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  • 1
    Online Resource
    Online Resource
    Clostridium difficile Testing in the Clinical Laboratory by Use of Multiple Testing Algorithms
    American Society for Microbiology ; 2010
    In:  Journal of Clinical Microbiology Vol. 48, No. 3 ( 2010-03), p. 889-893
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 48, No. 3 ( 2010-03), p. 889-893
    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.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.01801-09
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2010
    detail.hit.zdb_id: 1498353-9
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Comparison of Soil Bacterial Communities in Rhizospheres of Three Plant Species and the Interspaces in an Arid Grassland
    American Society for Microbiology ; 2002
    In:  Applied and Environmental Microbiology Vol. 68, No. 4 ( 2002-04), p. 1854-1863
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 68, No. 4 ( 2002-04), p. 1854-1863
    Abstract: Soil bacteria are important contributors to primary productivity and nutrient cycling in arid land ecosystems, and their populations may be greatly affected by changes in environmental conditions. In parallel studies, the composition of the total bacterial community and of members of the Acidobacterium division were assessed in arid grassland soils using terminal restriction fragment length polymorphism (TRF, also known as T-RFLP) analysis of 16S rRNA genes amplified from soil DNA. Bacterial communities associated with the rhizospheres of the native bunchgrasses Stipa hymenoides and Hilaria jamesii , the invading annual grass Bromus tectorum , and the interspaces colonized by cyanobacterial soil crusts were compared at three depths. When used in a replicated field-scale study, TRF analysis was useful for identifying broad-scale, consistent differences in the bacterial communities in different soil locations, over the natural microscale heterogeneity of the soil. The compositions of the total bacterial community and Acidobacterium division in the soil crust interspaces were significantly different from those of the plant rhizospheres. Major differences were also observed in the rhizospheres of the three plant species and were most apparent with analysis of the Acidobacterium division. The total bacterial community and the Acidobacterium division bacteria were affected by soil depth in both the interspaces and plant rhizospheres. This study provides a baseline for monitoring bacterial community structure and dynamics with changes in plant cover and environmental conditions in the arid grasslands.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.68.4.1854-1863.2002
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2002
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 3
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    Online Resource
    Practical Guidance for Clinical Microbiology Laboratories: Mycobacteria
    American Society for Microbiology ; 2018
    In:  Clinical Microbiology Reviews Vol. 31, No. 2 ( 2018-04)
    Details
    In: Clinical Microbiology Reviews, American Society for Microbiology, Vol. 31, No. 2 ( 2018-04)
    Abstract: Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.
    Type of Medium: Online Resource
    ISSN: 0893-8512 , 1098-6618
    URL: Article
    DOI: 10.1128/CMR.00038-17
    RVK:
    XA 36863
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 1497041-7
    SSG: 12
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  • 4
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    Online Resource
    Reconstitution and Minimization of a Micrococcin Biosynthetic Pathway in Bacillus subtilis
    American Society for Microbiology ; 2016
    In:  Journal of Bacteriology Vol. 198, No. 18 ( 2016-09-15), p. 2431-2438
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 198, No. 18 ( 2016-09-15), p. 2431-2438
    Abstract: Thiopeptides represent one of several families of highly modified peptide antibiotics that hold great promise for natural product engineering. These macrocyclic peptides are produced by a combination of ribosomal synthesis and extensive posttranslational modification by dedicated processing enzymes. We previously identified a compact, plasmid-borne gene cluster for the biosynthesis of micrococcin P1 (MP1), an archetypal thiopeptide antibiotic. In an effort to genetically dissect this pathway, we have reconstituted it in Bacillus subtilis . Successful MP1 production required promoter engineering and the reassembly of essential biosynthetic genes in a modular plasmid. The resulting system allows for rapid pathway manipulation, including protein tagging and gene deletion. We find that 8 processing proteins are sufficient for the production of MP1 and that the tailoring enzyme TclS catalyzes a C-terminal reduction step that distinguishes MP1 from its sister compound micrococcin P2. IMPORTANCE The emergence of antibiotic resistance is one of the most urgent human health concerns of our day. A crucial component in an integrated strategy for countering antibiotic resistance is the ability to engineer pathways for the biosynthesis of natural and derivatized antimicrobial compounds. In this study, the model organism B. subtilis was employed to reconstitute and genetically modularize a 9-gene system for the biosynthesis of micrococcin, the founding member of a growing family of thiopeptide antibiotics.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.00396-16
