1
|
Wagner TM, Pöntinen AK, Fenzel CK, Engi D, Janice J, Almeida-Santos AC, Tedim AP, Freitas AR, Peixe L, van Schaik W, Johannessen M, Hegstad K. Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium. FEMS MICROBES 2024; 5:xtae009. [PMID: 38606354 PMCID: PMC11008740 DOI: 10.1093/femsmc/xtae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
Enterococcus faecium (Efm) is a versatile pathogen, responsible for multidrug-resistant infections, especially in hospitalized immunocompromised patients. Its population structure has been characterized by diverse clades (A1, A2, and B (reclassified as E. lactis (Ela)), adapted to different environments, and distinguished by their resistomes and virulomes. These features only partially explain the predominance of clade A1 strains in nosocomial infections. We investigated in vitro interaction of 50 clinical isolates (clade A1 Efm) against 75 commensal faecal isolates from healthy humans (25 clade A2 Efm and 50 Ela). Only 36% of the commensal isolates inhibited clinical isolates, while 76% of the clinical isolates inhibited commensal isolates. The most apparent overall differences in inhibition patterns were presented between clades. The inhibitory activity was mainly mediated by secreted, proteinaceous, heat-stable compounds, likely indicating an involvement of bacteriocins. A custom-made database targeting 76 Bacillota bacteriocins was used to reveal bacteriocins in the genomes. Our systematic screening of the interactions between nosocomial and commensal Efm and Ela on a large scale suggests that, in a clinical setting, nosocomial strains not only have an advantage over commensal strains due to their possession of AMR genes, virulence factors, and resilience but also inhibit the growth of commensal strains.
Collapse
Affiliation(s)
- Theresa Maria Wagner
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Carolin Kornelia Fenzel
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Daniel Engi
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Jessin Janice
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Ana C Almeida-Santos
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CiberES CB22/06/00035), 28029 Madrid, Spain
| | - Ana R Freitas
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 1H- TOXRUN – One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, 4584-116 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mona Johannessen
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| |
Collapse
|
2
|
Apostolakos I, Paramithiotis S, Mataragas M. Comparative Genomic Analysis Reveals the Functional Traits and Safety Status of Lactic Acid Bacteria Retrieved from Artisanal Cheeses and Raw Sheep Milk. Foods 2023; 12:foods12030599. [PMID: 36766127 PMCID: PMC9914385 DOI: 10.3390/foods12030599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Lactic acid bacteria (LAB) are valuable for the production of fermented dairy products. We investigated the functional traits of LAB isolated from artisanal cheeses and raw sheep milk, assessed their safety status, and explored the genetic processes underlying the fermentation of carbohydrates. Lactiplantibacillus plantarum had the largest and more functional genome compared to all other LAB, while most of its protein-encoding genes had unknown functions. A key finding of our analysis was the overall absence of acquired resistance genes (RGs), virulence genes (VGs), and prophages, denoting that all LAB isolates fulfill safety criteria and can be used as starter or adjunct cultures. In this regard, the identified mobile genetic elements found in LAB, rather than enabling the integration of RGs or VGs, they likely facilitate the uptake of genes involved in beneficial functions and in the adaptation of LAB in dairy matrices. Another important finding of our study was that bacteriocins and CAZymes were abundant in LAB though each species was associated with specific genes, which in turn had different activity spectrums and identified applications. Additionally, all isolates were able to metabolize glucose, lactose, maltose, and sucrose, but Lactiplantibacillus plantarum was strongly associated with the fermentation of rhamnose, mannose, cellobiose, and trehalose whereas Levilactobacillus brevis with the utilization of arabinose and xylose. Altogether these results suggest that to fully exploit the beneficial properties of LAB, a combination of strains as food additives may be necessary. Interestingly, biological processes involved in the metabolism of carbohydrates that are not of direct interest for the dairy industry may yield valuable metabolites or activate pathways associated with beneficial health effects. Our results provide useful information for the development of new probiotic artisanal cheeses and probiotic starter cultures.
Collapse
Affiliation(s)
- Ilias Apostolakos
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece
| | - Spiros Paramithiotis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Marios Mataragas
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece
- Correspondence:
| |
Collapse
|
3
|
Suryaletha K, Savithri AV, Nayar SA, Asokan S, Rajeswary D, Thomas S. Demystifying Bacteriocins of Human Microbiota by Genome Guided Prospects: An Impetus to Rekindle the Antimicrobial Research. Curr Protein Pept Sci 2022; 23:811-822. [PMID: 36278460 DOI: 10.2174/1389203724666221019111515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 11/07/2022]
Abstract
The human microbiome is a reservoir of potential bacteriocins that can counteract multidrug resistant bacterial pathogens. Unlike antibiotics, bacteriocins selectively inhibit a spectrum of competent bacteria and are said to safeguard gut commensals, reducing the chance of dysbiosis. Bacteriocinogenic probiotics or bacteriocins of human origin will be more pertinent in human physiological conditions for therapeutic applications to act against invading pathogens. Recent advancement in the omics approach enables the mining of diverse and novel bacteriocins by identifying biosynthetic gene clusters from the human microbial genome, pangenome or shotgun metagenome, which is a breakthrough in the discovery line of novel bacteriocins. This review summarizes the most recent trends and therapeutic potential of bacteriocins of human microbial origin, the advancement in the in silico algorithms and databases in the discovery of novel bacteriocin, and how to bridge the gap between the discovery of bacteriocin genes from big datasets and their in vitro production. Besides, the later part of the review discussed the various impediments in their clinical applications and possible solution to bring them into the frontline therapeutics to control infections, thereby meeting the challenges of global antimicrobial resistance.
