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At least 1,279 records · Page 71Linked to original sources

PubMed1999

Vowel-specific effects in concurrent vowel identification.

An experiment investigated the effects of amplitude ratio (-35 to 35 dB in 10-dB steps) and fundamental frequency difference (0%, 3%, 6%, and 12%) on the identification of pairs of concurrent synthetic vowels. Vowels as weak as -25 dB relative to their competitor were easier to identify in the presence of a fundamental frequency difference (delta F0). Vowels as weak as -35 dB were not. Identification was generally the same at delta F0 = 3%, 6%, and 12% for all amplitude ratios: unfavorable amplitude ratios could not be compensated by larger delta F0's. Data for each vowel pair and each amplitude ratio, at delta F0 = 0%, were compared to the spectral envelope of the stimulus at the same ratio, in order to determine which spectral cues determined identification. This information was then used to interpret the pattern of improvement with delta F0 for each vowel pair, to better understand mechanisms of F0-guided segregation. Identification of a vowel was possible in the presence of strong cues belonging to its competitor, as long as cues to its own formants F1 and F2 were prominent. delta F0 enhanced the prominence of a target vowel's cues, even when the spectrum of the target was up to 10 dB below that of its competitor at all frequencies. The results are incompatible with models of segregation based on harmonic enhancement, beats, or channel selection.

Adolescent↗

PubMed2000

Noninvasive system identification for multichannel broadband active noise control

Many real-world applications of active noise control are characterized by transfer functions that vary significantly and unpredictably. The controller's transfer-function models must adapt to these variations. Presented here is a class of adaptive filters that accomplish quasiperiodic system identification updates for feedforward control by using blocks of input-output histories. The algorithms form a one-dimensional family linking normalized least-mean squares (LMS) adaptive filters and block recursive least-squares, termed "block projection" algorithms, and generalize the noninvasive system identification studied by Sommerfeldt and Tichy. The system identification proceeds noninvasively, producing nonparametric impulse responses. Simulations show that the algorithm's convergence is faster than that of normalized LMS, even after the additional overhead of computing the update is taken into account. Both the multichannel generalization and application of these algorithms to system identification are novel. Simulations of the algorithms' performance using measured data are presented here, while experimental results of an implemented algorithm are contained in the companion paper.

Journal Article↗

PubMed2026

A rapid CRISPR-based nanodroplet assay enables direct clinical identification of mycobacteria species.

The global incidence and mortality of nontuberculous mycobacterial infections have risen sharply with population aging. In some regions, they are now surpassing Mycobacterium tuberculosis complex infections, imposing a substantial clinical and economic burden. Because nontuberous mycobacteria exhibit species-level heterogeneity and require prolonged culture for identification, their diagnosis remains slow and is frequently inaccurate. Here, we describe a multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)-assisted nanodroplet differential identification (CANDI) diagnostic platform that integrates species-agnostic target amplification with species-specific CRISPR-associated protein 12a (Cas12a) detection in fluorescence-barcoded nanodroplets. By spatially compartmentalizing CRISPR reactions into color-encoded nanodroplets, CANDI overcomes the multiplexing limitations of conventional CRISPR diagnostics and enables simultaneous interrogation of multiple mycobacterial targets in a single assay. We designed a 16-plex panel that distinguishes 15 clinically relevant Mycobacterium species and subspecies. CANDI achieved high analytical sensitivity and accurate discrimination in samples containing coinfections with multiple species or subspecies. When applied to 230 clinical specimens, including sputum, tracheal aspirates, and other respiratory fluids, CANDI delivered subspecies-level results within 3.5 hours, achieving 97.08% sensitivity and 99.7% specificity relative to culture-based identification. By combining multiplexed, high-specificity CRISPR detection with scalable droplet-based engineering, CANDI has the potential to overcome the culture dependency of current diagnostics and enable species- and subspecies-level identification across the genetically complex Mycobacterium genus, offering a clinically adaptable framework for rapid, precision diagnosis of mycobacterial infections.

Humans↗

PubMed1988

Comparison of rapid NFT and API 20E with conventional methods for identification of gram-negative nonfermentative bacilli from pharmaceuticals and cosmetics.

