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PubMed2006

The identification of mycobacteria from solid media and directly from VersaTREK Myco bottles using the Sherlock Mycobacteria Identification HPLC system.

The Sherlock Mycobacteria Identification HPLC system correctly identified to the species level 61 (67.8%) of 90 isolates growing on solid media, and 73 (45.3%) of 161 isolates directly from positive VersaTREK Myco bottles. When these data were re-analysed with a revised database, correct identifications increased to 91.1% and 83.2%, respectively. All Mycobacterium tuberculosis isolates were identified correctly, regardless of the inoculum source or database used. The use of the revised database with isolates obtained directly from positive VersaTREK Myco bottles allows the identification of most isolates within clinically relevant time-frames.

Chromatography, High Pressure Liquid↗
PubMed1991

Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples.

A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a "standard") to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples.

Journal Article↗
PubMed1965

Application of replica plating and computer analysis for rapid identification of bacteria in some foods. I. Identification scheme.

A method was devised and tested for a quantitative identification of microbial flora in foods. The colonies developing on the initial isolation plates were picked with sterile toothpicks and inoculated on a master plate in prearranged spacing and order. The growth on the master plates was then replicated on a series of solid-agar plates containing differential or selective agents. The characteristic growth and physiological responses of microbial isolates to penicillin, tylosin, vancomycin, streptomycin, chloramphenicol, neomycin, colistin, and to S S Agar, Staphylococcus Medium No. 110, and Potato Dextrose Agar were recorded, together with Gram reaction and cell morphology. This information was then fed into an IBM 1410 digital computer which grouped and analyzed each isolate into 10 microbial genera, or groups, according to the identification key. The identification scheme was established by use of reference culture studies and from the literature. This system was used to analyze the microbial flora in dover sole (Microstomus pacificus) and ground beef. The method described in this article enables one to examine large numbers of microbial isolates with simplicity.

Animals↗
PubMed1971

Rapid identification of viruses by indirect immunofluorescence: isolation and identification of adenovirus types 4 and 7 and coxsackievirus type A21 in microcultures.

The indirect fluorescent-antibody test (IFAT), employing treated and standardized antiserum in a single pool, was earlier reported to have been used successfully for the preliminary identification of nine respiratory viruses in second to ninth passage multiplying in cells propagated on microscope slides. This report describes parameters affecting the isolation in first passage and the identification by IFAT of adenovirus types 4 and 7 and coxsackievirus type A21 present in stored clinical specimens inoculated into microcultures of WI-38 cells. Isolation frequency was comparable to that obtained in tube cultures, and identification by IFAT of viruses in microcultures could be accomplished in 3 to 4 hr after recognition of a cytopathogenic effect.

Adenoviridae↗
PubMed1989

Identification of Neisseria spp., Haemophilus spp., and other fastidious gram-negative bacteria with the MicroScan Haemophilus-Neisseria identification panel.

The Haemophilus-Neisseria identification (HNID) panel (American MicroScan, Sacramento, Calif.) is a 4-h microdilution format system for identification of Haemophilus and Neisseria spp., Branhamella (Moraxella) catarrhalis, and Gardnerella vaginalis. The HNID panel was evaluated by using 423 clinical isolates and stock strains of these organisms, and HNID identifications were compared with those obtained by conventional methods. In addition, 32 isolates representing six genera not included in the HNID data base were tested to determine whether these organisms would produce unique biotype numbers for possible inclusion in the data base. The HNID panel correctly identified 95.3% of 86 Neisseria gonorrhoeae strains, 96% of 25 G. vaginalis strains, and 100% of 28 Neisseria lactamica strains and 48 B. catarrhalis strains. Only 64.7% of 68 Neisseria meningitidis isolates were identified correctly owing to false-negative or equivocal carbohydrate and/or aminopeptidase reactions. Among the Haemophilus spp., 98.8% of 83 H. influenzae strains, 97.1% of 34 H. parainfluenzae strains, and 80% of 15 H. aphrophilus and H. paraphrophilus strains were correctly identified. Eight strains of Neisseria cinerea, a species not included in the data base, produced profiles identical with those for B. catarrhalis and N. gonorrhoeae. Isolates of other species not included in the data base, including Eikenella corrodens, Kingella spp., and Cardiobacterium hominis, produced unique biochemical reaction patterns on the panel. Modification of interpretative criteria for certain tests, expansion of the data base to include other species, and suggestions for additional confirmatory tests will increase the accuracy and utility of the HNID panel.

