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  • 1
    In: Journal for ImmunoTherapy of Cancer, BMJ, Vol. 4, No. S1 ( 2016-11)
    Type of Medium: Online Resource
    ISSN: 2051-1426
    Language: English
    Publisher: BMJ
    Publication Date: 2016
    detail.hit.zdb_id: 2719863-7
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  • 2
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 11, No. 3 ( 2023-06-15)
    Abstract: The ASTM E1174-21 Health Care Personnel Handwash method is prescribed by the U.S. Food and Drug Administration (FDA) to demonstrate the efficacy of antiseptic handwashing products. The standardized method allows for marker bacteria to be collected from the hands by using either a bag or a glove. Two recent studies utilizing the different collection methods testing the same product showed substantial differences in results. We sponsored two independent studies to compare the bag and glove collection methods following contamination with Serratia marcescens . Overall, there was no difference between collection methods for bacteria recovered ( P =  0.603). The distribution of recovery for the bag method was slightly less variable than for the glove method. Statistical differences were observed within each lab based on the collection day. The day-to-day variability is critical to consider for future multiple-day studies. Additionally, hand size appears to impact recovery, especially for the glove method, with both small and medium hand sizes resulting in higher recovery than large and extralarge hand sizes ( P =  0.015), whereas hand size did not impact recovery with the bag method ( P =  0.315). While it appears that both the bag and glove methods can be used, our findings suggest that gloves may not be the best option for subjects with large to extra-large hands. Additional work looking at bacterial recovery following product treatment is warranted to understand the impact of large hands in the bag versus glove recovery method. IMPORTANCE Antiseptic hand wash products are evaluated using the standard ASTM E1174-21 to demonstrate their antibacterial efficacy. Often products are tested at multiple labs, and the need to understand variables that may play a role in the outcome of the study is important. This work allows us to evaluate the impact that the two collection methods, bags and gloves, have on bacteria recovery. If differences are observed, standardization to one method may be critical to ensure similar test results when planning studies at multiple labs.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2807133-5
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  • 3
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 5 ( 2022-10-26)
    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the “gold standard” for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2807133-5
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  • 4
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 9, No. 2 ( 2021-10-31)
    Abstract: This study was conducted to determine the in vitro activities of gentamicin alone and in combination with ceftriaxone, ertapenem, and azithromycin against multidrug-resistant (MDR) Neisseria gonorrhoeae isolates. A total of 407 clinical isolates from Nanjing, China, obtained in 2016 to 2017, had MICs determined for gentamicin using the agar dilution method. MDR status was ascribed to 97 strains that displayed decreased susceptibility or resistance to extended-spectrum cephalosporins (ESCs) (ceftriaxone [MIC, ≥0.125 mg/liter] and cefixime [MIC, ≥0.25 mg/liter] ), plus resistance to at least two of the following antimicrobials: penicillin (MIC, ≥2 mg/liter), ciprofloxacin (MIC, ≥1 mg/liter), and azithromycin (MIC, ≥1 mg/liter). MDR strains underwent MIC determinations for antimicrobial combinations using the antimicrobial gradient epsilometer test (Etest). Results that ranged from synergy to antagonism were interpreted using the fractional inhibitory concentration (FICI). All 407 gonococcal isolates were susceptible to gentamicin; MICs ranged from 2 mg/liter to 16 mg/liter. Synergy was demonstrated in 16.5% (16/97), 27.8% (27/97), and 8.2% (8/97) of MDR strains when gentamicin was combined with ceftriaxone (geometric mean [GM] FICI, 0.747), ertapenem (GM FICI, 0.662), and azithromycin (GM FICI, 1.021), respectively. No antimicrobial antagonism was observed with any combination tested against MDR strains; overall, antimicrobial combinations were indifferent. The GM MICs of gentamicin were reduced by 2.63-, 3.80-, and 1.98-fold when tested in combination with ceftriaxone, ertapenem, and azithromycin, respectively. The GM MICs of the three additional antimicrobials individually were reduced by 3-, 2.57-, and 1.98-fold, respectively, when each was tested in combination with gentamicin. Gentamicin alone was effective in vitro against N. gonorrhoeae , including MDR isolates. Combination testing of MDR strains showed lower MICs against gentamicin and each of three antimicrobials (ceftriaxone, ertapenem, and azithromycin) when used in combination. IMPORTANCE Antimicrobial-resistant Neisseria gonorrhoeae is a major global public health concern. New treatment options are urgently needed to successfully treat multidrug-resistant (MDR) Neisseria gonorrhoeae infections. This study showed that gentamicin maintained excellent in vitro susceptibility against clinical gonococcal isolates collected in 2016 and 2017, including MDR isolates. Combinations of gentamicin plus ertapenem, ceftriaxone, and azithromycin produced synergistic effects against certain MDR isolates. No antagonism was observed in any of the antimicrobial combinations, which may prove useful to guide clinical testing of combination therapies.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2807133-5
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  • 5
    In: Microbiology Spectrum, American Society for Microbiology
