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Kouhi F, Mirzaei H, Nami Y, Khandaghi J, Javadi A. Potential probiotic and safety characterisation of enterococcus bacteria isolated from indigenous fermented motal cheese. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2021.105247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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2
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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Akazawa H, Tsujikawa Y, Fukuda I, Suzuki Y, Choi M, Katayama T, Mukai T, Osawa R. Isolation and identification of milk oligosaccharide-degrading bacteria from the intestinal contents of suckling rats. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2020; 40:27-32. [PMID: 33520566 PMCID: PMC7817515 DOI: 10.12938/bmfh.2020-024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/17/2020] [Indexed: 12/19/2022]
Abstract
We report the isolation of bacteria capable of degrading milk oligosaccharides from
suckling infant rats. The bacteria were successfully isolated via a selective enrichment
method, in which the serially diluted intestinal contents of infant rats were individually
incubated in an enrichment medium containing 3′-sialyllactose (3′-SL), followed by the
isolation of candidate strains from streaked agar plates and selection of 3′-SL-degrading
strains using thin-layer chromatography. Subsequent genomic and phenotypic analyses
identified all strains as Enterococcus gallinarum. The strains were
capable of degrading both 3′-SL and 6′-SL, which was not observed with the type strain of
E. gallinarum used as a reference. Furthermore, a time-course study
combining high-performance anion-exchange chromatography with pulsed amperometric
detection revealed that the representative strain AH4 degraded 3′-SL completely to yield
an equimolar amount of lactose and an approximately one-fourth equimolar amount of sialic
acid after 24 hr of anaerobic incubation. These findings point to a possibility that the
enterococci degrade rat milk oligosaccharides to “cross-feed” their degradants to other
members of concomitant bacteria in the gut of the infant rat.
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Affiliation(s)
- Hazuki Akazawa
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yuji Tsujikawa
- Central Research Institute, ITO EN, Ltd., 21 Mekami, Makinohara, Shizuoka 421-0516, Japan
| | - Itsuko Fukuda
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yoshihiro Suzuki
- School of Veterinary Medicine, Kitasato University, 23-35-1 Higashi, Towada, Aomori 034-8628, Japan
| | - Moonhak Choi
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takao Mukai
- School of Veterinary Medicine, Kitasato University, 23-35-1 Higashi, Towada, Aomori 034-8628, Japan
| | - Ro Osawa
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
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4
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Cho S, Jackson C, Frye J. The prevalence and antimicrobial resistance phenotypes of
Salmonella
,
Escherichia coli
and
Enterococcus
sp. in surface water. Lett Appl Microbiol 2020; 71:3-25. [DOI: 10.1111/lam.13301] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 12/25/2022]
Affiliation(s)
- S. Cho
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit United States Department of Agriculture, Agricultural Research Service Athens GA United States of America
| | - C.R. Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit United States Department of Agriculture, Agricultural Research Service Athens GA United States of America
| | - J.G. Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit United States Department of Agriculture, Agricultural Research Service Athens GA United States of America
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Immunization with the basic membrane protein (BMP) family ABC transporter elicits protection against Enterococcus faecium in a murine infection model. Microbes Infect 2020; 22:127-136. [DOI: 10.1016/j.micinf.2019.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022]
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Singh H, Das S, Yadav J, Srivastava VK, Jyoti A, Kaushik S. In search of novel protein drug targets for treatment of Enterococcus faecalis infections. Chem Biol Drug Des 2019; 94:1721-1739. [PMID: 31260188 DOI: 10.1111/cbdd.13582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022]
Abstract
Enterococcus faecalis (Ef) is one of the major pathogens involved in hospital-acquired infections. It can cause nosocomial bacteremia, surgical wound infection, and urinary tract infection. It is important to mention here that Ef is developing resistance against many commonly occurring antibiotics. The occurrence of multidrug resistance (MDR) and extensive-drug resistance (XDR) is now posing a major challenge to the medical community. In this regard, to combat the infections caused by Ef, we have to look for an alternative. Rational structure-based drug design exploits the three-dimensional structure of the target protein, which can be unraveled by various techniques such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. In this review, we have discussed the complete picture of Ef infections, the possible treatment available at present, and the alternative treatment options to be explored. This study will help in better understanding of novel biological targets against Ef and the compounds, which are likely to bind with these targets. Using these detailed structural informations, rational structure-based drug design is achievable and tight inhibitors against Ef can be prepared.
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Affiliation(s)
- Harpreet Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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7
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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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8
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Santiago M, Eysenbach L, Allegretti J, Aroniadis O, Brandt LJ, Fischer M, Grinspan A, Kelly C, Morrow C, Rodriguez M, Osman M, Kassam Z, Smith MB, Timberlake S. Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study. AIMS Microbiol 2019; 5:1-18. [PMID: 31384699 PMCID: PMC6646931 DOI: 10.3934/microbiol.2019.1.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/23/2018] [Indexed: 12/27/2022] Open
Abstract
The gastrointestinal microbiome is intrinsically linked to the spread of antibiotic resistance. Antibiotic treatment puts patients at risk for colonization by opportunistic pathogens like vancomycin resistant Enterococcus and Clostridioides difficile by destroying the colonization resistance provided by the commensal microbiota. Once colonized, the host is at a much higher risk for infection by that pathogen. Furthermore, we know that microbiome community differences are associated with disease states, but we do not have a good understanding of how we can use these changes to classify different patient populations. To that end, we have performed a multicenter retrospective analysis on patients who received fecal microbiota transplants to treat recurrent Clostridioides difficile infection. We performed 16S rRNA gene sequencing on fecal samples collected as part of this study and used these data to develop a microbiome disruption index. Our microbiome disruption index is a simple index that is predictive across cohorts, indications, and batch effects. We are able to classify pre-fecal transplant vs post-fecal transplant samples in patients with recurrent C. difficile infection, and we are able to predict, using previously-published data from a cohort of patients receiving hematopoietic stem cell transplants, which patients would go on to develop bloodstream infections. Finally, we also identified patients in this cohort that were initially colonized with vancomycin resistant Enterococcus and that 92% (11/12) were decolonized after the transplant, but the microbiome disruption index was unable to predict such decolonization. We, however, were able to compare the relative abundance of different taxa between the two groups, and we found that increased abundance of Enterobacteriaceae predicts whether patients were colonized with vancomycin resistant Enterococcus. This work is an early step towards a better understanding of how microbiome predictors can be used to help improve patient care and patient outcomes.
