1
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Schwartzman JA, Lebreton F, Salamzade R, Shea T, Martin MJ, Schaufler K, Urhan A, Abeel T, Camargo ILBC, Sgardioli BF, Prichula J, Guedes Frazzon AP, Giribet G, Van Tyne D, Treinish G, Innis CJ, Wagenaar JA, Whipple RM, Manson AL, Earl AM, Gilmore MS. Global diversity of enterococci and description of 18 previously unknown species. Proc Natl Acad Sci U S A 2024; 121:e2310852121. [PMID: 38416678 DOI: 10.1073/pnas.2310852121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/06/2023] [Indexed: 03/01/2024] Open
Abstract
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.
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Affiliation(s)
- Julia A Schwartzman
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, University of Southern California, Los Angeles, CA 90089
| | - Francois Lebreton
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Rauf Salamzade
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Melissa J Martin
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Katharina Schaufler
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- University of Greifswald, Institute of Pharmacy, Greifswald 17489, Germany
- Kiel University and University Medical Center Schleswig-Holstein, Institute of Infection Medicine, Kiel 24105, Germany
| | - Aysun Urhan
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Thomas Abeel
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Ilana L B C Camargo
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Bruna F Sgardioli
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Janira Prichula
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Federal University of Health Sciences of Porto Alegre, Porto Alegre - RS 90050-170, Brazil
| | - Ana Paula Guedes Frazzon
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre - RS, 90010-150, Brazil
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Daria Van Tyne
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA 15213
| | | | - Charles J Innis
- New England Aquarium, Animal Health Department and Anderson Cabot Center for Ocean Life, Boston, MA 02110
| | - Jaap A Wagenaar
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Ryan M Whipple
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Michael S Gilmore
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
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2
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Li G, Walker MJ, De Oliveira DMP. Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms 2022; 11:microorganisms11010024. [PMID: 36677316 PMCID: PMC9866002 DOI: 10.3390/microorganisms11010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.
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3
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Gooch HCC, Kiu R, Rudder S, Baker DJ, Hall LJ, Maxwell A. Enterococcus innesii sp. nov., isolated from the wax moth Galleria mellonella. Int J Syst Evol Microbiol 2021; 71:005168. [PMID: 34919037 PMCID: PMC8744253 DOI: 10.1099/ijsem.0.005168] [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] [Indexed: 01/05/2023] Open
Abstract
Four bacterial strains were isolated from two different colony sources of the wax moth Galleria mellonella. They were characterized by a polyphasic approach including 16S rRNA gene sequence analysis, core-genome analysis, average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), determination of G+C content, screening of antibiotic resistance genes, and various phenotypic analyses. Initial analysis of 16S rRNA gene sequence identities indicated that strain GAL7T was potentially very closely related to Enterococcus casseliflavus and Enterococcus gallinarum, having 99.5-99.9 % sequence similarity. However, further analysis of whole genome sequences revealed a genome size of 3.69 Mb, DNA G+C content of 42.35 mol%, and low dDDH and ANI values between the genomes of strain GAL7T and closest phylogenetic relative E. casseliflavus NBRC 100478T of 59.0 and 94.5 %, respectively, indicating identification of a putative new Enterococcus species. In addition, all novel strains encoded the atypical vancomycin-resistance gene vanC-4. Results of phylogenomic, physiological and phenotypic characterization confirmed that strain GAL7T represented a novel species within the genus Enterococcus, for which the name Enterococcus innesii sp. nov. is proposed. The type strain is GAL7T (=DSM 112306T=NCTC 14608T).
