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Results for “Automated phenotyping”

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PubMed2001

Genotype-phenotype correlation in gemistocytic astrocytomas.

OBJECTIVE: Gemistocytic astrocytomas often behave aggressively and carry the least favorable prognosis among diffuse astrocytomas. The frequency of p53 mutations has been reported to be significantly higher in the gemistocytic variant as compared with other astrocytomas. METHODS: Between 1985 and 1998, we selected 25 tumor samples from among 201 samples from patients with gemistocytic astrocytomas operated on at the Mayo Clinic. Exons 5 to 8 of the p53 gene were sequenced using an automated deoxyribonucleic acid sequencer. Morphometric characterization of individual gemistocytes was performed using an image analysis program. RESULTS: Of 25 tissue samples analyzed, 16 were found to carry a p53 missense mutation (three in exon 5, three in exon 6, one in exon 7, and nine in exon 8), and one sequence variant was synonymous. Mutations were clustered at codons 151 (2 of 17 mutations), 193 (3 of 17 mutations), and 273 (5 of 17 mutations) of the p53 gene. Patients whose tumors carried a p53 mutation were significantly younger than other patients, and their tumors tended to accumulate more p53 protein than those of other patients. Phenotype analysis of gemistocytes revealed that the sizes of tumor cell nuclei and of entire tumor cells in the same tissue area were positively correlated. Smaller tumor cell nuclei tended to be less circular or more atypical. In addition, more atypical gemistocytes were found in tumors lacking a wild-type p53 allele as well as in tissue from patients whose postoperative survival was shorter. CONCLUSION: Our data confirm that the frequency of p53 mutations is significantly higher (approximately twofold) in gemistocytic astrocytomas as compared with other astrocytoma subtypes. Whether the high frequency of p53 mutations contributes to the more aggressive behavior of gemistocytic astrocytomas, however, remains unclear.

Adult↗

PubMed2002

Using machine vision to analyze and classify Caenorhabditis elegans behavioral phenotypes quantitatively.

Mutants with abnormal patterns of locomotion, also known as uncoordinated (Unc) mutants, have facilitated the genetic dissection of many important aspects of nervous system function and development in the nematode Caenorhabditis elegans. Although a large number of distinct classes of Unc mutants can be distinguished by an experienced observer, precise quantitative definitions of these classes have not been available. Here we describe a new approach for using automatically-acquired image data to quantify the locomotion patterns of wild-type and mutant worms. We designed an automated tracking and imaging system capable of following an individual animal for long time periods and saving a time-coded series of digital images representing its motion and body posture over the course of the recording. We have also devised methods for measuring specific features from these image data that can be used by the classification and regression tree classification algorithm to reliably identify the behavioral patterns of specific mutant types. Ultimately, these tools should make it possible to evaluate with quantitative precision the behavioral phenotypes of novel mutants, gene knockout lines, or pharmacological treatments.

Algorithms↗

PubMed2004

Macular coloboma in siblings affected by different phenotypes of retinitis pigmentosa.

Purpose To report the clinical association between macular coloboma (early-onset macular dystrophies/atrophic changes) and different phenotypes of retinitis pigmentosa (RP). Methods Three young-adult siblings, two males and one female, were retrospectively studied. These patients underwent two complete ophthalmologic examinations (27-month follow-up), including orthoptic evaluation, colour vision test, visual field, corneal topography, electronystagmography, fluorescein angiography, and electroretinography. Eye check, automated visual field test, and complete electroretinographic study were also conducted on other asymptomatic members of the same family. Results All symptomatic siblings were affected by manifest congenital nystagmus, poor visual acuity, and progressive visual field impairment in both eyes, bilaterally presenting macular coloboma associated with three different RP patterns: classic RP; mild dystrophy of the retinal pigment epithelium, associated with subnormal electroretinographic findings (subclinical form of RP); and sector RP. The ophthalmologic reports regarding their deceased father documented that he had suffered from the same alterations of ocular movements and visual performances diagnosing, in both eyes, extensive atrophic changes of the macular area completely surrounded by pigmented bone spicules (RP-type tapeto-retinal dystrophy). The other investigated relatives did not show any specific and/or significant ocular disorder. Conclusions In these three adult members of the same family, the concomitance between macular coloboma and different intrafamilial RP phenotypes is described. This association represents an autosomal dominant clinical entity, hitherto observed only in non familial sporadic cases.Eye (2004) 18, 421-428. doi:10.1038/sj.eye.6700689

