The diversities of fluorescent pseudomonads, from two uncultivated soils and from the roots of two plant species cultivated in these two soils, were compared. The phenotypic diversity of the bacterial isolates was characterized on the basis of biochemical and physiological tests and on the basis of their ability to utilize 147 different organic compounds. The genotypic diversity of the isolates was characterized on the basis of the types of 16S genes coding for rRNA (rDNA), their repetitive extragenic palindromic patterns by PCR, and plasmid profiles. Taxonomic identification of the isolates was achieved with both biochemical and physiological tests and by comparing their 16S rDNA types to those of reference and type strains of fluorescent Pseudomonas spp. Numerical analysis of phenotypic characteristics allowed the clustering of isolates that showed high levels of similarity. This analysis indicated that both soil type and host plant had an effect on the diversity of fluorescent pseudomonads. However, of the two factors studied, the soil was clearly the dominating one. Indeed, the populations associated with the roots of each plant species varied from one soil to the other. This variation could possibly be ascribed to the differences recorded between the phenotypically diverse populations of fluorescent pseudomonads from the two uncultivated soils. The plant selection was, at least partly, plant specific. It was not related to bacterial species and biovars or to the presence of plasmid DNA. The phenotypic clustering of isolates was well correlated with genotypic characterization by repetitive extragenic palindrome-PCR fingerprinting.

A study was performed to evaluate a new manual miniaturized system, API Coryne (API-bioMerieux, Inc., La Balme les Grottes, France), in which conventional biochemical methods were used to identify 240 isolates of coryneform and related bacteria. A total of 40% of the isolates were excluded from the study because they could not be identified by conventional methods. Identifications of the 240 isolates obtained with API Coryne showed a 97.6% concordance with conventional methods (79% after 24 h of incubation, 21% after 48 h of incubation): 158 (65.8%) isolates were identified with no further testing, and extra testing was required for 76 (31.8%) isolates. In three (1.2%) cases, the organisms did not correspond to any key in the code book and could not be identified by the computer service of the manufacturer. Only three (1.2%) strains were misidentified. The system was shown to be reliable and rapid when compared with standard identification methods.

The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the LCA (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods.

A semi-automated commercial system (ID 32 E, bioMérieux) for 24-hour identification of Enterobacteriaceae and other gram-negative fermentative and nonfermentative bacteria encountered in diagnostic microbiology was evaluated. Overall, the system correctly identified 506 (91.5%) of the 553 strains tested, 94 (17.0%) strains requiring additional tests for complete identification. Six (1.1%) strains were misidentified and 33 (6.0%) strains were not identified. Eight (1.4%) strains were not present in the database and were misidentified or not identified. The system is a suitable alternative to existing systems for the identification of Enterobacteriaceae and other gram-negative bacteria frequently encountered in clinical samples.

A study was performed to compare the rapid identification system ATB 32E (API-bioMerieux SA, La Balme-les-Grottes, France) with conventional biochemical methods for identifying 414 isolates of the family Enterobacteriaceae and the genus Aeromonas, mainly of clinical origin. Overall, 395 strains (95.4%) were correctly identified, with 48 (11.6%) requiring extra tests for complete identification. Ten strains (2.4%) were not identified, and nine (2.9%) were misidentified. The ATB 32E is a suitable alternative for rapid identification of members of the family Enterobacteriaceae.