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Affiliation(s)
- Harriet C. C. Gooch
- Dept. Biochemisty & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Raymond Kiu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - David J. Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK,School of Life Sciences, ZIEL – Institute for Food &Health, Technical University of Munich, Freising, 85354, Germany,*Correspondence: Lindsay J. Hall,
| | - Anthony Maxwell
- Dept. Biochemisty & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK,*Correspondence: Anthony Maxwell,
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4
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Okumura N, Watanabe T, Teranishi S, Suzuki D, Hashimoto T, Takahashi K, Hara T. Successful treatment of aortic valve endocarditis caused by Enterococcus casseliflavus: a case report. BMC Infect Dis 2021; 21:447. [PMID: 34006246 PMCID: PMC8130351 DOI: 10.1186/s12879-021-06160-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 05/10/2021] [Indexed: 12/04/2022] Open
Abstract
Background Enterococcus casseliflavus is rarely isolated from human specimens. To the best of our knowledge, there are no reports on its detailed treatment course and prognosis. Here, we present the first known case of E. casseliflavus endocarditis with a detailed treatment course. Case presentation An 86-year-old Japanese woman was transferred to the emergency department with dyspnoea, wheezing, and lumbago. Her medical history included hypertension, chronic kidney disease, idiopathic interstitial pneumonia, and rectal carcinoma. Physical examination revealed expiratory wheezes and a diastolic murmur (Levine 2/6) at the 4th right sternal border. Chest radiography revealed bilateral interstitial opacities and slight cardiac dilatation. Transthoracic echocardiography demonstrated the presence of mobile vegetation with perforation, prolapse, and regurgitation of the aortic valve. With a suspicion of infective endocarditis, we started administering intravenous ampicillin/sulbactam. Thereafter, blood cultures identified E. casseliflavus through matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The antimicrobial treatment was then switched to ampicillin plus gentamicin. The patient underwent aortic valve replacement on the thirteenth hospital day. She was administered intravenous ampicillin and gentamicin for 6 weeks. The patient was discharged 8 weeks after admission. Conclusions Our case demonstrated that E. casseliflavus could cause infective endocarditis, which can be successfully treated with a 6-week regimen of ampicillin and gentamicin in combination with proper surgical treatment.
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Affiliation(s)
- Nobumasa Okumura
- Department of Respiratory Medicine, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan.
| | - Takashi Watanabe
- Department of Cardiology, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan
| | - Satoshi Teranishi
- Emergency Department, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan
| | - Daisuke Suzuki
- Department of Infectious Diseases, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan
| | - Takahiko Hashimoto
- Department of Respiratory Medicine, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan
| | - Kosuke Takahashi
- Department of Respiratory Medicine, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan
| | - Toru Hara
- Department of Respiratory Medicine, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan.,Department of Infectious Diseases, Anjo Kosei Hospital, Anjo-cho Higashi-Hirokute 28, Anjo City, Aichi Prefecture, Japan
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5
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Processing Wastewaters from Spanish-Style cv. Chalkidiki Green Olives: A Potential Source of Enterococcus Casseliflavus and Hydroxytyrosol. Microorganisms 2020; 8:microorganisms8091274. [PMID: 32825632 PMCID: PMC7564576 DOI: 10.3390/microorganisms8091274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to examine the isolation of indigenous lactic acid bacteria (LAB) with functional properties from Spanish-style cv. Chalkidiki green olive processing wastewaters (GOW). Predominant indigenous LAB could serve as bioaugmentation agents/starter culture for table olives production and protected designation of origin specification. Spontaneous fermentation of fresh GOW over different temperatures (15 °C to 50 °C) and pH values (3.5 to 11.5) for 30 d enabled the isolation/molecular identification of the lactic acid bacterium Enterococcus casseliflavus and the plant-associated bacterium Bacillus amyloliquefaciens subsp. plantarum. E. casseliflavus was found to reduce chemical oxygen demand by 72%. Its resistance to extreme pH values, salinity, and temperature was successfully modeled and the minimum inhibitory concentration of oleuropein against the bacterial growth was determined (0.9 g/L). Furthermore, hydroxytyrosol content was doubled (up to 553 mg/L) after GOW spontaneous fermentation under acidic conditions at 15 °C to 30 °C for 120 d, creating an additional source of input. These results highlight the significance and potential of E. casseliflavus in Spanish-style cv. Chalkidiki green olive processing.