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Affiliation(s)
- Marina Santiago
- Finch Therapeutics, 200 Inner Belt Rd, Somerville, MA 02143, USA
| | | | - Jessica Allegretti
- Division of Gastroenterology, Brigham and Women's Hospital, 75 Francis St, Boston, MA 02115, USA
| | - Olga Aroniadis
- Department of Medicine (Gastroenterology), Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Lawrence J Brandt
- Department of Medicine (Gastroenterology), Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Monika Fischer
- Division of Gastroenterology, Indiana University School of Medicine, 340 W. 10th St, Indianapolis, IN 46202, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029, USA
| | - Colleen Kelly
- Women's Medicine Collaborative, Brown Alpert Medial School, 222 Richmond St, Providence, RI 02903, USA
| | - Casey Morrow
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1720 2nd Ave S, Birmingham, AL 35294, USA
| | - Martin Rodriguez
- Division of Infectious Diseases, University of Alabama at Birmingham School of Medicine, 1670 University Blvd, Birmingham, AL 35233, USA
| | - Majdi Osman
- OpenBiome, 2067 Massachusetts Ave, Cambridge, MA 02140, USA
| | - Zain Kassam
- Finch Therapeutics, 200 Inner Belt Rd, Somerville, MA 02143, USA
| | - Mark B Smith
- Finch Therapeutics, 200 Inner Belt Rd, Somerville, MA 02143, USA
| | - Sonia Timberlake
- Finch Therapeutics, 200 Inner Belt Rd, Somerville, MA 02143, USA
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9
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Identification of vancomycin-susceptible major clones of clinical Enterococcus from Algeria. J Glob Antimicrob Resist 2016; 6:78-83. [DOI: 10.1016/j.jgar.2016.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 11/24/2022] Open
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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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Sun M, Wang Y, Chen Z, Zhu X, Tian L, Sun Z. The first report of the vanC₁ gene in Enterococcus faecium isolated from a human clinical specimen. Mem Inst Oswaldo Cruz 2014; 109:712-5. [PMID: 25317698 PMCID: PMC4238761 DOI: 10.1590/0074-0276140019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 06/20/2014] [Indexed: 11/21/2022] Open
Abstract
The vanC1 gene, which is chromosomally located, confers resistance to vancomycin and
serves as a species marker for Enterococcus gallinarum. Enterococcus
faecium TJ4031 was isolated from a blood culture and harbours the
vanC1gene. Polymerase chain reaction (PCR) assays were performed to
detect vanXYc and vanTc genes. Only the
vanXYc gene was found in the E. faecium TJ4031 isolate. The
minimum inhibitory concentrations ofvancomycin and teicoplanin were 2 µg/mL and 1 µg/mL, respectively. Real-time
reversetranscription-PCR results revealed that the vanC1and vanXYc genes were not expressed.Pulsed-field gel electrophoresis and southern hybridisation results showed
that the vanC1 gene was encoded in the chromosome. E. faecalis isolated
from animals has been reportedto harbour vanC1gene. However, this study is the first to report the presence of the
vanC1gene in E. faecium of human origin. Additionally, our
research showed the vanC1gene cannot serve as a species-specific gene of E. gallinarum
and that it is able to be transferredbetween bacteria. Although the resistance marker is not expressed in the
strain, ourresults showed that E. faecium could acquire the
vanC1gene from different species.
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Affiliation(s)
- Mingyue Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yue Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhongju Chen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuhui Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Tian
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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12
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Caro I, Bécares G, Fuentes L, Garcia-Armesto MR, Rúa J, Castro JM, Quinto EJ, Mateo J. Evaluation of three PCR primers based on the16S rRNAgene for the identification of lactic acid bacteria from dairy origin. CYTA - JOURNAL OF FOOD 2014. [DOI: 10.1080/19476337.2014.934297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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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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14
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Development of quantitative PCR assays targeting the 16S rRNA genes of Enterococcus spp. and their application to the identification of enterococcus species in environmental samples. Appl Environ Microbiol 2012; 79:196-204. [PMID: 23087032 DOI: 10.1128/aem.02802-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The detection of environmental enterococci has been determined primarily by using culture-based techniques that might exclude some enterococcal species as well as those that are nonculturable. To address this, the relative abundances of enterococci were examined by challenging fecal and water samples against a currently available genus-specific assay (Entero1). To determine the diversity of enterococcal species, 16S rRNA gene-based group-specific quantitative PCR (qPCR) assays were developed and evaluated against eight of the most common environmental enterococcal species. Partial 16S rRNA gene sequences of 439 presumptive environmental enterococcal strains were analyzed to study further the diversity of enterococci and to confirm the specificities of group-specific assays. The group-specific qPCR assays showed relatively high amplification rates with targeted species (>98%), although some assays cross-amplified with nontargeted species (1.3 to 6.5%). The results with the group-specific assays also showed that different enterococcal species co-occurred in most fecal samples. The most abundant enterococci in water and fecal samples were Enterococcus faecalis and Enterococcus faecium, although we identified more water isolates as Enterococcus casseliflavus than as any of the other species. The prevalence of the Entero1 marker was in agreement with the combined number of positive signals determined by the group-specific assays in most fecal samples, except in gull feces. On the other hand, the number of group-specific assay signals was lower in all water samples tested, suggesting that other enterococcal species are present in these samples. While the results highlight the value of genus- and group-specific assays for detecting the major enterococcal groups in environmental water samples, additional studies are needed to determine further the diversity, distributions, and relative abundances of all enterococcal species found in water.
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Phenotypic and genotypic characterization of Rhodococcus equi isolated from sputum. Braz J Infect Dis 2012; 16:409-15. [PMID: 22975169 DOI: 10.1016/j.bjid.2012.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Accepted: 03/13/2012] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Rhodococcus equi is an opportunistic pathogen, causing rhodococcosis, a condition that can be confused with tuberculosis. Often, without identifying M. tuberculosis, physicians initiate empiric treatment for tuberculosis. R. equi and M. tuberculosis have different susceptibility to drugs. Identification of R. equi is based on a variety of phenotypic, chromatographic, and genotypic characteristics. OBJECTIVE This study aimed to characterize bacterial isolates from sputum samples suggestive of R. equi. METHODS The phenotypic identification included biochemical assays; thin-layer chromatography (TLC) and polymerase chain reaction (PCR) were used for genotypic identification. RESULTS Among 78 Gram-positive and partially acid-fast bacilli isolated from the sputum of tuberculosis-suspected patients, 51 were phenotypically and genotypically characterized as R. equi based on literature data. Mycolic acid analysis showed that all suspected R. equi had compounds with a retention factor (R(f)) between 0.4-0.5. Genotypic characterization indicated the presence of the choE gene 959bp fragments in 51 isolates CAMP test positive. Twenty-two CAMP test negative isolates were negative for the choE gene. Five isolates presumptively identified as R. equi, CAMP test positive, were choE gene negative, and probably belonged to other bacterial species. CONCLUSIONS The phenotypic and molecular techniques used constitute a good methodological tool to identify R. equi.
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Schwaiger K, Bauer J, Hörmansdorfer S, Mölle G, Preikschat P, Kämpf P, Bauer-Unkauf I, Bischoff M, Hölzel C. Presence of the Resistance GenesvanC1andpbp5in Phenotypically Vancomycin and Ampicillin SusceptibleEnterococcus faecalis. Microb Drug Resist 2012; 18:434-9. [DOI: 10.1089/mdr.2011.0227] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Karin Schwaiger
- Chair of Animal Hygiene, Technische Universität München, Freising-Weihenstephan, Germany
| | - Johann Bauer
- Chair of Animal Hygiene, Technische Universität München, Freising-Weihenstephan, Germany
| | - Stefan Hörmansdorfer
- Bavarian Health and Food Safety Authority (LGL) Oberschleißheim, Oberschleißheim, Germany
| | - Gabriele Mölle
- Bavarian Health and Food Safety Authority (LGL) Erlangen, Erlangen, Germany
| | - Petra Preikschat
- Bavarian Health and Food Safety Authority (LGL) Erlangen, Erlangen, Germany
| | - Peter Kämpf
- Bavarian Health and Food Safety Authority (LGL) Oberschleißheim, Oberschleißheim, Germany
| | - Ilse Bauer-Unkauf
- Bavarian Health and Food Safety Authority (LGL) Erlangen, Erlangen, Germany
| | - Meike Bischoff
- Chair of Animal Hygiene, Technische Universität München, Freising-Weihenstephan, Germany
| | - Christina Hölzel
- Chair of Animal Hygiene, Technische Universität München, Freising-Weihenstephan, Germany
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Frolkova P, Ghosh A, Svec P, Zurek L, Literak I. Use of the manganese-dependent superoxide dismutase gene sodA for rapid identification of recently described enterococcal species. Folia Microbiol (Praha) 2012; 57:439-42. [PMID: 22570141 DOI: 10.1007/s12223-012-0115-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 03/08/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Petra Frolkova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1-3, 612 42 Brno, Czech Republic.
