Biochemical differences among human and animal streptococci of Lancefield group C or group G.

Pyogenic streptococci of Lancefield group C or group G from human or animal sources were examined with a view to increasing the number of diagnostic tests useful for their differentiation. Human strains of group G produced L-prolyl-L-arginine aminopeptidase but isolates of Streptococcus equisimilis (group C) did not. Tests for alpha-L-glutamate aminopeptidase together with fermentation of glycogen or sorbitol distinguished S. dysgalactiae from strains of S. equisimilis isolated from animals. It was confirmed that fermentation tests were helpful in the study of S. equi and S. zooepidemicus and that enzyme reactions helped distinguish between S. canis and the human strains of group G.

Identification of Brucella abortus, B. canis, B. melitensis, and B. suis by carbon substrate assimilation tests.

By using the results of seven carbon substrate assimilation tests from the Biotype 100 system (bioMérieux, Marcy-l'Etoile, France), we correctly identified 79 (85.9%) of 92 Brucella strains tested. The specificity of the method varied from 97.4 to 100% depending on the species. Although a biological safety cabinet must be used, this method represents an easy and fast alternative for the identification of Brucella species.

[Comparison of two systems for identifying coliform enterobacteria newly described or rarely found in clinical practice]. / Comparaison de deux systèmes d'identification d'entérobactéries coliformes nouvellement décrites ou rarement rencontrées en clinique.

The API 20 EC and ATB 32 GN identification systems were compared for their ability to identify 231 coliform bacteria strains. Agreement with the identification given by conventional methods was achieved for 96.1 p. cent of strains by the API 20 EC gallery and for 95.9 p. cent by the ATB 32 GN system. Complementary tests were needed to identify 9.5 p. cent of strains using the API 20 EC system but 30.3 per cent using the ATB 32 GN system.

Phenotypic drift inBradyrhizobium japonicum populations after introduction into soils as established by numerical analysis.

The degree of phenotypic variation of the bacterial strains USDA 125-Sp, USDA 138 and USDA 138-SmBradyrhizobium japonicum a long time after introduction was studied in three experimental fields. A total of 54 phenotypic characters were analyzed by constructing a dendrogram based on an hierarchic classification. Strong similarities (92.6, 94 and 95%) were found between the isolates introduced into soil 8, 10 and 13 years ago and between their respectiveB. japonicum parental clones. The dendrogrammic analysis detected a small amount of phenotypic drift, however, between soil isolates and parental clones belonging to the same serogroup (selective effects were found to have generated 0 to 3.9% variation for the USDA 125-Sp inoculum introduced 8 years ago, and 3.2-3.5% after 10 and 13 years, respectively, for the USDA 138 and USDA 138-Sm bacterial inocula) and within the serogroup 125 soil isolates (2.7%). We found a similar evolution of serogroup 125 isolates when compared with parental clones conserved on slant agar at 4°C. When a drift was observed, the isolates from soil presented a lower activity for several enzymes and lower diversity compared with the parental clones.

Carbon substrate assimilation patterns of clinical and environmental strains of Aeromonas hydrophila, Aeromonas sobria and Aeromonas caviae observed with a micromethod.

The assimilation of carbon substrates by 103 strains of Aeromonas of different origin identified by conventional methods was studied by means of a standardized micromethod containing 147 tests (API system). Six distinct groups could be recognized and the discriminating substrates were determined. 3 species of Aeromonas can be identified by means of conventional method: A. hydrophila, A. sobria and A. caviae. The method has a number of drawbacks: Some media are unreliable, others are difficult to read, strict preservation conditions are essential. The proposed micromethod for carbon substrate assimilation allows, in most cases, a simple separation of the 3 motile Aeromonas species.

Evaluation of the four-hour rapid 20E system for identification of members of the family Enterobacteriaceae.

A study was conducted to compare the API Rapid 20E 4-h system (API System S.A., France; commercially available in the U.S.A. under the name DMS Rapid E System; DMS Laboratories, Darts Mill, Flemington, N.J.), the API 20E 18- to 24-h system (Analytab Products, Plainview, N.Y.), and a conventional media system to measure the ability of each to identify members of the family Enterobacteriaceae. Comparison tables rather than simple percentage agreement tables were generated to define the particular strengths and weaknesses of each system and to allow the laboratory to best use the data. The Rapid 20E compared quite favorably with conventional media. It yielded correct identifications with 95.9% of the isolates tested (API 20E, 98% identification rate). In 2.5% of the isolates, the Rapid 20E gave only genus identifications, and in 1.4% the organisms did not correspond to any key in the code book and could not be identified by the manufacturer's computer service. The ease of inoculation and the 4-h capability make the Rapid 20E system an extremely attractive development in the field of bacterial identification.

Evaluation of API NH, a new 2-hour system for identification of Neisseria and Haemophilus species and Moraxella catarrhalis in a routine clinical laboratory.