The accuracy of the Rapid NFT and the API 20E identification systems was evaluated by comparing them with conventional biochemical methods for the identification of gram-negative, nonfermentative bacilli. The organisms were recovered from preserved, nonsterile pharmaceutical and cosmetic products. A total of 123 test isolates that are commonly encountered in these products were used. By using the criteria of accurate and reliable identification without employing additional tests, Rapid NFT was found to be more accurate after 48 h of incubation than API 20E for characterizing isolates to the species level. Therefore, close agreement between NFT and conventional methods for identification of industrial gram-negative isolates provides evidence that the Rapid NFT system is an improved and rapid method for identifying these organisms to the species level with minimal use of supplementary tests.

Cosmetics↗

PubMed1990

Identification of Salmonella somatic and flagellar antigens by modified serological methods.

This report describes two modified methods for the identification of Salmonella somatic (O) and flagellar (H) antigens. Over a period of 2 years, both modified methods were found to be approximately three times less labor intensive than the standard methods while requiring no more technical skill. The modified methods were as accurate as the standard methods in identifying the O and H antigens of 350 Salmonella isolates. Furthermore, 43 O antisera reacted exclusively with organisms possessing homologous O antigens when the modified and two standard methods were used. At the antiserum dilutions used for H antigen identification, H antisera did not react with O antigens or heterologous H antigens by either the modified or the standard method. Compared with the standard method for H antigen identification, the modified method was approximately 20 times more economical with respect to antisera and usually generated a 1.5- to 4-fold higher titer. Since the antisera stored for use in the modified method for H antigen identification were usually 100-fold more dilute than the antisera stored for the standard method, an antibody-stabilizing buffer was incorporated in the diluted antisera, allowing these reagents to be used for at least 9 to 16 months.

Agglutination Tests↗

PubMed1990

Evaluation and reliability of a simplified method for identification of food-borne yeasts.

A simplified identification key described by Deak and Beuchat (T. Deak and L. R. Beuchat, J. Food Prot. 50:243-264, 1987) and the computer method of Barnett et al. (J. A. Barnett, R. W. Payne, and D. Yarrow, Yeast Identification Program, 1985) were used to identify 12 reference strains and 382 yeasts isolated from cultured milk products. Because the simplified key failed to account for species variability with regard to physiological, morphological, and sexual reproduction characteristics, poor agreement of the identification results was obtained. A reevaluation of the basic theoretical assumptions of the simplified key only confirmed the practical results and indicates that this identification method is unsatisfactory.

Journal Article↗

PubMed1995

Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment.

Seventy-four bacterial strains were freshly isolated from a mine gallery. Using these bacteria, we have investigated how a molecular identification based on the analysis of small subunit rDNA sequences would compare in terms of precision and reliability to a more classical comparison of phenotypical descriptions (100 morphological and physiological traits). Our data clearly showed that a phylogenetic analysis of small subunit rDNA sequences is more efficient than classical phenotypic methods for the identification of bacterial strains freshly isolated from a natural environment, because occurrences of misidentification are very much decreased by this method. The lack of rDNA sequences for many described species is probably the major cause of a few failures in molecular identification, as the completeness of the database of small subunit rDNA sequences holds much importance in the degree of uncertainty in such identifications.

Journal Article↗

PubMed1998

Isolation and identification of Helicobacter spp. from canine and feline gastric mucosa.

