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Del Cerro A, Márquez I, Prieto JM. Genetic diversity and antimicrobial resistance of Flavobacterium psychrophilum isolated from cultured rainbow trout, Onchorynchus mykiss (Walbaum), in Spain. JOURNAL OF FISH DISEASES 2010; 33:285-291. [PMID: 20059636 DOI: 10.1111/j.1365-2761.2009.01120.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Flavobacterium psychrophilum is the causative agent of bacterial cold-water disease (CWD) and rainbow trout fry syndrome (RTFS) in salmonids. These diseases are a major problem in the aquaculture industry in Spain, and a better understanding of the epidemiology of F. psychrophilum isolates is necessary to improve management strategies. In this study, to investigate genetic variability of this bacterium, pulsed-field gel electrophoresis after DNA digestion with endonuclease StuI, plasmid profiling analysis and antimicrobial susceptibility testing were undertaken with 25 isolates of F. psychrophilum from Spain. These isolates were classified into 17 patterns by PFGE analysis, which were grouped into four clusters and seven independent branches. Twenty isolates (80%) possessed plasmids of 3.5 kb (n = 13) or 5.5 kb (n = 7). No plasmids were associated with antibiotic resistance to oxytetracycline (OTC) or florfenicol (FLO). Twenty isolates (80%) had minimum inhibitory concentrations (MICs) to OTC of between 2.4 and 9.7 microg mL(-1), and all isolates were susceptible to FLO. A relationship between the origin of the isolates and PFGE genotypes was found. Plasmid profile typing correlated with PFGE profile typing, whereas no correlation was found between antimicrobial susceptibility testing and PFGE profiles. These results suggest that the population of F. psychrophilum with pathogenic potential in northern Spain is quite heterogeneous.
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Affiliation(s)
- A Del Cerro
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Area de Sanidad Animal, Travesía del Hospital, Gijón, Spain.
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Jurkovic D, Krizková L, Sojka M, Takácová M, Dusinský R, Krajcovic J, Vandamme P, Vancanneyt M. Genetic diversity of Enterococcus faecium isolated from Bryndza cheese. Int J Food Microbiol 2007; 116:82-7. [PMID: 17300847 DOI: 10.1016/j.ijfoodmicro.2006.12.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 12/05/2006] [Accepted: 12/10/2006] [Indexed: 10/23/2022]
Abstract
One hundred and seventy-six Enterococcus faecium isolates from Slovak dairy product Bryndza were tested for the presence of plasmid DNA. Eighty-two isolates were positive and their plasmid DNA was isolated and digested by EcoRI and HindIII restriction endonucleases. The patterns obtained were compared with those obtained after pulsed-field gel electrophoresis of macrorestriction fragments (PFGE), (GTG)(5)-PCR and ERIC-PCR. All these molecular approaches were applied for the study of genetic variability and determination of strain relatednesses among plasmid-positive isolates of E. faecium. In general, all methods revealed a considerable genetic diversity of E. faecium isolates. Plasmid profiling and ERIC-PCR have offered a higher resolution than PFGE and (GTG)(5)-PCR.
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Affiliation(s)
- D Jurkovic
- Institute of Cell Biology, Faculty of Natural Sciences, Mlynská dolina, 84215 Bratislava, Slovakia.
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Rodríguez-Baño J, Ramírez E, Muniain MA, Santos J, Joyanes P, González F, García-Sánchez M, Martínez-Martínez L. Colonization by high-level aminoglycoside-resistant enterococci in intensive care unit patients: epidemiology and clinical relevance. J Hosp Infect 2005; 60:353-9. [PMID: 15893852 DOI: 10.1016/j.jhin.2004.12.024] [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] [Received: 11/30/2003] [Accepted: 12/15/2004] [Indexed: 11/30/2022]
Abstract
A cohort study was performed to investigate the risk factors for colonization with high-level aminoglycoside-resistant enterococci (HLARE) in intensive care unit (ICU) patients. Colonization was investigated by performing surveillance samples during ICU stay. Clonal relatedness of the isolates was assessed by pulsed-field gel electrophoresis. Eighty-six patients with an ICU stay of >48 h were included; two were colonized with HLARE at admission, and 24 (28.5%) acquired HLARE during their stay in the ICU. HLARE were initially isolated from rectal swabs alone. Thirty-five percent of Enterococcus faecalis and 57% of E. faecium showed high-level resistance to gentamicin or streptomycin. Most isolates were clonally unrelated. Using multi-variate analysis, the only variable associated with HLARE colonization was previous antimicrobial use. Five patients had HLARE isolated from clinical samples, three of them with infection; in all of these, colonization with the same clone had been detected previously by surveillance samples. We conclude that most infections due to HLARE in the ICU are preceded by previous colonization, and that antimicrobial use is the main risk factor for colonization.