Gardnerella vaginalis↗
PubMed1996

Evaluation of new computer-enhanced identification program for microorganisms: adaptation of BioBASE for identification of members of the family Enterobacteriaceae.

We report the use of BioBASE, a computer-enhanced numerical identification software package, as a valuable aid for the rapid identification of unknown enteric bacilli when using conventional biochemicals. We compared BioBASE identification results with those of the Centers for Disease Control and Prevention's mainframe computer to determine the former's accuracy in identifying both common and rare unknown isolates of the family Enterobacteriaceae by using the same compiled data matrix. Of 293 enteric strains tested by BioBASE, 278 (94.9%) were correctly identified to the species level; 13 (4.4%) were assigned unacceptable or low discrimination profiles, but 8 of these (2.7%) were listed as the first choice; and 2 (0.7%) were not identified correctly because of their highly unusual biochemical profiles. The software is user friendly, rapid, and accurate and would be of value to any laboratory that uses conventional biochemicals.

Bacteriological Techniques↗
PubMed1998

Improved identification of mycobacteria by using the microbial identification system in combination with additional trimethylsulfonium hydroxide pyrolysis.

The MIDI automated Microbial Identification System (MIS) uses gas chromatography (GC) analysis of whole-cell fatty acid methyl esters (FAMEs) between 9 and 20 carbons in length to characterize a wide range of bacterial genera and species, including mycobacteria. Mycolic acid cleavage products (MACPs) with chain lengths of C22 to C26 are not released by MIDI sample preparation of mycobacteria. Therefore, the MIS library search report often matches several mycobacterial species without any significant difference in the similarity indices. The problem is solved by adding trimethylsulfonium hydroxide (TMSH) instead of sodium sulfate in the last step of sample preparation, thus allowing the identification of MACPs in addition to FAMEs. Only one GC run parameter has to be changed: the temperature program must be extended from 260 to 310 degrees C. The MIS library search report for the identification of bacteria is not disturbed by TMSH. The combination of conventional library search report with the information of typical MACP patterns yields significantly better discrimination of mycobacterial species than the MIDI method allows.

Chromatography, Gas↗
PubMed1999

Rapid identification of Candida dubliniensis with commercial yeast identification systems.

Candida dubliniensis is a newly described species that is closely related phylogenetically to Candida albicans and that is commonly associated with oral candidiasis in human immunodeficiency virus-positive patients. Several recent studies have attempted to elucidate phenotypic and genotypic characteristics of use in separating the two species. However, results obtained with simple phenotypic tests were too variable and tests that provided more definitive data were too complex for routine use in the clinical laboratory setting. The objective of this study was to determine if reproducible identification of C. dubliniensis could be obtained with commercial identification kits. The substrate reactivity profiles of 80 C. dubliniensis isolates were obtained by using the API 20C AUX, ID 32 C, RapID Yeast Plus, VITEK YBC, and VITEK 2 ID-YST systems. The percentages of C. dubliniensis isolates capable of assimilating or hydrolyzing each substrate were compared with the percentages from the C. albicans profiles in each kit's database, and the results were expressed as percent C. dubliniensis and percent C. albicans. Any substrate that showed >50% difference in reactivity was considered useful in differentiating the species. In addition, assimilation of methyl-alpha-D-glucoside (MDG), D-trehalose (TRE), and D-xylose (XYL) by the same isolates was investigated by the traditional procedure of Wickerham and Burton (L. J. Wickerham and K. A. Burton, J. Bacteriol. 56:363-371, 1948). At 48 h (the time recommended by the manufacturer for its new database), we found that the assimilation of four carbohydrates in the API 20C AUX system could be used to distinguish the species, i.e., glycerol (GLY; 88 and 14%), XYL (0 and 88%), MDG (0 and 85%), and TRE (15 and 97%). Similarly, results with the ID 32 C system at 48 h showed that XYL (0 and 98%), MDG (0 and 98%), lactate (LAT; 0 and 96%), and TRE (30 and 96%) could be used to separate the two species. Phosphatase (PHS; 9 and 76%) and alpha-D-glucosidase (23 and 94%) proved to be the most useful for separation of the species in the RapID Yeast Plus system. While at 24 h the profiles obtained with the VITEK YBC system showed that MDG (10 and 95%), XYL (0 and 95%), and GLY (26 and 80%) could be used to separate the two species, at 48 h only XYL (6 and 95%) could be used to separate the two species. The most useful substrates in the VITEK 2 ID-YST system were TRE (1 and 89%), MDG (1 and 99%), LAT (4 and 98%), and PHS (83 and 1%). While the latter kit was not yet commercially available at the time of the study, it would appear to be the most valuable for the identification of C. dubliniensis. Although assimilation of MDG, TRE, and XYL proved to be the most useful for species differentiation by the majority of commercial systems, the results with these carbohydrates by the Wickerham and Burton procedure were essentially the same for both species, albeit following protracted incubation. Thus, it is the rapidity of the assimilation achieved with the commercial systems that allows the differentiation of C. dubliniensis from C. albicans.