It is known that virtually all healthy adult dogs and cats harbor spiral helicobacters in their gastric mucosa. Three species, Helicobacter felis, Helicobacter bizzozeronii, and Helicobacter salomonis have been isolated in vitro from the gastric mucosa of these animals. The aims of this study were to evaluate the efficacy of an isolation method for canine and feline gastric helicobacters that has been developed at the University of Helsinki; to estimate the prevalence and distribution of these taxa in the samples examined; and to assess the efficacy and validity of an extensive set of standardized conventional phenotypic tests, whole-cell protein profiling, and ultrastructural analysis in identifying the different species isolated from canine and feline gastric mucosa. We cultured 95 and 22 gastric mucosal biopsies from dogs and cats, respectively. Twenty-one H. bizzozeronii strains, 8 H. felis strains, 8 H. salomonis strains, 3 mixed cultures, 2 "Flexispira rappini"-like organisms, and 3 as yet uncharacterized strains were isolated from the dogs, and 3 H. felis strains were isolated from the cats. The methods used here yielded Helicobacter isolation rates of 51% from dogs and 13.6% from cats, which exceed those reported previously. The main difficulties were primary isolation, mixed cultures, and identification to the species level. In the species identification, a detailed morphological examination was found to yield important phenotypic characteristics. A large panel of biochemical and tolerance tests did not clearly differentiate the closely related species H. bizzozeronii, H. felis, and H. salomonis. Highly standardized whole-cell protein profiling was shown to be an excellent method for species identification. Improvements in culture conditions for these bacteria are still needed, especially for cats. A genetic identification method not requiring culture is needed for future studies of these very fastidious helicobacters, as the clinical significance and ecology of these species within the gastric mucosa of the domestic carnivores remain largely unknown.

Animals↗

PubMed2001

Comparison of statistical methods for identification of Streptococcus thermophilus, Enterococcus faecalis, and Enterococcus faecium from randomly amplified polymorphic DNA patterns.

Thermophilic streptococci play an important role in the manufacture of many European cheeses, and a rapid and reliable method for their identification is needed. Randomly amplified polymorphic DNA (RAPD) PCR (RAPD-PCR) with two different primers coupled to hierarchical cluster analysis has proven to be a powerful tool for the classification and typing of Streptococcus thermophilus, Enterococcus faecium, and Enterococcus faecalis (G. Moschetti, G. Blaiotta, M. Aponte, P. Catzeddu, F. Villani, P. Deiana, and S. Coppola, J. Appl. Microbiol. 85:25-36, 1998). In order to develop a fast and inexpensive method for the identification of thermophilic streptococci, RAPD-PCR patterns were generated with a single primer (XD9), and the results were analyzed using artificial neural networks (Multilayer Perceptron, Radial Basis Function network, and Bayesian network) and multivariate statistical techniques (cluster analysis, linear discriminant analysis, and classification trees). Cluster analysis allowed the identification of S. thermophilus but not of enterococci. A Bayesian network proved to be more effective than a Multilayer Perceptron or a Radial Basis Function network for the identification of S. thermophilus, E. faecium, and E. faecalis using simplified RAPD-PCR patterns (obtained by summing the bands in selected areas of the patterns). The Bayesian network also significantly outperformed two multivariate statistical techniques (linear discriminant analysis and classification trees) and proved to be less sensitive to the size of the training set and more robust in the response to patterns belonging to unknown species.

Bayes Theorem↗

PubMed2003

Molecular identification of ectomycorrhizal mycelium in soil horizons.

Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (> or = 99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had > or = 98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.

Basidiomycota↗

PubMed2003

Usefulness of rpoB gene sequencing for identification of Afipia and Bosea species, including a strategy for choosing discriminative partial sequences.

Bacteria belonging to the genera Afipia and Bosea are amoeba-resisting bacteria that have been recently reported to colonize hospital water supplies and are suspected of being responsible for intensive care unit-acquired pneumonia. Identification of these bacteria is now based on determination of the 16S ribosomal DNA sequence. However, the 16S rRNA gene is not polymorphic enough to ensure discrimination of species defined by DNA-DNA relatedness. The complete rpoB sequences of 20 strains were first determined by both PCR and genome walking methods. The percentage of homology between different species ranged from 83 to 97% and was in all cases lower than that observed with the 16S rRNA gene; this was true even for species that differed in only one position. The taxonomy of Bosea and Afipia is discussed in light of these results. For strain identification that does not require the complete rpoB sequence (4,113 to 4,137 bp), we propose a simple computerized method that allows determination of nucleotide positions of high variability in the sequence that are bordered by conserved sequences and that could be useful for design of universal primers. A fragment of 740 to 752 bp that contained the most highly variable area (positions 408 to 420) was amplified and sequenced with these universal primers for 47 strains. The variability of this sequence allowed identification of all strains and correlated well with results of DNA-DNA relatedness. In the future, this method could be also used for the determination of variability "hot spots" in sets of housekeeping genes, not only for identification purposes but also for increasing the discriminatory power of sequence typing techniques such as multilocus sequence typing.