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6
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Graham K, Stack H, Rea R. Safety, beneficial and technological properties of enterococci for use in functional food applications - a review. Crit Rev Food Sci Nutr 2020; 60:3836-3861. [PMID: 31924117 DOI: 10.1080/10408398.2019.1709800] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enterococci are ubiquitous lactic acid bacteria (LAB) that predominantly reside in the gastrointestinal tract of humans and animals but are also widespread in food and the environment due to their robust nature. Enterococci have the paradoxical position of providing several benefits of technological interest in food fermentations but are also considered as opportunistic pathogens capable of causing infection in immunocompromised patients. Several species of the genus have been correlated with disease development in humans such as bacteremia, urinary tract infections, and endocarditis. The pathogenesis of enterococci has been attributed to the increasing incidence of antibiotic resistance and the possession of virulence determinants. On the contrary, enterococci have led to improvements in the aroma, texture, and flavor of fermented dairy products, while their beneficial use as probiotic and protective cultures has also been documented. Furthermore, they have emerged as important candidates for the generation of bioactive peptides, particularly from milk, which provide new opportunities for the development of functional foods and nutraceuticals for human nutrition and health. The detection of pathogenic traits among some species is compromising their use in food applications and subsequently, the genus neither has Generally Regarded as Safe (GRAS) status nor has it been included in the Qualified Presumption of Safety (QPS) list. Nevertheless, the use of certain enterococcal strains in food has been permitted on the basis of a case-by-case assessment. Promisingly, enterococcal virulence factors appear strain specific and food isolates harbor fewer determinants than clinical isolates, while they also remain largely susceptible to clinically relevant antibiotics and thus, have a lower potential for pathogenicity. Ideally, strains considered for use in foods should not possess any virulence determinants and should be susceptible to clinically relevant antibiotics. Implementation of an appropriate risk/benefit analysis, establishment of a strain's innocuity, and consideration for relevant guidelines, legislation, and regulatory aspects surrounding functional food development, may help industry, health-staff and consumers accept enterococci, like other LAB, as important candidates for useful and beneficial applications in food biotechnology.
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Affiliation(s)
- Ken Graham
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Helena Stack
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Rosemary Rea
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
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7
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Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization's 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and outcomes are often poor. Whole-genome sequencing is providing important new insights into VREfm evolution, drug resistance and hospital adaptation, and is increasingly being used to track VREfm transmission within hospitals to detect outbreaks and inform infection control practices. This mini-review provides an overview of recent data on the use of genomics to understand and respond to the global problem of VREfm.
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Affiliation(s)
- Claire Gorrie
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Charlie Higgs
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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8
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Abstract
The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.
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Affiliation(s)
- Mónica García-Solache
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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9
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Ahmed MO, Baptiste KE. Vancomycin-Resistant Enterococci: A Review of Antimicrobial Resistance Mechanisms and Perspectives of Human and Animal Health. Microb Drug Resist 2017; 24:590-606. [PMID: 29058560 DOI: 10.1089/mdr.2017.0147] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistant infections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including "last resort antibiotics" ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.
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Affiliation(s)
- Mohamed O Ahmed
- 1 Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Tripoli , Tripoli, Libya
| | - Keith E Baptiste
- 2 Department of Veterinary Medicine, Danish Medicines Agency , Copenhagen South, Denmark
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10
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Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Klare I, Witte W, Wendt C, Werner G. [Vancomycin-resistant enterococci (VRE). Recent results and trends in development of antibiotic resistance]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2013; 55:1387-400. [PMID: 23114437 DOI: 10.1007/s00103-012-1564-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enterococci (mainly E. faecalis, E. faecium) are important nosocomial pathogens predominantly affecting older and/or immunocompromised patients. The bacteria possess a broad spectrum of intrinsic and acquired antibiotic resistance properties. Among these, the transferrable glycopeptide resistance of the vanA and vanB genotypes in vancomycin-resistant enterococci (VRE; reservoir: E. faecium) as well as resistance to last resort antibiotics (e.g. linezolid and tigecycline) are of special concern. Enterococci (including VRE) are easily transferred in hospitals; however, colonizations are far more frequent than infections. Resistance frequencies for vancomycin in clinical E. faecium isolates have remained at a relatively constant level of 8-15% (but with local or regional variations) in recent years whereas frequencies for teicoplanin resistance have shown a slight decrease. Glycopeptide resistance trends correlate with a spread of hospital-associated E. faecium strains carrying the vanA and, with rising frequency in recent years, the vanB gene cluster, the latter being associated with teicoplanin susceptibility. This increased occurrence of vanB-positive E. faecium strains may be caused by an increased use of antibiotics selecting enterococci and VRE as well as due to methodological reasons (e.g. reduced EUCAST MIC-breakpoints for glycopeptides; increased use and sensitive performance of chromogenic VRE agars, increased use of molecular diagnostic assays).
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Affiliation(s)
- I Klare
- Nationales Referenzzentrum für Staphylokokken und Enterokokken, Robert Koch-Institut, Burgstrasse 37, Wernigerode, Germany.