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 5
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    Online Resource
    Mercury Adaptation among Bacteria from a Deep-Sea Hydrothermal Vent
    American Society for Microbiology ; 2005
    In:  Applied and Environmental Microbiology Vol. 71, No. 1 ( 2005-01), p. 220-226
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 71, No. 1 ( 2005-01), p. 220-226
    Abstract: Since deep-sea hydrothermal vent fluids are enriched with toxic metals, it was hypothesized that (i) the biota in the vicinity of a vent is adapted to life in the presence of toxic metals and (ii) metal toxicity is modulated by the steep physical-chemical gradients that occur when anoxic, hot fluids are mixed with cold oxygenated seawater. We collected bacterial biomass at different distances from a diffuse flow vent at 9°N on the East Pacific Rise and tested these hypotheses by examining the effect of mercuric mercury [Hg(II)] on vent bacteria. Four of six moderate thermophiles, most of which were vent isolates belonging to the genus Alcanivorax , and six of eight mesophiles from the vent plume were resistant to 〉 10 μM Hg(II) and reduced it to elemental mercury [Hg(0)]. However, four psychrophiles that were isolated from a nearby inactive sulfide structure were Hg(II) sensitive. A neighbor-joining tree constructed from the deduced amino acids of a PCR-amplified fragment of merA , the gene encoding the mercuric reductase (MR), showed that sequences obtained from the vent moderate thermophiles formed a unique cluster (bootstrap value, 100) in the MR phylogenetic tree, which expanded the known diversity of this locus. The temperature optimum for Hg(II) reduction by resting cells and MR activity in crude cell extracts of a vent moderate thermophile corresponded to its optimal growth temperature, 45°C. However, the optimal temperature for activity of the MR encoded by transposon Tn 501 was found to be 55 to 65°C, suggesting that, in spite of its original isolation from a mesophile, this MR is a thermophilic enzyme that may represent a relic of early evolution in high-temperature environments. Results showing that there is enrichment of Hg(II) resistance among vent bacteria suggest that these bacteria have an ecological role in mercury detoxification in the vent environment and, together with the thermophilicity of MR, point to geothermal environments as a likely niche for the evolution of bacterial mercury resistance.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.71.1.220-226.2005
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2005
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
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    Online Resource
    Understanding, Verifying, and Implementing Emergency Use Authorization Molecular Diagnostics for the Detection of SARS-CoV-2 RNA
    American Society for Microbiology ; 2020
    In:  Journal of Clinical Microbiology Vol. 58, No. 8 ( 2020-07-23)
    Details
    In: Journal of Clinical Microbiology, American Society for Microbiology, Vol. 58, No. 8 ( 2020-07-23)
    Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has brought a new wave of challenges to health care, particularly in the area of rapid diagnostic test development and implementation. The diagnosis of acute coronavirus disease 2019 (COVID-19) is critically dependent on the detection of SARS-CoV-2 RNA from clinical specimens (e.g., nasopharyngeal swabs). While laboratory-developed testing for SARS-CoV-2 is an essential component of diagnostic testing for this virus, the majority of clinical microbiology laboratories are dependent on commercially available SARS-CoV-2 molecular assays. In contrast to assays approved or cleared by the U.S. Food and Drug Administration (FDA) for in vitro diagnostic use, assays for the detection of SARS-CoV-2 nucleic acids have emergency use authorization (EUA) from the FDA. Outside of highly specialized academic and commercial laboratory settings, clinical microbiology laboratories are likely unfamiliar with the EUA classification, and thus, assay verification can be daunting. Further compounding anxiety for laboratories are major issues with the supply chain that are dramatically affecting the availability of test reagents and requiring laboratories to implement multiple commercial EUA tests. Here, we describe guidance for the verification of assays with EUA for the detection of SARS-CoV-2 nucleic acid from clinical specimens.