AIDS-Related Opportunistic Infections↗
PubMed1999

Variation in Microbial Identification System accuracy for yeast identification depending on commercial source of Sabouraud dextrose agar.

The accuracy of the Microbial Identification System (MIS; MIDI, Inc. ) for identification of yeasts to the species level was compared by using 438 isolates grown on prepoured BBL Sabouraud dextrose agar (SDA) and prepoured Remel SDA. Correct identification was observed for 326 (74%) of the yeasts cultured on BBL SDA versus only 214 (49%) of yeasts grown on Remel SDA (P < 0.001). The commercial source of the SDA used in the MIS procedure significantly influences the system's accuracy.

Agar↗
PubMed1991

[STAPHYOGRAM, a new rapid identification kit for the aerobic, gram-positive, catalase-positive cocci--application of fluorometric microplate hybridization for the pre-identification of 386 isolates used].

A new simplified test kit, STAPHYOGRAM plate, was developed for 4-hr identification of aerobic, Gram-positive and catalase-positive cocci. The plate has 18 wells, in which different dehydrated substrates and nutrients are fixed. An 18-hr agar-culture suspension of a test strain with a turbidity of McFarland No. 4 was distributed into all wells in 50-microliters quantities. After 4-hr incubation at 37C, the profile number was obtained by summarizing positive reactions. The ability of the plate to differentiate the type strains of the 30 species of the three genera in the family Micrococcaceae was confirmed. These three genera are Staphylococcus, Micrococcus and Stomatococcus. The applicability of the fluorometric microplate hybridization technique to identification of aerobic, Gram-positive and catalase-positive cocci was confirmed by homologous hybridization among the type strains of the 30 species. Thus, 386 isolates of human and animal origin were pre-identified by microplate hybridization and used for evaluating the STAPHYOGRAM plate. Of the 236 profile numbers thus obtained with the 386 isolates, 218 (92.4%) were species-proper each and all for the 15 species of Staphylococcus and Stomatococcus mucilaginosus. A total of 342 (88.6%) of the 386 isolates were given such profile numbers, and were identified without any additional test. Among the 15 species identified primarily by the results of STAPHYOGRAM plate culture, S. caprae, S. lugdunensis, S. gallinarum and S. delphini were validly published after Approved Lists of Bacterial Names. The identified strains of S. caprae (48), S. haemolyticus (46), S. capitis (35) numbered between those of S. epidermidis (67) and S. saprophyticus (31). Profile numbers common to two species were seven (27 strains) and that to four species was one (17 strains). These 44 strains were identified with one to three additional tests. From these results, we were convinced that the STAPHYOGRAM test plate is useful for the rapid identification of members of family Micrococcaceae. By compiling STAPHYOGRAM plate data on genetically identified strains, an exclusive list of profile numbers will soon be prepared for perfection of the kit.

Animals↗
PubMed1986

"Bi-digital o-ring test molecular identification and localization method" and its application in imaging of internal organs and malignant tumors as well as identification and localization of neurotransmitters and micro-organisms--Part 1.

