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PubMed1992

Evaluation of a new commercial system for the identification of Enterobacteriaceae and non-fermentative bacteria.

The performance of a new commercial semi-automatic system (Cobas Micro, Becton Dickinson) for identification of gram-negative fermentative and non-fermentative bacilli was evaluated using strains of clinical origin belonging to 48 different species. Two groups of strains were tested: 510 strains using a long incubation period (21 hours) and 158 strains using a short incubation period (5 hours). The correct identification rate without additional tests was 95.5% and 94.3% for the tests using a long and short incubation period respectively. The findings suggest that the system is highly accurate in the identification of most clinically important gram-negative rods, but shows some shortcomings in the identification of non-fermentative bacteria. The system is easy to use, and with some changes in the database and the inclusion of gram-positive and anaerobic bacteria would offer a valuable alternative to currently available automatic identification systems.

Bacteriological Techniques↗

PubMed1994

Evaluation of an automated system for identification of anaerobic bacteria.

A fully automated computer-assisted system (ATB system, bioMérieux, France) which uses disposable microenzymatic panels was evaluated for its ability to identify 215 strains of anaerobic bacteria (clinical isolates and reference strains). All strains were examined using conventional identification protocols and by gas chromatographic analysis of short-chain fatty acids. Automated reading of Rapid ID32A test kits (bioMérieux, France) by the ATB system gave correct identification for 195 strains (90.7%): 92.25% of gram-negative anaerobes (116 strains) and 89% of gram-positive anaerobes (99 strains) were correctly identified. Twelve strains (5.6%) were incorrectly identified and 8 strains (3.7%) were not identified by the system. For some strains in the Bacteroides fragilis group, for Clostridium difficile and for the Fusobacterium genus, additional tests suggested by the ATB software were necessary to reach a final identification at the species or genus level. On the basis of the high incidence of correct identifications and the comparison of these results with those obtained previously using other commercially available kits, the ATB system was found to be a reliable method for identification of anaerobic bacteria in clinical laboratories.

Bacteria, Anaerobic↗

PubMed1983

Performance of two four-hour identification systems with atypical strains of Enterobacteriaceae.

Two four-hour systems (Rapid 20E and Micro-ID) for identification of Enterobacteriaceae were evaluated using 66 strains isolated from clinical specimens which could not be identified by conventional methods. API 20E was used as reference method. Both systems had an acceptable identification rate (84.8% for Rapid 20E and 74.2% for Micro-ID). After referral to API's computer facilities the identification rate of Rapid 20E rose to 92.4%. Micro-ID incorrectly identified 16.7% of the strains and Rapid 20E only 1.5%. On the other hand, no identification was achieved in 13.6% of the strains using Rapid 20E versus 6% using Micro-ID. On the basis of these findings Rapid 20E is considered the more suitable system for the rapid identification of Enterobacteriaceae strains which cannot be identified by conventional methods.

Bacteriological Techniques↗

PubMed1981

Comparison of four methods for identification of gram-negative non-fermenters: organisms less commonly encountered in clinical specimens.

Four commercial kits--Oxi/Ferm (OF), API 20E (AP), Minitek (MT), Flow N/F (NF) were evaluated, without additional tests, for identification of 105 opportunistic Gram-negative non-fermentative rods. Of correctly identified 42% of strains, with 35% as part (but not first) of a spectrum of identifications (SI) and 23% incorrect identification. MT yielded 75% correct identification, with 12% SI and 13% incorrect. AP correctly identified 64% of strains, with 26% SI, 10% incorrect. NF correctly speciated 70% of strains, with 24% SI, 6% incorrect. All 4 methods show deficiencies in identification of these rare but increasingly clinically encountered organisms. Addition of new tests/modification of existing ones would render these systems more capable of identifying this organisms group.

Alcaligenes↗

PubMed1994

Faster identification of mycobacteria using gas liquid and thin layer chromatography.