    Type of Medium: Online Resource
    ISSN: 0095-1137 , 1098-660X
    URL: Article
    DOI: 10.1128/JCM.00796-20
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 1498353-9
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  • 7
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    Online Resource
    Practical Evaluation of Methods for Detection and Specificity of Autoantibodies to Extractable Nuclear Antigens
    American Society for Microbiology ; 2004
    In:  Clinical and Vaccine Immunology Vol. 11, No. 2 ( 2004-03), p. 297-301
    Details
    In: Clinical and Vaccine Immunology, American Society for Microbiology, Vol. 11, No. 2 ( 2004-03), p. 297-301
    Abstract: Detection and specificity of autoantibodies against extractable nuclear antigens (ENA) play a critical role in the diagnosis and management of autoimmune disease. Historically, the detection of these antibodies has employed double immunodiffusion (DID). Autoantibody specificity was correlated with diagnoses by this technique. Enzyme immunoassays have been developed by multiple manufacturers to detect and identify the specificity ENA autoantibodies. To address the relationship of ENA detection by DID and enzyme immunoassay, the performances of five immunoassays were compared. These included two DID and three enzyme-linked immunoassays (ELISA) (both screening and individual antigen profile kits). The sample set included 83 ENA-positive, antinuclear-antibody (ANA)-positive specimens, 77 ENA-negative, ANA-positive specimens, and 20 ENA- and ANA-negative specimens. Sensitivity and specificity were calculated by two methods: first, by using the in-house DID result as the reference standard, and second, by using latent class analysis, which evaluates each kit result independently. Overall, the results showed that the ELISA methods were more sensitive for detection of ENA autoantibodies than DID techniques, but presence and/or specific type of ENA autoantibody did not always correlate with the patient's clinical presentation. Regardless of the testing strategy an individual laboratory uses, clear communication with the clinical staff regarding the significance of a positive result is imperative. The laboratory and the clinician must both be aware of the sensitivity and specificity of each testing method in use in the clinical laboratory.
    Type of Medium: Online Resource
    ISSN: 1556-6811 , 1556-679X
    URL: Article
    DOI: 10.1128/CDLI.11.2.297-301.2004
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2004
    detail.hit.zdb_id: 1496863-0
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  • 8
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    Online Resource
    Pharmacokinetics, Safety, and Tolerability of Caspofungin in Children and Adolescents
    American Society for Microbiology ; 2005
    In:  Antimicrobial Agents and Chemotherapy Vol. 49, No. 11 ( 2005-11), p. 4536-4545
    Details
    In: Antimicrobial Agents and Chemotherapy, American Society for Microbiology, Vol. 49, No. 11 ( 2005-11), p. 4536-4545
    Abstract: Caspofungin is a parenteral antifungal that inhibits beta-1,3- d -glucan synthesis. Although licensed for adult use, the appropriate caspofungin dosing regimen in pediatric patients is not yet known. We therefore investigated the pharmacokinetics and safety of caspofungin in pediatric patients. Thirty-nine children (ages 2 to 11 years) and adolescents (ages 12 to 17 years) with neutropenia were administered caspofungin using either a weight-based regimen (1 mg/kg of body weight/day) or a body surface area regimen (50 mg/m 2 /day or 70 mg/m 2 /day). Plasma samples for caspofungin profiles were collected on days 1 and 4. These results were compared to those from adults treated with either 50 or 70 mg/day for mucosal candidiasis. In children receiving 1 mg/kg/day (maximum, 50 mg/day), the area under the concentration-time curve over 24 h (AUC 0-24 ) was significantly smaller (46% after multiple doses) than that observed in adults receiving 50 mg/day ( P 〈 0.001). In children and adolescents receiving 50 mg/m 2 /day (maximum, 70 mg/day), the AUC 0-24 following multiple doses was similar to that for the exposure in adults receiving 50 mg/day. The AUC 0-24 and concentration trough (at 24 h) in pediatric patients receiving the 50-mg/m 2 daily regimen were consistent across the range of ages. Caspofungin was generally well tolerated in this study. None of the patients developed a serious drug-related adverse event or were discontinued for toxicity. These results demonstrate that caspofungin at 1 mg/kg/day in pediatric patients is suboptimal. Caspofungin administration at 50 mg/m 2 /day provides a comparable exposure to that of adult patients treated with 50 mg/day.