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Abstract
Identification of Corynebacterium species may be challenging. Corynebacterium species are occasional causes of prosthetic joint infection (PJI), but few data are available on the subject. Based on the literature, C. amycolatum, C. aurimucosum, C. jeikeium, and C. striatum are the most common Corynebacterium species that cause PJI. We designed a rapid PCR assay to detect the most common human Corynebacterium species, with a specific focus on PJI. A polyphosphate kinase gene identified using whole-genome sequence was targeted. The assay differentiates the antibiotic-resistant species C. jeikeium and C. urealyticum from other species in a single assay. The assay was applied to a collection of human Corynebacterium isolates from multiple clinical sources, and clinically relevant species were detected. The assay was then tested on Corynebacterium isolates specifically associated with PJI; all were detected. We also describe the first case of C. simulans PJI.
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19
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Identification of non-diphtheriae corynebacterium by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2011; 50:160-3. [PMID: 22075579 DOI: 10.1128/jcm.05889-11] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We evaluated the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for identification of 92 clinical isolates of Corynebacterium species in comparison to identification using rpoB or 16S rRNA gene sequencing. Eighty isolates (87%) yielded a score of ≥1.700, and all of these were correctly identified to the species level with the exception of Corynebacterium aurimucosum being misidentified as the closely related Corynebacterium minutissimum.
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20
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Vu J, Carvalho J. Enterococcus: review of its physiology, pathogenesis, diseases and the challenges it poses for clinical microbiology. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11515-011-1167-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Comparison of genotypic and phylogenetic relationships of environmental Enterococcus isolates by BOX-PCR typing and 16S rRNA gene sequencing. Appl Environ Microbiol 2011; 77:5050-5. [PMID: 21622792 DOI: 10.1128/aem.00130-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental Enterococcus spp. were compared by BOX-PCR genotyping and 16S rRNA gene sequencing to clarify the predictive relationship of BOX-PCR fingerprints to species designation. BOX-PCR and 16S rRNA gene relationships agreed for 77% of strains. BOX-PCR provided superior intraspecies discrimination but incorrectly identified some strains to the species level and divided some species into multiple groups.
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Velkers FC, van de Graaf-Bloois L, Wagenaar JA, Westendorp ST, van Bergen MAP, Dwars RM, Landman WJM. Enterococcus hirae-associated endocarditis outbreaks in broiler flocks: clinical and pathological characteristics and molecular epidemiology. Vet Q 2011; 31:3-17. [PMID: 22029817 DOI: 10.1080/01652176.2011.570107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND Enterococcus hirae-associated endocarditis, characterized by a peak in mortality during the second week of the grow-out, and occasionally lameness, was diagnosed at Dutch broiler farms. OBJECTIVES Field cases were studied to increase knowledge on clinical and pathological characteristics, pathogenesis and epidemiology of these infections. ANIMALS AND METHODS In total, 1266 birds of 25 flocks from 12 farms were examined. Post-mortem examinations, bacteriology, histopathology, PCR and DNA fingerprinting was carried out. Six flocks were followed longitudinally (n = 1017 birds). RESULTS Average mortality was 4.1% for the entire grow-out, of which 36% was attributed to endocarditis. Fibrinous thromboendocarditis of the right atrioventricular (AV) valve was found in 24% of hearts, compared to 7% and 4% with lesions of left and both AV valves, respectively. Thrombotic lesions were found in 24% (n = 432) of lungs, but only in larger branches of the Arteria pulmonalis. Occasionally, thrombi were found in the Arteria ischiadica externa and in liver and brain vessels. Enterococcus was cultured from 54% (n = 176) of heart and in 75% (n = 28), 62% (n = 106) and 31% (n = 16) of liver, bone marrow and lung samples, respectively. Further identification, using the Rapid ID Strep 32 API system and a PCR targeting mur-2 and mur-2(ed) genes was carried out on a subset of Enterococcus positive isolates (n = 65): both techniques identified the isolates as Enterococcus hirae. Pulsed-field gel electrophoresis did not indicate evidence of clonality between farms and flocks. CONCLUSIONS The relevance of these findings for pathogenesis and epidemiology of E. hirae infections is discussed. CLINICAL IMPORTANCE. This study may facilitate diagnosis of field cases and may contribute to the design of further research and development of control measures.
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Affiliation(s)
- F C Velkers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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Identification of enterococci from broiler products and a broiler processing plant and description of Enterococcus viikkiensis sp. nov. Appl Environ Microbiol 2010; 77:1196-203. [PMID: 21183650 DOI: 10.1128/aem.02412-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genus Enterococcus. Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in the Enterococcus avium group, with E. devriesei being the closest phylogenetic neighbor. The DNA-DNA hybridization levels with E. devriesei ranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The name Enterococcus viikkiensis sp. nov. is proposed, with strain DSM 24043(T) (LMG 26075(T)) being the type strain. Our study demonstrated that the identification of enterococci within the E. avium phylogenetic group demands polyphasic taxonomic approaches. The rpoA and pheS gene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) between E. viikkiensis and its closest phylogenetic neighbor, E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in the E. avium group were also highly similar, and some traits were found to be misleading for enterococci, such as E. viikkiensis does not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within the E. avium group.
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Zhu W, Murray PR, Huskins WC, Jernigan JA, McDonald LC, Clark NC, Anderson KF, McDougal LK, Hageman JC, Olsen-Rasmussen M, Frace M, Alangaden GJ, Chenoweth C, Zervos MJ, Robinson-Dunn B, Schreckenberger PC, Reller LB, Rudrik JT, Patel JB. Dissemination of an Enterococcus Inc18-Like vanA plasmid associated with vancomycin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2010; 54:4314-20. [PMID: 20660665 PMCID: PMC2944587 DOI: 10.1128/aac.00185-10] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/17/2010] [Accepted: 07/15/2010] [Indexed: 11/20/2022] Open
Abstract
Of the 9 vancomycin-resistant Staphylococcus aureus (VRSA) cases reported to date in the literature, 7 occurred in Michigan. In 5 of the 7 Michigan VRSA cases, an Inc18-like vanA plasmid was identified in the VRSA isolate and/or an associated vancomycin-resistant Enterococcus (VRE) isolate from the same patient. This plasmid may play a critical role in the emergence of VRSA. We studied the geographical distribution of the plasmid by testing 1,641 VRE isolates from three separate collections by PCR for plasmid-specific genes traA, repR, and vanA. Isolates from one collection (phase 2) were recovered from surveillance cultures collected in 17 hospitals in 13 states. All VRE isolates from 2 Michigan institutions (n = 386) and between 60 and 70 VRE isolates (n = 883) from the other hospitals were tested. Fifteen VRE isolates (3.9%) from Michigan were positive for an Inc18-like vanA plasmid (9 E. faecalis [12.5%], 3 E. faecium [1.0%], 2 E. avium, and 1 E. raffinosus). Six VRE isolates (0.6%) from outside Michigan were positive (3 E. faecalis [2.7%] and 3 E. faecium [0.4%]). Of all E. faecalis isolates tested, 6.0% were positive for the plasmid, compared to 0.6% for E. faecium and 3.0% for other spp. Fourteen of the 15 plasmid-positive isolates from Michigan had the same Tn1546 insertion site location as the VRSA-associated Inc18-like plasmid, whereas 5 of 6 plasmid-positive isolates from outside Michigan differed in this characteristic. Most plasmid-positive E. faecalis isolates demonstrated diverse patterns by PFGE, with the exception of three pairs with indistinguishable patterns, suggesting that the plasmid is mobile in nature. Although VRE isolates with the VRSA-associated Inc18-like vanA plasmid were more common in Michigan, they remain rare. Periodic surveillance of VRE isolates for the plasmid may be useful in predicting the occurrence of VRSA.
