Mycobacterial species identification: 138 mott isolates identified by PRA and by conventional typing

1994 ◽  
Vol 75 ◽  
pp. 41
Author(s):  
V. Thomsen ◽  
K. Fuursted
Keyword(s):  
Species Identification ◽  
Mycobacterial Species

Evaluation of Q Gene Mycobacteria: A novel and easy nucleic acid chromatography method for mycobacterial species identification

2019 ◽  
Vol 163 ◽  
pp. 105657 ◽  
Author(s):  
Kinuyo Chikamatsu ◽  
Akio Aono ◽  
Akiko Kawai ◽  
Hiroyuki Hata ◽  
Tomotada Iwamoto ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Species Identification ◽  
Mycobacterial Species ◽  
Chromatography Method ◽  
Q Gene

scholarly journals Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping

2017 ◽  
Vol 56 (2) ◽  
Author(s):  
T. Phuong Quan ◽  
Zharain Bawa ◽  
Dona Foster ◽  
Tim Walker ◽  
Carlos del Ojo Elias ◽  
...  
Keyword(s):  
Species Identification ◽  
Susceptibility Testing ◽  
Drug Susceptibility ◽  
Drug Susceptibility Testing ◽  
Line Probe Assay ◽  
Mycobacterial Species ◽  
Sequencing Data ◽  
First Line ◽  
Content Type ◽  
Probe Assay

ABSTRACTUse of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances of WGS and standard laboratory workflows prospectively, by parallel processing at a major mycobacterial reference service over the course of 1 year, for species identification, first-lineMycobacterium tuberculosisresistance prediction, and turnaround time. Among 2,039 isolates with line probe assay results for species identification, 74 (3.6%) failed sequencing or WGS species identification. Excluding these isolates, clinically important species were identified for 1,902 isolates, of which 1,825 (96.0%) were identified as the same species by WGS and the line probe assay. A total of 2,157 line probe test results for detection of resistance to the first-line drugs isoniazid and rifampin were available for 728M. tuberculosiscomplex isolates. Excluding 216 (10.0%) cases where there were insufficient sequencing data for WGS to make a prediction, overall concordance was 99.3% (95% confidence interval [CI], 98.9 to 99.6%), sensitivity was 97.6% (91.7 to 99.7%), and specificity was 99.5% (99.0 to 99.7%). A total of 2,982 phenotypic DST results were available for 777M. tuberculosiscomplex isolates. Of these, 356 (11.9%) had no WGS comparator due to insufficient sequencing data, and in 154 (5.2%) cases the WGS prediction was indeterminate due to discovery of novel, previously uncharacterized mutations. Excluding these data, overall concordance was 99.2% (98.7 to 99.5%), sensitivity was 94.2% (88.4 to 97.6%), and specificity was 99.4% (99.0 to 99.7%). Median processing times for the routine laboratory tests versus WGS were similar overall, i.e., 20 days (interquartile range [IQR], 15 to 31 days) and 21 days (15 to 29 days), respectively (P= 0.41). In conclusion, WGS predicts species and drug susceptibility with great accuracy, but work is needed to increase the proportion of predictions made.

scholarly journals Evaluation of the Ribosomal Protein S1 Gene (rpsA) as a Novel Biomarker forMycobacteriumSpecies Identification

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Hongfei Duan ◽  
Guan Liu ◽  
Xiaobo Wang ◽  
Yuhong Fu ◽  
Qian Liang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Ribosomal Protein ◽  
Species Identification ◽  
Comparative Sequence Analysis ◽  
Clinical Isolates ◽  
Species Differentiation ◽  
Alignment Algorithm ◽  
Mycobacterial Species ◽  
Ribosomal Protein S1

Objectives. To evaluate the resolution and reliability of therpsAgene, encoding ribosomal protein S1, as a novel biomarker for mycobacteria species identification.Methods. A segment of therpsAgene (565 bp) was amplified by PCR from 42 mycobacterial reference strains, 172 nontuberculosis mycobacteria clinical isolates, and 16M. tuberculosiscomplex clinical isolates. The PCR products were sequenced and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method.Results. Comparative sequence analysis of therpsAgene provided the basis for species differentiation within the genusMycobacterium. Slow- and rapid-growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. The sequences discrepancy was obvious betweenM. kansasiiandM. gastri, M. chelonaeandM. abscessus, M. aviumandM. intracellulare, andM. szulgaiandM. malmoense, which cannot be achieved by 16S ribosomal DNA (rDNA) homologue genes comparison. 183 of the 188 (97.3%) clinical isolates, consisting of 8 mycobacterial species, were identified correctly byrpsAgene blast.Conclusions. Our study indicates thatrpsAsequencing can be used effectively for mycobacteria species identification as a supplement to 16S rDNA sequence analysis.

scholarly journals Evaluation of a Low-Density Hydrogel Microarray Technique for Mycobacterial Species Identification

2015 ◽  
Vol 53 (4) ◽  
pp. 1103-1114 ◽  
Author(s):  
Danila V. Zimenkov ◽  
Elena V. Kulagina ◽  
Olga V. Antonova ◽  
Maria A. Krasnova ◽  
Ekaterina N. Chernyaeva ◽  
...  
Keyword(s):  
Species Identification ◽  
Clinical Samples ◽  
Probe Design ◽  
Clinical Microbiology Laboratory ◽  
Low Density ◽  
Pathogenic Species ◽  
Mycobacterial Species ◽  
Accurate Identification ◽  
Content Type ◽  
Species Specific

