Evaluation of commercial systems for the identification of clinical yeast isolates.

The Analytab Products Inc. (API), Micro-Drop (MD), and Uni-Yeast-Tek (UYT) systems for the presumptive identification of common clinical yeast isolates were compared with the oxidation-fermentation (OF) and a conventional procedure. With 229 coded isolates, the identification accuracies were API 94, MD 83, OF 82, and UYT 99%. The API system required the greatest technical ability. The MD materials were prone to malfunction. OF media, if incubated beyond 14 days, gave an accuracy of 87%, but this offered no advantage over the conventional procedure. The UYT system was the easiest to use.     

Evaluation of nonradioactive DNA probes for identification of mycobacteria.

Commercial chemiluminescent DNA probes (Accuprobe; Gen-Probe, San Diego, Calif.) for the identification of Mycobacterium tuberculosis (MTB) complex, M. avium complex (MAC), M. gordonae, and M. kansasii were evaluated with 134 clinical isolates. These included 36 MTB complex, 40 MAC, 27 M. gordonae, 9 M. kansasii, and 22 Mycobacterium spp. The specificity was 100% for the four probes. The sensitivity was 100% for the MTB complex and M. gordonae probes and 95.2% for the MAC probe. Five of the nine M. kansasii isolates tested were not detected with the probe.     

Evaluation of three test procedures for identification of Staphylococcus aureus from clinical sources.

A total of 520 clinical and environmental isolates of the family Micrococcaceae that fermented glucose anaerobically were tested for their ability to produce coagulase, thermostable nuclease, and deoxyribonuclease. Of these, 450 isolates coagulated rabbit plasma, produced thermostable nuclease, and were identified as Staphylococcus aureus, 447 of which produced a 3+ to 4+ clot. The remaining three isolates produced a 2+ clot, deoxyribonuclease, and thermostable nuclease. It was found that three of the S. aureus isolates failed to produce deoxyribonuclease. A total of 70 isolates which did not coagulate rabbit plasma and which were thermostable nuclease negative were identified as S. epidermidis. Three of them produced deoxyribonuclease. It is suggested that the thermostable nuclease test be performed on all isolates producing a 2+ (or 1+) clot in the coagulase test before identifying them as S. aureus.     

Evaluation of the new RapID-ANA II system for the identification of clinical anaerobic isolates.

The RapID-ANA II System (Innovative Diagnostic Systems, Inc., Atlanta, Ga.) is a recently revised and marketed 4-h system for the identification of anaerobic bacteria. The system was compared with conventional identification methods for its ability to identify 566 clinical anaerobic isolates. Overall, the system identified correctly to genus and species 68% of the total isolates (62% of 204 gram-negative bacilli, 70% of 69 nonsporeforming gram-positive bacilli, 74% of 130 Clostridium isolates, and 72% of 163 anaerobic cocci), without the use of additional tests. With the additional tests suggested by the manufacturer, 78% of the total isolates were identified correctly to species. The routine use of a few simple and practical tests (e.g., egg yolk agar for Clostridium spp.), in addition to the RapID-ANA II, would improve significantly the accuracy of the system in the identification of anaerobic bacteria. This second-generation system offers a number of improvements over the original system, including an updated data base and the option of overnight refrigeration of the system before the addition of reagents.     

Multiprimer PCR system for differential identification of mycobacteria in clinical samples.

A novel multiprimer PCR method with the potential to identify mycobacteria in clinical samples is presented. The assay relies on the simultaneous amplification of three bacterial DNA genomic fragments by using different sets of oligonucleotide primers. The first set of primers amplifies a 506-bp fragment from the gene for the 32-kDa antigen of Mycobacterium tuberculosis, which is present in most of the species belonging to the genus Mycobacterium. The second set of primers amplifies a 984-bp fragment from the IS6110 insertion sequence of the bacteria belonging to the M. tuberculosis complex. The third set of primers, derived from an M. tuberculosis species-specific sequence named MTP40, amplifies a 396-bp genomic fragment. Thus, while the multiprimer system would render three amplification fragments from the M. tuberculosis genome and two fragments from the Mycobacterium bovis genome, a unique amplification fragment would be obtained from nontuberculous mycobacteria. The results obtained, using reference mycobacterial strains and typed clinical isolates, show that the multiprimer PCR method may be a rapid, sensitive, and specific tool for the differential identification of various mycobacterial strains in a single-step assay.     