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Affiliation(s)
- Wenming Zhu
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Patrick R. Murray
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - W. Charles Huskins
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - John A. Jernigan
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Lawrence C. McDonald
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Nancye C. Clark
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Karen F. Anderson
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Linda K. McDougal
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Jeff C. Hageman
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Melissa Olsen-Rasmussen
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Mike Frace
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - George J. Alangaden
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Carol Chenoweth
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Marcus J. Zervos
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Barbara Robinson-Dunn
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Paul C. Schreckenberger
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - L. Barth Reller
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - James T. Rudrik
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
| | - Jean B. Patel
- Division of Healthcare Quality Promotion, Division of Scientific Resources, Centers for Disease Control and Prevention, MS-G08, 1600 Clifton Road, Atlanta, Georgia, National Institutes of Health Clinical Center, Bethesda, Maryland, College of Medicine, Mayo Clinic, Rochester, Minnesota, Detroit Medical Center, Detroit, Michigan, University of Michigan, Ann Arbor, Michigan, Henry Ford Hospital, Detroit, Michigan, William Beaumont Hospital, Royal Oak, Michigan, Loyola University Medical Center, Maywood, Illinois, Duke University Medical Center, Durham, North Carolina, Michigan Department of Community Health, Lansing, Michigan
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Watanabe S, Kobayashi N, Quiñones D, Hayakawa S, Nagashima S, Uehara N, Watanabe N. Genetic diversity of the low-level vancomycin resistance gene vanC-2/vanC-3 and identification of a novel vanC subtype (vanC-4) in Enterococcus casseliflavus. Microb Drug Resist 2010; 15:1-9. [PMID: 19216682 DOI: 10.1089/mdr.2009.0856] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An intrinsic low-level vancomycin resistance (VanC phenotype) in Enterococcus casseliflavus is conferred by either of two subtypes of vanC genes, that is, vanC-2 or vanC-3, which are genetically closely related. To know genetic diversity of vanC-2/C-3 genes among E. casseliflavus, nucleotide sequences of vanC-2/C-3 and other genetic components in vanC gene cluster (vanXYc, vanTc, vanRc, and vanSc) were analyzed for nine clinical isolates and four standard strains that showed low-level vancomycin resistance. While the vanC-2/C-3 gene sequences showed 93-100% identities among the strains examined, two genetic groups were discriminated by phylogenetic analysis: one closely related to the previously reported vanC-2 or vanC-3 genes (vanC-2/C-3 genotype) with 98-100% identity, and the other distinct from the vanC-2/C-3 genotype (93-95% identity). The latter group found in three clinical isolates was considered as a new subtype of vanC and tentatively designated as vanC-4. Between strains with the vanC-2/C-3 genotype and those with vanC-4, vanXYc genes were also genetically discriminated with 92-93% identity. Similar sequence diversity was observed for vanTc, vanRc, and vanSc (88-93% identity). Clonal relatedness among the E. casseliflavus strains was investigated by phylogenetic analysis of atpA gene. While among E. casseliflavus strains with vanC-2/C-3 genotype, extremely high sequence identities of atpA were found (98.7% or higher), these strains showed slightly lower identity to those with vanC-4 (94-96%). These two groups of E. casseliflavus strains were also discriminated by genotyping with arbitrarily primed PCR. These findings indicated that among E. casseliflavus there are at least two genetic lineages with the distinct vanC genes, that is, a single subtype including previously known vanC-2/C-3, and a novel subtype vanC-4.
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Affiliation(s)
- Shojiro Watanabe
- Department of Hygiene, Sapporo Medical University School of Medicine, Chuo-ku, Sapporo, Japan
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Graves A, Weaver R. Characterization of enterococci populations collected from a subsurface flow constructed wetland. J Appl Microbiol 2010; 108:1226-34. [DOI: 10.1111/j.1365-2672.2009.04516.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Medeiros AW, d'Azevedo P, Pereira RI, Cassenego AP, Van Der Sand S, Frazzon J, Frazzon APG. PCR-RFLP of 16S ribosomal DNA to confirm the identification of Enterococcus gallinarum and Enterococcus casseliflavus isolated from clinical and food samples. Rev Soc Bras Med Trop 2010; 43:100-1. [DOI: 10.1590/s0037-86822010000100023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 01/13/2010] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION: This study aimed to confirm the identification of Enterococcus gallinarum and Enterococcus casseliflavus isolated from clinical and food samples by PCR-RFLP. METHODS: Fifty-two strains identified by conventional biochemical exams were submitted to PCR amplification and digested with HinfI. Only 20 (38.5%) of the 52 strains showed a DNA pattern expected for E. gallinarum and E. casseliflavus. RESULTS: Analysis of the results of this study showed that E. gallinarum and E. casseliflavus are occasionally erroneously identified and confirmed the potential application of 16S rDNA analysis for accurate identification of these species. CONCLUSIONS: A correct identification is important to distinguish between intrinsic and acquired vancomycin resistance.
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Molecular and genetic characterization of a novel bacteriocin locus in Enterococcus avium isolates from infants. Appl Environ Microbiol 2009; 76:483-92. [PMID: 19933345 DOI: 10.1128/aem.01597-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are among the most common human intestinal lactic acid bacteria, and they are known to produce bacteriocins. In this study, fecal enterococci were isolated from infants and screened for bacteriocin production. Bacteriocin-producing Enterococcus avium isolates were obtained, and a new pediocin-like bacteriocin was purified and characterized. This bacteriocin, termed avicin A, was found to be produced by isolates from two healthy infants. It was purified to homogeneity from culture supernatant by ion-exchange and reversed-phase chromatography, and part of its amino acid sequence was obtained. The sequence of a 7-kb DNA fragment of a bacteriocin locus was determined by PCR and DNA sequencing. The bacteriocin locus was organized into four operon-like structures consisting of (i) the structural genes encoding avicin A and its immunity protein, (ii) a divergicin-like bacteriocin (avicin B) gene, (iii) an ABC bacteriocin transporter gene and two regulatory genes (histamine protein kinase- and response regulator-encoding genes), and (iv) induction peptide pheromone- and transport accessory protein-encoding genes. It was shown that the production of avicin A was regulated by the peptide pheromone-inducible regulatory system. Avicin A shows very high levels of similarity to mundticin KS and enterocin CRL35. This bacteriocin showed strong antimicrobial activity against many species of Gram-positive bacteria, including the food-borne pathogen Listeria monocytogenes. The avicin A locus is the first bacteriocin locus identified in E. avium to be characterized at the molecular level.
