TCS in the streptomycetes, with an emphasis on S. venezuelae.
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Affiliation(s)
- Thomas C McLean
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Rebecca Lo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Natalia Tschowri
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Mahmoud M Al Bassam
- Department of Paediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Nicolle F Som
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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Le Moigne V, Bernut A, Cortès M, Viljoen A, Dupont C, Pawlik A, Gaillard JL, Misguich F, Crémazy F, Kremer L, Herrmann JL. Lsr2 Is an Important Determinant of Intracellular Growth and Virulence in Mycobacterium abscessus. Front Microbiol 2019; 10:905. [PMID: 31114557 PMCID: PMC6503116 DOI: 10.3389/fmicb.2019.00905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium abscessus, a pathogen responsible for severe lung infections in cystic fibrosis patients, exhibits either smooth (S) or rough (R) morphotypes. The S-to-R transition correlates with inhibition of the synthesis and/or transport of glycopeptidolipids (GPLs) and is associated with an increase of pathogenicity in animal and human hosts. Lsr2 is a small nucleoid-associated protein highly conserved in mycobacteria, including M. abscessus, and is a functional homolog of the heat-stable nucleoid-structuring protein (H-NS). It is essential in Mycobacterium tuberculosis but not in the non-pathogenic model organism Mycobacterium smegmatis. It acts as a master transcriptional regulator of multiple genes involved in virulence and immunogenicity through binding to AT-rich genomic regions. Previous transcriptomic studies, confirmed here by quantitative PCR, showed increased expression of lsr2 (MAB_0545) in R morphotypes when compared to their S counterparts, suggesting a possible role of this protein in the virulence of the R form. This was addressed by generating lsr2 knock-out mutants in both S (Δlsr2-S) and R (Δlsr2-R) variants, demonstrating that this gene is dispensable for M. abscessus growth. We show that the wild-type S variant, Δlsr2-S and Δlsr2-R strains were more sensitive to H2O2 as compared to the wild-type R variant of M. abscessus. Importantly, virulence of the Lsr2 mutants was considerably diminished in cellular models (macrophage and amoeba) as well as in infected animals (mouse and zebrafish). Collectively, these results emphasize the importance of Lsr2 in M. abscessus virulence.
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Affiliation(s)
| | - Audrey Bernut
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France
| | | | - Albertus Viljoen
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France
| | - Christian Dupont
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France
| | - Alexandre Pawlik
- Unité de Pathogénomique Mycobactérienne, Institut Pasteur, Paris, France
| | - Jean-Louis Gaillard
- 2I, UVSQ, INSERM, Université Paris-Saclay, Versailles, France.,APHP, GHU PIFO, Hôpital Raymond-Poincaré - Hôpital Ambroise-Paré, Boulogne-Billancourt, France
| | | | | | - Laurent Kremer
- UMR 9004, Centre National de la Recherche Scientifique, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, Montpellier, France.,INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France
| | - Jean-Louis Herrmann
- 2I, UVSQ, INSERM, Université Paris-Saclay, Versailles, France.,APHP, GHU PIFO, Hôpital Raymond-Poincaré - Hôpital Ambroise-Paré, Boulogne-Billancourt, France
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15
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Characterization of a novel regulatory pathway for mannitol metabolism and its coordination with biofilm formation in Mycobacterium smegmatis. J Genet Genomics 2018; 45:477-488. [DOI: 10.1016/j.jgg.2018.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/26/2018] [Indexed: 01/03/2023]
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16
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Yang Y, Richards JP, Gundrum J, Ojha AK. GlnR Activation Induces Peroxide Resistance in Mycobacterial Biofilms. Front Microbiol 2018; 9:1428. [PMID: 30022971 PMCID: PMC6039565 DOI: 10.3389/fmicb.2018.01428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/11/2018] [Indexed: 12/31/2022] Open
Abstract
Mycobacteria spontaneously form surface-associated multicellular communities, called biofilms, which display resistance to a wide range of exogenous stresses. A causal relationship between biofilm formation and emergence of stress resistance is not known. Here, we report that activation of a nitrogen starvation response regulator, GlnR, during the development of Mycobacterium smegmatis biofilms leads to peroxide resistance. The resistance arises from induction of a GlnR-dependent peroxide resistance (gpr) gene cluster comprising of 8 ORFs (MSMEG_0565-0572). Expression of gpr increases the NADPH to NADP ratio, suggesting that a reduced cytosolic environment of nitrogen-starved cells in biofilms contributes to peroxide resistance. Increased NADPH levels from gpr activity likely support the activity of enzymes involved in nitrogen assimilation, as suggested by a higher threshold of nitrogen supplement required by a gpr mutant to form biofilms. Together, our study uniquely interlinks a nutrient sensing mechanism with emergence of stress resistance during mycobacterial biofilm development. The gpr gene cluster is conserved in several mycobacteria that can cause nosocomial infections, offering a possible explanation for their resistance to peroxide-based sterilization of medical equipment.
