Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “IDENTIFICATION”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources
PubMed2006

Reliable and rapid identification of Listeria monocytogenes and Listeria species by artificial neural network-based Fourier transform infrared spectroscopy.

Differentiation of the species within the genus Listeria is important for the food industry but only a few reliable methods are available so far. While a number of studies have used Fourier transform infrared (FTIR) spectroscopy to identify bacteria, the extraction of complex pattern information from the infrared spectra remains difficult. Here, we apply artificial neural network technology (ANN), which is an advanced multivariate data-processing method of pattern analysis, to identify Listeria infrared spectra at the species level. A hierarchical classification system based on ANN analysis for Listeria FTIR spectra was created, based on a comprehensive reference spectral database including 243 well-defined reference strains of Listeria monocytogenes, L. innocua, L. ivanovii, L. seeligeri, and L. welshimeri. In parallel, a univariate FTIR identification model was developed. To evaluate the potentials of these models, a set of 277 isolates of diverse geographical origins, but not included in the reference database, were assembled and used as an independent external validation for species discrimination. Univariate FTIR analysis allowed the correct identification of 85.2% of all strains and of 93% of the L. monocytogenes strains. ANN-based analysis enhanced differentiation success to 96% for all Listeria species, including a success rate of 99.2% for correct L. monocytogenes identification. The identity of the 277-strain test set was also determined with the standard phenotypical API Listeria system. This kit was able to identify 88% of the test isolates and 93% of L. monocytogenes strains. These results demonstrate the high reliability and strong potential of ANN-based FTIR spectrum analysis for identification of the five Listeria species under investigation. Starting from a pure culture, this technique allows the cost-efficient and rapid identification of Listeria species within 25 h and is suitable for use in a routine food microbiological laboratory.

Bacteriological Techniques↗
PubMed2001

Mycolic acid analysis by high-performance liquid chromatography for identification of Mycobacterium species.

Mycobacterium tuberculosis is the etiologic agent of tuberculosis and can be accurately detected by laboratories using commercial genetic tests. Nontuberculosis mycobacteria (NTM) causing other mycobacterioses can be difficult to identify. The identification processes are confounded by an increasing diversity of newly characterized NTM species. The ubiquitous nature of NTM, combined with their potential to be opportunistic pathogens in immunocompromised as well as nonimmunodeficient patients, further complicates the problem of their identification. Since clinical case management varies depending on the etiologic agent, laboratories must identify the species in a timely manner. However, only a few identification methods can detect the species diversity within the Mycobacterium genus. Over the last decade, high-performance liquid chromatography analysis of the mycolic acids has become an accepted method for identification of mycobacteria. In this review, we assess its development and usefulness as an identification technique for Mycobacterium species.

Bacterial Typing Techniques↗
PubMed2006

Species-specific identification of Leptospiraceae by 16S rRNA gene sequencing.

The genus Leptospira is classified into 13 named species and 4 genomospecies based upon DNA-DNA reassociation studies. Phenotypic tests are unable to distinguish between species of Leptospira, and there is a need for a simplified molecular approach to the identification of leptospires. 16S rRNA gene sequences are potentially useful for species identification of Leptospira, but there are a large number of sequences of various lengths and quality in the public databases. 16S rRNA gene sequences of near full length and bidirectional high redundancy were determined for all type strains of the species of the Leptospiraceae. Three clades were identified within the genus Leptospira, composed of pathogenic species, nonpathogenic species, and another clade of undetermined pathogenicity with intermediate 16S rRNA gene sequence relatedness. All type strains could be identified by 16S rRNA gene sequences, but within both pathogenic and nonpathogenic clades as few as two or three base pairs separated some species. Sequences within the nonpathogenic clade were more similar, and in most cases < or =10 bp distinguished these species. These sequences provide a reference standard for identification of Leptospira species and confirm previously established relationships within the genus. 16S rRNA gene sequencing is a powerful method for identification in the clinical laboratory and offers a simplified approach to the identification of Leptospira species.