Using the "Bi-Digital O-Ring Test Molecular Identification and Localization Method," one can identify and localize minute amounts of bioactive substances (including neurotransmitters), micro-organisms, toxic substances, or drugs, and, in addition, one can non-invasively image normal organs as well as screen for and image the distribution of specific types of cancer of specific internal organs without using any expensive instrumentation. One can also use this method to perform a qualitative analysis of neurotransmitters, neuromodulators, and hormones on different parts of the imaged organs. The molecule or substance being investigated is compared with a minute amount of a pure control reference substance, and if the substance identical to the control reference substance exists, then the electro-magnetic waves emitted by the identical substance will produce an electro-magnetic resonance phenomenon with the electro-magnetic waves of identical resonance frequency emitted by the control reference substance, and this resonance phenomenon is hypothesized to be the basis of the "Bi-Digital O-Ring Test Molecular Identification and Localization Method." The following substances have been used as control reference substances to identify and localize identical substances in vitro and in vivo: pure neurotransmitters (e.g. serotonin, beta-endorphin, methionine-enkephalin, norepinephrine, dopamine, L-dopa, substance P, etc.), as well as L-tryptophan and L-tyrosine; cholesterol; steroid hormones (including aldosterone, corticosterone, cortisol, progesterone, testosterone, etc.); peptide hormones; microscopic slides of normal organs; microscopic slides of specific cancer cells of specific organs (e.g. adenocarcinoma of the head of the pancreas, adenocarcinoma of the descending colon, etc.); microscopic slides of pure micro-organisms; toxic substances (e.g. lead, mercury, KCN); drugs (including non-steroidal anti-inflammatory drugs, antibiotics, beta-blockers, calcium channel blockers, etc.); and antibodies against specific substances or micro-organisms. An intensive network of serotonin and L-tryptophan was discovered, by using the "Bi-Digital O-Ring Test Molecular Identification and Localization Method," in different parts of the body. In general, in painful areas, frequently serotonin is markedly reduced, L-tryptophan is markedly increased, and substance P is markedly increased, while in non-painful areas, serotonin is markedly increased, L-tryptophan is markedly decreased, and substance P is markedly decreased.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗
PubMedDate not supplied

[Mitochondrial DNA typing--a new level for solving identification problems in forensic medical expert identification of unidentified remains of victims of terrorist acts in Moscow and the armed conflict in the Chechen Republic].

Two large-scale episodes described in this paper reflect the first in Russia use of molecular genetic matrilinear markers (analysis of polymorphism of sequences of amplified fragments of mitochondrial DNA hypervariable locuses) in solution of a complex identification problem: forensic medical identification of unidentified fragments of victims of explosions of houses in Moscow in September, 1999, and of soldiers dead in the war conflict in the Chechen Republic in 1994-1996. The results of this work and methodological experience gained in it essentially extend the potentialities of expert studies as regards forensic medical identification of victims of large scale disasters, terroristic acts, and war conflicts.

DNA, Mitochondrial↗
PubMed2003

World Trade Center human identification project: experiences with individual body identification cases.

AIM: To present individual body identification efforts, as part of the World Trade Center (WTC) mass disaster identification project. METHODS: More than 500 samples were tested by using polymerase chain reaction (PCR) amplification and short tandem repeat (STR) typing. The extent to which the remains were fragmented and affected by taphonomic factors complicated the identification project. Anthropologists reviewed 19,000 samples, and detected inconsistencies in 69, which were further split into 239 new cases and re-sampled by DNA specialists. RESULTS: The severity and nature of the disaster required an interdisciplinary effort. DNA profiling of 500 samples was successful in 75% of the cases. All discrepancies, which occurred between bone and tissue samples taken from the same body part, were resolved by re-sampling and re-testing of preferably bone tissue. Anthropologists detected inconsistencies in 69 cases, which were then split into 239 new cases. Out of 125 "split" cases, 65 were excluded from their original case. Of these 65 cases, 37 did not match any profiles in M-FISys, probably because profiles were incomplete or no exemplar for the victim was available. Out of the 60 remains not excluded from their original case, 30 were partial profiles and did not reach the statistical requirement to match their original case, because the population frequency of the DNA profile had to be </=1 in 10(9) for men and </=1 in 10(8) for women. CONCLUSION: Due to transfer of soft tissue and other commingling of remains, DNA testing alone would have led to problems if only soft tissue would have been tested. This was one of the reasons that forensic anthropologists were needed to evaluate the consistency between all linked body parts. Especially in disasters with a high potential for commingling, the described anthropological review process should be part of the investigation.

DNA Fingerprinting↗
PubMedDate not supplied

Gram-negative identification card for identification of Salmonella, Escherichia coli, and other Enterobacteriaceae isolated from foods: collaborative study.

Twelve laboratories evaluated the Gram-Negative Identification (GNI) Card to identify members of the Enterobacteriaceae. Eighty-four isolates, previously isolated from foods, were used in the collaborative study; the isolates represented 12 genera within the Enterobacteriaceae group. Each collaborator streaked each isolate on tryptic soy agar plates for purity. In the method, plates are incubated 18-24 h at 35 degrees C. Isolated colonies are then subcultured to tryptic soy agar slants and incubated 18-24 h at 35 degrees C. An emulsion is made from the growth on the slant in 1.8 mL 0.45% sodium chloride solution. The GNI Card is filled and placed in a reader/incubator. Isolates are identified and an identification is printed. The Vitek System correctly identified 96.7% of Salmonella sp., 97.0% of Escherichia coli, and an average of 93.8% of the other enteric genera. The method using the Vitek System and GNI Card has been approved interim official first action by AOAC as a screening method for the presumptive identification of Salmonella sp., E. coli, and other Enterobacteriaceae isolated from foods.