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Affiliation(s)
- Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Jacob P. Richards
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer Gundrum
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Anil K. Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States
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17
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Gray TA, Derbyshire KM. Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT. Mol Microbiol 2018; 108:601-613. [PMID: 29669186 DOI: 10.1111/mmi.13971] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2018] [Indexed: 12/16/2022]
Abstract
This review discusses a novel form of horizontal gene transfer (HGT) found in mycobacteria called Distributive Conjugal Transfer (DCT). While satisfying the criteria for conjugation, DCT occurs by a mechanism so distinct from oriT-mediated conjugation that it could be considered a fourth category of HGT. DCT involves the transfer of chromosomal DNA between mycobacteria and, most significantly, generates transconjugants with mosaic genomes of the parental strains. Multiple segments of donor chromosomal DNA can be co-transferred regardless of their location or the genetic selection and, as a result, the transconjugant genome contains many donor-derived segments; hence the name DCT. This distinguishing feature of DCT separates it from the other known mechanisms of HGT, which generally result in the introduction of a single, defined segment of DNA into the recipient chromosome (Fig. ). Moreover, these mosaic progeny are generated from a single conjugal event, which provides enormous capacity for rapid adaptation and evolution, again distinguishing it from the three classical modes of HGT. Unsurprisingly, the unusual mosaic products of DCT are generated by a conjugal mechanism that is also unusual. Here, we will describe the unique features of DCT and contrast those to other mechanisms of HGT, both from a mechanistic and an evolutionary perspective. Our focus will be on transfer of chromosomal DNA, as opposed to plasmid mobilization, because DCT mediates transfer of chromosomal DNA and is a chromosomally encoded process.
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Affiliation(s)
- Todd A Gray
- New York State Department of Health, Wadsworth Center, Albany, NY 12201, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
| | - Keith M Derbyshire
- New York State Department of Health, Wadsworth Center, Albany, NY 12201, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
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18
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Nesse LL, Simm R. Biofilm: A Hotspot for Emerging Bacterial Genotypes. ADVANCES IN APPLIED MICROBIOLOGY 2018; 103:223-246. [PMID: 29914658 DOI: 10.1016/bs.aambs.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bacteria have the ability to adapt to changing environments through rapid evolution mediated by modification of existing genetic information, as well as by horizontal gene transfer (HGT). This makes bacteria a highly successful life form when it comes to survival. Unfortunately, this genetic plasticity may result in emergence and dissemination of antimicrobial resistance and virulence genes, and even the creation of multiresistant "superbugs" which may pose serious threats to public health. As bacteria commonly reside in biofilms, there has been an increased interest in studying these phenomena within biofilms in recent years. This review summarizes the present knowledge within this important area of research. Studies on bacterial evolution in biofilms have shown that mature biofilms develop into diverse communities over time. There is growing evidence that the biofilm lifestyle may be more mutagenic than planktonic growth. Furthermore, all three main mechanisms for HGT have been observed in biofilms. This has been shown to occur both within and between bacterial species, and higher transfer rates in biofilms than in planktonic cultures were detected. Of special concern are the observations that mutants with increased antibiotic resistance occur at higher frequency in biofilms than in planktonic cultures even in the absence of antibiotic exposure. Likewise, efficient dissemination of antimicrobial resistance genes, as well as virulence genes, has been observed within the biofilm environment. This new knowledge emphasizes the importance of biofilm awareness and control.