Bacterial Typing Techniques↗
PubMed2006

Molecular identification of black-grain mycetoma agents.

Black-grain mycetomas are subcutaneous devastating chronic infections due to several dematiaceous fungi. They are diagnosed mostly in tropical countries. Identification of these fungi with standard mycological procedures is difficult because of their poor or delayed sporulation. The aim of this study was thus to assess the accuracy of molecular identification of these fungi. A total of 54 strains, mostly of clinical origin, were used, including 15 Madurella mycetomatis, 6 Madurella grisea, 12 Leptosphaeria senegalensis, 4 Leptosphaeria tompkinsii, 6 Pyrenochaeta spp., 4 Curvularia lunata, and 7 Exophiala jeanselmei strains. The internal transcribed spacer 1 (ITS1)-5.8S-ITS2 DNA region was amplified by using universal fungal primers and sequenced. Both intra- and interspecies sequence similarities were assessed. Madurella mycetomatis appeared to be a homogeneous species. More intraspecies variations were found for C. lunata and E. jeanselmei, leading, in some instances, to changes in the initial identification. L. senegalensis and L. tompkinsii showed intraspecies similarities of >99%, but similarity between the two species was <88%. Intergenera and interspecies variations were important, with sequence homologies of <81% between genera. In contrast, Pyrenochaeta romeroi and M. grisea appeared to be heterogeneous, with intraspecies similarities of 40 to 100% and 53 to 100%, respectively, which suggest either erroneous identification or the need for taxonomic revision. Epidemiological and therapeutic studies could benefit from a precise identification of the fungi responsible for black-grain mycetoma based not only on phenotypical characteristics but also on ITS sequencing.

DNA, Fungal↗
PubMed2006

Identification of Vibrio isolates by a multiplex PCR assay and rpoB sequence determination.

Vibrio, a diverse genus of aquatic bacteria, currently includes 72 species, 12 of which occur in human clinical samples. Of these 12, three species--Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus-account for the majority of Vibrio infections in humans. Rapid and accurate identification of Vibrio species has been problematic because phenotypic characteristics are variable within species and biochemical identification requires 2 or more days to complete. To facilitate the identification of human-pathogenic species, we developed a multiplex PCR that uses species-specific primers to amplify gene regions in four species (V. cholerae, V. parahaemolyticus, V. vulnificus, and V. mimicus). The assay was tested on a sample of 309 Vibrio isolates representing 26 named species (including 12 human pathogens) that had been characterized by biochemical methods. A total of 190 isolates that had been identified as one of the four target species all yielded results consistent with the previous classification. The assay identified an additional four V. parahaemolyticus isolates among the other 119 isolates. Sequence analysis based on rpoB was used to validate the multiplex results for these four isolates, and all clustered with other V. parahaemolyticus sequences. The rpoB sequences for 12 of 15 previously unidentified isolates clustered with other Vibrio species in a phylogenetic analysis, and three isolates appeared to represent unnamed Vibrio species. The PCR assay provides a simple, rapid, and reliable tool for identification of the major Vibrio pathogens in clinical samples, and rpoB sequencing provides an additional identification tool for other species in the genus Vibrio.

Bacterial Typing Techniques↗
PubMed1979

Nonfermentative bacilli: evaluation of three systems for identification.