Gas liquid chromatography (GLC) and thin layer chromatography (TLC) analysis of cell wall content was used for identification of mycobacteria isolated in primary cultures. GLC permitted determination of the fatty acid and alcohol profiles of Mycobacterium simiae and Mycobacterium marinum and detection of a peak in Mycobacterium ulcerans formerly described for Mycobacterium malmoense. Using the data obtained to fill some of the gaps in the dichotomic trees of Tisdall et al. and Jantzen et al., GLC analysis allowed full identification of 8 of 22 mycobacterial species after 24 hours. The other 14 species could be divided into four groups on the basis of similar findings on GLC. TLC was used for full identification of three species. The identification results of conventional methods were concordant with those of GLC and TLC in 161 of 169 strains (93%) representing 21 different species. Using primarily chromatography for analysis of cell wall content, and in the case of some species complementary biochemical tests, the identification procedure could be shortened to a maximum of three days after primary culture.

Chromatography, Gas↗

PubMed1982

Evaluation of Gram-stain screen and Micro-ID methods for direct identification of Enterobacteriaceae from urines.

A rapid method of urine screening and enterobacterial identification was evaluated. Results indicated that an average of 13.5 bacteria/oil immersion field (threshold value greater than or equal to 1) was observed in unsedimented urine of patients with significant bacteriuria, with an average of less than 1 bacterium/field in urines of patients without significant bacteriuria. In centrifuged urines, numbers of bacteria divided by amount of urine sedimented yielded similar results. Of 1758 urines studied, 136 yielded greater than or equal to 10(5) bacteria/ml, and 58 greater than 10(4) but less than 10(5) bacteria/ml, by conventional techniques. Gram-screening of unsedimented specimens gave sensitivity rates of 94.1%, specificity of 97.7%, and predictive positive and negative values of 78.5%, 99.5%, respectively; similar values were obtained with sedimented urines. Sensitivity rates of both screening methods for the 58 urines with greater than 10(4) but less than 10(5) bacteria/ml were 9.0%, 10.0%, respectively. Total correct enteric identification in 113 urines with positive screens and significant bacteriuria (greater than or equal to 10(5)/ml) was 82.3% and 90.3% with direct saline and broth Micro-ID methods, respectively. In 99 urines yielding pure or predominantly pure growth of 1 species of Enterobacteriaceae identification by direct saline and broth Micro-ID corresponded with isolated colony identification in 85.9%, 94.9% of cases, respectively. Gram-stain screening (together with back-up conventional plating in certain patient categories) and enterobacterial identification by direct broth Micro-ID, of urines with pure stains suggestive of greater than or equal to 10(5) Gram-negative rods/ml has been shown to be useful in laboratories without automated equipment for urine screening.

Bacteriological Techniques↗

PubMed2003

"Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping.

We describe here a new approach for the identification of affinity-bound proteins by proteolytic generation and mass spectrometric analysis of their antibody bound epitope peptides (epitope excision). The cardiac muscle protein troponin T was chosen as a protein antigen because of its diagnostic importance in myocardial infarct, and its previously characterised epitope structure. Two monoclonal antibodies (IgG1-1B10 and IgG1-11.7) raised against intact human troponin T were found to be completely cross reactive with bovine heart troponin T. A combination of immuno-affinity isolation, partial proteolytic degradation (epitope excision), mass spectrometric peptide mapping, and database analysis was used for the direct identification of Tn T from bovine heart cell lysate. Selective binding of the protein was achieved by addition of bovine heart cell lysate to the Sepharose-immobilised monoclonal antibodies, followed by removal of supernatant material containing unbound protein. While still bound to the affinity matrix the protein was partially degraded thereby generating a set of affinity-bound, overlapping peptide fragments comprising the epitope. Following dissociation from the antibody the epitope peptides were analysed by matrix assisted laser desorption-ionisation (MALDI) and electrospray-ionisation (ESI) mass spectrometry. The peptide masses identified by mass spectrometry were used to perform an automated database search, combined with a search for a common "epitope motif". This procedure resulted in the unequivocal identification of the protein from biological material with only a minimum number of peptide masses, and requiring only limited mass-determination accuracy. The dramatic increase of selectivity for identification of the protein by combining the antigen-antibody specificity with the redundancy of peptide sequences renders this "affinity-proteomics" approach a powerful tool for mass spectrometric identification of proteins from biological material.

Amino Acid Sequence↗

PubMed2006

Technical innovations for the automated identification of gel-separated proteins by MALDI-TOF mass spectrometry.

