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Acinetobacter — Microbiology
Published in E. Bergogne-Bénézin, M.L. Joly-Guillou, K.J. Towner, Acinetobacter, 2020
Characterisation of microorganisms by ribotyping has appeared useful in a number of reports (Owen, 1989; Grimont and Grimont, 1986). The method as used for Acinetobacter has been described in detail by Gerner-Smidt (1992). Briefly, it comprises purification of DNA, digestion by restriction enzymes, separation of resulting fragments by agarose gel electrophoresis, and transfer to nylon membrane by vacuo- blotting. Selective banding patterns are visualised by hybridisation with a non-radioactive digoxigenin-ll-dUTP-labelled probe of cDNA from rRNA of E. coli (see Appendix VIII). By this method Gerner-Smidt (1992) investigated 70 strains that were identified as either A. calcoaceticus, A. baumannii or the unnamed genomic species 3 and 13TU by DNA-DNA hybridisation. Patterns generated by restriction with EcoRI, Clal or Sall were specific for each genomic group and are thus useful for identification. Reproducibility was excellent, and the discriminatory power for typing by combined use of the three enzymes was high, with 52 different patterns in 70 unrelated strains.
Enterococcus
Published in Dongyou Liu, Laboratory Models for Foodborne Infections, 2017
PFGE represents the current standard in the clinical identification of Enterococcus spp. and strain typing, while ribotyping techniques allow accurate discrimination among species with reduced cost. Interestingly, MLST demonstrates an accuracy equivalent to that of PFGE for the identification of organisms to the subspecies level. de Been et al. [24] developed a core genome MLST (cgMLST) scheme for E. faecium that is capable of distinguishing between epidemiologically related and unrelated isolates, even between those of identical ST. Hullahalli et al. [25] showed that clustered, regularly interspaced short palindromic repeats (CRISPR) 2 analysis is an inexpensive alternative to MLST for assessing clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs. Other novel approaches for enterococcal identification include quantitative PCR (qPCR) targeting the esp gene of E. faecium (espfm), DNA microarrays, and use of bacteriophages specific to certain Enterococcus strains.
Mycobacterium tuberculosis – The Organism
Published in Peter D O Davies, Stephen B Gordon, Geraint Davies, Clinical Tuberculosis, 2014
Despite this work, many anomalies and confusions lingered in the nomenclature of the mycobacteria, as well as in other areas of bacterial taxonomy. In 1980, the Approved Lists of Bacterial Names were published to serve as the reference point for all further nomenclature [3]. These lists contained 41 species of mycobacteria, but many more have since been described. By 2012, more than 130 species were included in the List of Prokaryotic Names with Standing in Nomenclature (www.bacterio.cict.fr). For many years, a wide range of cultural and metabolic characteristics were used to define mycobacterial species until this approach was supplemented, and then largely superseded, by nucleic acid-based technology. Currently, the method of choice for defining mycobacterial species is ‘ribotyping’, based on differences in highly conserved regions of the genome, the DNA coding for 16S ribosomal ribonucleic acid (RNA) [4].
Various biofilm matrices of the emerging pathogen Staphylococcus lugdunensis: exopolysaccharides, proteins, eDNA and their correlation with biofilm mass
Published in Biofouling, 2020
Stefano Ravaioli, Davide Campoccia, Pietro Speziale, Giampiero Pietrocola, Beata Zatorska, Alessandra Maso, Elisabeth Presterl, Lucio Montanaro, Carla Renata Arciola
All 22 isolates were processed for automated ribotyping by a RiboPrinter® Microbial Characterization System (Qualicon, Wilmington, DE, USA). Pure culture samples were obtained from tryptic soy agar (TSA, Biolife) plates incubated for 24 h at 37 °C. The ribotyping was performed according to the instructions of the producer. EcoRI was the restriction enzyme used for the analysis. The isolates were taxonomically identified and automatically subtyped into ribogroups by the RiboPrinter®, based on the similarity of the ribotypes patterns generated. The identification of each isolate was obtained when the corresponding pattern matched one of the patterns of the DuPont Identification Library with a similarity > 0.85.
Shared detection of Porphyromonas gingivalis in cohabiting family members: a systematic review and meta-analysis
Published in Journal of Oral Microbiology, 2020
Maha Bennani, Hélène Rangé, Vincent Meuric, Francis Mora, Philippe Bouchard, Maria Clotilde Carra
Bacterial sampling was carried out on supra-gingival and/or subgingival plaque, stimulated saliva, or sampled from dorsum of the tongue, buccal mucosa, or tonsillar area. Detection methods included culture in 10 studies (38.4%), and Polymerase Chain Reaction (PCR) in 11 studies (42.3%). DNA restriction enzyme analysis (REA-DNA) was used in 4 studies (15.3%), pulsed field gel electrophoresis (PFGE) in 1 study, arbitrarily primed polymerase chain reaction (AP-PCR) in 2 (7.6%) studies, amplified fragment length polymorphism (AFLP-PCR) in 3, strain-specific identification of P. gingivalis I Isi 1126 PCR in 1, and Fim A genotyping in 3 studies. Serotyping characterization and ribotyping were reported in 2 studies, respectively.
Detection and elimination of a novel non-toxigenic Clostridioides difficile strain from the microbiota of a mouse colony
Published in Gut Microbes, 2020
Jeffrey R. Maslanka, Christopher H. Gu, Isma Zarin, Joshua E. Denny, Susan Broadaway, Bryton Fett, Lisa M. Mattei, Seth T. Walk, Michael C. Abt
PCR ribotyping was performed as previously described.56 DNA was isolated from either fecal pellets or from liquid culture using Qiagen DNeasy PowerSoil kit. Following DNA isolation, PCR ribotyping of the 16S gene region was performed (primer sequences listed in supplemental table 2), and PCR products were run on an agarose gel. Fluorescent PCR ribotyping was performed using a protocol as previously described.27,57