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Castillo-Rojas G, Mazari-Hiríart M, Ponce de León S, Amieva-Fernández RI, Agis-Juárez RA, Huebner J, López-Vidal Y. Comparison of Enterococcus faecium and Enterococcus faecalis Strains isolated from water and clinical samples: antimicrobial susceptibility and genetic relationships. PLoS One 2013; 8:e59491. [PMID: 23560050 PMCID: PMC3613387 DOI: 10.1371/journal.pone.0059491] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 02/14/2013] [Indexed: 11/26/2022] Open
Abstract
Enterococci are part of the normal intestinal flora in a large number of mammals, and these microbes are currently used as indicators of fecal contamination in water and food for human consumption. These organisms are considered one of the primary causes of nosocomial and environmental infections due to their ability to survive in the environment and to their intrinsic resistance to antimicrobials. The aims of this study were to determine the biochemical patterns and antimicrobial susceptibilities of Enterococcus faecalis and E. faecium isolates from clinical samples and from water (groundwater, water from the Xochimilco wetland, and treated water from the Mexico City Metropolitan Area) and to determine the genetic relationships among these isolates. A total of 121 enterococcus strains were studied; 31 and 90 strains were isolated from clinical samples and water (groundwater, water from the Xochimilco wetland, and water for agricultural irrigation), respectively. Identification to the species level was performed using a multiplex PCR assay, and antimicrobial profiles were obtained using a commercial kit. Twenty-eight strains were analyzed by pulsed-field gel electrophoresis (PFGE). E. faecium strains isolated from water showed an atypical biochemical pattern. The clinical isolates showed higher resistance to antibiotics than those from water. Both the enterococci isolated from humans, and those isolated from water showed high genetic diversity according to the PFGE analysis, although some strains seemed to be closely related. In conclusion, enterococci isolated from humans and water are genetically different. However, water represents a potential route of transmission to the community and a source of antimicrobial resistance genes that may be readily transmitted to other, different bacterial species.
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Affiliation(s)
- Gonzalo Castillo-Rojas
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, México
| | - Marisa Mazari-Hiríart
- Laboratorio de Ecología Química, Instituto de Ecología, Universidad Nacional Autónoma de México, México City, México
| | - Sergio Ponce de León
- Subdirector de Servicios Paramédicos, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México City, México
| | - Rosa I. Amieva-Fernández
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, México
| | - Raúl A. Agis-Juárez
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, México
| | - Johannes Huebner
- Division of Infectious Diseases, Department of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Yolanda López-Vidal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México City, México
- * E-mail:
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Sistek V, Maheux AF, Boissinot M, Bernard KA, Cantin P, Cleenwerck I, De Vos P, Bergeron MG. Enterococcus ureasiticus sp. nov. and Enterococcus quebecensis sp. nov., isolated from water. Int J Syst Evol Microbiol 2012; 62:1314-1320. [DOI: 10.1099/ijs.0.029033-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three enterococcal isolates, CCRI-16620, CCRI-16986T and CCRI-16985T, originating from water were characterized using morphological, biochemical and molecular taxonomic methods. 16S rRNA gene sequence analysis classified all three strains in the
Enterococcus faecalis
species group. The phylogenetic tree of 16S rRNA gene sequences showed that the three isolates form two separate branches. The first branch is represented by strains CCRI-16620 and CCRI-16986T and the second branch by strain CCRI-16985T. Further sequence analysis of the housekeeping genes rpoA (encoding RNA polymerase α subunit), pheS (phenylalanyl-tRNA synthase), tufA (elongation factor Tu) and atpD (ATP synthase β-subunit) as well as the results of amplified fragment length polymorphism (AFLP) DNA fingerprinting and DNA–DNA hybridization experiments confirmed the distinct status of these strains. Moreover, biochemical tests allowed phenotypic differentiation of the strains from the other species of the
E. faecalis
species group. On the basis of the results obtained, the names Enterococcus ureasiticus sp. nov. (type strain CCRI-16986T = CCUG 59304T = DSM 23328T = LMG 26304T) and Enterococcus quebecensis sp. nov. (type strain CCRI-16985T = CCUG 59306T = DSM 23327T = LMG 26306T) are proposed for the two hitherto undescribed species.