Evaluation of rapid tests for the identification of mycobacteria

The use of eight rapid tests for the identification of 1307 strains of mycobacteria belonging to 18 species was evaluated. The standard niacin, nitrate-reductase and catalase tests were supplemented by new tests for the detection of beta glucosidase, urease, penicillinase, trehalase and cephalosporinase. This combination of eight rapid tests was not able to replace more conventional procedures but in some cases was of value in discriminating between closely related species.     

Evaluation of Mast-ID 15 system for identification of fresh clinical isolates of Enterobacteriaceae and Acinetobacter.

AIMS: To assess the accuracy of the Mast-ID 15 system compared with API 20 E for the identification of stock and fresh clinical strains of Enterobacteriaceae and Acinetobacter spp; to compare the accuracy of 19 pin and 36 pin multipoint inoculator heads. METHODS: One hundred frozen stock cultures of Enterobacteriaceae and Acinetobacter spp which had previously been identified by the API 20E were classified by the Mast-ID using 19 and 36 pin multipoint inoculator heads. Reproducibility was determined by testing 36 randomly selected organisms in duplicate. Four hundred and sixty nine consecutive fresh clinical isolates of Enterobacteriaceae and Acinetobacter spp were identified by the Mast-ID using a 36 pin multipoint inoculator and by the API 20E. Reproducibility for the fresh isolates was determined by testing 96 randomly selected strains in duplicate. RESULTS: The Mast-ID 15 identified 82% and 85% of frozen strains to species level and reproducibility was 80% and 86% using 19 and 36 pin inoculator heads, respectively. Of the 469 fresh clinical isolates, the Mast-ID identified 70% of strains to species level; 19% were not identified and 11% were identified incorrectly by comparison with the API 20E. The Mast-ID achieved a reproducibility level of 80% with the fresh clinical isolates. CONCLUSIONS: The use of a 36 pin multipoint inoculator head in preference to the standard 19 pin head for the Mast-ID was advantageous as it allowed greater numbers of strains to be identified at a reduced cost. Unfortunately, in our hands, the Mast-ID system was insufficiently accurate for routine use in the clinical laboratory. Modifications to some of the problematic tests may result in a sufficient increase in accuracy and reproducibility to make the system beneficial in the routine clinical laboratory.     

Evaluation of Staf-Sistem 18-R for identification of staphylococcal clinical isolates to the species level.

The accuracy and efficiency of Staf-Sistem 18-R (Liofilchem s.r.l., Roseto degli Abruzzi, Teramo, Italy) were compared with those of conventional biochemical methods to identify 523 strains belonging to 16 different human Staphylococcus species. Overall, 491 strains (93.9%) were correctly identified (percentage of identification, > or = 90.0), with 28 (5.4%) requiring supplementary tests for complete identification. For 14 isolates (2.8%), the strains did not correspond to any key in the codebook and could not be identified by the manufacturer's computer service. Only 18 isolates (3.4%) were misidentified. The system is simple to use, is easy to handle, gives highly reproducible results, and is inexpensive. With the inclusion of more discriminating tests and adjustment in supplementary code numbers for some species, such as Staphylococcus lugdunensis and Staphylococcus schleiferi, Staf-Sistem 18-R is a suitable alternative for identification of human coagulase-positive and coagulase-negative Staphylococcus species in microbiological laboratories.     

Mycolic acid analysis for clinical identification of Mycobacterium avium and related mycobacteria.

We examined the mycolic acid composition of 133 strains belonging to MAIS complex (Mycobacterium avium-M. intracellulare-M. scrofulaceum) and MAIS intermediate strains and the related species M. asiaticum, M. malmoense, M. shimoidei, and M. simiae. The analysis revealed that about 10% of the strains identified as M. avium-M. intracellulare complex by conventional cultural and biochemical tests were in fact M. simiae strains according to their mycolate composition. Of 25 strains previously studied by the International Working Group on Mycobacterial Taxonomy, 2 (MAIS intermediate and M. asiaticum) presented patterns incompatible with the clusters to which they had been assigned. M. malmoense and both M. simiae serovars shared the same pattern with alpha-, alpha'-, and ketomycolates. We describe here the method used to identify the mycolic acid profiles in detail. We found it to be highly reproducible and convenient for use in mycobacterial reference laboratories.     