Collapse
Affiliation(s)
- Karthika Suryaletha
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Akhila Velappan Savithri
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Seema A Nayar
- Department of Microbiology, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Sijo Asokan
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Divya Rajeswary
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Sabu Thomas
- Cholera & Biofilm Research Laboratory, Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| |
Collapse
|
4
|
Omi M, Matsuo Y, Araki-Sasaki K, Oba S, Yamada H, Hirota K, Takahashi K. 16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study. BMJ Open Ophthalmol 2022; 7:bmjophth-2021-000910. [PMID: 36161861 PMCID: PMC9131114 DOI: 10.1136/bmjophth-2021-000910] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Objective We conducted a feasibility study to verify the effectiveness of 16S ribosomal RNA (rRNA) gene analysis using the nanopore sequencer MinION for identifying causative bacteria in several types of ocular infections. Methods and Analysis Four cases of corneal ulcers, one case of endophthalmitis and one case of a conjunctival abscess were included in this study. DNA was extracted from corneal scraping, vitreous samples and secretions from the conjunctival abscess. We conducted 16S rRNA gene amplicon sequencing using MinION and metagenomic DNA analysis. The efficacy of bacterial identification was verified by comparing the conventional culture method with smear observations. Results 16S rRNA gene sequencing analysis with MinION identified the causative organisms promptly with high accuracy in approximately 4 hours, from ophthalmic specimens. The results of the conventional culture method and 16S rRNA gene sequencing were consistent in all cases. In four of the six cases, a greater variety of organisms was found in the 16S rRNA gene analysis than in bacterial culture. Conclusion Using our workflow, 16S rRNA gene analysis using MinION enabled rapid and accurate identification possible in various kinds of bacterial ocular infections.
Collapse
Affiliation(s)
- Masatoshi Omi
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Kansai Medical University, Hirakata, Japan
| | | | - Shimpei Oba
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Haruhiko Yamada
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Kansai Medical University, Hirakata, Japan
| | - Kanji Takahashi
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| |
Collapse
|
5
|
Mousa WK, Chehadeh F, Husband S. Recent Advances in Understanding the Structure and Function of the Human Microbiome. Front Microbiol 2022; 13:825338. [PMID: 35185849 PMCID: PMC8851206 DOI: 10.3389/fmicb.2022.825338] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
Trillions of microbes live within our bodies in a deep symbiotic relationship. Microbial populations vary across body sites, driven by differences in the environment, immunological factors, and interactions between microbial species. Major advances in genome sequencing enable a better understanding of microbiome composition. However, most of the microbial taxa and species of the human microbiome are still unknown. Without revealing the identity of these microbes as a first step, we cannot appreciate their role in human health and diseases. A shift in the microbial balance, termed dysbiosis, is linked to a broad range of diseases from simple colitis and indigestion to cancer and dementia. The last decade has witnessed an explosion in microbiome research that led to a better understanding of the microbiome structure and function. This understanding leads to potential opportunities to develop next-generation microbiome-based drugs and diagnostic biomarkers. However, our understanding is limited given the highly personalized nature of the microbiome and its complex and multidirectional interactions with the host. In this review, we discuss: (1) our current knowledge of microbiome structure and factors that shape the microbial composition, (2) recent associations between microbiome dysbiosis and diseases, and (3) opportunities of new microbiome-based therapeutics. We analyze common themes, promises, gaps, and challenges of the microbiome research.
Collapse
Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
- Department of Biology, Whitman College, Walla Walla, WA, United States
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Fadia Chehadeh
- Department of Biology, Whitman College, Walla Walla, WA, United States
| | - Shannon Husband
- Department of Biology, Whitman College, Walla Walla, WA, United States
| |
Collapse
|
6
|
Almeida-Santos AC, Novais C, Peixe L, Freitas AR. Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context. Antibiotics (Basel) 2021; 10:antibiotics10101215. [PMID: 34680796 PMCID: PMC8532689 DOI: 10.3390/antibiotics10101215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/10/2023] Open
Abstract
Enterococcus spp. are one of the most frequent producers of bacteriocins (enterocins), which provides them with an advantage to compete in their natural environment, which is the gut of humans and many animals. The enterocins’ activity against microorganisms from different phylogenetic groups has raised interest in Enterococcus spp. in different contexts throughout the last decades, especially in the food industry. Nevertheless, some species can also cause opportunistic life-threatening infections and are frequently multidrug-resistant (MDR). Vancomycin-resistant Enterococcus (VRE), in particular, are an ongoing global challenge given the lack of therapeutic options. In this scenario, bacteriocins can offer a potential solution to this persistent threat, either alone or in combination with other antimicrobials. There are a handful of studies that demonstrate the advantages and applications of bacteriocins, especially against VRE. The purpose of this review is to present a current standpoint about the dual role of Enterococcus spp., from important producers to targets needed to be controlled, and the crucial role that enterocins may have in the expansion of enterococcal populations. Classification and distribution of enterocins, the current knowledge about the bacteriocinome of clinical enterococci, and the challenges of bacteriocin use in the fight against VRE infections are particularly detailed.
Collapse
Affiliation(s)
- Ana C. Almeida-Santos
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Carla Novais
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
| | - Ana R. Freitas
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN–Toxicology Research Unit, Department of Sciences, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
| |
Collapse
|
7
|
Alternatives to Fight Vancomycin-Resistant Staphylococci and Enterococci. Antibiotics (Basel) 2021; 10:antibiotics10091116. [PMID: 34572698 PMCID: PMC8471638 DOI: 10.3390/antibiotics10091116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
Gram positive pathogens are a significant cause of healthcare-associated infections, with Staphylococci and Enterococci being the most prevalent ones. Vancomycin, a last resort glycopeptide, is used to fight these bacteria but the emergence of resistance against this drug leaves some patients with few therapeutic options. To counter this issue, new generations of antibiotics have been developed but resistance has already been reported. In this article, we review the strategies in place or in development to counter vancomycin-resistant pathogens. First, an overview of traditional antimicrobials already on the market or in the preclinical or clinical pipeline used individually or in combination is summarized. The second part focuses on the non-traditional antimicrobials, such as antimicrobial peptides, bacteriophages and nanoparticles. The conclusion is that there is hitherto no substitute equivalent to vancomycin. However, promising strategies based on drugs with multiple mechanisms of action and treatments based on bacteriophages possibly combined with conventional antibiotics are hoped to provide treatment options for vancomycin-resistant Gram-positive pathogens.