The combination of gel-based two-dimensional protein separations with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is the workhorse for the large-scale analyses of proteomes. Such high-throughput proteomic approaches require automation of all post-separation steps and the in-gel digest of proteins especially is often the bottleneck in the protein identification workflow. With the objective of reaching the same high performance of manual low-throughput in-gel digest procedures, we have developed a novel stack-type digestion device and implemented it into a commercially available robotic liquid handling system. This modified system is capable of performing in-gel digest, extraction of proteolytic peptides, and subsequent sample preparation for MALDI-MS without any manual intervention, but with a performance at least identical to manual procedures as indicated on the basis of the sequence coverage obtained by peptide mass fingerprinting. For further refinement of the automated protein identification workflow, we have also developed a motor-operated matrix application device to reproducibly obtain homogenous matrix preparation of high quality. This matrix preparation was found to be suitable for the automated acquisition of both peptide mass fingerprint and fragment ion spectra from the same sample spot, a prerequisite for high confidence protein identifications on the basis of peptide mass and sequence information. Due to the implementation of the stack-type digestion device and the motor-operated matrix application device, the entire platform works in a reliable, cost-effective, and sensitive manner, yielding high confidence protein identifications even for samples in the concentration range of as low as 100 fmol protein per gel plug.

Automation↗

PubMed2002

Identification of transcription factor binding sites in the human genome sequence.

The identification of transcription factor binding sites (TFBS) is an important initial step in determining the DNA signals that regulate transcription of the genome. We tested the performance of three distinct computational methods for the identification of TFBS applied to the human genome sequence, as judged by their ability to recover the location of experimentally determined, and uniquely mapped, TFBS taken from the TRANSFAC database. These identification methods all attempt to filter the quantity of TFBS identified by aligning positional weight matrices that describe the binding site and employ either (i) a P-value threshold for accepting a site, (ii) an over-representation measure of neighboring sites, or (iii) conservation with the mouse genome and application of P-value thresholds. The results show that the best recognition of TFBS is achieved by combining the identification of TFBS in regions of human-mouse conservation and also by applying a high stringency P-value to the TFBS identified in non-coding regions that are not conserved. Additionally, we find that only half of the 481 experimentally mapped sites can be found in sequence regions conserved with mouse, but the predictive power of the binding site identification method is up to threefold higher in the conserved regions.

Animals↗

PubMed2005

Could earprint identification be computerised? An illustrated proof of concept paper.

To date, the ear remains an under-utilised part of the human body for use in forensic practice. Although the ear has been used since the nineteenth century as part of the process of human identification, in this particular function its use, to date, remains low and in the case of earprints, controversial. A limited number of publications exist related to methods used for the purpose of ear image identification and the growing field of ear biometrics but to date, a computerised system for earprint identification does not exist. This paper illustrates the concept of a computerised earprint identification system. To assist those considering similar developments we share the concept problems and possible solutions we have identified and encountered to date, and highlight the advantages for such a system over traditional manual methods used for earprint identification.

Adult↗

PubMed1998

Computer-aided virus identification on the World Wide Web.

An attempt has been made to devise computer software that will aid virologists to identify unknown virus isolates using the World Wide Web. Computerized information from the Animal Virus Information System was used to obtain data on various characters of a virus species. Sequence data banks are used to obtain the molecular data. A probabilistic method of virus identification based on Willcox's implementation of Bayes' theorem is implemented. The program provides hints to the users to carry out additional tests required to obtain higher confidence in identification of virus species. Signature peptides of the virus can also be used to confirm identification. The software is implemented on a UNIX machine and is written in C, UNIX shell scripts and HTML to run on the World Wide Web. This is the first species identification software that allows the user to carry out identification online through Internet.

Computer Communication Networks↗

PubMed2002

Comparison of porphyrin-based, growth factor-based, and biochemical-based testing methods for identification of Haemophilus influenzae.