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Affiliation(s)
- J Rodríguez-Baño
- Sección de Enfermedades Infecciosas, Hospital Universitario Virgen Macarena, Avda. Dr. Fedriani, 3, 41071 Sevilla, Spain.
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Domig KJ, Mayer HK, Kneifel W. Methods used for the isolation, enumeration, characterisation and identification of Enterococcus spp. Int J Food Microbiol 2003; 88:165-88. [PMID: 14596988 DOI: 10.1016/s0168-1605(03)00178-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper reviews the methodology applied for the identification and characterisation of enterococci and covers phenotypic, genotypic and phylogenetic techniques. Although conventional phenotypic typing schemes are useful for rapid and simple identification of enterococcal species for routine applications, other methods like standardised sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE), multilocus enzyme electrophoresis (MLEE), antimicrobial susceptibility testing, serotyping, pyrolysis mass spectrometry (pyMS) and vibrational spectroscopic methods allow a more in-depth characterisation of enterococci. Many of the recently described enterococcal species exhibit deviations from hitherto so-called classical enterococci with regard to their phenotypical properties. Therefore, genotypic methods have to be used to clarify their possible assignment to the genus Enterococcus. In this review, special emphasis is given on recently developed polymerase chain reaction (PCR)-based typing methods such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), specific and random amplification (SARA) and modifications of PCR-ribotyping as well as pulsed-field gel electrophoresis (PFGE) and partial sequence analysis. The use of PCR and probes for genus and species identification of enterococci is also considered like the application of sequence data of conserved DNA regions (e.g., ribosomal ribonucleic acid (rRNA) genes) in the case of species identification.
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Affiliation(s)
- Konrad J Domig
- Department of Dairy Research and Bacteriology, University of Natural Resources and Applied Life Sciences, Gregor Mendel Strasse 33, 1180 Vienna, Austria
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Larrasa J, Garcia A, Ambrose NC, Alonso JM, Parra A, de Mendoza MH, Salazar J, Rey J, de Mendoza JH. A simple random amplified polymorphic DNA genotyping method for field isolates of Dermatophilus congolensis. JOURNAL OF VETERINARY MEDICINE. B, INFECTIOUS DISEASES AND VETERINARY PUBLIC HEALTH 2002; 49:135-41. [PMID: 12019944 DOI: 10.1046/j.1439-0450.2002.00521.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Dermatophilus congolensis is the pathogenic actinomycete that causes dermatophilosis in cattle, lumpy wool in sheep and rain scald in horses. Phenotypic variation between isolates has previously been described, but its genetic basis, extent and importance have not been investigated. Standard DNA extraction methods are not always successful for D. congolensis due to its complex life cycle, one stage of which is encapsulated. Here we describe the development of rapid and reliable DNA extraction and random amplified polymorphic DNA (RAPD) methods that can be used for genotyping D. congolensis field isolates. Our results suggest that genotypic variation between isolates correlates with host species. Several DNA extraction methods and RAPD protocols were compared. An extraction method based on incubation of the bacterium in lysozyme, sodium dodecyl sulphate (SDS) and proteinase K treatments and phenolic extraction yielded high-quality DNA, which was used to optimize RAPD-polymerase chain reaction (PCR) protocols for two random primers. An alternative rapid, non-phenolic extraction method based on proteinase K treatment and thermal shock was selected for routine RAPD typing of isolates. DNA extracted from reference strains from cattle, sheep and horse using either method gave reproducible banding patterns with different DNA batches and different thermal cyclers. The rapid DNA extraction method and RAPD-PCR were applied to 38 D. congolensis field isolates. The band patterns of the field and type isolates correlated with host species but not with geographical location.