API NH is a new 2-h system (bioMérieux, La Balme-les-Grottes, France) for the identification of most Neisseria and Haemophilus spp. of clinical significance and of Moraxella catarrhalis and for the detection of penicillinase production. Furthermore, this system allows the biotyping of Haemophilus influenzae and Haemophilus parainfluenzae. Three hundred eighteen strains belonging to these species, previously identified by conventional methods, were tested. Among the 305 strains belonging to species included in the data base, 225 (73.8%) were identified without additional tests, 79 (25.9%) were correctly identified after extra tests, and 1 strain (0.3%) was misidentified. For 131 (90.3%) of the 145 H. influenzae and H. parainfluenzae strains, results of biotyping were in agreement with results of standard methods. API NH is an accurate and reliable method for the routine identification of these bacteria in a clinical laboratory, for biotyping of Haemophilus spp., and for the detection of penicillinase-producing strains. The system is ready to use and time saving; inoculation of the system and reading of results are easy.

Evaluation of a semi-automated 24-hour commercial system for identification of Enterobacteriaceae and other gram-negative bacteria.

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.

Difficulties in identifying Klebsiella strains of clinical origin.

Two hundred and four strains of Gram-negative bacteria of clinical origin, initially identified as Klebsiella using the API 20 E system, and 10 reference strains were further analysed with the API 20 EC test system and the API 50 CH, API 50 AO, API 50 AA assimilation systems. Four clusters corresponding to the species Klebsiella pneumoniae subsp. pneumoniae, K. oxytoca, K. planticola, and K. terrigena were formed after numerical analysis of 155 selected tests and the 26 most discriminating tests were determined. A comparison was made between conventional identification using the API 20 E system and the results of the numerical analysis. The conventional method resulted in incorrect identification of 13% of the strains tested, especially for the new species: K. planticola and K. terrigena. After numerical analysis, 17 out of 204 strains (8.3%) of clinical origin were identified as K. planticola. Only 1 strain of clinical origin was identified as K. terrigena, and 1 strain as K. ornithinolytica.

Description and evaluation of the semiautomated 4-hour rapid ID 32 Strep method for identification of streptococci and members of related genera.

The rapid ID 32 Strep system (bioMérieux, La Balme les Grottes, France) is a new system which allows the identification in 4 h of most streptococci and members of related genera encountered in medical and veterinary bacteriology. Four hundred thirty-three isolates first identified by conventional methods and belonging to the genera Streptococcus, Lactococcus, Enterococcus, Aerococcus, Gemella, Leuconostoc, Erysipelothrix, Gardnerella, and Listeria were tested. Overall, rapid ID 32 Strep correctly identified 413 (95.3%) of the strains, with 109 (25.1%) requiring extra tests for complete identification. Sixteen strains (3.7%) were not identified, and 4 (1.0%) were misidentified. The rapid ID 32 Strep system is a suitable alternative for rapid identification of members of the genus Streptococcus and of related genera.

Effect of Two Plant Species, Flax (Linum usitatissinum L.) and Tomato (Lycopersicon esculentum Mill.), on the Diversity of Soilborne Populations of Fluorescent Pseudomonads.

Suppression of soilborne disease by fluorescent pseudomonads may be inconsistent. Inefficient root colonization by the introduced bacteria is often responsible for this inconsistency. To better understand the bacterial traits involved in root colonization, the effect of two plant species, flax (Linum usitatissinum L.) and tomato (Lycopersicon esculentum Mill.), on the diversity of soilborne populations was assessed. Fluorescent pseudomonads were isolated from an uncultivated soil and from rhizosphere, rhizoplane, and root tissue of flax and tomato cultivated in the same soil. Species and biovars were identified by classical biochemical and physiological tests. The ability of bacterial isolates to assimilate 147 different organic compounds and to show three different enzyme activities was assessed to determine their intraspecific phenotypic diversity. Numerical analysis of these characteristics allowed the clustering of isolates showing a high level (87.8%) of similarity. On the whole, the populations isolated from soil were different from those isolated from plants with respect to their phenotypic characteristics. The difference in bacteria isolated from uncultivated soil and from root tissue of flax was particularly marked. The intensity of plant selection was more strongly expressed with flax than with tomato plants. The selection was, at least partly, plant specific. The use of 10 different substrates allowed us to discriminate between flax and tomato isolates. Pseudomonas fluorescens biovars II, III, and V and Pseudomonas putida biovar A and intermediate type were well distributed among the isolates from soil, rhizosphere, and rhizoplane. Most isolates from root tissue of flax and tomato belonged to P. putida bv. A and to P. fluorescens bv. II, respectively. Phenotypic characterization of bacterial isolates was well correlated with genotypic characterization based on repetitive extragenic palindromic PCR fingerprinting.

The use of biochemical markers, serotype and fimbriation in the detection of Escherichia coli clones.

