Publications (11)35.55 Total impact
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Article: Evaluation of the Cepheid Xpert MTB/RIF assay for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.
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ABSTRACT: A total of 217 specimens submitted for routine smear and culture from three different sites within the western United States were used to evaluate the GeneXpert MTB/RIF assay (for research use only) (Cepheid, Sunnyvale, CA). Overall agreement compared to culture was 89% (98% for smear positives and 72% for smear negatives) for detection of Mycobacterium tuberculosis.Journal of clinical microbiology 02/2011; 49(4):1621-3. · 4.16 Impact Factor -
Article: Impact of strain type on detection of toxigenic Clostridium difficile: comparison of molecular diagnostic and enzyme immunoassay approaches.
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ABSTRACT: A multicenter clinical trial assessed the performance of the Cepheid Xpert C. difficile assay on stool specimens collected from patients suspected of having Clostridium difficile infection (CDI). A total of 2,296 unformed stool specimens, collected from seven study sites, were tested by Xpert C. difficile enrichment culture followed by cell culture cytotoxicity testing of the isolates (i.e., toxigenic culture with enrichment) and the study sites' standard C. difficile test methods. The methods included enzyme immunoassay (EIA), direct cytotoxin testing, and two- and three-step algorithms using glutamate dehydrogenase (GDH) screening followed by either EIA or EIA and an in-house PCR assay. All C. difficile strains were typed by PCR-ribotyping. Compared to results for toxigenic culture with enrichment, the sensitivity, specificity, and positive and negative predictive values of the Xpert assay were 93.5, 94.0, 73.0, and 98.8%, respectively. The overall sensitivity of the EIAs compared to that of enrichment culture was 60.0%, and the sensitivity of combined GDH algorithms was 72.9%; both were significantly lower than that of Xpert C. difficile (P < 0.001 and P = 0.03, respectively). The sensitivity of the EIA was significantly lower than that of the Xpert C. difficile assay for detection of ribotypes 002, 027, and 106 (P < 0.0001, P < 0.0001, and P = 0.004, respectively, Fisher's exact test), and the sensitivity of GDH algorithms for ribotypes other than 027 was lower than that for Xpert C. difficile (P < 0.001). The Xpert C. difficile assay is a simple, rapid, and accurate method for detection of toxigenic C. difficile in unformed stool specimens and is minimally affected by strain type compared to EIA and GDH-based methods.Journal of clinical microbiology 10/2010; 48(10):3719-24. · 4.16 Impact Factor -
Article: Clostridium difficile testing in the clinical laboratory by use of multiple testing algorithms.
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ABSTRACT: The incidence of Clostridium difficile infection (CDI) has risen almost 3-fold in the United States over the past decade, emphasizing the need for rapid and accurate tests for CDI. The Cepheid Xpert C. difficile assay is an integrated, closed, nucleic acid amplification system that automates sample preparation and real-time PCR detection of the toxin B gene (tcdB). A total of 432 stool specimens from symptomatic patients were tested by a glutamate dehydrogenase (GDH) assay, a toxin A and B enzyme immunoassay (EIA), the Xpert C. difficile assay, and a cell culture cytotoxicity neutralization assay (CCCN). The results of these methods, used individually and in combination, were compared to those of toxigenic culture. Results for the Xpert C. difficile assay alone showed a sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of 94.4, 96.3, 84.0, and 98.8%, while the EIA alone gave corresponding values of 58.3, 94.7, 68.9, and 91.9%, respectively. An algorithm using the GDH assay and the EIA (plus the CCCN if the EIA was negative) showed corresponding values of 83.1, 96.7, 83.1, and 96.1%. The Xpert C. difficile assay was statistically superior to the EIA (P, <0.001 by Fisher's exact test) and to the GDH-EIA-CCCN algorithm (P, 0.0363). Combining the GDH and Xpert C. difficile assays lowered both the sensitivity and the NPV of the Xpert assay. The GDH-EIA-CCCN procedure required, on average, 2 days to complete testing on GDH-positive results, while testing by the Xpert C. difficile assay was completed, on average, in less than 1 h. Xpert C. difficile testing yielded the highest sensitivity and NPV, in the least amount of time, of the individual- and multiple-test algorithms evaluated in this study.Journal of clinical microbiology 03/2010; 48(3):889-93. · 4.16 Impact Factor -
Article: Performance of the GeneXpert enterovirus assay for detection of enteroviral RNA in cerebrospinal fluid.