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Layton BA, Walters SP, Boehm AB. Distribution and diversity of the enterococcal surface protein (esp) gene in animal hosts and the Pacific coast environment. J Appl Microbiol 2009; 106:1521-31. [PMID: 19187132 DOI: 10.1111/j.1365-2672.2008.04113.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS This study sought to evaluate the distribution of the enterococcal surface protein (esp) gene in Enterococcus faecium in the Pacific coast environment as well as the distribution and diversity of the gene in Northern California animal hosts. METHODS AND RESULTS Over 150 environmental samples from the Pacific coast environment (sand, surf zone, fresh/estuarine, groundwater, and storm drain) were screened for the esp gene marker in E. faecium, and the marker was found in 37% of the environmental samples. We examined the host specificity of the gene by screening various avian and mammalian faecal samples, and found the esp gene to be widespread in nonhuman animal faeces. DNA sequence analysis performed on esp polymerase chain reaction amplicons revealed that esp gene sequences were not divergent between hosts. CONCLUSIONS Our data confirm recent findings that the E. faecium variant of the esp gene is not human-specific. SIGNIFICANCE AND IMPACT OF THE STUDY Our results suggest that the use of the esp gene for microbial source tracking applications may not be appropriate at all recreational beaches.
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Affiliation(s)
- B A Layton
- Environmental and Water Studies, Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
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Martín B, Corominas L, Garriga M, Aymerich T. Identification and tracing ofEnterococcusspp. by RAPD-PCR in traditional fermented sausages and meat environment. J Appl Microbiol 2009; 106:66-77. [DOI: 10.1111/j.1365-2672.2008.03976.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
The aim of this study was to screen two cheese starter cultures and cheese-borne microbial communities with the potential to produce biogenic amines in cheese during ripening. Bacteria of the genera Enterococcus and Lactobacillus and coliform bacteria were isolated from Dutch-type semi-hard cheese at the beginning of the ripening period. Statistically significant counts of bacterial isolates were screened for the presence of specific DNA sequences coding for tyrosine decarboxylase (tyrDC) and histidine decarboxylase (hDC) enzymes. The PCR analysis of DNA from 14 Enterococcus and 3 Lactobacillus isolates confirmed the presence of the targetted DNA sequences. Simultaneously, 13 tyrDC- and 3 hDC-positive isolates were grown in decarboxylase screening medium and this was followed by HPLC analysis of the produced tyramine and histamine. Conventional and molecular taxonomic analyses of the above-mentioned isolates identified the following species: Enterococcus durans (7 strains), Enterococcus faecalis (3 strains), Enterococcus faecium (1 strain), Enterococcus casseliflavus (3 strains), Lactobacillus curvatus (1 strain), Lactobacillus lactis (1 strain) and Lactobacillus helveticus (1 strain). All of the above Enterococcus and two of the Lactobacillus strains originated from contaminating microbial communities. The L. helveticus strain, which was tyrosine decarboxylase-positive and exhibited tyramine production, originated from starter culture 1 used for cheese production. Comparison of partial tyrDC sequences of positive Enterococcus isolates revealed 89% sequence similarity, and that of hDC-positive Lactobacillus isolates revealed 99% sequence similarity.
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Affiliation(s)
- Radka Burdychova
- Department of Food Technology, Mendel University of Agriculture and Forestry in Brno, Brno, Czech Republic.
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Tung SK, Teng LJ, Vaneechoutte M, Chen HM, Chang TC. Array-based identification of species of the genera Abiotrophia, Enterococcus, Granulicatella, and Streptococcus. J Clin Microbiol 2006; 44:4414-24. [PMID: 17065265 PMCID: PMC1698397 DOI: 10.1128/jcm.01712-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some species of enterococci and streptococci are difficult to differentiate by phenotypic traits. The feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. The aim of this study was to expand the array to identify species of Abiotrophia (1 species), Enterococcus (18 species), Granulicatella (3 species), and Streptococcus (31 species and 6 subspecies). The method consisted of PCR amplification of the ribosomal DNA intergenic spacer (ITS) regions, followed by hybridization of the digoxigenin-labeled PCR products to a panel of oligonucleotide probes (16- to 30-mers) immobilized on a nylon membrane. Probes could be divided into three categories: species specific, group specific, and supplemental probes. All probes were designed either from the ITS regions or from the 3' ends of the 16S rRNA genes. A collection of 312 target strains (162 reference strains and 150 clinical isolates) and 73 nontarget strains was identified by the array. Most clinical isolates were isolated from blood cultures or deep abscesses, and only those strains having excellent species identification with the Rapid ID 32 STREP system (bioMérieux Vitek, Taipei, Taiwan) were used for array testing. The test sensitivity and specificity of the array were 100% (312/312) and 98.6% (72/73), respectively. The whole procedure of array hybridization took about 8 h, starting from isolated colonies, and the hybridization patterns could be read by the naked eye. The oligonucleotide array is accurate for identification of the above microorganisms and could be used as a reliable alternative to phenotypic identification methods.
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Affiliation(s)
- Sheng Kai Tung
- Department of Medical Laboratory Science and Biotechnology, School of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Belgium
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Batdorj B, Dalgalarrondo M, Choiset Y, Pedroche J, Métro F, Prévost H, Chobert JM, Haertlé T. Purification and characterization of two bacteriocins produced by lactic acid bacteria isolated from Mongolian airag. J Appl Microbiol 2006; 101:837-48. [PMID: 16968295 DOI: 10.1111/j.1365-2672.2006.02966.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The aim of this study was to isolate and identify bacteriocin-producing lactic acid bacteria (LAB) issued from Mongolian airag (traditional fermented mare's milk), and to purify and characterize bacteriocins produced by these LAB. METHODS AND RESULTS Identification of the bacteria (Enterococcus durans) was carried out on the basis of its morphological, biochemical characteristics and carbohydrate fermentation profile and by API50CH kit and 16S rDNA analyses. The pH-neutral cell-free supernatant of this bacterium inhibited the growth of several Lactobacillus spp. and food-borne pathogens including Escherichia coli, Staphylococcus aureus and Listeria innocua. The antimicrobial agent (enterocin A5-11) was heat stable and was not sensitive to acid and alkaline conditions (pH 2-10), but was sensitive to several proteolytic enzymes. Its inhibitory activity was completely eliminated after treatment with proteinase K and alpha-chymotrypsin. The activity was however not completely inactivated by other proteases including trypsin and pepsin. Three-step purification procedure with high recovery yields was developed to separate two bacteriocins. The applied procedure allowed the recovery of 16% and 64% of enterocins A5-11A and A5-11B, respectively, present in the culture supernatant with purity higher than 99%. SDS-PAGE analyses revealed that enterocin A5-11 has a molecular mass of 5000 Da and mass spectrometry analyses demonstrates molecular masses of 5206 and 5218 Da for fractions A and B, respectively. Amino acid analyses of both enterocins indicated significant quantitative difference in their contents in threonine, alanine, isoleucine and leucine. Their N-termini were blocked hampering straightforward Edman degradation. CONCLUSIONS Bacteriocins A5-11A and B from Ent. durans belong to the class II of bacteriocins. SIGNIFICANCE AND IMPACT OF THE STUDY Judging from molecular masses, amino acid composition and spectrum of activities, bacteriocins A5-11A and B from Ent. durans show high degree of similarity with enterocins L50A and L50B isolated from Enterococcus faecium (Cintas et al. 1998, 2000) and with enterocin I produced by Ent. faecium 6T1a, a strain originally isolated from a Spanish-style green olive fermentation (Floriano et al. 1998).