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Affiliation(s)
- Viridiana Sistek
- Département de microbiologie-infectiologie et d’immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
- Centre de recherche en infectiologie de l’Université Laval, Centre de recherche du CHUQ, Pavillon CHUL, 2705 boulevard Laurier, RC-709, Québec, QC, G1V 4G2, Canada
| | - Andrée F. Maheux
- Département de microbiologie-infectiologie et d’immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
- Centre de recherche en infectiologie de l’Université Laval, Centre de recherche du CHUQ, Pavillon CHUL, 2705 boulevard Laurier, RC-709, Québec, QC, G1V 4G2, Canada
| | - Maurice Boissinot
- Département de microbiologie-infectiologie et d’immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
- Centre de recherche en infectiologie de l’Université Laval, Centre de recherche du CHUQ, Pavillon CHUL, 2705 boulevard Laurier, RC-709, Québec, QC, G1V 4G2, Canada
| | - Kathryn A. Bernard
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Health Canada H5040-1015 Arlington St, Winnipeg, MB, Canada
| | - Philippe Cantin
- Centre d’Expertise en Analyse Environnementale du Québec, Ministère du Développement Durable de l’Environnement et des Parcs, Québec, QC, Canada
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, Ghent, Belgium
| | - Paul De Vos
- LM-UGent, Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, Ghent, Belgium
| | - Michel G. Bergeron
- Département de microbiologie-infectiologie et d’immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada
- Centre de recherche en infectiologie de l’Université Laval, Centre de recherche du CHUQ, Pavillon CHUL, 2705 boulevard Laurier, RC-709, Québec, QC, G1V 4G2, Canada
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Chakravorty S, Aladegbami B, Burday M, Levi M, Marras SAE, Shah D, El-Hajj HH, Kramer FR, Alland D. Rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique. J Clin Microbiol 2010; 48:258-67. [PMID: 19923485 PMCID: PMC2812257 DOI: 10.1128/jcm.01725-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 10/25/2009] [Accepted: 11/07/2009] [Indexed: 11/20/2022] Open
Abstract
A real-time PCR assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. Current real-time PCR technologies cannot accomplish this task due to severe limitations in multiplexing ability. To this end, we developed a new assay system which supports very high degrees of multiplexing. We developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelting temperature (T(m)) signature approach to bacterial species identification. Sloppy molecular beacons were exceptionally versatile, and they were able to generate specific T(m) values for DNA sequences that differed by as little as one nucleotide to as many as 23 polymorphisms. Combining the T(m) values generated by several probe-target hybrids resulted in T(m) signatures that served as highly accurate sequence identifiers. Using this method, PCR assays with as few as six sloppy molecular beacons targeting bacterial 16S rRNA gene segments could reproducibly classify 119 different sequence types of pathogenic and commensal bacteria, representing 64 genera, into 111 T(m) signature types. Blinded studies using the assay to identify the bacteria present in 270 patient-derived clinical cultures including 106 patient blood cultures showed a 95 to 97% concordance with conventional methods. Importantly, no bacteria were misidentified; rather, the few species that could not be identified were classified as "indeterminate," resulting in an assay specificity of 100%. This approach enables highly multiplexed target detection using a simple PCR format that can transform infectious disease diagnostics and improve patient outcomes.
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Affiliation(s)
- Soumitesh Chakravorty
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Bola Aladegbami
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Michele Burday
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Michael Levi
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Salvatore A. E. Marras
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Darshini Shah
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Hiyam H. El-Hajj
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Fred Russell Kramer
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - David Alland
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
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Velasco D, Perez S, Peña F, Dominguez MA, Cartelle M, Molina F, Moure R, Villanueva R, Bou G. Lack of correlation between phenotypic techniques and PCR-based genotypic methods for identification of Enterococcus spp. Diagn Microbiol Infect Dis 2004; 49:151-6. [PMID: 15246503 DOI: 10.1016/j.diagmicrobio.2004.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Accepted: 03/17/2004] [Indexed: 11/28/2022]
Abstract
A total of 123 genetically-unrelated strains of Enterococcus spp. strains (51 Enterococcus faecalis, 57 Enterococcus faecium, 10 Enterococcus gallinarum, and 5 Enterococcus casseliflavus) were phenotypically identified by biochemical profiles and by using an automated method. The strains were also analyzed by a PCR assay to assess the accuracy of the phenotypically-based methods for identification of Enterococcus spp. With this aim, a PCR assay using different cell targets, which allows simultaneous detection of glycopeptide-resistant genotypes as well as identification to the species level by means of different gene targets, was used as the gold standard method. All 51 strains of E. faecalis were correctly identified, whereas 48 of 57 strains (84.2%) of E. faecium, were correctly identified. All of the strains of E. gallinarum and 3 out of 5 strains of E. casseliflavus were also correctly identified. The overall results showed that it is possible to identify Enterococcus spp. at the molecular level in less than 30 hours, compared with the 48-96 hours required for the phenotypically-based methods. The excellent accuracy of the PCR assay in identifying these species, particularly E. faecium, must also be emphasized. These findings may have implications for the routine clinical identification of enterococci species.
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Affiliation(s)
- David Velasco
- Servicio de Microbiologia, Complejo Hospitalario Universitario Juan Canalejo, La Coruña, Spain
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