Adult↗

PubMed2000

Automated oxyhemoglobin dissociation curve construction to assess sickle cell anemia therapy.

Oxyhemoglobin dissociation curves measure the most important function of red blood cells - the affinity for oxygen and its delivery to the tissues. This function may be deranged in sickle cell anemia and some other hemoglobinopathies. An automated oxyhemoglobin dissociation curve analyzer constructed dissociation curves in 55 patients with hemoglobinopathies and in 24 control subjects while maintaining constant temperature and pH. Sigmoid curves were converted to rectilinear ones using the Hill equation. Oxygen affinity of red cells was assessed by calculation of P50 (the PO2 at which hemoglobin is half saturated). Results revealed separation of oxyhemoglobin dissociation Hill plots according to phenotype but with wide variability. Mean oxygen affinity of fetal hemoglobin was greatest, whereas that of sickle hemoglobin was least. Other hemoglobins were intermediate. A positive correlation between decreased oxygen affinity and carboxyhemoglobin confirmed the decreased oxygen affinity of sickle hemoglobin and decreased oxygen affinity and increased diphosphoglycerate in red cells. Hill plots are less sensitive discriminators of oxygen affinity than traditional sigmoid dissociation curves and offer no particular advantage. Serial studies in a subset of three sickle cell anemia patients treated conservatively suggest automated oxyhemoglobin dissociation curves may be useful in assessment of effectiveness of newer therapies of sickle cell anemia after refinement of the method and studies of larger populations.

Adult↗

PubMed1997

[Laboratory-evaluation of antimicrobial susceptibility testings to detect vancomycin-resistant enterococci].

The emergence and dissemination of vancomycin-resistant enterococci (VRE) emphasizes the need for laboratories to be able to correctly detect them. The study described was conducted to evaluate the test methods presently available in Japan to discriminate between the isolates of VRE and those susceptible (VSE). Among the phenotypic test methods evaluated, an agar screening method which utilized 8 micrograms per ml of vancomycin in Mueller-Hinton agar plate appeared to have a sufficient accuracy. When 23 isolates of vanA positive, 31 of vanB positive, 4 of both positive and 60 of both negative were tested, the sensitivity and specificity to detect VRE were estimated to be 98.3% and 100%, respectively. Also, all the VRE isolates were interpreted as being resistant or intermediate by the E test recently approved in Japan, when the results were read after 48 hr-incubation. Whereas, two disk diffusion tests, Showa disk and NCCLS-based Sensi-disc, were evaluated, but both methods failed to discriminate between VRE and VSE, in particular, between the isolates with vanB positive and negative. The automated system, Vitek GPS-TA produced high frequencies of very major errors; 8.7% for vanA positives and 58% for vanB positives. A total of 1,214 enterococcal isolates from multisite laboratories in Japan, comprising 7 different species, were first tested onto agar screening test plates, but none of isolates represented phenotypic vancomycin resistance. With these results, it can be recommended to detect VRE in clinical microbiology laboratories as follows: First, all the enterococcal isolates will be tested onto the agar screening plates or by the E test. Then, if the isolate is interpreted as being resistant or intermediate, the laboratory should confirm whether it is positive for vanA or vanB by polymerase chain reaction (PCR) specified.

Anti-Bacterial Agents↗

PubMed1992

Phenotypic overlaps between pleomorphic malignant T-cell lymphomas and mixed-cellularity Hodgkin's disease.

