Identification of Clinically Important Anaerobic Bacteria by an Oligonucleotide Array

• Published in: Journal of Clinical Microbiology Vol. 48; no. 4; pp. 1283 - 1290
• Main Authors: Lin, Yu Tzu, Vaneechoutte, Mario, Huang, Ay Huey, Teng, Lee Jene, Chen, Hung-Mo, Su, Shu-Li, Chang, Tsung Chain
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01.04.2010; American Society for Microbiology (ASM)
• Subjects: Bacteria, Anaerobic - classification; Bacteria, Anaerobic - genetics; Bacteria, Anaerobic - isolation & purification; Bacterial Infections - diagnosis; Bacterial Infections - microbiology; Bacteriological Techniques - methods; Bacteriology; Bacteroides vulgatus; DNA Primers - genetics; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal Spacer - chemistry; DNA, Ribosomal Spacer - genetics; Humans; Molecular Sequence Data; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis - methods; Polymerase Chain Reaction - methods; Sensitivity and Specificity; Sequence Analysis, DNA; Veillonella
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/JCM.01620-09

Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and VEILLONELLA: The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.