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19
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Biofilms: Survival and defense strategy for pathogens. Int J Med Microbiol 2017; 307:481-489. [PMID: 28950999 DOI: 10.1016/j.ijmm.2017.09.016] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 01/20/2023] Open
Abstract
Studies on biofilm related infections are gaining prominence owing to their involvement in majority of clinical infections. Biofilm, considered as a generic mechanism for survival used by pathogenic as well as non-pathogenic microorganisms, involves surface attachment and growth of heterogeneous cells encapsulated within a matrix. The matrix provides ecological niche where partnership of cells endows a community like behaviour that not only enables the cohort to survive local microenvironment stress but also channelizes them to evolve, disseminate and cause resurgence of infections. In this mini-review we highlight the mechanisms used by microbes to develop and sustain biofilms, including the influence of the microbiota. Several strategies to target biofilms have been validated on certain groups of microorganisms and these basically target different stages in the life cycle of biofilm, however comprehensive methods to target microbial biofilms are relatively unknown. In the backdrop of recent reports suggesting that biofilms can harbour multiple species of organisms, we need to relook and devise newer strategies against biofilms. Effective anti-biofilm strategies cannot be confined to a single methodology that can disrupt one pathway but should simultaneously target the various routes adopted by the microorganisms for survival within their ecosystem. An overview of the currently available drugs, their mode of action, genomic targets and translational therapies against biofilm related infection are discussed.
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20
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Yang Y, Thomas J, Li Y, Vilchèze C, Derbyshire KM, Jacobs WR, Ojha AK. Defining a temporal order of genetic requirements for development of mycobacterial biofilms. Mol Microbiol 2017. [PMID: 28628249 DOI: 10.1111/mmi.13734] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Most mycobacterial species spontaneously form biofilms, inducing unique growth physiologies and reducing drug sensitivity. Biofilm growth progresses through three genetically programmed stages: substratum attachment, intercellular aggregation and architecture maturation. Growth of Mycobacterium smegmatis biofilms requires multiple factors including a chaperonin (GroEL1) and a nucleoid-associated protein (Lsr2), although how their activities are linked remains unclear. Here it is shown that Lsr2 participates in intercellular aggregation, but substratum attachment of Lsr2 mutants is unaffected, thereby genetically distinguishing these developmental stages. Further, a suppressor mutation in a glycopeptidolipid synthesis gene (mps) that results in hyperaggregation of cells and fully restores the form and functions of Δlsr2 mutant biofilms was identified. Suppression by the mps mutation is specific to Δlsr2; it does not rescue the maturation-deficient biofilms of a ΔgroEL1 mutant, thereby differentiating the process of aggregation from maturation. Gene expression analysis supports a stepwise process of maturation, highlighted by temporally separated, transient inductions of iron and nitrogen import genes. Furthermore, GroEL1 activity is required for induction of nitrogen, but not iron, import genes. Together, the findings begin to define molecular checkpoints during development of mycobacterial biofilms.
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Affiliation(s)
- Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Joseph Thomas
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yunlong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Keith M Derbyshire
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.,Howard Hughes Medical Institute, Bronx, NY, USA
| | - Anil K Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
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Abstract
Bacteria have a natural propensity to grow as sessile, matrix-encapsulated, multicellular communities called biofilms. Formation of biofilms proceeds through genetically programmed, distinct developmental stages signaled by intricate networks of communication among the constituent population and their environment. Growing in the complex and heterogeneous microenvironments of biofilms, the resident bacteria acquire unique phenotypes that are generally not associated with their planktonic counterparts. Most notable among these is an extraordinary level of tolerance to a variety of environmental stresses, including antibiotics. Although mycobacteria have long been observed to spontaneously form complex multicellular structures in vitro, it has only recently become apparent that these structures are not only formed through dedicated genetic pathways but are also tolerant to antibiotics. In this article, we review the recent advances in the understanding of mycobacterial biofilms in vitro. We further consider the possible linkage between biofilm-like lifestyles and characteristic persistence of mycobacterial infections against host-defense mechanisms as well as antibiotics.
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22
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Abstract
A major factor complicating efforts to control the tuberculosis epidemic is the long duration of treatment required to successfully clear the infection. One reason that long courses of treatment are required may be the fact that mycobacterial cells arise during the course of infection that are less susceptible to antibiotics. Here we describe the paradigms of phenotypic drug tolerance and resistance as they apply to mycobacteria. We then discuss the mechanisms by which phenotypically drug-tolerant and -resistant cells arise both at a population level and in specialized subpopulations of cells that may be especially important in allowing the bacterium to survive in the face of treatment. These include general mechanisms that have been shown to alter the susceptibility of mycobacteria to antibiotics including growth arrest, efflux pump induction, and biofilm formation. In addition, we discuss emerging data from single-cell studies of mycobacteria that have identified unique ways in which specialized subpopulations of cells arise that vary in their frequency, in their susceptibility to drug, and in their stability over time.