Histologically diagnosed, or in part questionable, malignant pleomorphic peripheral T-cell lymphomas (pPTCLs, n = 16) and mixed-cellularity Hodgkin's disease (MCHD, n = 12) were objectively compared by the use of combined immunohistochemistry on paraffin sections, test-point analysis of tissue components, and semi-automated nuclear morphometry on semi-thin resin sections. Classical, qualitative histomorphological distinction of these sub-types of lymphomas proved to be valid and is probably still the best method. Quantitative discriminant features, in order of decreasing significance, were: (i) expression by large atypical cells (LACs) of CD45R0, CD43 and CD45 in pPTCLs, and of CD30 and CD15 in MCHD; (ii) means and standard deviations (SDs) of LAC nuclear-profile areas (greater in MCHD than in pPTCLs); (iii) expression of CD3 by LACs in pPTCLs; (iv) prominence of small lymphoid cells in MCHD; (v) higher percentage of medium-sized lymphoid cells in pPTCLs; and (vi) higher SDs of nuclear-profile circularity factor of small lymphoid cells in MCHD. The medians of the largest nucleolar profile areas in LACs per field did not differ in pPTCLs and MCHD, but dispersion of individual values towards higher levels was significantly greater in the latter. Stepwise discriminant analysis of test point and nucleometric variables that best distinguished pPTCLs from MCHD revealed considerable overlaps, and questionable cases tended to be intermediate between the two. In conclusion, our results confirm and expand the notion of intra-group heterogeneity, with indistinct borders and the existence of intermediate phenotypes between these two taxonomic categories of malignant lymphomas.

Adolescent↗

PubMed2000

Molecular and phenotypic identification of the yeast pathogen Candida dubliniensis.

Candida dubliniensis is an emerging yeast pathogen generally misclassified as Candida albicans by standard diagnostic procedures. This study examined the efficiency of molecular identification, based on a discriminative PCR test, in a prospective study on the prevalence of C. dubliniensis among 103 oropharyngeal isolates from HIV-infected individuals or transplant recipients, and 30 vaginal isolates. All of the isolates had been classified as C. albicans by standard laboratory procedures. The PCR was evaluated in a blinded fashion against classification achieved by sequencing rDNA. Sequencing results corresponded 100% to the results of the discriminative PCR, indicating the validity of this rapid test. Twenty-one C. dubliniensis isolates were identified, all of them from HIV-infected individuals (prevalence 30%). The internal transcribed spacer regions of the C. dubliniensis isolates were sequenced. Phenotypic features of C. dubliniensis, namely abundant chlamydospore formation, atypical color on CHROMagar, growth defect at 45 degrees C, and colony morphology on Staib agar, were evaluated in a blinded fashion with respect to their discriminative potential, facilitating the design of further epidemiological studies. Carbohydrate assimilation patterns were determined for C. dubliniensis with a novel automated system showing that, in contrast to previous reports, C. dubliniensis is able to utilize D-xylose and trehalose. In evaluating these tests we present a rational approach to identification of the new species and characterization of C. dubliniensis isolates.

AIDS-Related Opportunistic Infections↗

PubMed2025

Evaluating 12 automated, whole-genome sequencing analysis pipelines for Mycobacterium tuberculosis complex: a comparative study.