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Affiliation(s)
- B Batdorj
- Fonctions et Interactions des Protéines Laitières/Biopolymères, Interactions, Assemblages, INRA, Nantes Cedex 3, France
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Moore DF, Zhowandai MH, Ferguson DM, McGee C, Mott JB, Stewart JC. Comparison of 16S rRNA sequencing with conventional and commercial phenotypic techniques for identification of enterococci from the marine environment. J Appl Microbiol 2006; 100:1272-81. [PMID: 16696674 DOI: 10.1111/j.1365-2672.2006.02879.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To compare accuracy of genus and species level identification of presumptive enterococci isolates from the marine environment using conventional biochemical testing, four commercial identification systems and 16S rRNA sequence analysis. METHODS AND RESULTS Ninety-seven environmental bacterial isolates identified as presumptive enterococci on mEI media were tested using conventional and Enterococcus genus screen biochemical tests, four commercial testing systems and 16S rRNA sequencing. Conventional and Enterococcus genus screen biochemical testing, 16S rRNA sequencing and two commercial test systems achieved an accuracy of > or = 94% for Enterococcus genus confirmation. Conventional biochemical testing and 16S rRNA sequencing achieved an accuracy of > or = 90% for species level identification. CONCLUSIONS For confirmation of Enterococcus genus from mEI media, conventional or genus screen biochemical testing, 16S rRNA sequencing and the four commercial systems were correct 79-100% of the time. For speciation to an accuracy of 90% or better, either conventional biochemical testing or 16S rRNA sequencing is required. SIGNIFICANCE AND IMPACT OF THE STUDY Accurate identification of presumptive environmental Enterococcus isolates to genus and species level is an integral part of laboratory quality assurance and further characterization of Enterococcus species from pollution incidents. This investigation determines the ability of six different methods to correctly identify environmental isolates.
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Affiliation(s)
- D F Moore
- Orange County Public Health Laboratory, Newport Beach, CA 92660, USA
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Shanks OC, Santo Domingo JW, Graham JE. Use of competitive DNA hybridization to identify differences in the genomes of bacteria. J Microbiol Methods 2006; 66:321-30. [PMID: 16469400 DOI: 10.1016/j.mimet.2005.12.006] [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] [Received: 12/08/2005] [Accepted: 12/19/2005] [Indexed: 11/20/2022]
Abstract
Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, comparisons of closely related bacterial species and individual isolates by whole-genome sequencing approaches remains prohibitively expensive for most laboratories. Here we report the development and testing of a biochemical approach for targeted sequencing of only those chromosomal regions that differ between two DNA preparations. The method, designated GFE (genome fragment enrichment) uses competitive solution hybridization and positive selection to obtain genomic DNA fragments that are present in one pool of fragments but not another. Repeated comparisons of the genomes of Enterococcus faecalis and E. faecium led to the identification of 225 putative genome-specific DNA fragments. Species and strain variations within these fragments were confirmed by both experimental and bioinformatic analyses. The E. faecalis genome-specific sequences identified included both a preponderance of those predicted to encode surface-exposed proteins, as well as several previously described unique marker regions embedded within highly conserved rrn operons. The GFE strategy we describe efficiently identified genomic differences between two enterococcal genomes, and will be widely applicable for studying genetic variation among closely related bacterial species.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH, USA
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PIPER KERRYLE, HANSSEN ARLEND, LEWALLEN DAVIDG, MATTESON ERICL, OSMON DOUGLASR, DUFFY MARYC, HAGAN ROCHELLEA, STECKELBERG JAMESM, PATEL ROBIN. Lack of detection of human retrovirus-5 proviral DNA in synovial tissue and blood specimens from individuals with rheumatoid arthritis or osteoarthritis. ACTA ACUST UNITED AC 2006; 55:123-5. [PMID: 16463423 PMCID: PMC1464419 DOI: 10.1002/art.21690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Prior studies have suggested an association of human retrovirus 5 with rheumatoid arthritis. The purpose of this study was to determine if human retrovirus-5 proviral DNA is present in synovial tissue and blood specimens from patients with rheumatoid arthritis or osteoarthritis, or those without joint disease. METHODS Synovial tissue and whole blood from 75 patients with rheumatoid arthritis, 75 patients with osteoarthritis, and 50 patients without a primary arthritis diagnosis were assayed by real-time quantitative polymerase chain reaction (PCR) using primers that amplify a 186-bp fragment of human retrovirus-5 proviral DNA. RESULTS A total of 200 tissue specimens, 200 mononuclear cells, and 196 of 200 granulocyte specimens tested negative for human retrovirus-5 proviral DNA. No association between human retrovirus 5 and rheumatoid arthritis or osteoarthritis (P = 0.516) was identified. Granulocyte specimens from 4 patients, 2 with rheumatoid arthritis and 2 with osteoarthritis, yielded a low positive human retrovirus-5 proviral DNA signal (83-1,365 copies of human retrovirus-5 proviral DNA/ml blood). CONCLUSION Contrary to prior reports, we did not find an association between human retrovirus 5 and rheumatoid arthritis or osteoarthritis using a real-time PCR assay. Our findings are consistent with the recent finding that human retrovirus 5 is actually rabbit endogenous retrovirus H.
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Affiliation(s)
| | | | | | | | | | | | | | | | - ROBIN PATEL
- Address correspondence to Robin Patel, MD, Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905. E-mail:
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Manero A, Vilanova X, Cerdà-Cuéllar M, Blanch AR. Vancomycin- and erythromycin-resistant enterococci in a pig farm and its environment. Environ Microbiol 2006; 8:667-74. [PMID: 16584478 DOI: 10.1111/j.1462-2920.2005.00945.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A high prevalence of vancomycin- and erythromycin-resistant enterococci (VRE and ERE respectively) in a pig farm and its environment was observed. A similar structure and composition of enterococcal populations was detected between urban sewage and those associated with the pig environment. Enterococcus faecium was the most predominant species among VRE isolates from both animal and human origin. The high population similarity index (Sp) obtained comparing VRE and ERE isolates from urban sewage and pig slurry suggests that there are certain strains circulating through the food chain from farms to humans. Erythromycin resistance was present in a wider variety of clones and species of enterococci in both pigs and humans than vancomycin resistance.
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Affiliation(s)
- Albert Manero
- Laboratori d'Anàlisi Mediambiental, Secció Microbiologia, Aigües de Terrassa, S.A., Carrer del Nord, 88, E 08221 Terrassa (Barcelona), Catalonia, Spain
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Botina SG, Sukhodolets VV. Speciation in bacteria: Comparison of the 16S rRNA gene for closely related Enterococcus species. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406030033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Naser SM, Vancanneyt M, Hoste B, Snauwaert C, Vandemeulebroecke K, Swings J. Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004. Int J Syst Evol Microbiol 2006; 56:413-416. [PMID: 16449449 DOI: 10.1099/ijs.0.63891-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic relatedness between the speciesEnterococcus casseliflavusandEnterococcus flavescensand betweenEnterococcus italicusandEnterococcus saccharominimuswas investigated. Literature data had already indicated the synonymy betweenE. casseliflavusandE. flavescens, but this observation had not been formally published. Additional evidence that the two taxa represent a single species was provided by comparison of the partial sequences for three housekeeping genes, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the alpha subunit of ATP synthase (atpA). Additional genomic data derived from DNA–DNA hybridization demonstrated that the two species are synonymous. ForE. italicusandE. saccharominimus, two recently described taxa, a high 16S rRNA gene sequence similarity of >99 % and analogous phenotypic features indicated a close taxonomic relatedness. The same multilocus sequence analysis scheme for the three housekeeping genes was also applied forE. italicusandE. saccharominimusand indicated possible conspecificity, an observation that was also confirmed by a high DNA–DNA hybridization value (⩾78 %). Data from the present study led to the proposal thatE. flavescensshould be reclassified as a later synonym ofE. casseliflavusand thatE. saccharominimusshould be reclassified as a later synonym ofE. italicus.