Three systems for the identification of nonfermentative bacilli were evaluated for their rapidity and accuracy of identification of 217 strains. Two of the systems, API 20E (API) and Oxi/Ferm tube (OxiF), are available as kits; the oxidative attack (OA) system is not commerically available. The overall accuracies of the OA, API, and OxiF systems were 91, 69, and 50%, respectively. Identification within 48 h was achieved for 98% of the strains by OA, for 50% by API, and for 18% by OxiF. Most of the organisms that were either misidentified or not identified by API and OxiF were those nonfermentative bacilli which are relatively more fastidious or rarely encountered or both. All three systems accurately identified nonfermentative bacilli commonly isolated at Olive View Medical Center, namely, Pseudomonas aeruginosa, Acinetobacter anitratus, Pseudomonas maltophilia, Acinetobacter lwoffi, saccharolytic flavobacteria (CDC IIb), moraxellae, Pseudomonas fluorescens, and Pseudomonas putida. The OA system identified 100% of the above organisms correctly, API identified 99.4%, and OxiF identified 99.3%. Since these organisms comprise 92% of the total number of nonfermentative bacilli isolated at Olive View Medical Center, we conclude that both API and OxiF may be useful alternatives to conventional methods, based on accuracy of identification alone. These two systems were considered substantially inferior to the OA system when both accuracy and rapidity of identification were taken into account.

Bacteria↗
PubMed1979

Clinical evaluation of the MICRO-ID, API 20E, and conventional media systems for identification of Enterobacteriacea.

MICRO-ID (General Diagnostics, Morris Plains, N.J.) is a new kit system designed for the identification of Enterobacteriaceae in 4 h. It consists of 15 biochemical tests of paper disks. Each test is in its own compartment in a molded plastic tray. Only one reagent need be added to the system (2 drops of 20% KOH, which is added to the Voges-Proskauer test). Based on the pattern of positive and negative biochemical test results, a five-digit octal code number is calculated. An identification is derived from a computer-generated identification manual. A study was conducted to compare three systems-the MICRO-ID 4-h and the API 20E (Analytab Products Inc., Plainview, N.Y.) 18- to 24-h systems 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 allow the laboratory to best use the data. The MICRO-ID compared quite favorably with conventional media. MICRO-ID yielded incorrect identifications with 1.5% of the isolates tested (API 20E, 4.7% misidentification rate). Half the MICRO-ID misidentifications occurred when the system identified a Citrobacter diversus as a lysine-negative Escherichia coli; all gave one octal number. A direct comparison of the MICRO-ID and API 20E was of limited value because percentage agreements were merely the sums of the errors of each. The ease of inoculation, the requirement for the addition of only one reagent, and the 4-h capability make the MICRO-ID system an extremely attractive development in the field of bacterial identification.

Bacteriological Techniques↗
PubMed1979

Evaluation of the new API 20C strip for yeast identification against a conventional method.

The new API 20C yeast identification system together with appropriate microscopic morphology determinations achieved a 97% correlation with a rapid conventional method. Whereas a group composed of Candida, Torulopsis, Saccharomyces, and Rhodotorula was identified with ease (98% overall correlation), a second group, containing Cryptococcus, Trichosporon, and Geotrichum species, appeared to give the system the most difficulty (90% correlation). Within this group particular difficulty was encountered in identifying varieties of Cryptococcus albidus, C. terreus, C. laurentii, Trichosporon beigelli, and Geotrichum spp. as to species. The API 20C system should be incubated the full 72 h prescribed by the manufacturer. However, when used in conjunction with appropriate morphological tests, presumptive identifications of some Candida and Torulopsis species may be made at 24 to 48 h. To facilitate identifications of the more difficult group of yeasts, ancillary tests for determining nitrate reductase, urease, and phenol oxidase activities should be considered as additions to the strip. Incorporating the phenol oxidase test would be especially important for identification of Cryptococcus neoformans, a yeast which should be identified as quickly and as accurately as possible. The API 20C system with computer assistance has proved to be an easy-to-inoculate, versatile, and fairly rapid method of yeast identification, giving results comparable to those obtained by conventional methodologies.

Candida↗
PubMed1980

Evaluation of the Minitek system for identification of nonfermentative and nonenteric fermentative Gram-negative bacteria.