BACKGROUND: Reliance on complex, custom-built bioinformatics pipelines is a barrier to the implementation of whole-genome sequencing (WGS) of Mycobacterium tuberculosis in high-burden settings in some low-income and middle-income countries (LMICs). Automated analysis pipelines could address this inequity in access to WGS-based diagnostics and surveillance. This study aimed to systematically evaluate the performance and usability of publicly available WGS pipelines for M tuberculosis. METHODS: We identified automated M tuberculosis WGS analysis pipelines through searches of PubMed and GitHub from database inception up to Aug 31, 2024. Accuracy, cost, accessibility, and scalability were assessed for each pipeline. We evaluated the accuracy of genotypic drug susceptibility testing (gDST) using publicly available sequences with phenotypic susceptibility data for 12 antituberculosis drugs. We estimated pooled sensitivity and specificity for each pipeline, across all drugs, by conducting a bivariate meta-analysis, with random effects representing between-drug variability. Lineage classifications were compared, and a previously epidemiologically well-characterised dataset was used to compare measures of genomic relatedness. FINDINGS: Among 28 candidate pipelines, 16 were excluded as they were unmaintained and inexecutable. 12 pipelines (11 compatible with Illumina and four compatible with Nanopore), all free to use, were included for evaluation. Six pipelines processed and stored data remotely, but for five of these six, scalability was limited by the need to upload sequences through web portals. For local processing pipelines, scalability was dependent on substantial local computational resources, data storage capacity, and command-line interfaces that limited user-friendliness. Only one of six remote-processing pipelines removed human DNA sequences before server upload. gDST was similarly accurate across ten of 11 Illumina-compatible pipelines and three of four Nanopore-compatible pipelines. All pipelines classified the main lineages consistently, although there were differences at sublineage resolution. Outputs from three of four pipelines reporting genomic relatedness were compatible with commonly cited single nucleotide polymorphism difference thresholds. INTERPRETATION: Numerous automated analysis pipelines capable of enhancing equity in M tuberculosis WGS are available. Given the overall similarities between the pipelines evaluated in this study in terms of gDST performance, lineage classification, and genomic relatedness inference, non-functional attributes such as availability, accessibility, scalability, and privacy could represent the point of difference for prospective users in LMICs with a high burden of tuberculosis. FUNDING: The Rhodes Trust, Wellcome, Ellison Institute of Technology, and the UK National Institute for Health and Care Research Oxford Biomedical Research Centre.

Mycobacterium tuberculosis↗

PubMed2005

Classification of fundus autofluorescence patterns in early age-related macular disease.

PURPOSE: To describe and classify patterns of abnormal fundus autofluorescence (FAF) in eyes with early nonexudative age-related macular disease (AMD). METHODS: FAF images were recorded in eyes with early AMD by confocal scanning laser ophthalmoscopy (cSLO) with excitation at 488 nm (argon or OPSL laser) and emission above 500 or 521 nm (barrier filter). A standardized protocol for image acquisition and generation of mean images after automated alignment was applied, and routine fundus photographs were obtained. FAF images were classified by two independent observers. The kappa statistic was applied to assess intra- and interobserver variability. RESULTS: Alterations in FAF were classified into eight phenotypic patterns including normal, minimal change, focal increased, patchy, linear, lacelike, reticular, and speckled. Areas with abnormal increased or decreased FAF signals may or may not have corresponded to funduscopically visible alterations. For intraobserver variability, kappa of observer I was 0.80 (95% confidence interval [CI]0.71-0.89) and of observer II, 0.74. (95% CI, 0.64-0.84). For interobserver variability, kappa was 0.77 (95% CI, 0.67-0.87). CONCLUSIONS: Various phenotypic patterns of abnormal FAF can be identified with cSLO imaging. Distinct patterns may reflect heterogeneity at a cellular and molecular level in contrast to a nonspecific aging process. The results indicate that the classification system yields a relatively high degree of intra- and interobserver agreement. It may be applicable for determination of novel prognostic determinants in longitudinal natural history studies, for identification of genetic risk factors, and for monitoring of future therapeutic interventions to slow the progression of early AMD.

Fluorescence↗

PubMed1987

[Demonstration of individual predisposition to myocardial infarct based on immunogenetic status].

Statusometry, a method of automated quantitative assessment of the state of composite multiparametrical objects, is proposed for the detection of genetic predisposition to myocardial infarction as an instrument of integral quantitative assessment of systemic immunogenetic status on the basis of HLA phenotype. The prognostic error does not exceed 15%. Large-scale application of the new method appears a promising approach to individualization and better efficiency of preventive cardiologic treatment.