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12
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Morandi S, Cremonesi P, Povolo M, Brasca M. Enterococcus lactis sp. nov., from Italian raw milk cheeses. Int J Syst Evol Microbiol 2012; 62:1992-1996. [DOI: 10.1099/ijs.0.030825-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ten atypical
Enterococcus
strains were isolated from Italian raw milk cheeses. The 16S rRNA gene, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the 16S–23S rRNA intergenic transcribed spacer (ITS) sequences, randomly amplified polymorphic DNA (RAPD) PCR and the phenotypic properties revealed that the isolates represent a novel enterococcal species. On the basis of 16S rRNA gene sequence analysis, the isolates were closely related to
Enterococcus hirae
ATCC 8043T,
Enterococcus durans
CECT 411T and
Enterococcus faecium
ATCC 19434T, with 98.8, 98.9 and 99.4 % sequence similarity, respectively. On the basis of sequence analysis of the housekeeping gene pheS, the reference strain, BT159T, occupied a position separate from
E. faecium
LMG 16198. The group of isolates could be easily differentiated from recognized species of the genus
Enterococcus
by 16S–23S rRNA ITS analysis, RAPD-PCR and phenotypic characteristics. The name Enterococcus lactis sp. nov. is proposed, with BT159T ( = DSM 23655T = LMG 25958T) as the type strain.
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Affiliation(s)
- Stefano Morandi
- Institute of Sciences of Food Production, Italian National Research Council (CNR ISPA), Via Celoria 2, 20133 Milan, Italy
| | - Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council (CNR IBBA), Via Bassini 15, 20133 Milan, Italy
| | - Milena Povolo
- CRA, Fodder and Dairy Productions Research Centre, Via A. Lombardo 11, 26900 Lodi, Italy
| | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council (CNR ISPA), Via Celoria 2, 20133 Milan, Italy
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13
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Borgo F, Ferrario C, Ricci G, Fortina MG. Genotypic intraspecies heterogeneity of Enterococcus italicus: data from dairy environments. J Basic Microbiol 2012; 53:20-8. [PMID: 22581461 DOI: 10.1002/jobm.201100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/26/2011] [Indexed: 11/08/2022]
Abstract
The diversity of a collection of 19 Enterococcus italicus strains isolated from different dairy sources was explored using a molecular polyphasic approach, comprising random amplification of polymorphic DNA (RAPD-PCR), repetitive element PCR (REP-PCR), plasmid profiling and ribotyping. The data obtained showed a high-level of biodiversity, not always correlated to the niche of isolation. Particularly, REP-PCR with primer BOXA1R and plasmid profiling allowed the best discrimination at strain level. Exploiting the genome shotgun sequence of the type strain of the species, available in public database, genes related to insertion sequences present on enterococcal Pathogenic Islands (ISEf1, IS905), determinants related to virulence factors (codifying for hemolysin and cell wall surface proteins), exogenously DNA (conjugal transfer protein, replication plasmid protein, pheromone shutdown protein, phage integrase/recombinase) and penicillin binding proteins system were detected. The presence of most of these genes seemed a common genetic trait in the Enterococcus genus, sur gene (cell wall surface protein) was only detected in strains of E. italicus. To our knowledge, this is the first time that specific primers, with the expection of the species-specific probe targeted to 16S rRNA gene, have been designed for this species.
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Affiliation(s)
- Francesca Borgo
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Sezione di Microbiologia Industriale, Università degli Studi di Milano, Milan, Italy.
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14
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Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2011; 35:7-18. [PMID: 22172557 DOI: 10.1016/j.syapm.2011.10.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 08/17/2011] [Accepted: 10/06/2011] [Indexed: 11/29/2022]
Abstract
Streptomyces hygroscopicus and related species are the most well known candidate producers of antibiotics and many other industrially and agronomically important secondary metabolites in the genus Streptomyces. Multilocus sequence analysis (MLSA) has shown to be a powerful and pragmatic molecular method for unraveling streptomycete diversities. In this investigation, a multilocus phylogeny of 58 representatives of the S. hygroscopicus 16S rRNA gene clade including S. violaceusniger and related species was examined. The result demonstrated that the MLSA data were helpful in defining members of the S. hygroscopicus clade, providing further evidence that the MLSA scheme of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is a valuable alternative for creating and maintaining operational protocols for the Streptomyces species assignment. DNA-DNA hybridization (DDH) between strains with representative MLSA evolutionary distances, combined with previous data from S. griseus and S. albidoflavus clades, revealed a high correlation between MLSA and DDH, and sustains that the five-gene nucleotide sequence distance of 0.007 could be considered as the species cut-off for the whole genus. This significant correlation thus makes the MLSA scheme applicable to construction of a theory-based taxonomy for both ecology and bioprospecting of streptomycetes. Based on the MLSA and DDH data, as well as phenotypic characteristics, 10 species and three subspecies of the S. hygroscopicus clade are considered to be later heterotypic synonyms of eight genomic species, and Streptomyces glebosus sp. nov., comb. nov. (type strain CGMCC 4.1873(T)=LMG 19950(T)=DSM 40823(T)) and Streptomyces ossamyceticus sp. nov., comb. nov. (type strain CGMCC 4.1866(T)=LMG 19951(T)=DSM 40824(T)) are also proposed.