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23
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Sharma IM, Petchiappan A, Chatterji D. Quorum sensing and biofilm formation in mycobacteria: Role of c-di-GMP and methods to study this second messenger. IUBMB Life 2014; 66:823-34. [DOI: 10.1002/iub.1339] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 12/04/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Indra Mani Sharma
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
| | - Anushya Petchiappan
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
| | - Dipankar Chatterji
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
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Mortimer TD, Pepperell CS. Genomic signatures of distributive conjugal transfer among mycobacteria. Genome Biol Evol 2014; 6:2489-500. [PMID: 25173757 PMCID: PMC4202316 DOI: 10.1093/gbe/evu175] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis. We have tested popular LGT detection methods on whole-genome sequence data from experimental DCT transconjugants and used the best performing methods to compare genomic signatures of DCT with those of LGT through natural transformation, conjugative plasmids, and mobile genetic elements (MGE). We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT. We used the best performing methods to characterize LGT in Mycobacterium canettii, the mycobacterial species most closely related to Mycobacterium tuberculosis. Patterns of LGT among M. canettii were highly distinctive. Gene flow appeared unidirectional, from lineages with minimal evidence of LGT to isolates with a substantial proportion (6–13%) of sites identified as recombinant. Among M. canettii isolates with evidence of LGT, recombinant fragments were larger and more evenly distributed relative to bacteria that undergo LGT through natural transformation, conjugative plasmids, and MGE. Spatial bias in M. canettii was also unusual in that patterns of recombinant fragment sharing mirrored overall phylogenetic structure. Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.
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Affiliation(s)
- Tatum D Mortimer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison
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25
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Chimileski S, Franklin MJ, Papke RT. Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer. BMC Biol 2014; 12:65. [PMID: 25124934 PMCID: PMC4180959 DOI: 10.1186/s12915-014-0065-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/31/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Archaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2. RESULTS Biofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 μm in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 μm in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method. CONCLUSIONS The developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.
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27
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Van Meervenne E, De Weirdt R, Van Coillie E, Devlieghere F, Herman L, Boon N. Biofilm models for the food industry: hot spots for plasmid transfer? Pathog Dis 2014; 70:332-8. [PMID: 24436212 DOI: 10.1111/2049-632x.12134] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/03/2014] [Accepted: 01/04/2014] [Indexed: 12/26/2022] Open
Abstract
Biofilms represent a substantial problem in the food industry, with food spoilage, equipment failure, and public health aspects to consider. Besides, biofilms may be a hot spot for plasmid transfer, by which antibiotic resistance can be disseminated to potential foodborne pathogens. This study investigated biomass and plasmid transfer in dual-species (Pseudomonas putida and Escherichia coli) biofilm models relevant to the food industry. Two different configurations (flow-through and drip-flow) and two different inoculation procedures (donor-recipient and recipient-donor) were tested. The drip-flow configuration integrated stainless steel coupons in the setup while the flow-through configuration included a glass flow cell and silicone tubing. The highest biomass density [10 log (cells cm-²)] was obtained in the silicone tubing when first the recipient strain was inoculated. High plasmid transfer ratios, up to 1/10 (transconjugants/total bacteria), were found. Depending on the order of inoculation, a difference in transfer efficiency between the biofilm models could be found. The ease by which the multiresistance plasmid was transferred highlights the importance of biofilms in the food industry as hot spots for the acquisition of multiresistance plasmids. This can impede the treatment of foodborne illnesses if pathogens acquire this multiresistance in or from the biofilm.
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Affiliation(s)
- Eva Van Meervenne
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Gent, Belgium; Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium; Laboratory of Food Microbiology and Food Preservation (LFMFP), Ghent University, Gent, Belgium
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28
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Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One 2013; 8:e78237. [PMID: 24250794 PMCID: PMC3826726 DOI: 10.1371/journal.pone.0078237] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. PRINCIPAL FINDINGS Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. SIGNIFICANCE For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.