HLA Antigens↗

PubMed2004

Extended-Spectrum beta-lactamase (ESBL) producing Enterobacter aerogenes phenotypically misidentified as Klebsiella pneumoniae or K. terrigena.

BACKGROUND: Enterobacter aerogenes and Klebsiella pneumoniae are common isolates in clinical microbiology and important as producers of extended spectrum beta-lactamases (ESBL). The discrimination between both species, which is routinely based on biochemical characteristics, is generally accepted to be straightforward. Here we report that genotypically unrelated strains of E. aerogenes can be misidentified as K. pneumoniae by routine laboratories using standard biochemical identification and using identification automates. RESULTS: Ten clinical isolates, identified as K. pneumoniae or K. terrigena with the routinely used biochemical tests and with API-20E, were identified as E. aerogenes by tDNA-PCR - an identification that was confirmed by 16S rRNA gene sequencing for five of these isolates. Misidentification also occurred when using the automated identification systems Vitek 2 and Phoenix, and was due to delayed positivity for ornithine decarboxylase and motility. Subculture and prolonged incubation resulted in positive results for ornithine decarboxylase and for motility. It could be shown by RAPD-analysis that the E. aerogenes strains belonged to different genotypes. CONCLUSIONS: Clinical E. aerogenes isolates can be easily misidentified as Klebsiella due to delayed positivity for ornithine decarboxylase and motility. The phenomenon may be widespread, since it was shown to occur among genotypically unrelated strains from different hospitals and different isolation dates. A useful clue for correct identification is the presence of an inducible beta-lactamase, which is highly unusual for K. pneumoniae. In several instances, the use of genotypic techniques like tDNA-PCR may circumvent problems of phenotypic identification.

Bacterial Typing Techniques↗

PubMed2003

A new web-based data mining tool for the identification of candidate genes for human genetic disorders.

To identify the gene underlying a human genetic disorder can be difficult and time-consuming. Typically, positional data delimit a chromosomal region that contains between 20 and 200 genes. The choice then lies between sequencing large numbers of genes, or setting priorities by combining positional data with available expression and phenotype data, contained in different internet databases. This process of examining positional candidates for possible functional clues may be performed in many different ways, depending on the investigator's knowledge and experience. Here, we report on a new tool called the GeneSeeker, which gathers and combines positional data and expression/phenotypic data in an automated way from nine different web-based databases. This results in a quick overview of interesting candidate genes in the region of interest. The GeneSeeker system is built in a modular fashion allowing for easy addition or removal of databases if required. Databases are searched directly through the web, which obviates the need for data warehousing. In order to evaluate the GeneSeeker tool, we analysed syndromes with known genesis. For each of 10 syndromes the GeneSeeker programme generated a shortlist that contained a significantly reduced number of candidate genes from the critical region, yet still contained the causative gene. On average, a list of 163 genes based on position alone was reduced to a more manageable list of 22 genes based on position and expression or phenotype information. We are currently expanding the tool by adding other databases. The GeneSeeker is available via the web-interface (http://www.cmbi.kun.nl/GeneSeeker/).

Computational Biology↗

PubMed2000

Screening assay for promigratory/antimigratory compounds.

Large-scale screening strategies aimed at finding anticancer drugs traditionally focus on identifying cytotoxic compounds that attack actively dividing cells. Because progression to malignancy involves acquisition of an aggressively invasive phenotype in addition to hyperproliferation, simple and effective screening strategies for finding compounds that target the invasive aspects of cancer progression may prove valuable for identifying alternative and preventative cancer therapies. Here, we describe a fluorescence-based automated assay for identifying antimigratory compounds, with the ability to discern cytotoxic from noncytotoxic modes of action. With this assay, we analyzed the effects of two drugs on tumorigenic (MDA-MB-435) and nontumorigenic (MCF-10A) human breast cell lines. We chose to compare carboxyamidotriazole (CAI), an experimental compound shown to inhibit migration of various cell types, with tamoxifen, a common preventative and therapeutic anticancer compound. Our assay demonstrated that both these compounds inhibit migration at sublethal concentrations. Furthermore, CAI was more effective than tamoxifen at inhibiting chemotactic and haptotactic migration of both cell lines at all concentrations tested.