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Affiliation(s)
- Xiaoying Rong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Rong X, Huang Y. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol 2010; 60:696-703. [DOI: 10.1099/ijs.0.012419-0] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.
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Affiliation(s)
- Xiaoying Rong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Rong X, Guo Y, Huang Y. Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA–DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens. Syst Appl Microbiol 2009; 32:314-22. [DOI: 10.1016/j.syapm.2009.05.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Indexed: 11/30/2022]
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Scheirlinck I, Van der Meulen R, Vrancken G, De Vuyst L, Settanni L, Vandamme P, Huys G. Polyphasic taxonomic characterization of Lactobacillus rossiae isolates from Belgian and Italian sourdoughs reveals intraspecific heterogeneity. Syst Appl Microbiol 2009; 32:151-6. [PMID: 19201563 DOI: 10.1016/j.syapm.2008.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 12/22/2008] [Indexed: 11/24/2022]
Abstract
(GTG)5-PCR fingerprinting and pheS sequence analysis of 18 Lactobacillus rossiae isolates, mainly originating from Belgian and Italian artisan sourdoughs, revealed intraspecies grouping as evidenced by the delineation of three and two subgroups, respectively. On the other hand, 16S rRNA and rpoA gene sequence analysis and DNA-DNA hybridizations supported the accommodation of all isolates in a single species. No correlation between genetic and phenotypic heterogeneity was observed. Collectively, these data do not warrant taxonomic division of L. rossiae. On the other hand, the considerable differences in intraspecies sequence variation of L. rossiae isolates displayed by the pheS (9.8%) and rpoA (1.1%) genes highlight that the discriminatory power of housekeeping genes as alternative genomic markers for the 16S rRNA gene in the identification of Lactobacillus species may significantly differ from gene to gene. In conclusion, this study has demonstrated that a polyphasic approach remains highly useful for identification of isolates belonging to genotypically heterogeneous species such as L. rossiae.
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Affiliation(s)
- Ilse Scheirlinck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Fornasari ME, Rossetti L, Remagni C, Giraffa G. Quantification of Enterococcus italicus in traditional Italian cheeses by fluorescence whole-cell hybridization. Syst Appl Microbiol 2008; 31:223-30. [DOI: 10.1016/j.syapm.2008.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 04/03/2008] [Accepted: 04/09/2008] [Indexed: 10/21/2022]
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Designation of the provisional new enterococcus species CDC PNS-E2 as Enterococcus sanguinicola sp. nov., isolated from human blood, and identification of a strain previously named Enterococcus CDC PNS-E1 as Enterococcus italicus Fortina, Ricci, Mora, and Manachini 2004. J Clin Microbiol 2008; 46:3473-6. [PMID: 18667594 DOI: 10.1128/jcm.00603-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have previously characterized two new enterococcal species (provisionally designated CDC PNS-E1 and CDC PNS-E2) recovered from clinically significant specimens associated with invasive infections in humans. In the present report we provide additional data and propose formal denominations for isolates of these two species of Enterococcus. Results of 16S rRNA gene sequencing, sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of whole-cell protein profiles, and DNA-DNA reassociation experiments indicated that the blood isolate ATCC BAA-780 (SS 1728; CDC PNS-E1) corresponds to Enterococcus italicus, whose species epithet was proposed to designate isolates from artisanal Italian cheese. Strain ATCC BAA-781 (CCUG 47861; SS 1729; CDC PNS-E2), a vancomycin-resistant isolate recovered from the blood of a patient in the United States, was found to be highly related at the species level to another blood isolate (SS 1743; CCUG 47884) from Sweden, and for these we propose the designation Enterococcus sanguinicola sp. nov.