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Affiliation(s)
- Lillian G. Acuña
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Juan Pablo Cárdenas
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Paulo C. Covarrubias
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | | | | | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingenieria, Universidad de Talca, Talca, Chile
| | | | - Jorge Valdés
- Center for Systems Biotechnology, Fraunhofer Chile, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Douglas E. Rawlings
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - David S. Holmes
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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Yuan J, Chen Y, Zhou G, Chen H, Gao H. Investigation of roles of divalent cations in Shewanella oneidensis pellicle formation reveals unique impacts of insoluble iron. Biochim Biophys Acta Gen Subj 2013; 1830:5248-57. [PMID: 23911985 DOI: 10.1016/j.bbagen.2013.07.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND Bacteria adopt a variety of lifestyles in their natural habitats and can alternate among different lifestyles in response to environmental changes. At high cell densities, bacteria can form extracellular matrix encased cell population on submerged tangible surfaces (biofilms), or at the air-liquid interface (pellicles). Compared to biofilm, pellicle lifestyle allows for better oxygen access, but is metabolically more costly to maintain. Further understanding of pellicle formation and environmental cues that influence cellular choices between these lifestyles will definitely improve our appreciation of bacterial interaction with their environments. METHODS Shewanella oneidensis cells were cultured in 24-well plates with supplementation of varied divalent cations, and pellicles formed under such conditions were evaluated. Mutants defective in respiration of divalent cations were used to further characterize and confirm unique impacts of iron. RESULTS AND CONCLUSIONS Small amount of Fe(2+) was essential for pellicle formation, but presence of over-abundant iron (0.3mM Fe(2+) or Fe(3+)) led to pellicle disassociation without impairing growth. Such impacts were found due to S. oneidensis-mediated formation of insoluble alternative electron acceptors (i.e., Fe3O4) under physiologically relevant conditions. Furthermore, we demonstrated that cells preferred a lifestyle of forming biofilm and respiring on such insoluble electron acceptors under tested conditions, even to living in pellicles. GENERAL SIGNIFICANCE Our finding suggests that bacterial lifestyle choice involves balanced evaluation of multiple aspects of environmental conditions, and yet-to-be-characterized signaling mechanism is very likely underlying such processes.
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Affiliation(s)
- Jie Yuan
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Gray TA, Krywy JA, Harold J, Palumbo MJ, Derbyshire KM. Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus. PLoS Biol 2013; 11:e1001602. [PMID: 23874149 PMCID: PMC3706393 DOI: 10.1371/journal.pbio.1001602] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 05/24/2013] [Indexed: 01/01/2023] Open
Abstract
We find that genome-wide DNA transfer by conjugation in mycobacteria affords bacteria that reproduce by binary fission the same advantages of sexual reproduction, and may explain the genomic evolution of Mycobacterium tuberculosis. Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism. Bacteria reproduce by binary fission, generating two clones of the original; this restricts the genomic diversity of the population, which brings with it inherent evolutionary drawbacks. This problem can be eased by conjugation, which transfers DNA from a donor to a recipient bacterium. Understanding the potential of conjugal DNA transfer for generating genetic diversity is necessary for estimating gene flow through populations and for predicting rates of bacterial evolution. The influence of chromosomal conjugal DNA transfer on mycobacterial diversity has not been previously addressed. Here, we determine and compare the complete genome sequences of independent progeny from bacterial matings between defined donor and recipient strains of Mycobacterium smegmatis. We find the resulting hybrid bacteria to be extremely diverse blends of the parental strains, reminiscent of the genetic mixing that occurs through meiotic recombination in sexual organisms. This novel mechanism of conjugation can create genome-wide mosaicism in a single event, generating segments of donor DNA that range from small (∼0.05 kb) to large (∼250 kb), widely distributed around the recipient chromosome. We exploit this mixing by using genetic tools originally developed for finding mammalian disease genes to locate the genes that confer a donor phenotype in M. smegmatis. We speculate that similar genomic mosaicism observed in pathogenic mycobacteria arose from conjugation between ancestral progenitor strains.
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Affiliation(s)
- Todd A Gray
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.