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ABSTRACT: The GeneXpert Dx System allows for automated extraction, processing, amplification and real-time detection of target nucleic acids. To evaluate the performance of the Cepheid Xpert enterovirus (EV) assay for detection of EV RNA compared to a nucleic acid sequence based amplification (NASBA) assay and a user-developed TaqMan RT-PCR assay. Assays were evaluated using a 12-member proficiency panel and up to 138 CSF specimens. Samples in which EV RNA was detected by two or more assays were considered true positives. The GeneXpert, NASBA, and TaqMan assays correctly identified 10, 8, and 7 of 12 proficiency panel members, respectively. For detection of EV RNA in CSF, the sensitivities of the GeneXpert, NASBA, and TaqMan were 100%, 87.5%, and 96%, respectively. There were no false positives. Two samples tested by GeneXpert and NASBA yielded indeterminate or invalid results and could not be resolved. The Xpert EV assay is a sensitive and specific method for detection of EV RNA in CSF specimens. The ease of use, random access capability, and minimal hands-on time with the automated GeneXpert system affords laboratories with little molecular diagnostics expertise an opportunity to complete a clinically useful testing within 2.5 h.Journal of Clinical Virology 09/2008; 43(1):110-3. · 3.97 Impact Factor -
Article: Sensitivity and specificity of a rapid rRNA gene probe assay for simultaneous identification of Staphylococcus aureus and detection of mecA.
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ABSTRACT: rRNA gene sequences were used for identification and target adequacy controls in a DNA probe assay to identify isolates as Staphylococcus and, more specifically, as S. aureus within 1 hour. mecA status was simultaneously determined using a specific DNA probe. The target adequacy control guarded against false-negative mecA results.Journal of Clinical Microbiology 08/2005; 43(7):3438-42. · 4.15 Impact Factor -
Article: Application of an rRNA probe matrix for rapid identification of bacteria and fungi from routine blood cultures.
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ABSTRACT: One of the most important functions of the clinical microbiology laboratory is the identification of the etiology of sepsis. For this study, aliquots from 405 positive blood cultures were tested against a unique array of DNA probes directed against rRNA subsequences of bacteria and fungi for identification. Another 280 samples that were negative after 5 days of incubation were also tested. Blood culture bottles were incubated in a BacT/Alert3D instrument. For the rRNA assay, a 0.4-ml aliquot was removed, and the cells were pelleted by centrifugation. The pellet was washed and frozen at -70 degrees C. Analysis of the pellet involved a lysis step and then the addition of samples to the reaction wells containing the probes in a microtiter plate format. Analysis was performed by using a hybridization protection assay. Results were taken through a series of deductive steps to obtain species, or in some cases genus, identification. Batch sample preparation required approximately 15 min, and sample analysis required another 60 min. Probe results were compared to conventional biochemical identifications. The probe test was negative for the 280 samples that were negative by the BacT/Alert 3D system and for another 21 samples that were false positive (the instrument signaled, but there was no growth). Microorganisms from the remaining 384 signal-positive samples included 60 Enterobacteriaceae, 10 Pseudomonas aeruginosa, 10 other gram-negative bacteria, 40 Staphylococcus aureus, 152 coagulase-negative staphylococci, 28 streptococci, 22 enterococci, 21 other gram-positive bacteria, 8 anaerobes, and 16 yeast organisms. Seventeen cultures were polymicrobial, and one was gram positive and culture negative. Discordance between probe and conventional identification results was noted for only 12 (1.75%) samples. This novel rapid molecular approach to the identification of bacteria and yeast in blood cultures was highly sensitive (100%) and specific (96%).Journal of Clinical Microbiology 12/2003; 41(11):5127-33. · 4.15 Impact Factor -
Article: Conventional and molecular methods for verification of results obtained with BacT/Alert Nonvent blood culture bottles.
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ABSTRACT: A strategy comparing molecular and conventional methods for verification of the BacT/Alert nonvent blood culture bottles (Organon Teknika, Durham, N.C.) was performed with seeded isolates. The bottles were evaluated with 12 common organisms from bloodstream infections. Overall, the bottles were equivalent as determined by conventional and molecular methods.Journal of Clinical Microbiology 04/2003; 41(3):1266-9. · 4.15 Impact Factor -
Article: Practical therapeutic application of the oxoid PBP2' latex agglutination test for the rapid identification of methicillin-resistant Staphylococcus aureus in blood cultures.