Afipia↗

PubMed2003

Rapid identification of Candida species by using nuclear magnetic resonance spectroscopy and a statistical classification strategy.

Nuclear magnetic resonance (NMR) spectra were acquired from suspensions of clinically important yeast species of the genus Candida to characterize the relationship between metabolite profiles and species identification. Major metabolites were identified by using two-dimensional correlation NMR spectroscopy. One-dimensional proton NMR spectra were analyzed by using a staged statistical classification strategy. Analysis of NMR spectra from 442 isolates of Candida albicans, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis resulted in rapid, accurate identification when compared with conventional and DNA-based identification. Spectral regions used for the classification of the five yeast species revealed species-specific differences in relative amounts of lipids, trehalose, polyols, and other metabolites. Isolates of C. parapsilosis and C. glabrata with unusual PCR fingerprinting patterns also generated atypical NMR spectra, suggesting the possibility of intraspecies discontinuity. We conclude that NMR spectroscopy combined with a statistical classification strategy is a rapid, nondestructive, and potentially valuable method for identification and chemotaxonomic characterization that may be broadly applicable to fungi and other microorganisms.

Candida↗

PubMed2006

Oligonucleotide array for identification and detection of pythium species.

A DNA array containing 172 oligonucleotides complementary to specific diagnostic regions of internal transcribed spacers (ITS) of more than 100 species was developed for identification and detection of Pythium species. All of the species studied, with the exception of Pythium ostracodes, exhibited a positive hybridization reaction with at least one corresponding species-specific oligonucleotide. Hybridization patterns were distinct for each species. The array hybridization patterns included cluster-specific oligonucleotides that facilitated the recognition of species, including new ones, belonging to groups such as those producing filamentous or globose sporangia. BLAST analyses against 500 publicly available Pythium sequences in GenBank confirmed that species-specific oligonucleotides were unique to all of the available strains of each species, of which there were numerous economically important ones. GenBank entries of newly described species that are not putative synonyms showed no homology to sequences of the spotted species-specific oligonucleotides, but most new species did match some of the cluster-specific oligonucleotides. Further verification of the specificity of the DNA array was done with 50 additional Pythium isolates obtained by soil dilution plating. The hybridization patterns obtained were consistent with the identification of these isolates based on morphology and ITS sequence analyses. In another blind test, total DNA of the same soil samples was amplified and hybridized on the array, and the results were compared to those of 130 Pythium isolates obtained by soil dilution plating and root baiting. The 13 species detected by the DNA array corresponded to the isolates obtained by a combination of soil dilution plating and baiting, except for one new species that was not represented on the array. We conclude that the reported DNA array is a reliable tool for identification and detection of the majority of Pythium species in environmental samples. Simultaneous detection and identification of multiple species of soilborne pathogens such as Pythium species could be a major step forward for epidemiological and ecological studies.

Oligonucleotide Array Sequence Analysis↗

PubMed2004

Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases.

The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.

Bacteria↗

PubMed1992

Automated systems for identification of microorganisms.

Automated instruments for the identification of microorganisms were introduced into clinical microbiology laboratories in the 1970s. During the past two decades, the capabilities and performance characteristics of automated identification systems have steadily progressed and improved. This article explores the development of the various automated identification systems available in the United States and reviews their performance for identification of microorganisms. Observations regarding deficiencies and suggested improvements for these systems are provided.

Bacteria↗

PubMed2006

Identification of Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides species by repetitive-sequence-based PCR.