Biochemical reactions, O and K serotypes and presence of P-fimbriae were analysed in 116 Escherichia coli strains isolated in blood cultures from patients with bacteraemia and in 99 faecal strains isolated from healthy individuals. By using biochemical typing, the strains could be grouped into six main clusters with similarity index less than 0.8 (Gower, 1971) and altogether 16 subclusters with similarity index 0.82-0.89. The most discriminating tests between the clusters were fermentation of D-tagatose, saccharose, salicin and sorbose. No single biochemical property could differentiate bacteraemic isolates from faecal strains, although strains isolated from blood were significantly more often found in certain subclusters, whereas other subclusters contained mainly control strains. Bacteraemic strains possessed P-fimbriae more often, especially strains isolated from patients with E. coli in the urine concomitantly with bacteraemia. Equally, no single reaction could separate P-fimbriated from non-P-fimbriated strains. D-Tagatose was fermented more often by the P-fimbriated strains; on the other hand, melibiose and lactose fermentation tests were less often positive. Certain O serotypes (O1, O4, O6, O7, O18 and O25) were more common among bacteraemic isolates than controls. K serotypes such as K1, K5 and K52 were also more frequent among blood isolates. We conclude that a combination of biochemical tests, fimbriation and serotyping might be used to identify potentially pathogenic clusters of E. coli.

Description and evaluation of the semiautomated 4-hour ATB 32E method for identification of members of the family Enterobacteriaceae.

A study was performed to compare the rapid identification system ATB 32E (API-bioMérieux 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.

Evaluation of API Coryne in comparison with conventional methods for identifying coryneform bacteria.

A study was performed to evaluate a new manual miniaturized system, API Coryne (API-bioMérieux, 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.

International collaborative evaluation of the ATB 32 staph gallery for identification of the Staphylococcus species.

This international collaborative study evaluates a new system (ATB 32 Staph) for the identification of staphylococci taking into account the new novobiocin-sensitive and -resistant species reported. This study involved eight laboratories and 792 strains were tested. The reproducibility obtained for the cumulative results of the inter- and intra-laboratory tests was more than 90%. For 713 strains relevant of a species 95.5% were correctly identified by the system. Eight strains (1.2%) were misidentified and 24 strains (3.3%) were not identified. For 79 strains initially considered as not-classified, 62% were identified at the species level by the new system. The newer ATB 32 Staph gallery is a performant and useful method for routine identification of the currently described staphylococci species from clinical and animal origin.

Potential impact of the VITEK 2 system and the Advanced Expert System on the clinical laboratory of a university-based hospital.

A study was designed to assess the impact of the VITEK 2 automated system and the Advanced Expert System (AES) on the clinical laboratory of a typical university-based hospital. A total of 259 consecutive, nonduplicate isolates of Enterobacteriaceae members, Pseudomonas aeruginosa, and Staphylococcus aureus were collected and tested by the VITEK 2 system for identification and antimicrobial susceptibility testing, and the results were analyzed by the AES. The results were also analyzed by a human expert and compared to the AES analyses. Among the 259 isolates included in this study, 245 (94.6%) were definitively identified by VITEK 2, requiring little input from laboratory staff. For 194 (74.9%) isolates, no inconsistencies between the identification of the strain and the antimicrobial susceptibility determined by VITEK 2 were detected by the AES. Thus, no input from laboratory staff was required for these strains. The AES suggested one or more corrections to results obtained with 65 strains to remove inconsistencies. The human expert thought that most of these corrections were appropriate and that some resulted from a failure of the VITEK 2 system to detect certain forms of resistance. Antimicrobial phenotypes assigned to the strains by the AES for beta-lactams, aminoglycosides, quinolones, macrolides, tetracyclines, and glycopeptides were similar to those assigned by the human expert for 95.7 to 100% of strains. These results indicate that the VITEK 2 system and AES can provide accurate information in tests for most of the clinical isolates examined and remove the need for human analysis of results for many. Certain problems were identified in the study that should be remediable with further work on the software supporting the AES.

Ability of the VITEK 2 advanced expert system To identify beta-lactam phenotypes in isolates of Enterobacteriaceae and Pseudomonas aeruginosa.

The Advanced Expert System (AES) was used in conjunction with the VITEK 2 automated antimicrobial susceptibility test system to ascertain the beta-lactam phenotypes of 196 isolates of the family Enterobacteriaceae and the species Pseudomonas aeruginosa. These isolates represented a panel of strains that had been collected from laboratories worldwide and whose beta-lactam phenotypes had been characterized by biochemical and molecular techniques. The antimicrobial susceptibility of each isolate was determined with the VITEK 2 instrument, and the results were analyzed with the AES to ascertain the beta-lactam phenotype. The results were then compared to the beta-lactam resistance mechanism determined by biochemical and molecular techniques. Overall, the AES was able to ascertain a beta-lactam phenotype for 183 of the 196 (93.4%) isolates tested. For 111 of these 183 (60.7%) isolates, the correct beta-lactam phenotype was identified definitively in a single choice by the AES, while for an additional 46 isolates (25.1%), the AES identified the correct beta-lactam phenotype provisionally within two or more choices. For the remaining 26 isolates (14.2%), the beta-lactam phenotype identified by the AES was incorrect. However, for a number of these isolates, the error was due to remediable problems. These results suggest that the AES is capable of accurate identification of the beta-lactam phenotypes of gram-negative isolates and that certain modifications can improve its performance even further.