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31
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Pacheco SA, Hsu FF, Powers KM, Purdy GE. MmpL11 protein transports mycolic acid-containing lipids to the mycobacterial cell wall and contributes to biofilm formation in Mycobacterium smegmatis. J Biol Chem 2013; 288:24213-22. [PMID: 23836904 DOI: 10.1074/jbc.m113.473371] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A growing body of evidence indicates that MmpL (mycobacterial membrane protein large) transporters are dedicated to cell wall biosynthesis and transport mycobacterial lipids. How MmpL transporters function and the identities of their substrates have not been fully elucidated. We report the characterization of Mycobacterium smegmatis MmpL11. We showed previously that M. smegmatis lacking MmpL11 has reduced membrane permeability that results in resistance to host antimicrobial peptides. We report herein the further characterization of the M. smegmatis mmpL11 mutant and identification of the MmpL11 substrates. We found that biofilm formation by the M. smegmatis mmpL11 mutant was distinct from that by wild-type M. smegmatis. Analysis of cell wall lipids revealed that the mmpL11 mutant failed to export the mycolic acid-containing lipids monomeromycolyl diacylglycerol and mycolate ester wax to the bacterial surface. In addition, analysis of total lipids indicated that the mycolic acid-containing precursor molecule mycolyl phospholipid accumulated in the mmpL11 mutant compared with wild-type mycobacteria. MmpL11 is encoded at a chromosomal locus that is conserved across pathogenic and nonpathogenic mycobacteria. Phenotypes of the M. smegmatis mmpL11 mutant are complemented by the expression of M. smegmatis or M. tuberculosis MmpL11, suggesting that MmpL11 plays a conserved role in mycobacterial cell wall biogenesis.
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Affiliation(s)
- Sophia A Pacheco
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239, USA
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32
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Islam MS, Richards JP, Ojha AK. Targeting drug tolerance in mycobacteria: a perspective from mycobacterial biofilms. Expert Rev Anti Infect Ther 2013; 10:1055-66. [PMID: 23106280 DOI: 10.1586/eri.12.88] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Multidrug chemotherapy for 6-9-months is one of the primary treatments in effective control of tuberculosis, although the mechanisms underlying the persistence of its etiological agent, Mycobacterium tuberculosis, against antibiotics remain unclear. Ever-mounting evidence indicates that the survival of many environmental and pathogenic microbial species against antibiotics is influenced by their ability to grow as surface-associated multicellular communities called biofilms. In recent years, several mycobacterial species, including M. tuberculosis, have been found to form drug-tolerant biofilms in vitro through genetically controlled mechanisms. In this review, the authors discuss the relevance of the in vitro mycobacterial biofilms in understanding the antibiotic recalcitrance of tuberculosis infections.
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Affiliation(s)
- Mohammad S Islam
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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33
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Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley S, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet 2013; 45:172-9. [PMID: 23291586 PMCID: PMC3856870 DOI: 10.1038/ng.2517] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 12/06/2012] [Indexed: 11/09/2022]
Abstract
Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5× coverage), 454/Roche (13-18× coverage) and/or Illumina DNA sequencing (45-105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
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Affiliation(s)
- Philip Supply
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Michael Marceau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Sophie Mangenot
- CNRS-UMR 8030 , Evry, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope, LABGeM, Evry, France
| | - David Roche
- CNRS-UMR 8030 , Evry, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope, LABGeM, Evry, France
| | - Carine Rouanet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Varun Khanna
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Laleh Majlessi
- Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Paris, France
- INSERM U1041, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Genotyping of Pathogens and Public Health (PF8), Paris, France
| | - Julien Tap
- Institut Pasteur, Genotyping of Pathogens and Public Health (PF8), Paris, France
| | - Alexandre Pawlik
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Laurence Fiette
- Institut Pasteur, Unité d’Histopathologie Humaine et Modèles Animaux, Paris, France
- Université Versailles-Saint Quentin en Yvelines, Faculté de Médecine, DER Histologie, Versailles, France
| | - Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Michel Fabre
- Laboratoire de Biologie Clinique, HIA Percy, Clamart, France
| | - Cécile Parmentier
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Roxane Simeone
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Eva C. Boritsch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Anne-Sophie Debrie
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Eve Willery
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | | | | | - Laurence Ma
- Institut Pasteur, Genopole, Platform Genomics PF1, Paris, France
| | | | - Grégory Salvignol
- CNRS-UMR 8030 , Evry, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope, LABGeM, Evry, France
| | - Fadel Sayes
- Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Paris, France
- INSERM U1041, Paris, France
| | | | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton, Australia
| | - Valérie Barbe