The performance of repetitive-sequence-based PCR (rep-PCR) using the DiversiLab system for identification of Coccidioides species, Blastomyces dermatitidis, and Histoplasma capsulatum was assessed by comparing data obtained to colony morphology and microscopic characteristics and to nucleic acid probe results. DNA from cultures of 23 Coccidioides, 24 B. dermatitidis, 24 H. capsulatum, 3 Arthrographis, and 2 Malbranchea isolates was extracted using a microbial DNA isolation kit as recommended by Bacterial Barcodes, Inc. Rep-PCR and probe results agreed for 97.2% of the dimorphic fungi when > or =85% similarity was used as the criterion for identification. Two H. capsulatum isolates were not identified, but no isolates were misidentified. From 43 of those cultures (15 Coccidioides, 14 B. dermatitidis, 14 H. capsulatum, 3 Arthrographis, and 2 Malbranchea), DNA also was extracted using an IDI lysis kit, a simpler method. Rep-PCR and probe results agreed for 97.7% of the dimorphic fungi when a criterion of > or =90% similarity was used for identification. One H. capsulatum isolate could not be identified; no isolates were misidentified. Using > or =85% similarity for identification resulted in one misidentification. These data suggest that the DiversiLab system can be used to identify Coccidioides and B. dermatitidis and, possibly, H. capsulatum isolates.

Blastomyces↗

PubMed2006

Array-based identification of species of the genera Abiotrophia, Enterococcus, Granulicatella, and Streptococcus.

Some species of enterococci and streptococci are difficult to differentiate by phenotypic traits. The feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. The aim of this study was to expand the array to identify species of Abiotrophia (1 species), Enterococcus (18 species), Granulicatella (3 species), and Streptococcus (31 species and 6 subspecies). The method consisted of PCR amplification of the ribosomal DNA intergenic spacer (ITS) regions, followed by hybridization of the digoxigenin-labeled PCR products to a panel of oligonucleotide probes (16- to 30-mers) immobilized on a nylon membrane. Probes could be divided into three categories: species specific, group specific, and supplemental probes. All probes were designed either from the ITS regions or from the 3' ends of the 16S rRNA genes. A collection of 312 target strains (162 reference strains and 150 clinical isolates) and 73 nontarget strains was identified by the array. Most clinical isolates were isolated from blood cultures or deep abscesses, and only those strains having excellent species identification with the Rapid ID 32 STREP system (bioMérieux Vitek, Taipei, Taiwan) were used for array testing. The test sensitivity and specificity of the array were 100% (312/312) and 98.6% (72/73), respectively. The whole procedure of array hybridization took about 8 h, starting from isolated colonies, and the hybridization patterns could be read by the naked eye. The oligonucleotide array is accurate for identification of the above microorganisms and could be used as a reliable alternative to phenotypic identification methods.

Bacteriological Techniques↗

PubMed1979

Identification of clinical isolates of mycobacteria with gas-liquid chromatography alone.

Identification of 18 mycobacterial species was performed by analysis of profiles obtained by using gas-liquid chromatography. Organisms were saponified in methanolic NaOH, and the reaction mixture was treated with BF(3) in methanol and extracted with a hexane-chloroform mixture. An identification scheme was developed from 128 stock strains and tested against a collection of 79 clinical isolates. By using gas-liquid chromatographic profiles alone, 58% of specimens were correctly identified to species level, and an additional 41% were correctly identified to a group of two or three organisms. Use in a clinical laboratory over a 2-month period proved chromatography to be as accurate as and more rapid than concurrent biochemical testing. Of 81 isolates tested, 64% were identified to species level by chromatography alone. An additional 35% were differentiated to the same groups of two or three organisms as found in our analysis of stock strains. These groups consisted of: Mycobacterium tuberculosis, M. bovis, and M. xenopi; M. avium complex, M. gastri, and M. scrofulaceum; or M. fortuitum and M. chelonei. Identification to species level from these groups could usually be done by colonial morphology alone and could always be done by the addition of one selected biochemical test. This study demonstrated the practical application of gas-liquid chromatography in the identification of mycobacteria in a clinical laboratory. In particular, all strains of M. gordonae and M. kansasii were identified to species level. M. tuberculosis was definitively identified in 85% of cases. When it could not be definitely identified, the only alternatives were M. bovis and M. xenopi, both of which are rare causes of infection.

Chromatography, Gas↗