Antineoplastic Agents↗

PubMed2001

Investigation of an outbreak caused by methicillin-resistant Staphylococcus aureus in a cardiovascular surgery unit by ribotyping, randomly amplifed polymorphic DNA and pulsed-field gel electrophoresis.

An outbreak caused by rapid spread of methicillin-resistant Staphylococcus aureus (MRSA) in an intensive care unit for cardiovascular surgery was investigated by phenotypic and genotypic methods. Fourteen isolates were collected during a 2-month period from clinical and environmental specimens in the unit recently re-opened after reconstruction. The isolates were tested for antibiotic susceptibility patterns and genotyped by automated ribotyping, randomly amplified polymorphic DNA-PCR (RAPD) analysis and pulsed-field gel electrophoresis (PFGE). Automated ribotyping applying EcoRI digestion proved to be of no value in separating the isolates. In contrast, PFGE grouped the isolates into four clusters different from the reference strain. These results fully correlated with the antibiograms. Twelve of the isolates were grouped into two clonally related clusters. RAPD analyses grouped the isolates into five clusters. Except for two isolates of one patient, which had different RAPD patterns, PFGE and RAPD analyses presented very similar results. The results verified the usefulness of PFGE in studies of MRSA epidemics. A combination of these two methods reduces the time to identification of an outbreak and increases the accuracy in detection of intraspecies differences.

Base Sequence↗

PubMedDate not supplied

Analysis of methylation patterns in the regulatory region of the latent Epstein-Barr virus promoter BCR2 by automated fluorescent genomic sequencing.

We analyzed the methylation patterns of CpG dinucleotides in the regulatory region of the latent Epstein-Barrvirus (EBV) promoter BCR2 (also called C promoter, Cp) using automated fluorescent genomic sequencing after bisulfite-induced modification of DNA. BCR2 is one of the alternative promoters for transcripts encoding the growth-transformation-associated nuclear antigens EBNA 1-6 which are expressed in a host cell phenotype dependent manner. Well characterized clones isolated from the Burkitt's lymphoma (BL) line Mutu differing from each other as to their phenotype and EBV latent gene expression were used in the present study. We found that in Mutu BL III clone 99 which is actively using the BCR2 promoter the regulatory sequences are unmethylated with two exceptions (position 10702 and 10799). In contrast, there are 15 methylated cytosines in the same region in Mutu BL I clone 216 where the BCR2 promoter is silent. Cytosines which are potential targets of DNA methyltransferase in the immediate vicinity or within the attachment sites of cellular C promoter binding factors CBF1 and CBF2 remained hypomethylated in Mutu BL I clone 216. This suggests a role for a hypermethylated region (nucleotides 10666 -10865, -639 to -440 bases upstream from the beginning of the TATA box at position 11305) in silencing of the BCR2 promoter in these cells.

Base Sequence↗

PubMed2004

A simplified low-cost approach to antibiotic resistance profiling for faecal source tracking.

Antibiotic resistance profiling (ARP) is a potentially useful method for distinguishing faecal bacteria according to host source. This phenotypic approach has cost benefits over genotypic methods, but existing protocols are time-consuming and manual data handling is open to human error. A simplified, low-cost approach to the ARP technique was developed that used automated data recording techniques combined with simple statistical analyses to compare isolates of the genus Enterococcus from various faecal sources. An initial battery of 21 antibiotics (at up to four concentrations) was chosen for source discrimination. Images of growth or non-growth in microplate wells were stored as bitmaps and converted to binary data to form a database of known antibiotic resistance profiles. Discriminant function analysis (DFA) showed that the average rate of isolates correctly classified by the database (wastewater vs non-wastewater) was 86%. Once the more discriminating antibiotics and their concentrations had been identified, it was possible to reduce the number of tests from 80 to 18 whilst increasing the number of correctly classified human isolates. ARP could offer a low-cost and rapid means of identifying sources of faecal pollution. As such, the technique may be of particular benefit to developing countries, where water quality may have a significant impact on health and where cost is a major factor when choosing environmental management technology.