Collapse
|
8
|
Inactivation of GalU Leads to a Cell Wall-Associated Polysaccharide Defect That Reduces the Susceptibility of Enterococcus faecalis to Bacteriolytic Agents. Appl Environ Microbiol 2021; 87:AEM.02875-20. [PMID: 33483312 DOI: 10.1128/aem.02875-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Enterococcal plasmid-encoded bacteriolysin Bac41 is a selective antimicrobial system that is considered to provide a competitive advantage to Enterococcus faecalis cells that carry the Bac41-coding plasmid. The Bac41 effector consists of the secreted proteins BacL1 and BacA, which attack the cell wall of the target E. faecalis cell to induce bacteriolysis. Here, we demonstrated that galU, which encodes UTP-glucose-1-phosphate uridylyltransferase, is involved in susceptibility to the Bac41 system in E. faecalis Spontaneous mutants that developed resistance to the antimicrobial effects of BacL1 and BacA were revealed to carry a truncation deletion of the C-terminal amino acid (aa) region 288 to 298 of the translated GalU protein. This truncation resulted in the depletion of UDP-glucose, leading to a failure to utilize galactose and produce the enterococcal polysaccharide antigen (EPA), which is expressed abundantly on the cell surface of E. faecalis This cell surface composition defect that resulted from galU or EPA-specific genes caused an abnormal cell morphology, with impaired polarity during cell division and alterations of the limited localization of BacL1 Interestingly, these mutants had reduced susceptibility to beta-lactams besides Bac41, despite their increased susceptibility to other bacteriostatic antimicrobial agents and chemical detergents. These data suggest that a complex mechanism of action underlies lytic killing, as exogenous bacteriolysis induced by lytic bacteriocins or beta-lactams requires an intact cell physiology in E. faecalis IMPORTANCE Cell wall-associated polysaccharides of bacteria are involved in various physiological characteristics. Recent studies demonstrated that the cell wall-associated polysaccharide of Enterococcus faecalis is required for susceptibility to bactericidal antibiotic agents. Here, we demonstrated that a galU mutation resulted in resistance to the enterococcal lytic bacteriocin Bac41. The galU homologue is reported to be essential for the biosynthesis of species-specific cell wall-associated polysaccharides in other Firmicutes In E. faecalis, the galU mutant lost the E. faecalis-specific cell wall-associated polysaccharide EPA (enterococcal polysaccharide antigen). The mutant also displayed reduced susceptibility to antibacterial agents and an abnormal cell morphology. We demonstrated here that galU was essential for EPA biosynthesis in E. faecalis, and EPA production might underlie susceptibility to lytic bacteriocin and antibiotic agents by undefined mechanisms.
Collapse
|
9
|
Tiwari SK, Dicks LMT, Popov IV, Karaseva A, Ermakov AM, Suvorov A, Tagg JR, Weeks R, Chikindas ML. Probiotics at War Against Viruses: What Is Missing From the Picture? Front Microbiol 2020; 11:1877. [PMID: 32973697 PMCID: PMC7468459 DOI: 10.3389/fmicb.2020.01877] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/16/2020] [Indexed: 01/07/2023] Open
Abstract
Our world is now facing a multitude of novel infectious diseases. Bacterial infections are treated with antibiotics, albeit with increasing difficulty as many of the more common causes of infection have now developed broad spectrum antimicrobial resistance. However, there is now an even greater challenge from both old and new viruses capable of causing respiratory, enteric, and urogenital infections. Reports of viruses resistant to frontline therapeutic drugs are steadily increasing and there is an urgent need to develop novel antiviral agents. Although this all makes sense, it seems rather strange that relatively little attention has been given to the antiviral capabilities of probiotics. Over the years, beneficial strains of lactic acid bacteria (LAB) have been successfully used to treat gastrointestinal, oral, and vaginal infections, and some can also effect a reduction in serum cholesterol levels. Some probiotics prevent gastrointestinal dysbiosis and, by doing so, reduce the risk of developing secondary infections. Other probiotics exhibit anti-tumor and immunomodulating properties, and in some studies, antiviral activities have been reported for probiotic bacteria and/or their metabolites. Unfortunately, the mechanistic basis of the observed beneficial effects of probiotics in countering viral infections is sometimes unclear. Interestingly, in COVID-19 patients, a clear decrease has been observed in cell numbers of Lactobacillus and Bifidobacterium spp., both of which are common sources of intestinal probiotics. The present review, specifically motivated by the need to implement effective new counters to SARS-CoV-2, focusses attention on viruses capable of co-infecting humans and other animals and specifically explores the potential of probiotic bacteria and their metabolites to intervene with the process of virus infection. The goal is to help to provide a more informed background for the planning of future probiotic-based antiviral research.