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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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The Lactic Acid Enterococci Enterococcus faecium and Enterococcus durans: Nucleotide Sequence Diversity in 16S rRNA Genes. Microbiology (Reading) 2005. [DOI: 10.1007/s11021-005-0127-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Waar K, Degener JE, van Luyn MJ, Harmsen HJ. Fluorescent in situ hybridization with specific DNA probes offers adequate detection of Enterococcus faecalis and Enterococcus faecium in clinical samples. J Med Microbiol 2005; 54:937-944. [PMID: 16157547 DOI: 10.1099/jmm.0.46022-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are among the leading causes of hospital-acquired infections. Reliable and quick identification of E. faecalis and E. faecium is important for accurate treatment and understanding their role in the pathogenesis of infections. Fluorescent in situ hybridization (FISH) of whole bacterial cells with oligonucleotides targeted at the 16S rRNA molecule leads to a reduced time to identification. In clinical practice, FISH therefore can be used in situations in which quick identification is necessary for optimal treatment of the patient. Furthermore, the abundance, spatial distribution and bacterial cell morphology can be observed in situ. This report describes the design of two fluorescent-labelled oligonucleotides that, respectively, detect the 16S rRNA of E. faecalis and the 16S rRNA of E. faecium, Enterococcus hirae, Enterococcus mundtii, Enterococcus villorum and Enterococcus saccharolyticus. Different protocols for the application of these oligonucleotides with FISH in different clinical samples such as faeces or blood cultures are given. Enterococci in a biofilm attached to a biomaterial were also visualized. Embedding of the biomaterial preserved the morphology and therefore the architecture of the biofilm could be observed. The usefulness of other studies describing FISH for detection of enterococci is generally hampered by the fact that they have only focused on one material and one protocol to detect the enterococci. However, the results of this study show that the probes can be used both in the routine laboratory to detect and determine the enterococcal species in different clinical samples and in a research setting to enumerate and detect the enterococci in their physical environment.
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Affiliation(s)
- Karola Waar
- Departments of Medical Microbiology1, and Pathology and Laboratory Medicine2, Section Medical Biology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - John E Degener
- Departments of Medical Microbiology1, and Pathology and Laboratory Medicine2, Section Medical Biology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marja J van Luyn
- Departments of Medical Microbiology1, and Pathology and Laboratory Medicine2, Section Medical Biology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hermie Jm Harmsen
- Departments of Medical Microbiology1, and Pathology and Laboratory Medicine2, Section Medical Biology, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Alyaseen SA, Piper KE, Rouse MS, Steckelberg JM, Patel R. Selection of cross-resistance following exposure of Pseudomonas aeruginosa clinical isolates to ciprofloxacin or cefepime. Antimicrob Agents Chemother 2005; 49:2543-5. [PMID: 15917569 PMCID: PMC1140511 DOI: 10.1128/aac.49.6.2543-2545.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Exposure of ciprofloxacin- and cefepime-susceptible Pseudomonas aeruginosa isolates to increasing concentrations of ciprofloxacin selected for ciprofloxacin resistance in 26/27 and cefepime nonsusceptibility in 7/27 isolates. Exposure of the isolates to increasing concentrations of cefepime selected for cefepime nonsusceptibility in 20/27 isolates but not for ciprofloxacin resistance.
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Affiliation(s)
- Samer A Alyaseen
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN 55905, USA
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Naser S, Thompson FL, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I, Thompson CC, Vancanneyt M, Swings J. Phylogeny and identification of Enterococci by atpA gene sequence analysis. J Clin Microbiol 2005; 43:2224-30. [PMID: 15872246 PMCID: PMC1153757 DOI: 10.1128/jcm.43.5.2224-2230.2005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relatedness among 91 Enterococcus strains representing all validly described species was investigated by comparing a 1,102-bp fragment of atpA, the gene encoding the alpha subunit of ATP synthase. The relationships observed were in agreement with the phylogeny inferred from 16S rRNA gene sequence analysis. However, atpA gene sequences were much more discriminatory than 16S rRNA for species differentiation. All species were differentiated on the basis of atpA sequences with, at a maximum, 92% similarity. Six members of the Enterococcus faecium species group (E. faecium, E. hirae, E. durans, E. villorum, E. mundtii, and E. ratti) showed > 99% 16S rRNA gene sequence similarity, but the highest value of atpA gene sequence similarity was only 89.9%. The intraspecies atpA sequence similarities for all species except E. faecium strains varied from 98.6 to 100%; the E. faecium strains had a lower atpA sequence similarity of 96.3%. Our data clearly show that atpA provides an alternative tool for the phylogenetic study and identification of enterococci.
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Affiliation(s)
- S Naser
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium.
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45
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Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P, Vancanneyt M, Swings J. Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology (Reading) 2005; 151:2141-2150. [PMID: 16000705 DOI: 10.1099/mic.0.27840-0] [Citation(s) in RCA: 304] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to evaluate the use of RNA polymeraseαsubunit (rpoA) and phenylalanyl-tRNA synthase (pheS) gene sequences as species identification tools for enterococci. Ninety-six representative strains comprising all currently recognizedEnterococcusspecies were examined.rpoAgene sequences generated a robust classification into species groups similar to the one based on 16S rRNA gene sequence analysis. On the other hand, thepheSgene is a fast-evolving clock even better suited for species delineation than therpoAgene, but not for recognition of species groups withinEnterococcusas determined by bothrpoAand 16S rRNA genes. All enterococcal species were clearly differentiated on the basis of theirrpoAandpheSsequences. Evaluation of intraspecies variation showed that bothrpoAandpheSgenes have a high degree of homogeneity among strains of the same species. Strains of the same enterococcal species have at least 99 %rpoAand 97 %pheSgene sequence similarity, whereas, different enterococcal species have at maximum 97 %rpoAand 86 %pheSgene sequence similarity. It was concluded that both genes can be used as reliable tools for identification of clinical and environmental species ofEnterococcusand are efficient screening methods for the detection of novel species. The sequence data obtained in this study were compared to the availableatpAand 16S rRNA gene sequences. The MLSA approach toEnterococcustaxonomy provides portable, highly reproducible data with lower costs for rapid identification of all enterococcal species.
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Affiliation(s)
- Sabri M Naser
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Fabiano L Thompson
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Bart Hoste
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Dirk Gevers
- Bioinformatics and Evolutionary Genomics, Ghent University/VIB, Technologiepark 927, Ghent 9052, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Peter Dawyndt
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Jean Swings
- BCCM/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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He JW, Jiang S. Quantification of enterococci and human adenoviruses in environmental samples by real-time PCR. Appl Environ Microbiol 2005; 71:2250-5. [PMID: 15870308 PMCID: PMC1087545 DOI: 10.1128/aem.71.5.2250-2255.2005] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 12/07/2004] [Indexed: 11/20/2022] Open
Abstract
Pathogenic bacteria and enteric viruses can be introduced into the environment via human waste discharge. Methods for rapid detection and quantification of human viruses and fecal indicator bacteria in water are urgently needed to prevent human exposure to pathogens through drinking and recreational waters. Here we describe the development of two real-time PCR methods to detect and quantify human adenoviruses and enterococci in environmental waters. For real-time quantification of enterococci, a set of primers and a probe targeting the 23S rRNA gene were used. The standard curve generated using Enterococcus faecalis genomic DNA was linear over a 7-log-dilution series. Serial dilutions of E. faecalis suspensions resulted in a lower limit of detection (LLD) of 5 CFU/reaction. To develop real-time PCR for adenoviruses, degenerate primers and a Taqman probe targeting a 163-bp region of the adenovirus hexon gene were designed to specifically amplify 14 different serotypes of human adenoviruses, including enteric adenovirus serotype 40 and 41. The standard curve generated was linear over a 5-log-dilution series, and the LLD was 100 PFU/reaction using serial dilutions of purified adenoviral particles of serotype 40. Both methods were optimized to be applicable to environmental samples. The real-time PCR methods showed a greater sensitivity in detection of adenoviruses in sewage samples than the viral plaque assay and in detection of enterococci in coastal waters than the bacterial culture method. However, enterococcus real-time PCR overestimated the number of bacteria in chlorinated sewage in comparison with the bacterial culture method. Overall, the ability via real-time PCR to detect enterococci and adenoviruses rapidly and quantitatively in the various environmental samples represents a considerable advancement and a great potential for environmental applications.