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Enterococcus thailandicus sp. nov., isolated from fermented sausage ('mum') in Thailand. Int J Syst Evol Microbiol 2008; 58:1630-4. [DOI: 10.1099/ijs.0.65535-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Wang LT, Lee FL, Tai CJ, Kuo HP. Bacillus velezensis is a later heterotypic synonym of Bacillus amyloliquefaciens. Int J Syst Evol Microbiol 2008; 58:671-5. [DOI: 10.1099/ijs.0.65191-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Maietti L, Bonvini B, Huys G, Giraffa G. Incidence of antibiotic resistance and virulence determinants among Enterococcus italicus isolates from dairy products. Syst Appl Microbiol 2007; 30:509-17. [PMID: 17587527 DOI: 10.1016/j.syapm.2007.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
The main objective of this work was to investigate the biosafety of Enterococcus italicus, a recently described enterococcal species widely diffused in dairy products. For this purpose, the antibiotic susceptibility and the incidence of virulence factors among 30 E. italicus isolates originating mainly from different Italian cheeses were tested. Although not all 30 isolates showed unique genotypes, PCR fingerprinting evidenced a notable genotypic diversity among the E. italicus collection under study. All isolates were susceptible to vancomycin, gentamicin, erythromycin, ampicillin, chloramphenicol and bacitracin. Five isolates corresponding to three unique genotypes exhibited phenotypic resistance to tetracycline with MICs ranging from 64-256mug/ml. By PCR-based detection, the genetic basis of the Tet(R) phenotype in these strains was linked to the tet(S) gene whereas detection of tet(L) and tet(M) genes and the integrase element int of the Tn916/Tn1545 family of transposons were negative. Likewise, none of the strains appeared to contain any of the tested virulence genes gelE, asaI, cpd, agg, cylA, cylB, cylM, ace and hyl(Efm). The results of this study warrant further research into the environmental dissemination of Tet(R)E. italicus and into the potential transferability of its tet(S) genes.
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Sukontasing S, Tanasupawat S, Moonmangmee S, Lee JS, Suzuki KI. Enterococcus camelliae sp. nov., isolated from fermented tea leaves in Thailand. Int J Syst Evol Microbiol 2007; 57:2151-2154. [PMID: 17766890 DOI: 10.1099/ijs.0.65109-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive and catalase-negative coccus that formed chains, strain FP15-1T, isolated from fermented tea leaves (‘miang’), was studied systematically. The strain was facultatively anaerobic and producedl-lactic acid from glucose. Demethylmenaquinone (DMK-7) was the major menaquinone. Straight-chain unsaturated fatty acids C16 : 1and C18 : 1were the dominant components. The DNA G+C content was 37.8 mol%. On the basis of 16S rRNA and RNA polymeraseαsubunit (rpoA) gene sequence analysis, strain FP15-1Twas closely related toEnterococcus italicusKCTC 5373T, with 99.2 and 93.8 % similarity, respectively. The strain could be clearly distinguished fromE. italicusATCC 5373Tby low DNA–DNA relatedness (≤33.8 %) and phenotypic characteristics. Therefore, this strain represent a novel species of the genusEnterococcus, for which the nameEnterococcus camelliaesp. nov. is proposed. The type strain is FP15-1T(=KCTC 13133T=NBRC 101868T=NRIC 0105T=TISTR 932T=PCU 277T).
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Enterococcus/classification
- Enterococcus/genetics
- Enterococcus/isolation & purification
- Enterococcus/metabolism
- Fatty Acids/analysis
- Food Microbiology
- Genes, rRNA
- Glucose/metabolism
- Lactic Acid/metabolism
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Plant Leaves/microbiology
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Tea/microbiology
- Thailand
- Vitamin K 2/analysis
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Affiliation(s)
- Sirapan Sukontasing
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somporn Moonmangmee
- Thailand Institute of Scientific and Technological Research, Pathumthani 12120, Thailand
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong, Daejeon 305-806, Korea
| | - Ken-Ichiro Suzuki
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, Kisarazu, Chiba 292-0818, Japan
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Fortina MG, Ricci G, Borgo F, Manachini PL. Rapid identification of Enterococcus italicus by PCR with primers targeted to 16S rRNA gene. Lett Appl Microbiol 2007; 44:443-6. [PMID: 17397485 DOI: 10.1111/j.1472-765x.2006.02082.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To develop a species-specific PCR assay with primers targeted to 16S rRNA gene for the identification of Enterococcus italicus, a new species of Enterococcus, involved in the production of Italian cheeses. METHODS AND RESULTS The type strain of E. italicus (DSM 15952(T) - 16S rRNA gene accession no. AJ582753) and other strains of the species were subjected to a rapid identification by PCR using primer pairs located within the 16S rRNA gene. A species-specific PCR product of approximately 323 bp was obtained after amplification of all E. italicus strains tested. The specificity of the primers was validated with representatives of the most closely related genera and species and a number of other bacterial species. In addition, the technique enabled the recognition of E. italicus from cheeses. CONCLUSIONS The protocol was highly efficient and sensitive, enabling the identification of E. italicus from cheeses. SIGNIFICANCE AND IMPACT OF THE STUDY The species-specific PCR offers a reliable and rapid alternative to conventional phenotypic methods for the identification of E. italicus within the heterogeneous genus Enterococcus.