Collapse
Affiliation(s)
- Santosh Kumar Tiwari
- Department of Genetics, Maharshi Dayanand University, Rohtak, India,*Correspondence: Santosh Kumar Tiwari,
| | - Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Igor V. Popov
- Center for Agro-Biotechnology, Faculty of Bioengineering and Veterinary Medicine, Don State Technical University, Rostov-on-Don, Russia
| | - Alena Karaseva
- Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Alexey M. Ermakov
- Center for Agro-Biotechnology, Faculty of Bioengineering and Veterinary Medicine, Don State Technical University, Rostov-on-Don, Russia
| | - Alexander Suvorov
- Institute of Experimental Medicine, Saint Petersburg, Russia,Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Richard Weeks
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, Brunswick, NJ, United States
| | - Michael L. Chikindas
- Center for Agro-Biotechnology, Faculty of Bioengineering and Veterinary Medicine, Don State Technical University, Rostov-on-Don, Russia,Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, Brunswick, NJ, United States
| |
Collapse
|
10
|
Melegh S, Nyul A, Kovács K, Kovács T, Ghidán Á, Dombrádi Z, Szabó J, Berta B, Lesinszki V, Pászti J, Tóth Á, Mestyán G. Dissemination of VanA-TypeEnterococcus faeciumIsolates in Hungary. Microb Drug Resist 2018; 24:1376-1390. [DOI: 10.1089/mdr.2017.0296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Szilvia Melegh
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Adrienn Nyul
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Krisztina Kovács
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | | | - Ágoston Ghidán
- Department of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Dombrádi
- Department of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | - Judit Szabó
- Department of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | | | | | - Judit Pászti
- National Public Health Institute, Budapest, Hungary
| | - Ákos Tóth
- National Public Health Institute, Budapest, Hungary
| | - Gyula Mestyán
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| |
Collapse
|
11
|
Todokoro D, Eguchi H, Suzuki T, Suzuki M, Nakayama-Imaohji H, Kuwahara T, Nomura T, Tomita H, Akiyama H. Genetic diversity and persistent colonization of Enterococcus faecalis on ocular surfaces. Jpn J Ophthalmol 2018; 62:699-705. [PMID: 30324322 DOI: 10.1007/s10384-018-0630-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/30/2018] [Indexed: 01/03/2023]
Abstract
PURPOSE Enterococcus faecalis causes severe acute endophthalmitis and often leads to poor visual outcomes. Conjunctival bacterial cultures occasionally grow atypical bacteria including E. faecalis, which can potentially contribute to the development of postoperative endophthalmitis. However, the characteristics of these ocular E. faecalis strains are unknown. This study is the first attempt to determine the population characteristics of E. faecalis clinical isolates from eye infections and ocular commensals. STUDY DESIGN Retrospective METHODS: Twenty-eight E. faecalis ocular isolates were collected from 23 patients at 3 referring hospitals. The multilocus sequence typing (MLST) data were analyzed using the eBURST program. Phenotypes of cytolysin and gelatinase, antibiotic susceptibility, and mutations of the quinolone resistance-determining regions (QRDRs) of gyrA and parC were also examined. Pulsed-field gel electrophoresis (PFGE) was performed for strains from the same patients. RESULTS PFGE revealed that 3 patients retained identical strains for 10 months to 2 and a half years. MLST identified 12 sequence types (STs), which were clustered into 3 clonal complexes (CCs) and 8 singletons, with ST179 the largest. Thirteen of the 23 isolates (56.5%) belonged to CC58, CC8, or CC2, which have previously been reported to be major CCs. Six of the 23 strains (26.0%) exhibited high-level quinolone resistance derived from mutations of the QRDRs in both gyrA and parC. CONCLUSIONS The sequence types of E. faecalis ocular isolates were divergent, with no eye-specific lineages observed. Persistent colonization of E. faecalis on the ocular surface was demonstrated in patients with chronic ocular surface diseases.
Collapse
Affiliation(s)
- Daisuke Todokoro
- Department of Ophthalmology, Gunma University Graduate School of Medicine, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
| | - Hiroshi Eguchi
- Department of Ophthalmology, Kindai University, Osaka, Japan
| | - Takashi Suzuki
- Department of Ophthalmology, School of Medicine, Toho University, Tokyo, Japan
| | - Motoo Suzuki
- Department of Molecular Microbiology, Faculty of Medicine, Kagawa University, Kita-gun, Japan
| | | | - Tomomi Kuwahara
- Department of Molecular Microbiology, Faculty of Medicine, Kagawa University, Kita-gun, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hideo Akiyama
- Department of Ophthalmology, Gunma University Graduate School of Medicine, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| |
Collapse
|
12
|
Enterococcus faecium produces membrane vesicles containing virulence factors and antimicrobial resistance related proteins. J Proteomics 2018; 187:28-38. [DOI: 10.1016/j.jprot.2018.05.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/25/2018] [Accepted: 05/29/2018] [Indexed: 11/19/2022]
|
13
|
Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A. Gut microbiota as a source of novel antimicrobials. Gut Microbes 2018; 10:1-21. [PMID: 29584555 PMCID: PMC6363078 DOI: 10.1080/19490976.2018.1455790] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 02/08/2023] Open
Abstract
Bacteria, Archaea, Eukarya and viruses coexist in the human gut, and this coexistence is functionally balanced by symbiotic or antagonistic relationships. Antagonism is often characterized by the production of antimicrobials against other organisms occupying the same environmental niche. Indeed, close co-evolution in the gut has led to the development of specialized antimicrobials, which is attracting increased attention as these may serve as novel alternatives to antibiotics and thereby help to address the global problem of antimicrobial resistance. The gastrointestinal (GI) tract is especially suitable for finding novel antimicrobials due to the vast array of microbes that inhabit it, and a considerable number of antimicrobial producers of both wide and narrow spectrum have been described. In this review, we summarize some of the antimicrobial compounds that are produced by bacteria isolated from the gut environment, with a special focus on bacteriocins. We also evaluate the potential therapeutic application of these compounds to maintain homeostasis in the gut and the biocontrol of pathogenic bacteria.