The Minitek identification system (MT) was compared with a conventional testing battery for the characterization of 735 isolates which included 57 species and groups of nonfermentative (NF) and nonenteric fermentative (NEF) gram-negative bacteria. The MT correctly identified 585 of 616 NF (94,96%) and 115 of 119 NEF (96.65%) bacteria and 700 of 735 strains (95.24%) overall. A total of 31 NF and NEF (4.22%) bacteria were misidentified, and no identification was determined for four strains (0.69%). All strains of Acinetobacter anitratus, Pseudomonas maltophilia, P. fluroescens, and P. putida and all but one strain of P. aeruginosa were correctly identified. The most frequently misidentified taxa were CDC group Va-1, P. pickettii (Va-2), P. mendocina, and Moraxella urethralis (M-4). Supplemental tests were needed for the complete identification of 214 strains (29.11%). An average of 1.54 supplemental tests were used with each of these strains. A total of 134 strains (18.23%) had their identification delayed by 1 day due to supplemental testing. We recommend the use of the 42 degree C growth test with the MT. When used in accord with the manufacturer's instructions and with the MT code book the MT was found to be a valuable system for the identification of a wide variety of common and infrequently encountered NF and NEF bacteria.

Bacteria↗
PubMed1980

Evaluation of the four-hour Micro-ID technique for direct identification of oxidase-negative, Gram-negative rods from blood cultures.

A 4-h Micro-ID technique for direct identification of oxidase-negative gram-negative rods from positive blood cultures was compared to subculture and species identification of single colonies by API 20E and Micro-ID, using standardized inocula. A total of 127 patients (220 positive cultures) were studied. Isolates included 96 Escherichia coli, 46 Klebsiella pneumoniae, 7 Klebsiella oxytoca, 8 Enterobacter aerogenes, 17 Enterobacter cloacae, 19 Serratia marcescens, 2 Serratia liquefaciens, 8 Proteus mirabilis, 1 Salmonella species, 1 Morganella morganii, 6 Haemophilus influenzae, 2 Haemophilus parainfluenzae, 3 Bacteroides fragilis, 3 Acinetobacter calcoaceticus biotype anitratus, and 1 Pseudomonas maltophilia. In 90% of the cultures, identification by Micro-ID was identical to that obtained after subculture; if the 15 non-enterobacterial isolates were excluded, the corresponding figure was 96.6%. Enterobacteria identified incorrectly by direct Micro-ID were three S. marcescens (two identified as S. liquefaciens, one as Hafnia alvei), two S. liquefaciens (both identified as E. cloacae), and two K. pneumoniae (one identified as Klebsiella ozaenae, the other as Serratia rubidaea). None of the 15 non-enterobacterial cultures were correctly identified by Micro-ID (non-identifiable, or classified as Providencia/Yersinia/Klebsiella species). Although biochemical discrepancies between direct and final Micro-ID tests occurred in 41% of the enterobacterial cultures, this did not seriously interfere with identification. Direct species identification of Enterobacteriaceae from blood cultures by direct Micro-ID is accurate and easily performed and identified organisms within 4 h compared to at least 24 h by most other methods; the direct Micro-ID technique would be rendered even more valuable by the additional capability of identifying non-enterobacterial gram-negative isolates.

Acinetobacter↗
PubMed1980

Comparison of the automicrobic system with API, enterotube, micro-ID, micro-media systems, and conventional methods for identification of Enterobacteriaceae.

Identification of Enterobacteriaceae by the AutoMicrobic System Enterobacteriaceae Biochemical Card was evaluated. Recent clinical isolates of enteric gram-negative bacilli (192) and glucose nonfermenters (3) were identified by the AutoMicrobic System, Micro-Media Systems, Micro-ID, API, and Enterotube II in comparison with conventional methods. The AutoMicrobic System and Micro-Media Systems correctly identified 97% of the organisms tested. Micro-ID, API, and Enterotube II correctly identified 94, 92, and 84% of the organisms, respectively. In addition to a high degree of identification accuracy, the AutoMicrobic System was convenient to operate and produced identification results in 8 h. Operation of the AutoMicrobic System also required minimal personnel time because it automatically monitored and interpreted the biochemical reactions and reported organism identifications. The AutoMicrobic System appears to be an efficient and accurate system for the identification of Enterobacteriaceae.

