Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli - PubMed (original) (raw)

Comparative Study

Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli

Y W Tang et al. J Clin Microbiol. 1998 Dec.

Abstract

Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. We used identification systems based on cellular fatty acid profiles (Sherlock; MIDI, Inc., Newark, Del.), carbon source utilization (Microlog; Biolog, Inc., Hayward, Calif.), and 16S rRNA gene sequence (MicroSeq; Perkin-Elmer Applied Biosystems Division, Foster City, Calif.) to evaluate 72 unusual aerobic gram-negative bacilli isolated from clinical specimens at the Mayo Clinic. Compared to lengthy conventional methods, Sherlock, Microlog, and MicroSeq were able to identify 56 of 72 (77.8%), 63 of 72 (87.5%), and 70 of 72 (97.2%) isolates to the genus level (P = 0.002) and 44 to 65 (67.7%), 55 of 65 (84.6%), and 58 of 65 (89.2%) isolates to the species level (P = 0.005), respectively. Four Acinetobacter and three Bordetella isolates which could not be identified to the species level by conventional methods were identified by MicroSeq. In comparison to the full 16S rDNA sequences, the first 527 bp provided identical genus information for all 72 isolates and identical species information for 67 (93.1%) isolates. These data show that MicroSeq provides rapid, unambiguous identification of clinical bacterial isolates. The improved turnaround time provided by genotypic identification systems may translate into improved clinical outcomes.

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Figures

FIG. 1

FIG. 1

Flowchart of the MicroSeq process from culture to sequence. The total elapsed time was 15.5 to 18.5 h, comprising bacterial DNA extraction (A), PCR (B), sequencing reaction preparation (C), cycle sequencing (D), and analysis (E). The time required for each step is indicated.

FIG. 2

FIG. 2

Neighbor-joining analysis of DNA sequences from several Enterobacter spp. Phylogenetic analysis was based on full 16S rRNA gene sequences, and the scale reflects relative phylogenetic distance. Isolates with names beginning with Mayo were evaluated in this study. Isolates with names beginning with accession numbers were retrieved from GenBank (15, 16). The remaining isolates, whose names begin with ATCC numbers, were type strains stored in the MicroSeq database.

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