Evaluation of the DMS Rapid E system for identification of clinical isolates of the family Enterobacteriaceae.

A total of 387 unique clinical isolates of the family Enterobacteriaceae were examined with the new DMS Rapid E gram-negative identification system (DMS Laboratories, Inc., Flemington, N.J.) and the API 20E procedure (Analytab Products, Plainview, N.Y.). Altogether, 376 strains (97.2%) were correctly identified to species level within 4 h with the DMS Rapid E system; 366 strains (94.6%) were correctly identified with the API 20E after overnight incubation.     

Bacteremia due to Rochalimaea henselae in a child: practical identification of isolates in the clinical laboratory.

Two closely related species of Rochalimaea, Rochalimaea quintana and Rochalimaea henselae, are nutritionally fastidious but can be cultivated on bacteriologic media from the blood of patients with diverse clinical presentations. We report a case of culture-proven R. henselae bacteremia in a child with persistent fever. Serologic evidence of infection by R. henselae was ascertained by testing sera at two intervals for immunoglobulin G or immunoglobulin M antibodies by enzyme immunoassay and immunoblot. The case isolate and a collection of other strains (R. henselae, R. quintana, and related organisms) were used to test commercial identification systems for their comparative utility in the identification of Rochalimaea spp. on a practical basis. Of six systems designed for testing of either fastidious or anaerobic isolates of bacteria, the MicroScan Rapid Anaerobe Panel was the only system that distinguished R. henselae from R. quintana. Four of five others gave reactions that were unique within their data bases but did not distinguish Rochalimaea isolates at the species level.     

Simple amidase test for identification of mycobacteria.

A modified amidase test for differentiation of mycobacteria is described. A total of 224 atypical mycobacteria, 154 Mycobacterium tuberculosis, and 26 M. bovis strains were classified by this procedure. Of the 404 strains of various species studied, 400 exhibited an amidase spectrum identical to the established pattern. The simplicity of this method may promote its application in routine examinations.     

Reliable urease test for identification of mycobacteria.

A simple, modified formation for urea broth gave consistent, reliable results to aid in the differentiation of Mycobacterium species. In a study of 1,346 isolates representing 17 different species, tests read after 7 days were distinct and reproducible. The use of this test facilitates the identification of Mycobacterium species, such as M. scrofulaceum, the M. avium complex, the M. terrae complex, and M. triviale.     

Molecular technique for rapid identification of mycobacteria.

Identification of mycobacteria through conventional microbiological methods is cumbersome and time-consuming. Recently we have developed a novel bacterial identification method to accurately and rapidly identify different mycobacteria directly from water and clinical isolates. The method utilizes the PCR to amplify a portion of the small subunit rRNA from mycobacteria. The 5' PCR primer has a fluorescent label to allow detection of the amplified product. The PCR product is digested with restriction endonucleases, and an automated DNA sequencer is employed to determine the size of the labeled restriction fragments. Since the PCR product is labeled only at the 5' end, the analysis identifies only the restriction fragment proximal to the 5' end. Each mycobacterial species has a unique 5' restriction fragment length for each specific endonuclease. However, frequently the 5' restriction fragments from different species have similar or identical lengths for a given endonuclease. A set of judiciously chosen restriction enzymes produces a unique set of fragments for each species, providing us with an identification signature. Using this method, we produced a library of 5' restriction fragment sizes corresponding to different clinically important mycobacteria. We have characterized mycobacterial isolates which had been previously identified by biochemical test and/or nucleic acid probes. An analysis of these data demonstrates that this protocol is effective in identifying 13 different mycobacterial species accurately. This protocol has the potential of rapidly (less than 36 h) identifying mycobacterial species directly from clinical specimens. In addition, this protocol is accurate, sensitive, and capable of identifying multiple organisms in a single sample.     