- CNRS-UMR 8030 , Evry, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope, LABGeM, Evry, France
| | - Camille Locht
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Maria-Cristina Gutierrez
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019, Center for Infection and Immunity of Lille, Lille, France
- Centre National de la Recherche Scientifique (CNRS), Unite mixte de recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France
- Univ Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- Institut Pasteur, Department d’Infection et d’Epidemiologie, Paris, France
| | - Claude Leclerc
- Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Paris, France
- INSERM U1041, Paris, France
| | | | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health (PF8), Paris, France
| | - Claudine Médigue
- CNRS-UMR 8030 , Evry, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope, LABGeM, Evry, France
| | | | - Stéphane Cruveiller
- CNRS-UMR 8030 , Evry, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope, LABGeM, Evry, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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Fröls S, Dyall-Smith M, Pfeifer F. Biofilm formation by haloarchaea. Environ Microbiol 2012; 14:3159-74. [DOI: 10.1111/j.1462-2920.2012.02895.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 08/10/2012] [Accepted: 08/28/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Sabrina Fröls
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstrasse 10; 64287; Darmstadt; Germany
| | - Mike Dyall-Smith
- School of Biomedical Sciences; Charles Sturt University; Wagga Wagga; NSW; 2678; Australia
| | - Felicitas Pfeifer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstrasse 10; 64287; Darmstadt; Germany
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35
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Amábile-Cuevas CF. Antibiotic resistance: from Darwin to Lederberg to Keynes. Microb Drug Resist 2012; 19:73-87. [PMID: 23046150 DOI: 10.1089/mdr.2012.0115] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The emergence and spread of antibiotic-resistant bacteria reflects both, a gradual, completely Darwinian evolution, which mostly yields slight decreases in antibiotic susceptibility, along with phenotypes that are not precisely characterized as "resistance"; and sudden changes, from full susceptibility to full resistance, which are driven by a vast array of horizontal gene transfer mechanisms. Antibiotics select for more than just antibiotic resistance (i.e., increased virulence and enhanced gene exchange abilities); and many non-antibiotic agents or conditions select for or maintain antibiotic resistance traits as a result of a complex network of underlying and often overlapping mechanisms. Thus, the development of new antibiotics and thoughtful, integrated anti-infective strategies is needed to address the immediate and long-term threat of antibiotic resistance. Since the biology of resistance is complex, these new drugs and strategies will not come from free-market forces, or from "incentives" for pharmaceutical companies.
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36
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Alavi M, Stojadinovic A, Izadjoo M. An overview of biofilm and its detection in clinical samples. J Wound Care 2012; 21:376-83. [DOI: 10.12968/jowc.2012.21.8.376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- M.R. Alavi
- Diagnostics and Translational Research Center, Henry M. Jackson Foundation for Advancement of Military Medicine, Maryland, USA
- Combat Wound Initiative Program, Maryland, USA
| | - A. Stojadinovic
- Combat Wound Initiative Program, Maryland, USA
- Uniformed Services University of the Health Sciences, Maryland, USA
| | - M.J. Izadjoo
- Diagnostics and Translational Research Center, Henry M. Jackson Foundation for Advancement of Military Medicine, Maryland, USA
- Combat Wound Initiative Program, Maryland, USA
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37
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Bastian FO, Elzer PH, Wu X. Spiroplasma spp. biofilm formation is instrumental for their role in the pathogenesis of plant, insect and animal diseases. Exp Mol Pathol 2012; 93:116-28. [PMID: 22552100 DOI: 10.1016/j.yexmp.2012.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 03/20/2012] [Accepted: 04/11/2012] [Indexed: 01/25/2023]
Abstract
Spiroplasma spp. are important phyto and insect pathogens, and candidate causal agent/s of transmissible spongiform encephalopathies (TSE) in man and animals. These filterable wall-less bacteria are widely distributed in nature with an unspecified environmental reservoir. In this study we showed by scanning electron microscopy that spiroplasma form biofilm on an assortment of hard surfaces including mica, nickel and stainless steel. Spiroplasma were stuck to the surfaces by fibrillar threads consistent with curli fibers (an amyloid protein found in bacterial biofilms). After a lengthy time in cultures (6 weeks), spiroplasma in biofilm bound to mica disks lost their spiral shapes and formed coccoid forms interconnected by long (>2 μm) branched membranous nanotubules, therein representing direct conjugate connections between the cells. The affinity of spiroplasma biofilms for mica and nickel, and the membrane communications suggest that soil could be a reservoir for these bacteria. The persistence of clay bound spiroplasma in soil could serve as the mechanism of lateral spread of TSEs by ingestion of soil by ruminants. Spiroplasma binding to stainless steel wire supports bacterial contamination of surgical instruments following surgery on dementia patients as a mechanism of iatrogenic transmission of TSEs, especially with resistance of spiroplasma in biofilms to drying or exposure to 50% glutaraldehyde. The discovery of biofilm formation by spiroplasma addresses questions regarding environmental persistence of these organisms in nature and suggests novel mechanisms of intercellular communication and transmission.