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Affiliation(s)
- M G Fortina
- Industrial Microbiology Section, Department of Food Science and Microbiology, University of Milan, Milan, Italy.
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Naser SM, Vancanneyt M, Hoste B, Snauwaert C, Swings J. Lactobacillus cypricasei Lawson et al. 2001 is a later heterotypic synonym of Lactobacillus acidipiscis Tanasupawat et al. 2000. Int J Syst Evol Microbiol 2006; 56:1681-1683. [PMID: 16825650 DOI: 10.1099/ijs.0.64229-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The applicability of a multilocus sequence analysis (MLSA)-based identification system for lactobacilli was evaluated. Two housekeeping genes that code for the phenylalanyl-tRNA synthase alpha-subunit (pheS) and RNA polymerase alpha-subunit (rpoA) were sequenced and analysed for members of the Lactobacillus salivarius species group. The type strains of Lactobacillus acidipiscis and Lactobacillus cypricasei were investigated further using a third gene that encodes the alpha-subunit of ATP synthase (atpA). The MLSA data revealed close relatedness between L. acidipiscis and L. cypricasei, with 99.8-100 % pheS, rpoA and atpA gene sequence similarities. Comparison of the 16S rRNA gene sequences of the type strains of the two species confirmed the close relatedness (99.8 % gene sequence similarity) between the two taxa. Similar phenotypes and high DNA-DNA binding values in the range of 84 to 97.5 % confirmed that L. acidipiscis and L. cypricasei are synonymous species. On the basis of the present study, it is proposed that Lactobacillus cypricasei is a later heterotypic synonym of Lactobacillus acidipiscis.
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Affiliation(s)
- Sabri M Naser
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Marc Vancanneyt
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Bart Hoste
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Cindy Snauwaert
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Jean Swings
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
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Jurkovic D, Krizková L, Sojka M, Belicová A, Dusinský R, Krajcovic J, Snauwaert C, Naser S, Vandamme P, Vancanneyt M. Molecular identification and diversity of enterococci isolated from Slovak Bryndza cheese. J GEN APPL MICROBIOL 2006; 52:329-37. [PMID: 17325446 DOI: 10.2323/jgam.52.329] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Three hundred and eight presumed enterococcal isolates were recovered from Bryndza, a soft sheep milk cheese. The cheese samples were obtained from five different commercial distributors in Slovakia and were taken at three different seasonal intervals. All isolates were identified to the species level using genotypic tools. Species-specific PCR using ddl genes highlighted the predominance of Enterococcus faecium (176 isolates) and assigned 50 isolates to the species Enterococcus faecalis. The remaining 82 isolates were classified using repetitive element sequence-based polymerase chain reaction (PCR) with primer (GTG)(5)-(GTG)(5)-PCR, in combination with phenylalanyl-tRNA synthase gene (pheS) sequence analysis and by whole-cell protein analysis (SDS-PAGE). These strains were identified as Enterococcus durans (59 strains), Enterococcus italicus (8 strains), Enterococcus casseliflavus (3 strains), Enterococcus gallinarum (3 strains), Enterococcus hirae (1 strain), and 8 strains were members of the species Lactococcus lactis. Of the seven enterococcal species isolated, three of them, E. durans, E. faecalis and E. faecium were present in all samples studied, with E. faecium as the predominant one. The precise identification of enterococci in Bryndza cheese is an essential step in the process of evaluation of their functional properties which will be further studied and assessed.
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Affiliation(s)
- Dusan Jurkovic
- Institute of Cell Biology, Faculty of Natural Sciences, Mlynská dolina, Bratislava, Slovak Republic
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