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Affiliation(s)
- J Larrasa
- Cátedra de Patologia Infecciosa, Universidad de Extremadura, Facultad de Veterinaria, Cáceres, Spain
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Nallapareddy SR, Duh RW, Singh KV, Murray BE. Molecular typing of selected Enterococcus faecalis isolates: pilot study using multilocus sequence typing and pulsed-field gel electrophoresis. J Clin Microbiol 2002; 40:868-76. [PMID: 11880407 PMCID: PMC120268 DOI: 10.1128/jcm.40.3.868-876.2002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present study compared the recently developed multilocus sequence typing (MLST) approach with a well-established molecular typing technique, pulsed-field gel electrophoresis (PFGE), for subspecies differentiation of Enterococcus faecalis isolates. We sequenced intragenic regions of three E. faecalis antigen-encoding genes (ace, encoding a collagen and laminin adhesin; efaA, encoding an endocarditis antigen; and salA, encoding a cell wall associated antigen) and one housekeeping gene (pyrC) of 22 E. faecalis isolates chosen largely for their temporal and geographical diversity, but also including some outbreak isolates. MLST analysis of polymorphic regions of these four genes identified 13 distinct sequence types (STs) with different allelic profiles; the composite sequences generated from the four sequenced gene fragments of individual isolates showed 98.3 to 100% identity among the 22 isolates. We also found that the allelic profiles from two sequences, ace and salA, were sufficient to distinguish all 13 STs of this study. The 13 STs corresponded to 12 different PFGE types, with one previously designated PFGE clone (a widespread U.S. clone of beta-lactamase-producing isolates) being classified into two highly related STs which differed at 2 of 2,894 bases, both in the same allele. MLST also confirmed the clonal relationships among the isolates of two other PFGE clonal groups, including vancomycin resistant isolates. Thus, this pilot study with representative E. faecalis isolates suggests that, similar to PFGE, the sequence-based typing method may be useful for differentiating isolates of E. faecalis to the subspecies level in addition to identifying outbreak isolates.
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Affiliation(s)
- Sreedhar R Nallapareddy
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School, Houston, Texas 77030, USA
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Dicuonzo G, Gherardi G, Lorino G, Angeletti S, Battistoni F, Bertuccini L, Creti R, Di Rosa R, Venditti M, Baldassarri L. Antibiotic resistance and genotypic characterization by PFGE of clinical and environmental isolates of enterococci. FEMS Microbiol Lett 2001; 201:205-11. [PMID: 11470363 DOI: 10.1111/j.1574-6968.2001.tb10758.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fifty-four Enterococcus faecalis and 20 Enterococcus faecium isolates from clinical and non-human sources in Rome, Italy, were characterized by antibiotic resistance and pulsed field gel electrophoresis (PFGE). Resistance to vancomycin, teicoplanin, ampicillin, and ciprofloxacin was more frequent in E. faecium than in E. faecalis, whereas high-level resistance to aminoglycoside was found primarily in E. faecalis. Multi-resistance was found primarily among clinical isolates, but was also observed among environmental isolates. Common genotypes shared among clinical and environmental isolates were observed, however, the majority of isolates occurred as unique, source-specific clones. Several PFGE types were associated with shared features in their antibiotic resistance patterns; evidences of clonal spread between and within wards were also noted. This is the first report indicating clonal relatedness between human and environmental enterococci isolated in Italy.
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Affiliation(s)
- G Dicuonzo
- Departimento di Medicina di Laboratorio e Microbiologia, Università Campus Biomedica, Rome, Italy.
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Turabelidze D, Kotetishvili M, Kreger A, Morris JG, Sulakvelidze A. Improved pulsed-field gel electrophoresis for typing vancomycin-resistant enterococci. J Clin Microbiol 2000; 38:4242-5. [PMID: 11060099 PMCID: PMC87572 DOI: 10.1128/jcm.38.11.4242-4245.2000] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A rapid protocol for subtyping vancomycin-resistant enterococci by pulsed-field gel electrophoresis is reported. The procedure is simple and potentially cost-effective and allows reproducible subtyping of the strains in approximately 1 day.
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Affiliation(s)
- D Turabelidze
- Division of Molecular Epidemiology, Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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Mannu L, Paba A, Pes M, Floris R, Scintu MF, Morelli L. Strain typing among enterococci isolated from home-made Pecorino Sardo cheese. FEMS Microbiol Lett 1999; 170:25-30. [PMID: 9919649 DOI: 10.1111/j.1574-6968.1999.tb13351.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Three molecular techniques (RAPD-polymerase chain reaction analysis, plasmid profile and pulsed-field gel electrophoresis) were used for a preliminary approach to type, at strain level, enterococci isolated from a 24-h-old home-made Pecorino Sardo (protected designation of origin) cheese. A high genetic polymorphism was found. Clusters obtained by the RAPD technique and plasmid profile analysis contained different strains. Pulsed-field gel electrophoresis proved to be an efficient and highly reproducible typing method. In addition, by combining the results from plasmid profile analysis and pulsed-field gel electrophoresis, it was possible to identify closely related strains probably belonging to the same clonal lineage.
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Affiliation(s)
- L Mannu
- Istituto Zootecnico e Caseario per la Sardegna, Olmedo, Italy.
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