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ABSTRACT: The Oxoid PBP2' latex agglutination test (OLA; Oxoid, Basingstoke, England) was evaluated in a controlled prospective study examining Staphylococcus aureus from 25 positive blood cultures. Subcultures of positive blood cultures with coagulase-positive, gram-positive cocci in clusters were batched, and the OLA was performed at the end of the working day, once growth was seen on the plate. Results were sent to the infectious disease pharmacist for therapy evaluation, and the 24-hour minimum inhibitory concentration (MIC) was confirmed the next day. Blood culture OLA results correlated 100% with oxacillin MIC results for the patient, and results were available in as little as 3 hours after the blood culture was positive. The mean time difference between the OLA and MIC reports was 19.4 hours. This test allowed same-day resistance marker reporting and was easily incorporated into the work flow of the clinical laboratory.American Journal of Clinical Pathology 09/2002; 118(2):287-91. · 2.60 Impact Factor -
Article: Application of a Reverse Transcription-PCRassay to monitor regulation of the catabolicnahAc gene during phenanthrene degradation
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ABSTRACT: Biodegradation of polycyclic aromatic hydrocarbons (PAH), such as phenanthrene, in environmental samples is often limited by low bioavailability whichresults from a combination of low aqueous solubility and/or high sorption. The purpose of thisstudy was to investigate the influence of agents that increase PAH bioavailability on expressionof the PAH catabolic gene nahAc. Phenanthrene was used as a model PAH andPseudomonas putida PpG7, which contains the NAH7 plasmid that encodes the genesresponsible for naphthalene and phenanthrene degradation, was used as a model degrader.PAH bioavailability was altered by the addition of two biosurfactants, rhamnolipid andhydroxypropyl--cyclodextrin (HPCD). Gene expression was determined by extraction of bacterialmRNA followed by RT-PCR amplification of two transcripts; nahAc, a naphthalenedioxygenase gene, and rpoD, a housekeeping gene. Results indicate that the lag period precedingnahAc gene induction decreased from 312 to 48 h in the presence of biosurfactants.Expression of the nahAc gene, as measured by RT-PCR, in the presence of surfactants wasbimodal on a temporal basis, indicating that induction stopped briefly during biodegradation.Cessation of induction could have resulted from the up-regulation of alternate pathways or theaccumulation of toxic intermediates. In contrast, expression of the rpoD gene wasmaintained throughout the duration of each experiment. This research demonstrates thatthe use of a gene expression assay to monitor the impact of substrate bioavailability on substrateutilization provides unique information concerning the biodegradation process that cannot beobtained from more traditional biodegradation assays such as cell growth or substrate disappearance.Gene expression assays also have the potential for use in assessing the impact of otherenvironmental factors on biodegradation.Biodegradation 07/2002; 13(4):251-260. · 2.02 Impact Factor -
Article: Application of a reverse transcription-PCR assay to monitor regulation of the catabolic nahAc gene during phenanthrene degradation.
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ABSTRACT: Biodegradation of polycyclic aromatic hydrocarbons (PAH), such as phenanthrene, in environmental samples is often limited by low bioavailability which results from a combination of low aqueous solubility and/or high sorption. The purpose of this study was to investigate the influence of agents that increase PAH bioavailability on expression of the PAH catabolic gene nahAc. Phenanthrene was used as a model PAH and Pseudomonasputida PpG7, which contains the NAH7 plasmid that encodes the genes responsible for naphthalene and phenanthrene degradation, was used as a model degrader. PAH bioavailability was altered by the addition of two biosurfactants, rhamnolipid and hydroxypropyl-beta-cyclodextrin (HPCD). Gene expression was determined by extraction of bacterial mRNA followed by RT-PCR amplification of two transcripts; nahAc, a naphthalene dioxygenase gene, and rpoD, a housekeeping gene. Results indicate that the lag period preceding nahAc gene induction decreased from 312 to 48 h in the presence of biosurfactants. Expression of the nahAc gene, as measured by RT-PCR, in the presence of surfactants was bimodal on a temporal basis, indicating that induction stopped briefly during biodegradation. Cessation of induction could have resulted from the up-regulation of alternate pathways or the accumulation of toxic intermediates. In contrast, expression of the rpoD gene was maintained throughout the duration of each experiment. This research demonstrates that the use of a gene expression assay to monitor the impact of substrate bioavailability on substrate utilization provides unique information concerning the biodegradation process that cannot be obtained from more traditional biodegradation assays such as cell growth or substrate disappearance. Gene expression assays also have the potential for use in assessing the impact of other environmental factors on biodegradation.Biodegradation 02/2002; 13(4):251-60. · 2.02 Impact Factor -
Article: Cyclodextrin-Enhanced Biodegradation of Phenanthrene
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ABSTRACT: The effectiveness of in situ bioremediation in many systems may be constrained by low contaminant bioavailability due to limited aqueous solubility or a large magnitude of sorption. The objective of this research was to evaluate the effect of hydroxypropyl-β-cyclodextrin (HPCD) on phenanthrene solubilization and biodegradation. Results showed that analytical-grade HPCD can significantly increase the apparent solubility of phenanthrene. The increase in apparent solubility had a major impact on the biodegradation rate of phenanthrene. For example, in the presence of 105 mg L-1 HPCD, the substrate utilization rate increased from 0.17 mg h-1 to 0.93 mg h-1 while the apparent solubility was increased from 1.3 mg L-1 to 161.3 mg L-1. As a result, only 0.3% of the phenanthrene remained at the end of a 48 h incubation for the highest concentration of HPCD tested (105 mg L-1). In contrast, 45.2% of the phenanthrene remained in the absence of HPCD. Technical-grade HPCD, which contains the biodegradable impurity propylene glycol, also increased the substrate utilization rate, although to a lesser extent than the analytical-grade HPCD. On the basis of these results, it appears that HPCD can significantly increase the bioavailability, and thereby enhance the biodegradation, of phenanthrene.05/1998;
Top co-authors
Top Journals
Institutions
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2008–2011
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Kaiser Permanente
Oakland, CA, USA
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2003
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Harbor-UCLA Medical Center
Torrance, CA, USA
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2002
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VA Greater Los Angeles Healthcare System
Los Angeles, CA, USA -
The University of Arizona
- Department of Soil, Water, and Environmental Science
Tucson, AZ, USA
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