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Affiliation(s)
- Jian-Wen He
- Dept. of Environmental Health, Science, and Policy, University of California, Irvine, CA 92697, USA
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Higashide T, Takahashi M, Kobayashi A, Ohkubo S, Sakurai M, Shirao Y, Tamura T, Sugiyama K. Endophthalmitis caused by Enterococcus mundtii. J Clin Microbiol 2005; 43:1475-6. [PMID: 15750139 PMCID: PMC1081296 DOI: 10.1128/jcm.43.3.1475-1476.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus mundtii has rarely been isolated from environmental or human sources. We report the identification of E. mundtii as a pathogen of human infectious disease by DNA sequencing of 16S rRNA and sodA genes in a case of endophthalmitis developed in a 66-year-old immunocompetent gardener.
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Affiliation(s)
- Tomomi Higashide
- Department of Ophthalmology, Kanazawa University Graduate School of Medical Science, 13-1 Takara-machi, Kanazawa, Ishikawa 9208641, Japan.
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Ennahar S, Cai Y. Biochemical and genetic evidence for the transfer of Enterococcus solitarius Collins et al. 1989 to the genus Tetragenococcus as Tetragenococcus solitarius comb. nov. Int J Syst Evol Microbiol 2005; 55:589-592. [PMID: 15774629 DOI: 10.1099/ijs.0.63205-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of 16S rRNA gene sequences revealed thatEnterococcus solitariusis not a member of the genusEnterococcus, but is related to species of the genusTetragenococcus. On a phylogenetic tree,E. solitariusclustered withTetragenococcus halophilusandTetragenococcus muriaticus, with which it showed the highest 16S rRNA gene sequence similarity level (about 94 %). Phenotypic studies indicated thatE. solitariuswas also unable to produce acid from lactose, providing further evidence of its affiliation to the genusTetragenococcus. DNA hybridization studies indicated thatE. solitariuswas clearly a separate species, different fromT. halophilusandT. muriaticus(reassociation levels of about 23 and 54 %, respectively). As suggested in previous studies,E. solitariusis closely related to but clearly distinct fromT. halophilus. Based upon properties that taxonomically distinguish it from species of the genusEnterococcus, it is proposed thatE. solitariusbe transferred to the genusTetragenococcusand reclassified asTetragenococcus solitariuscomb. nov. (type strain, 885/78T=ATCC 49428T=CCUG 29293T=CIP 103330T=DSM 5634T=JCM 8736T=LMG 12890T=NCTC 12193T).
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Affiliation(s)
- Saïd Ennahar
- Laboratoire de Chimie Analytique et Sciences de l'Aliment (UMR 7512), Faculté de Pharmacie, Université Louis Pasteur, 74, route du Rhin, 67400 Illkirch, France
- National Institute of Livestock and Grassland Science, Department of Animal Feeding and Management, Nishinasuno, Tochigi 329-2793, Japan
| | - Yimin Cai
- National Institute of Livestock and Grassland Science, Department of Animal Feeding and Management, Nishinasuno, Tochigi 329-2793, Japan
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Tsai JC, Hsueh PR, Lin HM, Chang HJ, Ho SW, Teng LJ. Identification of clinically relevant enterococcus species by direct sequencing of groES and spacer region. J Clin Microbiol 2005; 43:235-41. [PMID: 15634977 PMCID: PMC540105 DOI: 10.1128/jcm.43.1.235-241.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We determined the groESL sequences (groES, groEL, and the intergenic spacer) of 10 clinically relevant Enterococcus species and evaluated the feasibility of identifying Enterococcus species on the basis of these sequences. Seven common clinical Enterococcus species, E. faecalis, E. faecium, E. casseliflavus, E. gallinarum, E. avium, E. raffinosus, and E. hirae, and three less common Enterococcus species, E. cecorum, E. durans, and E. mundtii, were examined in this study. We found that the groES genes of these enterococcal species are identical in length (285 nucleotides) and contain an unusual putative start codon, GTG. The lengths and sequences of the intergenic regions (spacers between the groES and groEL genes) are quite variable (17 to 57 bp in length) among Enterococcus species but are conserved in strains within each species, with only a few exceptions. Considerable variation of groES or groEL sequences was also observed. The evolutionary trees of groES or groEL sequences revealed similarities among Enterococcus species. However, the overall intraspecies variation of groES was less than that of groEL. The high interspecies variation and low intraspecies variation indicate that the groES and spacer sequences are more useful than groEL for identification of clinically relevant Enterococcus species. The sequences of these two genetic traits, groES and spacer, can be determined by a single PCR and direct sequencing and may provide important information for the differentiation of closely related species of Enterococcus.
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Affiliation(s)
- Jui-Chang Tsai
- Division of Neurosurgery, Department of Surgery, National Taiwan University College of Medicine, No. 1, Chang-Te St., Taipei, Taiwan
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Sedgley CM, Nagel AC, Shelburne CE, Clewell DB, Appelbe O, Molander A. Quantitative real-time PCR detection of oral Enterococcus faecalis in humans. Arch Oral Biol 2004; 50:575-83. [PMID: 15848151 DOI: 10.1016/j.archoralbio.2004.10.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 10/25/2004] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Enterococcus faecalis is consistently associated with recurrent root canal infections. Only low concentrations of E. faecalis in the human mouth have been demonstrated by culture techniques. Quantitative detection strategies more sensitive than culturing, such as quantitative PCR (qPCR), could provide more illuminating data. DESIGN Thirty outpatients attending the University of Michigan Graduate Endodontic Clinic for endodontic treatment provided oral rinse samples that were analysed for E. faecalis using qPCR and microbiological culturing. A SYBR Green I qPCR protocol was developed for the quantifiable detection of E. faecalis and total bacteria in oral rinse samples using primers designed to target the 16S rRNA gene. Annealing temperature and primer, magnesium ion, and dimethyl sulfoxide concentrations were investigated for optimisation of the protocol; a minimum sensitivity limit of 23 rRNA copies (an estimated six E. faecalis cells) was established for E. faecalis in pure culture, and 104 rRNA copies (an estimated 26 E. faecalis cells) in mixed culture. RESULTS In qPCR assays, based on extrapolation from estimated rRNA gene copy numbers, E. faecalis comprised 0.0006-0.0047% of a total bacteria load that ranged from 5.92 x 10(5) to 5.69 x 10(7) cells/ml of oral rinse. E. faecalis was detected in five (17%) samples in concentrations from 114 to 490 cells/ml. In parallel culture assays E. faecalis were detected in only two samples (7%) of the five identified by qPCR and in concentrations 30 and 240 CFU/ml. CONCLUSIONS qPCR reported a higher incidence of E. faecalis in oral rinse samples than culture techniques and afforded greater sensitivity.
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Affiliation(s)
- C M Sedgley
- Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan, Ann Arbor, MI 48109-1078, USA.
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