The accurate identification of Haemophilus spp. is essential for optimizing the role of the clinical microbiology laboratory in the diagnosis and management of Haemophilus infections. One laboratory-prepared medium and eight commercially available test systems were examined in parallel as a means of identifying 378 clinical isolates of Haemophilus spp. as either Haemophilus influenzae or non- Haemophilus influenzae spp. At least one discordant result was noted with 187 (49.5%) of the isolates tested. Discordant results were resolved either by majority rule for isolates with less than three discordant test results or by confirming the identity using conventional biochemical tests for isolates with three or more discordant test results ( n=20). Among these 20 isolates, 2 were judged not to belong to the Haemophilus genus. Comparisons of three porphyrin-based methods, three growth factor-based methods (1 of which also incorporates a porphyrin testing component), and three biochemical-based methods revealed varying discrepancy rates within each testing method. In general, porphyrin-based methods, with overall discrepancy rates of 1.3% or less, outperformed other testing methods. One important exception was the performance of the porphyrin testing component of the Haemophilus Identification Test Kit (Remel, USA), which produced an overall discrepancy rate of 28.5% and a false-negative rate of 52.2% with non- Haemophilus influenzae isolates. Growth factor-based methods yielded overall discrepancy rates ranging from 1.6% ( Haemophilus Identification Agar Quad; Remel) to 10.4% (hemin and nicotinamide adenine dinucleotide disk component of the Haemophilus Identification Test Kit). Biochemical-based assays produced overall discrepancy rates ranging from 4.5% (API NH; bioMérieux Vitek, USA) to 10.1% ( Neisseria Haemophilus Identification Card; bioMérieux Vitek). Collectively, these results suggest that porphyrin-based testing methods represent the most reliable means for identifying Haemophilus spp.

Bacterial Typing Techniques↗

PubMed1998

Comparative evaluation of a commercial system for identification of gram-positive cocci.

The performance of a new commercial system for the identification of different groups of gram-positive cocci [BBL Crystal Gram-Positive (GP) Identification System; Becton Dickinson Microbiology Systems, Germany] was evaluated in comparison with two currently used commercial systems, the API Staph and the API Strep (bioMérieux Diagnostic, Germany). A total of 191 strains from seven different gram-positive genera comprising 32 different species were tested. For the BBL Crystal GP system, the correct identification rate without additional tests was 89.5% at the species level and 97.9% at the genus level. The findings suggest that the newly introduced BBL Crystal GP ID system provides an accurate method for the identification of gram-positive cocci, with an overall rate of correct species identification of about 90%, similar to that of the established API systems. Its major advantage is the extended spectrum of taxa included in a single test panel in contrast to the two different API test kits. Furthermore, the simplicity of use and the safe and rapid handling in a closed system conveniently accommodate existing laboratory workflow.

Bacteriological Techniques↗

PubMed2000

Cost-effective algorithm for detection and identification of vancomycin-resistant enterococci in surveillance cultures.

A study was undertaken to develop an easy-to-use and cost-effective algorithm for the detection and identification of vancomycin-resistant enterococci (VRE) in surveillance cultures, because the incidence of VRE outbreaks in institutions across Canada has made continuous surveillance a necessity. Enterococcus faecium and Enterococcus faecalis carry transferable resistance genes and hence are a problem for infection control. In laboratory surveillance, however, Enterococcus gallinarum and Enterococcus casseliflavus, which exhibit low-level nontransferable resistance, are also encountered and often create confusion in identification. Included in this study were a total of 218 strains of enterococci and other streptococci isolated from surveillance cultures. Conventional methods were used to determine their biochemical activities, and speciation was attempted in 121 strains using a rapid multiplex polymerase chain reaction (PCR) method that utilized primers for the vanA, B, C1, C2/C3 and ddl genes. The results indicated that by using only a few tests (Gram stain, pyrrolidonyl arylamidase activity, motility, xylose and methyl-alpha-D-glucopyranoside utilization), Enterococcus faecium/faecalis strains could be accurately differentiated from Enterococcus gallinarum/casseliflavus strains. For the 121 strains on which PCR was performed, there was a 100% correlation with the biochemical identification, with the added advantage that the presence of van genes could be determined at the same time. The cost of identification using minimal biochemical testing and PCR was less than that of identification using automated systems or a battery of conventional biochemical methods. The algorithm presented here may be used in the microbiology laboratory.

Algorithms↗

PubMed2004

The efficacy of a nerve stimulator (CaverMap) to enhance autonomic nerve identification and confirm nerve preservation during total mesorectal excision.