Preliminary identification of mycobacteria isolated from clinical specimens

From March 1979 to June 1980, we preliminary identified mycobacteria at the time of their initial isolation by colonial morphology, pigmentation, and growth rate. The definitive identifications were predicted accurately for 92% of the mycobacteria isolated from 108 patients. For laboratories that isolate relatively few different species of mycobacteria, the advantages of this approach are its simplicity and the speed with which presumptive identifications can be made available for clinical use.     

Evaluation of the Rapid Strep system for the identification of clinical isolates of Streptococcus species

A total of 247 strains of streptococci isolated from humans were tested for identification in the Rapid Strep system. The identification rates and identification levels were different for each Streptococcus species. Our data indicate that the Rapid Strep system will identify nearly all the beta-hemolytic Streptococcus species if serological procedures are used in conjunction with the rapid physiological procedures. Of the group D streptococci, 98% of the enterococci and 95% of the non-enterococci were correctly identified. Of the commonly occurring viridans species, 85% were correctly identified, but only 10% of the less frequently occurring viridans species were identified. A total of 90% of the Streptococcus pneumoniae and 60% of the Aerococcus strains were correctly identified.     

Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria

An evaluation of the Vitek 2 ANC card (bioMérieux, Marcy l'Etoile, France) was performed with 301 anaerobic isolates. Each strain was identified by 16S rRNA gene sequencing, which is considered to be the reference method. The Vitek 2 ANC card correctly identified 239 (79.4%) of the 301 clinical isolates to the genus level, including 100 species that were not represented in the database. Correct species identification was obtained for 60.1% (181/301) of the clinical isolates. For the isolates not identified to the species level, a correct genus identification was obtained for 47.0% of them (47/100), and 16 were accurately designated not identified. Although the Vitek 2 ANC card allows the rapid and acceptable identification of the most common clinically important anaerobic bacteria within 6 h, improvement is required for the identification of members of the genera Fusobacterium, Prevotella, and Actinomyces and certain Gram-positive anaerobic cocci (GPAC).     

Curvilinear-gradient high-performance liquid chromatography for identification of mycobacteria.

Over a 1-year period, 502 mycobacterial cultures submitted to the Microbial Diseases Laboratory were identified by high-performance liquid chromatography (HPLC) in parallel with standard biochemical methods. Identification by HPLC using a curvilinear gradient was achieved by comparing the chromatograms of the unknown cultures to chromatograms for known reference strains, together with calculation of peak height or peak area ratios, as necessary. The overall agreement between HPLC and biochemical identification was 97.2%. In addition, 7 of 12 cultures of Mycobacterium bovis were identified by HPLC as the BCG strain. Of 111 cultures biochemically identified as members of the M. avium complex (MAC), 108 were confirmed as MAC by DNA probe and 106 were confirmed by HPLC. Of the latter 106, 58 probe-positive strains were identified as M. avium, 38 were identified as M. intracellulare, and 10 were identified as Mycobacterium sp. strain "X" by HPLC. Of the remaining five nonchromogenic cultures, four had MAC-like chromatograms that did not match any in our library sufficiently to permit definitive identification. Of the latter four, two were confirmed as MAC strains by DNA probe and two were not. The last of the cultures biochemically identified as MAC (1 of 111) was a mixture of MAC and non-MAC strains. Overall, only 2 of 502 cultures yielded results by HPLC that differed from those obtained by standard biochemical methods. The HPLC result was confirmed in both cases by an independent national reference laboratory. In the 12 instances in which HPLC did not provide identification, the chromatograms were either uninterpretable or did not match available reference chromatograms. These findings show that the identification obtained by HPLC concurs well with that obtained by both the standard biochemical methods and the DNA probes. Thus, identification by HPLC provides mycobacteriology laboratories with a reproducible and specific method for accurate and timely identification of most medically important mycobacteria.     

Development of reference systems for automatic identification of clinical isolates of bacteria.

The reported work describes experiments on automatic identification based on a material of 636 clinical isolates of bacteria. It is shown that three different and mutually independent automatic identification principles produce almost identical identification conclusions. It is also shown that an automatic procedure which continuously corrects the basic classification gives results which are independent of the classification background. Automatic correction logics develop conventionally-based, as well as numerically-based initial reference systems toward almost similar solutions. This may indicate that automated identification methods based on numerical classifications possess general validity.