Bacteriological Techniques↗
PubMed1981

Accurate automated identification of selected Enterobacteriaceae at four hours.

The Enterobacteriaceae Biochemical Card of the AutoMicrobic system Vitek Systems, Inc., Hazelwood, Mo.) provides completely automated identification of members of this family within an 8-h test period. Identification of 776 clinical and stock isolates to species level by the Enterobacteriaceae Biochemical Card under routine operating conditions correlated at 96% with our present 18- to 24-h methods of identification. Further, utilizing a special program, we investigated presumptive identification of certain organisms within 4-h--an interval that provides greater practical clinical usefulness on a real-time rapid basis. In a single year, 1978, 97% of 23,464 Enterobacteriaceae isolated in our diagnostic laboratory belonged to 11 species of six genera. Our results suggest that, by limiting the number of the identified Enterobacteriaceae that could be actually presumptively reported to those 11 species of six genera. Our results suggest that, by limiting the number of the identified Enterobacteriaceae that could be actually presumptively reported to those 11 species with the highest frequency of occurrence, we could have correctly identified and presumptively reported 83% of these to genus or species after only 4 h. Approximately 2% of the isolates would have been presumptively identified and reported incorrectly, whereas the identification of the remaining 15% would not have been reported before the completed 8-h incubation period.

Autoanalysis↗
PubMed1981

Rapid identification and antimicrobial susceptibility testing of gram-negative bacilli from blood cultures by the AutoMicrobic system.

A procedure was developed which allows direct identification and antimicrobial susceptibility testing of fermentative and nonfermentative gram-negative bacilli from positive blood cultures. A 10-ml sample was removed from turbid blood culture bottles, and the bacteria were washed and concentrated by centrifugation. The bacterial pellet was used to inoculate an Enterobacteriaceae Plus Identification Card and a Gram-Negative General Susceptibility Card of the AutoMicrobic system. Results with these cards were compared with results obtained with standard technique for 196 blood cultures seeded with recent clinical isolates. Identification of most cultures was available in 8 h, whereas the antimicrobial susceptibility results were available in an average of 4.7 h for all organisms. Direct identification was correct for 95% of the cultures, whereas the antimicrobial susceptibility data had an average agreement of 87% with 3.8% very major and 1.4% major errors. In using this procedure it was possible to provide accurate preliminary identification and results of antimicrobial susceptibility tests for gram-negative bacilli on the same day that a blood culture was determined to be positive.

Anti-Bacterial Agents↗
PubMed1982

Comparison of Enteric-Tek with API 20E and conventional methods for identification of Enterobacteriaceae.

Enteric-Tek (Flow Laboratories, Inc., Roslyn, N.Y.) is a new system designed for the identification of Enterobacteriaceae and consists of a round, multicompartmented plastic plate with 11 peripheral wells and 1 center well incorporating 14 biochemical reactions. Only one reagent (Kovacs reagent) is required to complete the biochemical test results for generation of a five-digit number for computer code identification. The identification accuracy of the Enteric-Tek system was compared with those obtained by conventional methods and API 20E. The Enteric-Tek system was found to be not only a convenient and simple method for rapid identification of Enterobacteriaceae, but also to be highly reliable, giving excellent identification performance as compared to API 20E and conventional methods.

Enterobacteriaceae↗
PubMed1982

Comparison of micro-ID and API 20E in rapid identification of Enterobacteriaceae.