PURPOSE: Sexual dysfunction after total mesorectal excision may be caused by injury to the autonomic nerves. During surgery, nerve identification is not always achieved, and, to date, there has been no method to objectively confirm nerve preservation. The aim of this study was to assess the efficacy of a nerve-stimulating device (CaverMap) to assist in the intraoperative identification of the autonomic nerves during total mesorectal excision, and objectively confirm nerve preservation after proctectomy is completed. PATIENTS AND METHODS: Sexually active consecutive male patients undergoing total mesorectal excision were prospectively enrolled in this study. During pelvic dissection, the surgeon attempted to localize the hypogastric and cavernous nerves. CaverMap was used to confirm these findings and to facilitate the identification in cases of uncertainty. At the completion of proctectomy, the nerves were restimulated to ensure preservation. Factors that could affect the surgeon's ability to localize the nerves and CaverMap to confirm this were evaluated. RESULTS: Twenty-nine male patients with a median age of 58 years were enrolled in this study. An attempt to visualize the hypogastric nerves during dissection was made in 26 patients; the surgeon was able to identify the nerves in 19 (73 percent) patients. CaverMap successfully identified the nerves in six of the seven remaining patients, and failed to identify them in only one case. An attempt to localize the cavernous nerves during dissection was made in 13 patients, of which localization was successful in 8 (61.5 percent) patients. CaverMap improved the identification rate in four of the remaining five patients. After proctectomy, CaverMap successfully confirmed the preservation of both hypogastric and cavernous nerves in 27 of 29 (93 percent) patients. A history of previous surgery statistically correlated with failure to identify the hypogastric nerves by the surgeon (P = 0.005). There were no adverse events related to use of the device. CONCLUSION: CaverMap may be a useful tool to facilitate identification of the pelvic autonomic nerves during total mesorectal excision and to objectively confirm nerve preservation.

Autonomic Pathways↗

PubMed2005

The efficacy of a nerve stimulator (Cavermap) to enhance autonomic nerve identification and confirm nerve preservation during total mesorectal excision.

Autonomic Pathways↗

PubMed2007

Identification of youth psychosocial problems during pediatric primary care visits.

This investigation applied the Gateway Provider Model (GPM) of child mental health services to investigate whether characteristics of the child, family, visit, and provider were related to the identification of youth psychosocial problems during primary care visits. Data were gathered during 774 visits to 54 primary care providers (PCPs) at 13 clinics. Similar to previous investigations in primary care settings, 42% of youth demonstrated at least a sub-threshold clinical mental health problem. Most PCPs reported high job satisfaction and control, but reported varying access to mental health specialists. PCPs generally had positive attitudes and beliefs about treating psychosocial problems but many reported that doing so was burdensome. Identification was more likely when the visit was for a mental health problem, when issues related to psychosocial problems were discussed during the visit, when the youth demonstrated mental health symptoms, impairment, or burden to the family, and when the youth was older, uninsured, or received Medicaid. Identification was less likely when the PCP reported greater burden associated with treating psychosocial problems and when the PCP reported greater accessibility to mental health specialists. These results suggest that identification is associated with the interaction of multilevel factors and that the GPM is a useful model to investigate points of intervention for improving the identification of children's mental health problems in primary care settings.

Adolescent↗

PubMed2006

Performance enhancement for audio-visual speaker identification using dynamic facial muscle model.

Science of human identification using physiological characteristics or biometry has been of great concern in security systems. However, robust multimodal identification systems based on audio-visual information has not been thoroughly investigated yet. Therefore, the aim of this work to propose a model-based feature extraction method which employs physiological characteristics of facial muscles producing lip movements. This approach adopts the intrinsic properties of muscles such as viscosity, elasticity, and mass which are extracted from the dynamic lip model. These parameters are exclusively dependent on the neuro-muscular properties of speaker; consequently, imitation of valid speakers could be reduced to a large extent. These parameters are applied to a hidden Markov model (HMM) audio-visual identification system. In this work, a combination of audio and video features has been employed by adopting a multistream pseudo-synchronized HMM training method. Noise robust audio features such as Mel-frequency cepstral coefficients (MFCC), spectral subtraction (SS), and relative spectra perceptual linear prediction (J-RASTA-PLP) have been used to evaluate the performance of the multimodal system once efficient audio feature extraction methods have been utilized. The superior performance of the proposed system is demonstrated on a large multispeaker database of continuously spoken digits, along with a sentence that is phonetically rich. To evaluate the robustness of algorithms, some experiments were performed on genetically identical twins. Furthermore, changes in speaker voice were simulated with drug inhalation tests. In 3 dB signal to noise ratio (SNR), the dynamic muscle model improved the identification rate of the audio-visual system from 91 to 98%. Results on identical twins revealed that there was an apparent improvement on the performance for the dynamic muscle model-based system, in which the identification rate of the audio-visual system was enhanced from 87 to 96%.

Adult↗