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Affiliation(s)
- Frank O Bastian
- Department of Veterinary Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA.
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38
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Bridier A, Briandet R, Thomas V, Dubois-Brissonnet F. Resistance of bacterial biofilms to disinfectants: a review. BIOFOULING 2011; 27:1017-32. [PMID: 22011093 DOI: 10.1080/08927014.2011.626899] [Citation(s) in RCA: 533] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A biofilm can be defined as a community of microorganisms adhering to a surface and surrounded by a complex matrix of extrapolymeric substances. It is now generally accepted that the biofilm growth mode induces microbial resistance to disinfection that can lead to substantial economic and health concerns. Although the precise origin of such resistance remains unclear, different studies have shown that it is a multifactorial process involving the spatial organization of the biofilm. This review will discuss the mechanisms identified as playing a role in biofilm resistance to disinfectants, as well as novel anti-biofilm strategies that have recently been explored.
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Affiliation(s)
- A Bridier
- AgroParisTech, UMR MICALIS, F-91300 Massy, France
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39
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Cook L, Chatterjee A, Barnes A, Yarwood J, Hu WS, Dunny G. Biofilm growth alters regulation of conjugation by a bacterial pheromone. Mol Microbiol 2011; 81:1499-510. [PMID: 21843206 DOI: 10.1111/j.1365-2958.2011.07786.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conjugation is an important mode of horizontal gene transfer in bacteria, enhancing the spread of antibiotic resistance. In clinical settings, biofilms are likely locations for antibiotic resistance transfer events involving nosocomial pathogens such as Enterococcus faecalis. Here we demonstrate that growth in biofilms alters the induction of conjugation by a sex pheromone in E. faecalis. Mathematical modelling suggested that a higher plasmid copy number in biofilm cells would enhance a switch-like behaviour in the pheromone response of donor cells with a delayed, but increased response to the mating signal. Alterations in plasmid copy number, and a bimodal response to induction of conjugation in populations of plasmid-containing donor cells were both observed in biofilms, consistent with the predictions of the model. The pheromone system may have evolved such that donor cells in biofilms are only induced to transfer when they are in extremely close proximity to potential recipients in the biofilm community. These results may have important implications for development of chemotherapeutic agents to block resistance transfer and treat biofilm-related clinical infections.
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Affiliation(s)
- Laura Cook
- Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, USA
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Increased transfer of a multidrug resistance plasmid in Escherichia coli biofilms at the air-liquid interface. Appl Environ Microbiol 2011; 77:5079-88. [PMID: 21642400 DOI: 10.1128/aem.00090-11] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although biofilms represent a common bacterial lifestyle in clinically and environmentally important habitats, there is scant information on the extent of gene transfer in these spatially structured populations. The objective of this study was to gain insight into factors that affect transfer of the promiscuous multidrug resistance plasmid pB10 in Escherichia coli biofilms. Biofilms were grown in different experimental settings, and plasmid transfer was monitored using laser scanning confocal microscopy and plate counting. In closed flow cells, plasmid transfer in surface-attached submerged biofilms was negligible. In contrast, a high plasmid transfer efficiency was observed in a biofilm floating at the air-liquid interface in an open flow cell with low flow rates. A vertical flow cell and a batch culture biofilm reactor were then used to detect plasmid transfer at different depths away from the air-liquid interface. Extensive plasmid transfer occurred only in a narrow zone near that interface. The much lower transfer frequencies in the lower zones coincided with rapidly decreasing oxygen concentrations. However, when an E. coli csrA mutant was used as the recipient, a thick biofilm was obtained at all depths, and plasmid transfer occurred at similar frequencies throughout. These results and data from separate aerobic and anaerobic matings suggest that oxygen can affect IncP-1 plasmid transfer efficiency, not only directly but also indirectly, through influencing population densities and therefore colocalization of donors and recipients. In conclusion, the air-liquid interface can be a hot spot for plasmid-mediated gene transfer due to high densities of juxtaposed donor and recipient cells.
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