The effectiveness of Micro-ID and API 20E as same-day identification systems for Enterobacteriaceae was evaluated in comparison with conventional identification by using 315 clinical isolates and 90 stock strains. The API 20E system was heavily inoculated according to manufacturer's recommendations for same-day identification. We found that 83 and 81% of isolates provided adequate inocula for Micro-ID and API 20E, respectively, and purity of the heavy inocula was not a problem with either system. Overall agreement with conventional identification at genus and species levels was 93.5% with Micro-ID and 90.2% with API 20E. However, when Klebsiella pneumoniae and K. oxytoca were considered as a single species and Proteus morganii was equated with Morganella morganii, agreement was 95.8 and 90.5%, respectively. Only 83.% of isolates were identified on the day of inoculation by API 20E, in contrast to 94.3% with Micro-ID. The remaining isolates required supplementary overnight testing. Provisional (low selectivity) determinations were constant with conventional identification with 49.3% of isolates with API 20E and 82.6% with Micro-ID. Telephone consultations with the manufacturers to resolve unprinted octal codes required a maximum of 15 min with Micro-ID and from 2 to greater than 48 h with API 20E.

Bacteriological Techniques↗
PubMed1982

Evaluation of a rapid system for species identification of alpha-hemolytic streptococci.

A new 4-h commercial system (API 20S; Analytab Products, Plainview, N.Y.) for the identification of streptococci was compared with the conventional biochemical profile method in the species identification of alpha-hemolytic streptococci. A total of 194 clinical isolates (including 74 isolated from blood cultures, 64 isolated from wound cultures, and 56 isolated from respiratory cultures) and 20 reference strains were tested. Only 4 of the 20 reference strains were correctly identified to species level by the API 20S system. Six were identified to group level (viridans), four were incorrectly identified, and six did not conform to the identification key. Of the 194 clinical isolates tested, 79 (39%) were correctly identified to species level, 34 (17.5%) were identified to group level, 34 (17.5%) were incorrectly identified, and 50 (25.8%) did not conform to the identification key. Of the 12 different species of alpha-hemolytic streptococci isolated from clinical specimens, the API 20S system consistently identified Streptococcus faecalis and Streptococcus faecium, but consistently misidentified the other 10 species, especially Streptococcus mitis. Our results indicate that for identification to species level, the API 20S system is of little value for alpha-hemolytic streptococci other than enterococci.

Bacteriological Techniques↗
PubMed1982

Development and evaluation of a biochemical scheme for identification of endocervical lactobacilli.

A biochemical scheme for the species identification of endocervical lactobacilli was developed and evaluated with 10 isolates obtained from the American Type Culture Collection (ATCC) and 106 endocervical isolates obtained from women reporting to a local venereal disease clinic and a local hospital clinic. The scheme consisted of two stages. Stage I included six tests and was tested and modified with results obtained with ATCC strains. From the modified stage I, stage II was developed. Tests to be performed in this stage were determined from expected characteristics of lactobacilli. Stage II was also tested with the ATCC strains. Of the 106 endocervical isolates, 78 (74%) were identified with the two-stage scheme as developed with the ATCC strains. Unexpected results were obtained in one or both stages with the other 28 isolates. For 10 isolates, the final species identified were not previously expected to be recovered. A "best-fit" method was used to determine the most likely identification of the remaining 18 isolates. In a few instances, the use of a third stage was necessary to reach an identification. The final identification scheme, although complicated in appearance, generated a species identification with a total of 12 tests with a range of 7 to 10 tests per isolate.

Cervix Uteri↗
PubMed1982

Automated identification of gram-positive bacteria.

A total of 451 strains of gram-positive bacteria were identified with a prototype of the Gram-Positive Identification card used in conjunction with the AutoMicrobic system (Vitek Systems, Inc., Hazelwood, Mo.). Of the species that the Gram-Positive Identification card is capable of identifying, 85% of staphylococcal, 50% of beta-hemolytic group A, B, C, F, and G streptococcal, 91% of group D streptococcal, 100% of pneumococcal, 63% of viridans streptococcal, and 100% of Listeria monocytogenes strains tested displayed Gram-Positive Identification card identifications that were in agreement with identifications obtained by conventional methods.

Bacteriological Techniques↗