    Type of Medium: Online Resource
    ISSN: 0066-4804 , 1098-6596
    URL: Article
    DOI: 10.1128/AAC.49.11.4536-4545.2005
    RVK:
    XA 24552
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2005
    detail.hit.zdb_id: 1496156-8
    SSG: 12
    SSG: 15,3
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  • 9
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    A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides ( Clostridium ) difficile in Adults
    American Society for Microbiology ; 2019
    In:  Clinical Microbiology Reviews Vol. 32, No. 3 ( 2019-06-19)
    Details
    In: Clinical Microbiology Reviews, American Society for Microbiology, Vol. 32, No. 3 ( 2019-06-19)
    Abstract: The evidence base for the optimal laboratory diagnosis of Clostridioides ( Clostridium ) difficile in adults is currently unresolved due to the uncertain performance characteristics and various combinations of tests. This systematic review evaluates the diagnostic accuracy of laboratory testing algorithms that include nucleic acid amplification tests (NAATs) to detect the presence of C. difficile . The systematic review and meta-analysis included eligible studies (those that had PICO [population, intervention, comparison, outcome] elements) that assessed the diagnostic accuracy of NAAT alone or following glutamate dehydrogenase (GDH) enzyme immunoassays (EIAs) or GDH EIAs plus C. difficile toxin EIAs (toxin). The diagnostic yield of NAAT for repeat testing after an initial negative result was also assessed. Two hundred thirty-eight studies met inclusion criteria. Seventy-two of these studies had sufficient data for meta-analysis. The strength of evidence ranged from high to insufficient. The uses of NAAT only, GDH-positive EIA followed by NAAT, and GDH-positive/toxin-negative EIA followed by NAAT are all recommended as American Society for Microbiology (ASM) best practices for the detection of the C. difficile toxin gene or organism. Meta-analysis of published evidence supports the use of testing algorithms that use NAAT alone or in combination with GDH or GDH plus toxin EIA to detect the presence of C. difficile in adults. There is insufficient evidence to recommend against repeat testing of the sample using NAAT after an initial negative result due to a lack of evidence of harm (i.e., financial, length of stay, or delay of treatment) as specified by the Laboratory Medicine Best Practices (LMBP) systematic review method in making such an assessment. Findings from this systematic review provide clarity to diagnostic testing strategies and highlight gaps, such as low numbers of GDH/toxin/PCR studies, in existing evidence on diagnostic performance, which can be used to guide future clinical research studies.
    Type of Medium: Online Resource
    ISSN: 0893-8512 , 1098-6618
    URL: Article
    DOI: 10.1128/CMR.00032-18
    RVK:
    XA 36863
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
    detail.hit.zdb_id: 1497041-7
    SSG: 12
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  • 10
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    Correction for Kraft et al., “A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides ( Clostridium ) difficile in Adults”
    American Society for Microbiology ; 2019
    In:  Clinical Microbiology Reviews Vol. 32, No. 4 ( 2019-09-18)
    Details
    In: Clinical Microbiology Reviews, American Society for Microbiology, Vol. 32, No. 4 ( 2019-09-18)
    Type of Medium: Online Resource
    ISSN: 0893-8512 , 1098-6618
    URL: Article
    DOI: 10.1128/CMR.00128-19
    RVK:
    XA 36863
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
    detail.hit.zdb_id: 1497041-7
    SSG: 12
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