In addition to the obligatory pathogenic species of theMycobacterium tuberculosiscomplex andMycobacterium leprae, the genusMycobacteriumalso includes conditionally pathogenic species that in rare cases can lead to the development of nontuberculous mycobacterial diseases. Because tuberculosis and mycobacteriosis have similar clinical signs, the accurate identification of the causative agent in a clinical microbiology laboratory is important for diagnostic verification and appropriate treatment. This report describes a low-density hydrogel-based microarray containing oligonucleotide probes based on the species-specific sequences of thegyrBgene fragment for mycobacterial species identification. The procedure included the amplification of a 352-nucleotide fragment of the gene and its hybridization on a microarray. The triple-species-specific probe design and the algorithm for hybridization profile recognition based on the calculation of Pearson correlation coefficients, followed by the construction of a profile database, allowed for the reliable and accurate identification of mycobacterial species, including mixed-DNA samples. The assay was used to evaluate 543 clinical isolates from two regions of Russia, demonstrating its ability to detect 35 mycobacterial species, with 99.8% sensitivity and 100% specificity when usinggyrB, 16S, and internal transcribed spacer (ITS) fragment sequencing as the standard. The testing of clinical samples showed that the sensitivity of the assay was 89% to 95% for smear-positive samples and 36% for smear-negative samples. The large number of identified species, the high level of sensitivity, the ability to detect mycobacteria in clinical samples, and the up-to-date profile database make the assay suitable for use in routine laboratory practice.

Chemical Species Identification in an SEM by Changes in Emitted X-Ray Energies

1974 ◽  
Vol 32 ◽  
pp. 570-571
Author(s):  
R. H. Duff
Keyword(s):  
Species Identification ◽  
Valence Electron ◽  
Chemical Species ◽  
X Rays ◽  
Chemical Bonds ◽  
Small Shift ◽  
X Ray ◽  
Electron Transitions ◽  
Peak Energy ◽  
Chemical Combination

A material irradiated with electrons emits x-rays having energies characteristic of the elements present. Chemical combination between elements results in a small shift of the peak energies of these characteristic x-rays because chemical bonds between different elements have different energies. The energy differences of the characteristic x-rays resulting from valence electron transitions can be used to identify the chemical species present and to obtain information about the chemical bond itself. Although these peak-energy shifts have been well known for a number of years, their use for chemical-species identification in small volumes of material was not realized until the development of the electron microprobe.

Beetles of the family Cryptophagidae (Coleoptera) in the collection of Zoological Museum of Taras Shevchenko National University of Kyiv

2019 ◽  
Vol 17 (2) ◽  
pp. 10-24 ◽  
Author(s):  
K. Ocheretna
Keyword(s):  
Species Identification ◽  
Broad Sense ◽  
Zoological Museum ◽  
World War ◽  
Identification Number ◽  
Comprehensive List ◽  
Carpathian Region ◽  
The Family ◽  
National University ◽  
Collection Sites

The Cryptophagidae collection (Coleoptera: Cucujoidea) deposited at the Zoological Museum of the Taras Shevchenko National University of Kyiv (ZMKU) is described. The main authors of the collection are well-known researchers from the 1910–1930s, Orest Marcu and Karl Penecke. This is the largest collection of cryptophagids among the natural museums of Ukraine containing 304 specimens belonging to 85 species of 13 genera. In addition, 15 specimens of 5 species belonging to the families Erotylidae, Biphyllidae and Languriidae were among Cryptophagidae specimens. The collection, according to information available in the ZMKU, came to the museum not earlier than 1947 as the indemnity for the results of the II World War, most likely from Chernivtsi, where Marcu and Penecke worked. The vast majority of specimens is collected in the territory of modern Romania and Ukraine, and many specimens came from Chernivtsi. A table with an overview of all key details of the specimens is given, in which there are 6 fields: the name of the species on the label, details on the species identification, number of specimens, collection locality with the name of collector and remarks on the specimen, in particular, the instructions for decoding collection sites from the original labels. Annotations are made on the amount of the collection and the most important specimens and re-identification for each of the 13 genera. Some specimens are lost, probably during numerous collection migrations. In particular, some species (Cryptophagus simplex, C. lapidicola, C. nitidulus, Caenoscelis subdeplanata, Atomaria grandicollis, A. peltata, etc.) are represented in the collection only by the labels. The collection is important for the analysis of the composition of the fauna of the Carpathian region in the broad sense, since some species are encountered in the collection rarely; therefore it is important to clarify their locations to form the most comprehensive list of species of the Cryptophagids in the region. Several species of the family were included on the actual list of the fauna of the region on the basis of the study of this collection, in particular: Atomaria linearis, A. analis, A. apicalis, A. gravidula, Cryptophagus fasciatus, C. setulosus, etc.

Species identification of raw and cooked bivalves using electrophoresis

2000 ◽  
Vol 20 (3) ◽  
pp. 367-377 ◽  
Author(s):  
Monique Etienne ◽  
Marc Jérôme ◽  
Joël Fleurence
Keyword(s):  
Species Identification
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