Collapse
Affiliation(s)
- Enriqueta Garcia-Gutierrez
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
- Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Melinda J. Mayer
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
| | - Paul D. Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
- APC Microbiome, Ireland
| | - Arjan Narbad
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
| |
Collapse
|
14
|
Todokoro D, Suzuki T, Kobayakawa S, Tomita H, Ohashi Y, Akiyama H. Postoperative Enterococcus faecalis endophthalmitis: virulence factors leading to poor visual outcome. Jpn J Ophthalmol 2017; 61:408-414. [DOI: 10.1007/s10384-017-0527-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 06/15/2017] [Indexed: 12/30/2022]
|
15
|
Abstract
Enterococci belong to the group of lactic acid bacteria (LAB), and inhabit the gastrointestinal tracts of a wide variety of animals from insects and to human, and the commensal organism in humans and animals. The commensal/probiotic role of enterococci has evolved through thousands of years in mutual coexistence. Enterococcus have many favorable traits that have been appreciated in food fermentation and preservation, and many serve as probiotics to promote health. While lactobacillus have been shown to confer numerous benefits on and often regarded as health bringing organisms, enterococci have become more recognized as emerging human pathogens in recent years. Mac Callum and Hastings characterized an organism, now known to be Enterococcal faecalis, which was isolated from a lethal case of endocarditis on 1899. The report was the first detailed description of its pathogenic capabilities. Over the past few decades, multi-drug resistance enterococci have become as important health-care associated pathogen, and leading causes of drug resistance infection. The modern life style including the broad use of antibiotics in medical practice and animal husbandry have selected for the convergence of potential virulence factors to the specific enterococcus species such as E. faecium and E. faecalis. The development of modern medical care of intensive and invasive medical therapies and treatments for human disease, and existence of severe compromised patients in hospitals has contributed to the increased prevalence of these opportunistic organisms. The virulence factors converged in E. faecalis and E. faecium which have been isolated in nosocomial infections, include antibiotic resistance, extracellular proteins (toxins), extrachromosome and mobile genetic elements, cell wall components, biofilm formation, adherence factors, and colonization factor such as bacteriocin, etc. In these potential virulence factors, I presented characteristics of enterococcal conjugative plasmid, cytolysin, collagen binding protein of adhesion, bacteriocins, and drug resistances. I made reference to our original reports, and review books for this review. The review books are "Enterococci: from Commensals to Leading Causes of Drug Resistant Infection, NCBI Bookshelf. A service of the National Library of Medicine, National Institute of Health. Ed. by Michael S Gilmore, Don B Clewell, Yasuyoshi Ike, and Nathan Shankar", and "The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance, Gilmore M., Clewell D., Courvadin P., Dunny G., Murray B., Rice L., (ed) 2002. ASM Press".
Collapse
Affiliation(s)
- Yasuyoshi Ike
- Professor Emeritus, Gunma University Graduate School of Medicine
- Representative Director, Association for Education in Bacterial Drug Resistance
| |
Collapse
|
16
|
Kurushima J, Ike Y, Tomita H. Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains. J Bacteriol 2016; 198:2379-90. [PMID: 27353651 PMCID: PMC4984558 DOI: 10.1128/jb.00348-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen Enterococcus faecalis Its genetic determinant consists of bacL1 (effector), bacL2 (regulator), bacA (effector), and bacI (immunity). The secreted effectors BacL1 and BacA coordinate to induce the lytic cell death of E. faecalis Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer, E. faecalis, against the action of BacL1 and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of E. faecalis screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the E. faecalis strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from bacA Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among E. faecalis strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage. IMPORTANCE Bacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among E. faecalis clinical strains and the Bac41 subtypes with partial diversity. The Bac41-like bacteriocins were found to be classified into type I, type IIa, and type IIb by variation of the cognate immunity factors. The antibacterial activity of the respective effectors was specifically inhibited by the immunity factor from the same type of Bac41 but not the other types. This specificity of effector-immunity pairs suggests that bacteriocin genes might have evolved to change the immunity specificity to acquire an advantage in interbacterial competition.
Collapse
Affiliation(s)
- Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Yasuyoshi Ike
- Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| |
Collapse
|
17
|
Liu H, Zhang L, Yi H, Han X, Gao W, Chi C, Song W, Li H, Liu C. A novel enterocin T1 with anti-Pseudomonas activity produced by Enterococcus faecium T1 from Chinese Tibet cheese. World J Microbiol Biotechnol 2016; 32:21. [PMID: 26745981 DOI: 10.1007/s11274-015-1973-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/28/2015] [Indexed: 11/26/2022]
Abstract
An enterocin-producing Enterococcus faecium T1 was isolated from Chinese Tibet cheese. The enterocin was purified by SP-Sepharose and reversed phase HPLC. It was identified as unique from other reported bacteriocins based on molecular weight (4629 Da) and amino acid compositions; therefore it was subsequently named enterocin T1. Enterocin T1 was stable at 80-100 °C and over a wide pH range, pH 3.0-10.0. Protease sensitivity was observed to trypsin, pepsin, papain, proteinase K, and pronase E. Importantly, enterocin T1 was observed to inhibit the growth of numerous Gram-negative and Gram-positive bacteria including Pseudomonas putida, Pseudomonas aeruginosa, Pseudomonas fluorescens, Escherichia coli, Salmonella typhimurium, Shigella flexneri, Shigella sonnei, Staphylococcus aureus, Listeria monocytogenes. Take together, these results suggest that enterocin T1 is a novel bacteriocin with the potential to be used as a bio-preservative to control Pseudomonas spp. in food.