Culture Media↗
PubMedDate not supplied

Identification of Vibrio vulnificus by cellular fatty acid composition using the Hewlett-Packard 5898A Microbial Identification System: collaborative study.

A gas chromatographic method using a capillary column for rapid identification of Vibrio vulnificus was examined in a collaborative study. Identifications were performed by analysis of cellular fatty acid profiles which were automatically searched against reference profiles stored in a computer-generated library. Each of the 13 collaborators was sent 15 unknown isolates, which included 10 V. vulnificus isolates and 5 negative control isolates. Each collaborator was furnished with a computer-generated library, developed by the Dallas U.S. Food and Drug Administration laboratory, which contained entries for V. vulnificus, V. cholerae, V. fluvialis, V. parahaemolyticus, V. mimicus, and Aeromonas hydrophila. Of the 195 isolates sent to the collaborators, results for 190 isolates were received. The other 5 isolates were nonviable before analyses began. Of the 126 V. vulnificus isolates analyzed, 118 (93.7%) were correctly identified. Of the 65 negative control isolates sent, one was nonviable, one was misidentified as V. vulnificus, and 2 were misidentified as V. parahaemolyticus. Of the 64 negative controls analyzed, 95.3% were correctly identified. Statistical analysis shows a sensitivity rate of 0.872, specificity rate of 0.982, false positive rate of 0.010, and false negative rate of 0.206. The gas chromatographic method for identification of Vibrio vulnificus by microbial fatty acid profile has been adopted first action by AOAC INTERNATIONAL.

Chromatography, Gas↗
PubMedDate not supplied

[Voice identification in the Dr. Schneider case. Problems in speaker identification by lay persons].

In this case report a number of problems with speaker identification by lay persons are discussed. It is argued that specific circumstances of the identification procedure(s) and factors such as subjects' emotional states, personal attitudes towards the speaker in question, short-term changes in the speaker's vocal behaviour and the semantic content and type of speech material used may heavily bias subjects' judgements. On the other hand, a 'conventional' forensic voice comparison carried out by professionals provided clear-cut results even under severe time constraints. It is argued that speaker identification by lay persons, if indispensable in a case, should be carried out by means of a formalized, classical voice line-up experiment.

Expert Testimony↗
PubMed2002

Facing sexual violence in a rape emergency room: identification, projective identification, and the myth of nemesis.

This article focuses on the relationship between identification and sexual abuse. Three subsequent levels are considered, namely, the relationship between (1) the abuser and the victim, (2) the gynecologist or social worker of the Rape Emergency Room (RER) and the victim, and (3) the gynecologist or social worker and the entire RER staff. In the relationship with a rape victim, the gynecologist and the social worker may perceive unexpected negative feelings such as fear, horror, impotence, despair, or even anger which can interfere in the identification with the victim. Rape can be considered also as a concrete form of devaluation through concrete penetration of the victim. As an example, a myth of sexual abuse will be presented: the rape of Nemesis by Zeus.

Crime Victims↗
PubMed1999

Identification of a D579G homozygote cystic fibrosis patient with pancreatic sufficiency and minor lung involvement. Mutations in brief no. 221. Online.

Here we describe the identification of an italian patient homozygote for the D579G mutation affected by a mild form of Cystic Fibrosis with pancreatic sufficiency, minor lung involvement and marked viscosity of the cervical mucous. The D579G mutation causes an A1868G transition, a substitution of an aspartic acid to a glycine residue, generating an important amino acid change (charged to hydrophobic) in the nucleotide-binding domain (NBD). The mutation was first described by Brancolini et al. (1995) on two pancreatic sufficient CF patients, compound heterozygotes for delta508F. Patients were from Southern Italy (Puglia) as the D579G homozygote one, who is a 30 years old woman from Taranto (Puglia), daughter of second cousins born in Bari (Puglia). The identification of a homozygote D579G patient might confirm that this mutation does correlate with pancreatic sufficiency and a mild pulmonary phenotype.

Adult↗