title: Array-based identification of species of the genera Abiotrophia, Enterococcus, Granulicatella, and Streptococcus.
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.
authors.affiliation: 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.
authors.forename: Sheng Kai
authors.initials: SK
authors.lastname: Tung
authors.forename: Lee Jene
authors.initials: LJ
authors.lastname: Teng
authors.forename: Mario
authors.initials: M
authors.lastname: Vaneechoutte
authors.forename: Hung Mo
authors.initials: HM
authors.lastname: Chen
authors.forename: Tsung Chain
authors.initials: TC
authors.lastname: Chang
mesh_terms: D001431:Bacteriological Techniques; D001769:Blood / Q000382:microbiology; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D016983:Enterococcus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D006094:Gram-Positive Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D006801:Humans; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013291:Streptococcus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer; D015345:Oligonucleotide Probes