Collapse
Affiliation(s)
- Hui Liu
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Lanwei Zhang
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China.
| | - Huaxi Yi
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China.
| | - Xue Han
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Wei Gao
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Chunliang Chi
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Wei Song
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Haiying Li
- College of Life Sciences, Heilongjiang University, Harbin, 150070, Heilongjiang, China
| | - Chunguang Liu
- College of Life Sciences, Heilongjiang University, Harbin, 150070, Heilongjiang, China
| |
Collapse
|
18
|
Mikalsen T, Pedersen T, Willems R, Coque TM, Werner G, Sadowy E, van Schaik W, Jensen LB, Sundsfjord A, Hegstad K. Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis. BMC Genomics 2015; 16:282. [PMID: 25885771 PMCID: PMC4438569 DOI: 10.1186/s12864-015-1407-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/27/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST)17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses. RESULTS The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep 17/pRUM , rep 2/pRE25 , rep 14/EFNP1 and rep 20/pLG1 dominating in E. faecium and rep 9/pCF10 , rep 2/pRE25 and rep 7 in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. CONCLUSIONS The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST.
Collapse
Affiliation(s)
- Theresa Mikalsen
- Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| | - Rob Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. .,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany.
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, ul, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Lars Bogø Jensen
- Division of Food Microbiologyt, National Food Institute, Danish Technical University, Copenhagen V, Denmark.
| | - Arnfinn Sundsfjord
- Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. .,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| | - Kristin Hegstad
- Research group for Host-microbe Interactions, Department of Medical Biology, Faculty of Health Science, UiT - The Arctic University of Norway, Tromsø, Norway. .,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| |
Collapse
|
19
|
Bacteriocin protein BacL1 of Enterococcus faecalis targets cell division loci and specifically recognizes L-Ala2-cross-bridged peptidoglycan. J Bacteriol 2014; 197:286-95. [PMID: 25368300 DOI: 10.1128/jb.02203-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacteriocin 41 (Bac41) is produced from clinical isolates of Enterococcus faecalis and consists of two extracellular proteins, BacL1 and BacA. We previously reported that BacL1 protein (595 amino acids, 64.5 kDa) is a bacteriolytic peptidoglycan D-isoglutamyl-L-lysine endopeptidase that induces cell lysis of E. faecalis when an accessory factor, BacA, is copresent. However, the target of BacL1 remains unknown. In this study, we investigated the targeting specificity of BacL1. Fluorescence microscopy analysis using fluorescent dye-conjugated recombinant protein demonstrated that BacL1 specifically localized at the cell division-associated site, including the equatorial ring, division septum, and nascent cell wall, on the cell surface of target E. faecalis cells. This specific targeting was dependent on the triple repeat of the SH3 domain located in the region from amino acid 329 to 590 of BacL1. Repression of cell growth due to the stationary state of the growth phase or to treatment with bacteriostatic antibiotics rescued bacteria from the bacteriolytic activity of BacL1 and BacA. The static growth state also abolished the binding and targeting of BacL1 to the cell division-associated site. Furthermore, the targeting of BacL1 was detectable among Gram-positive bacteria with an L-Ala-L-Ala-cross-bridging peptidoglycan, including E. faecalis, Streptococcus pyogenes, or Streptococcus pneumoniae, but not among bacteria with alternate peptidoglycan structures, such as Enterococcus faecium, Enterococcus hirae, Staphylococcus aureus, or Listeria monocytogenes. These data suggest that BacL1 specifically targets the L-Ala-L-Ala-cross-bridged peptidoglycan and potentially lyses the E. faecalis cells during cell division.
Collapse
|
20
|
Kurushima J, Hayashi I, Sugai M, Tomita H. Bacteriocin protein BacL1 of Enterococcus faecalis is a peptidoglycan D-isoglutamyl-L-lysine endopeptidase. J Biol Chem 2013; 288:36915-25. [PMID: 24235140 DOI: 10.1074/jbc.m113.506618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enterococcus faecalis strains are commensal bacteria in humans and other animals, and they are also the causative agent of opportunistic infectious diseases. Bacteriocin 41 (Bac41) is produced by certain E. faecalis clinical isolates, and it is active against other E. faecalis strains. Our genetic analyses demonstrated that the extracellular products of the bacL1 and bacA genes, which are encoded in the Bac41 operon, coordinately express the bacteriocin activity against E. faecalis. In this study, we investigated the molecular functions of the BacL1 and BacA proteins. Immunoblotting and N-terminal amino acid sequence analysis revealed that BacL1 and BacA are secreted without any processing. The coincidental treatment with the recombinant BacL1 and BacA showed complete bacteriocin activity against E. faecalis, but neither BacL1 nor BacA protein alone showed the bacteriocin activity. Interestingly, BacL1 alone demonstrated substantial degrading activity against the cell wall fraction of E. faecalis in the absence of BacA. Furthermore, MALDI-TOF MS analysis revealed that BacL1 has a peptidoglycan D-isoglutamyl-L-lysine endopeptidase activity via a NlpC/P60 homology domain. These results collectively suggest that BacL1 serves as a peptidoglycan hydrolase and, when BacA is present, results in the lysis of viable E. faecalis cells.
Collapse
|
21
|
Cui Y, Zhang C, Wang Y, Shi J, Zhang L, Ding Z, Qu X, Cui H. Class IIa bacteriocins: diversity and new developments. Int J Mol Sci 2012; 13:16668-707. [PMID: 23222636 PMCID: PMC3546714 DOI: 10.3390/ijms131216668] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/10/2012] [Accepted: 11/12/2012] [Indexed: 12/02/2022] Open
Abstract
Class IIa bacteriocins are heat-stable, unmodified peptides with a conserved amino acids sequence YGNGV on their N-terminal domains, and have received much attention due to their generally recognized as safe (GRAS) status, their high biological activity, and their excellent heat stability. They are promising and attractive agents that could function as biopreservatives in the food industry. This review summarizes the new developments in the area of class IIa bacteriocins and aims to provide uptodate information that can be used in designing future research.