Anti-Bacterial Agents↗

PubMed1992

Characterization of mutations in phenotypic variants of hypoxanthine phosphoribosyltransferase deficiency.

The Lesch-Nyhan disease is caused by an almost complete lack of the enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT). Partial HPRT-deficiency, associated with less severe phenotype, has also been identified. We have characterized mutations occurring in HPRT cDNA isolated from patients with HPRT-deficiency with an emphasis on examining the more unusual partial variants of HPRT-deficiency. HPRT cDNA was amplified by PCR, cloned and analyzed by automated DNA sequence analysis. Twenty-two, unrelated individuals with HPRT deficiency were studied including eight classic Lesch-Nyhan patients and fourteen patients representing the different groups of partial HPRT deficiency. We found a diverse pattern of mutations with point mutations accounting for the majority of abnormal HPRT genes. Nonsense mutations and exon deletions were only found in HPRT cDNA isolated from classic Lesch-Nyhan patients. Mutations associated with partial HPRT-deficiency were frequently located in the amino terminal part of the molecule. A CpG mutational hot spot was identified at the position for Arg-51 in the HPRT protein. Two hyperuricemic patients exhibited unusual splice site mutations: in one this led to the creation of an additional exon in the HPRT gene and in the other part of exon 6 was missing in a subpopulation of the transcripts, producing the effect of a dominant, negative mutation.

Amino Acid Sequence↗

PubMed2006

Rapid phenotypic assay of antimycobacterial susceptibility pattern by direct mycobacteria growth indicator tube and phage amplified biological assay compared to BACTEC 460 TB.

The performance of antimycobacterial susceptibility testing for the first line drugs (isoniazid, streptomycine, rifampicin and ethambutol) with mycobacteria growth indicator tube (MGIT) and by bacteriophage amplified biological assay by FAST-plaque TB-MDR were compared to automated radiometric BACTEC 460 TB system. This study was carried on 84 sputum samples of positive Zhiel-Neelsen (ZN) smears. Sputum samples were subjected to culture and antimycobacterial susceptibility testing by BACTEC 460 TB. Samples were also tested by direct susceptibility tests for isoniazid (INH), ethambutol, rifampicin (RIF) and streptomycine by MGIT. Sensitive and resistant isolates for RIF were further studied by FAST-plaque TB-MDR for RIF resistance. The commonest resistance pattern by BACTEC 460 TB was for INH (32%) followed by RIF (24%) either alone or in combination with other drugs. Multiple drugs resistance was 20%. The agreement between BACTEC 460 TB and direct MGIT for resistant strains was 100% for INH and ethambutol, 91.7% for rifampicin, 80% for streptomycine and was 90% for MDR. FAST-plaque TB-MDR detected correctly all RIF resistant strains and 97.2% of the sensitive strains. For majority of strains direct susceptibility tests were available within 6.34-6.404 days (95% confidence interval) with direct mycobacteria growth tube, while results for FAST-plaque TB-MDR appear within 10.5-11.5 days from the time that the sputum was received in the laboratory (95% confidence interval). From this study, we could conclude that direct MGIT AST is the quickest method for screening antimycobacterial susceptibility pattern for the drugs commonly used (INH, RIF, etambutol, streptomycin) as results were available within 6.34-6.404 days. Also FAST-plaque TB-MDR method is accurate for detection of rifampicin resistance after primary culture which can be used as a surrogate marker for presence of MDR strains and the results were available within 10.5-11.5 days.

Adult↗