Collapse
Affiliation(s)
- Yanhua Cui
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China; E-Mails: (Y.C.); (C.Z.); (Z.D.)
| | - Chao Zhang
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China; E-Mails: (Y.C.); (C.Z.); (Z.D.)
| | - Yunfeng Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; E-Mail:
| | - John Shi
- Guelph Food Research Center, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada; E-Mail:
| | - Lanwei Zhang
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China; E-Mails: (Y.C.); (C.Z.); (Z.D.)
| | - Zhongqing Ding
- School of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China; E-Mails: (Y.C.); (C.Z.); (Z.D.)
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010, China; E-Mail:
| | - Hongyu Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; E-Mail:
| |
Collapse
|
22
|
Devi SM, Halami PM. Detection of mobile genetic elements in pediocin PA-1 like producing lactic acid bacteria. J Basic Microbiol 2012; 53:555-61. [DOI: 10.1002/jobm.201200079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 04/21/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Sundru Manjulata Devi
- Food Microbiology Department; CSIR-Central Food Technological Research Institute; Mysore; 570020; India
| | - Prakash M. Halami
- Food Microbiology Department; CSIR-Central Food Technological Research Institute; Mysore; 570020; India
| |
Collapse
|
23
|
Genetic organization and mode of action of a novel bacteriocin, bacteriocin 51: determinant of VanA-type vancomycin-resistant Enterococcus faecium. Antimicrob Agents Chemother 2011; 55:4352-60. [PMID: 21709077 DOI: 10.1128/aac.01274-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriocin 51 (Bac 51) is encoded on the mobile plasmid pHY (6,037 bp), which was isolated from vancomycin-resistant Enterococcus faecium VRE38. Bacteriocin 51 is active against E. faecium, E. hirae, and E. durans. Sequence analysis of pHY showed that it encodes nine open reading frames (ORFs) from ORF1 to ORF9 (in that order). Genetic analysis suggested that ORF1 and ORF2, which were designated bacA and bacB, respectively, are the bacteriocin and immunity genes. bacA encodes a 144-amino-acid protein. The deduced BacA protein has a typical signal sequence at its amino terminus, and a potential signal peptidase-processing site corresponding to the V-E-A sequence is located between the 37th and 39th amino acids. The predicted mature BacA protein consists of 105 amino acids. A potential promoter sequence was identified upstream of the start codon. bacB encodes a 55-amino-acid protein. No obvious promoter or terminator sequence was identified between bacA and bacB. Northern blot analysis of bacA and bacB with a bacA RNA probe produced a transcript of approximately 700 nucleotides, which corresponded to the combined nucleotide sizes of bacA and bacB, indicating that transcription was initiated from the promoter upstream of bacA, continued through bacB, and was terminated at the terminator downstream of bacB. The transcription start site was determined to be the T nucleotide located 6 nucleotides downstream from the -10 promoter sequence. These results indicate that bacA and bacB constitute an operon and that bacA is the bacteriocin structural gene while bacB is the immunity gene. The purified C-terminally His tagged BacA protein of Bac 51 showed bacteriostatic activity against the indicator strain. The purified C-terminally His tagged BacA protein of Bac 32 (whose mature BacA protein has 54 amino acids) and the culture filtrates of the Bac 31- and Bac 43-producing E. faecalis strain FA2-2 showed bactericidal activity. Bac 31 and Bac 43 are pore-forming bacteriocins, unlike the newly characterized bacteriocin Bac 51.
Collapse
|
24
|
Hegstad K, Mikalsen T, Coque TM, Werner G, Sundsfjord A. Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium. Clin Microbiol Infect 2011; 16:541-54. [PMID: 20569265 DOI: 10.1111/j.1469-0691.2010.03226.x] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mobile genetic elements (MGEs) including plasmids and transposons are pivotal in the dissemination and persistence of antimicrobial resistance in Enterococcus faecalis and Enterococcus faecium. Enterococcal MGEs have also been shown to be able to transfer resistance determinants to more pathogenic bacteria such as Staphylococcus aureus. Despite their importance, we have a limited knowledge about the prevalence, distribution and genetic content of specific MGEs in enterococcal populations. Molecular epidemiological studies of enterococcal MGEs have been hampered by the lack of standardized molecular typing methods and relevant genome information. This review focuses on recent developments in the detection of MGEs and their contribution to the spread of antimicrobial resistance in clinically relevant enterococci.
Collapse
Affiliation(s)
- K Hegstad
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North-Norway.
| | | | | | | | | |
Collapse
|
25
|
Ortolani MBT, Moraes PM, Perin LM, Viçosa GN, Carvalho KG, Silva Júnior A, Nero LA. Molecular identification of naturally occurring bacteriocinogenic and bacteriocinogenic-like lactic acid bacteria in raw milk and soft cheese. J Dairy Sci 2010; 93:2880-6. [PMID: 20630205 DOI: 10.3168/jds.2009-3000] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/28/2010] [Indexed: 11/19/2022]
Abstract
Lactic acid bacteria (LAB) are currently used by food industries because of their ability to produce metabolites with antimicrobial activity against gram-positive pathogens and spoilage microorganisms. The objectives of this study were to identify naturally occurring bacteriocinogenic or bacteriocinogenic-like LAB in raw milk and soft cheese and to detect the presence of nisin-coding genes in cultures identified as Lactococcus lactis. Lactic acid bacteria cultures were isolated from 389 raw milk and soft cheese samples and were later characterized for the production of antimicrobial substances against Listeria monocytogenes. Of these, 58 (14.9%) LAB cultures were identified as antagonistic; the nature of this antagonistic activity was then characterized via enzymatic tests to confirm the proteinaceous nature of the antimicrobial substances. In addition, 20 of these antagonistic cultures were selected and submitted to genetic sequencing; they were identified as Lactobacillus plantarum (n=2) and Lactococcus lactis ssp. lactis (n=18). Nisin genes were identified by polymerase chain reaction in 7 of these cultures. The identified bacteriocinogenic and bacteriocinogenic-like cultures were highly variable concerning the production and activity of antimicrobial substances, even when they were genetically similar. The obtained results indicated the need for molecular and phenotypic methodologies to properly characterize bacteriocinogenic LAB, as well as the potential use of these cultures as tools to provide food safety.
Collapse
Affiliation(s)
- M B T Ortolani
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | | | | | | | | |
Collapse
|
26
|
Tomita H. [Highly conjugative plasmids in enterococci]. Nihon Saikingaku Zasshi 2009; 64:343-355. [PMID: 19721337 DOI: 10.3412/jsb.64.343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| |
Collapse
|
27
|
Criado R, Gutiérrez J, Budin-Verneuil A, Hernández PE, Hartke A, Cintas LM, Auffray Y, Benachour A. Molecular analysis of the replication region of the pCIZ2 plasmid from the multiple bacteriocin producer strain Enterococcus faecium L50. Plasmid 2008; 60:181-9. [PMID: 18692522 DOI: 10.1016/j.plasmid.2008.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 07/08/2008] [Accepted: 07/15/2008] [Indexed: 11/25/2022]
Abstract
The sequence analysis of the 7383 bp plasmid pCIZ2 from Enterococcus faecium L50 enabled the identification of a DNA region involved in its replication. The structural organization of the pCIZ2 replication region is highly similar to those of well-known theta-replicating plasmids. It contains an untranslated region, the putative replication origin (ori), constituted by two sets of direct repeats of 12 and 22 bp (iterons), and followed by three open-reading frames (orf8 to orf10). orf8 encodes the replication initiation protein (RepE). The transcriptional start site of the replication locus was identified 13 nucleotides upstream of the repE start codon. A two-dimensional agarose gel electrophoresis analysis revealed pCIZ2 intermediates profile typical of the theta-type replication mechanism. Subcloning of different DNA fragments of the pCIZ2 replication region in Escherichia coli and, subsequently, in the plasmidless E. faecium L50/14-2 allowed the determination of the minimal replicon on a 1.2kb DNA fragment containing only the overall ori and repE which also act in trans. The involvement of orf9 in the plasmid copy number and in the plasmid stability was investigated. The pCIZ2 recombinant plasmids constitute narrow-host range shuttle cloning vectors (E. coli-E. faecium) that could be very useful for enterococcal genes studies, allowing an easy identification due to their histochemical recognition.
Collapse
Affiliation(s)
- R Criado
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040-Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
28
|
A "retrocidal" plasmid in Enterococcus faecalis: passage and protection. Plasmid 2008; 59:217-30. [PMID: 18295881 DOI: 10.1016/j.plasmid.2008.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 12/19/2007] [Accepted: 01/04/2008] [Indexed: 11/20/2022]
Abstract
Enterococcus faecalis MC4 harbors a 130 kb conjugative, pheromone (cCF10)-responding plasmid, pAMS1, conferring chloramphenicol, streptomycin and tetracycline resistances. A plasmid-borne class IIa bacteriocin (MC4-1) determinant and cognate immunity gene were present, but not expressed in MC4. However, pAMS1 transfer to E. faecalis JH2-2 (but not to the non-isogenic OG1SS) generated the surprising ability to express bacteriocin activity against the plasmid donor, MC4. The bacteriocin target spectrum includes E. faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae, and Listeria monocytogenes. Those donors unable to express bacteriocin or immunity could protect themselves from the "retrocidal" behavior of transconjugants by a switch to bacteriocin resistance at a frequency of approximately 10(-3). Reversion to sensitivity occurred at a relatively high frequency, suggestive of involvement of a phase variation event. These observations concerning a conjugative plasmid with novel "retrocidal" properties, coupled with a defense mechanism independent of plasmid-borne immunity functions, may relate to phenomena exploiting regulatory features with broader ecological and evolutionary implications.
Collapse
|
29
|
Franz CMAP, van Belkum MJ, Holzapfel WH, Abriouel H, Gálvez A. Diversity of enterococcal bacteriocins and their grouping in a new classification scheme. FEMS Microbiol Rev 2007; 31:293-310. [PMID: 17298586 DOI: 10.1111/j.1574-6976.2007.00064.x] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Enterococci are lactic acid bacteria of importance in food, public health and medical microbiology. Many strains produce bacteriocins, some of which have been well characterized. This review describes the structural and genetic characteristics of enterocins, the bacteriocins produced by enterococci. Some of these can be grouped with typical bacteriocins produced by lactic acid bacteria according to traditional classification, whereas others are atypical and structurally distinct from the general classes of bacteriocins. These atypical enterocins recently played an important role in and prompted reclassification of the class II bacteriocins into a new scheme. In this review, a more simplified classification scheme for enterocins based on amino acid sequence homologies is proposed. Enterocins are of interest for their diversity and potential for use as food biopreservatives. The emergence of multiple antibiotic-resistant enterococci among agents of nosocomial disease and the presence of virulence factors among food isolates requires a careful safety evaluation of isolates intended for potential biotechnical use. Nevertheless, enterococcal bacteriocins produced by heterologous hosts or added as cell-free preparations may still be attractive for application in food preservation.
Collapse
Affiliation(s)
- Charles M A P Franz
- Federal Research Centre for Nutrition and Food, Institute for Hygiene and Toxicology, Karlsruhe, Germany
| | | | | | | | | |
Collapse
|