    Abstract: Management of infections with multi-drug resistant Klebsiella pneumoniae is a major challenge in hospital settings, with few treatment options. In this study, the authors aim to assess the in vitro susceptibility of these clinical isolates to cefiderocol, a novel siderophore. Comparators are colistin, ceftazidime-avibactam, and ceftazidime-avibactam/aztreonam synergy, which are currently available options for treatment in this region. Baseline-resistance rates against cefiderocol are higher than those in the previously published studies, with MIC50 and MIC90 at 2 and 8 µg/mL, respectively.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2807133-5
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  • 6
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 11, No. 3 ( 2023-06-15)
    Abstract: Population-based HIV Impact Assessments (PHIAs) are national household (HH) surveys that provide HIV diagnosis and CD4 testing with an immediate return of results. Accurate CD4 results improve HIV-positive participants’ clinical care and inform the effectiveness of HIV programs. Here, we present CD4 results from the PHIA surveys that were conducted in 11 countries in sub-Saharan Africa between 2015 and 2018. All of the HIV-positive participants and 2 to 5% of the HIV-negative participants were offered Pima CD4 (Abbott, IL, USA) point-of-care (POC) tests. The quality of the CD4 test was ensured by conducting instrument verification, comprehensive training, quality control, a review of testing errors and an analysis of unweighted CD4 data by HIV status, age, gender, and antiretroviral (ARV) treatment status. Overall, CD4 testing was completed for 23,085 (99.5%) of the 23,209 HIV-positive and 7,329 (2.7%) of the 270,741 negative participants in 11 surveys. The instrument error rate was 11.3% (range, 4.4% to 15.7%). The median CD4 values among HIV-positive and HIV-negative participants (aged 15+) were 468 cells/mm 3 (interquartile range [IQR], 307 to 654) and 811 cells/mm 3 (IQR, 647 to 1,013), respectively. Among the HIV-positive participants (aged 15+), those with detectable ARVs had higher CD4 values (508 cells/mm 3 ) than those with undetectable ARVs (385.5 cells/mm 3 ). Among the HIV-positive participants (aged 15+), 11.4% (2,528/22,253) had a CD4 value of less than 200 cells/mm 3 , and approximately half of them (1,225/2,528 = 48.5%) had detectable ARVs, whereas 51.5% (1,303/2,528) had no detectable ARVs ( P 〈 0.0001). We successfully implemented high quality POC CD4 testing using Pima instruments. Our data come from nationally representative surveys in 11 countries and provide unique insights regarding the CD4 distribution among HIV-positive individuals as well as the baseline CD4 values among HIV-negative individuals. IMPORTANCE The manuscript describes CD4 levels among HIV-positive individuals and baseline CD4 levels among HIV-negative individuals from 11 sub-Saharan countries, thereby highlighting the importance of CD4 markers in the context of the HIV epidemic. Despite increased ARV access in each country, advanced HIV disease (CD4  〈  200 cells/mm 3 ) persists among approximately 11% of HIV-positive individuals. Therefore, it is important that our findings are shared with the scientific community to assist with similar implementations of point-of-care testing and to conduct a review of HIV programmatic gaps.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2807133-5
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  • 7
    Online Resource
    Online Resource
    Public Library of Science (PLoS) ; 2014
    In:  PLoS ONE Vol. 9, No. 2 ( 2014-2-28), p. e83728-
    In: PLoS ONE, Public Library of Science (PLoS), Vol. 9, No. 2 ( 2014-2-28), p. e83728-
    Type of Medium: Online Resource
    ISSN: 1932-6203
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2014
    detail.hit.zdb_id: 2267670-3
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  • 8
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 9, No. 1 ( 2021-09-03)
    Abstract: The use of molecular-based diagnostic testing, such as the Luminex Verigene system, to rapidly identify the most common bacterial isolates from blood cultures is an important tool that reduces the duration of inappropriate antibiotics and decreases mortality. However, 5 to 15% of microorganisms recovered from blood culture are unable to be identified by the Verigene Gram-negative (BC-GN) or Gram-positive (BC-GP) assays. In this retrospective, observational study, we evaluate the identities and antimicrobial susceptibility patterns of 229 isolates that were not identified by either the Verigene BC-GN or BC-GP assay. The results presented here suggest that important, clinically relevant information about antimicrobial susceptibility patterns can still be inferred even when isolates are not identified by Verigene. We also examined changes in antibiotic use for patients with “unidentified” Verigene results at our institution and found that this subgroup represents an opportunity to optimize empirical antibiotic therapy. IMPORTANCE Rapid diagnostic testing to identify bloodstream pathogens has arisen as an important tool both to ensure adequate antimicrobial therapy is given early and to aid in antimicrobial stewardship by allowing for more rapid deescalation of inappropriate antimicrobial therapy. However, there is a paucity of data regarding the significance of isolates that are not able to be identified by rapid diagnostic testing. In this study, we report the identification to the species level and antimicrobial susceptibilities among isolates that were not identified by one such rapid diagnostic platform, the Verigene system. This study provides important insight into how a strong understanding of the strengths and limitations of a given rapid diagnostic platform, coupled with insight into local antibiotic susceptibility patterns, can allow for more nuanced and thoughtful empirical antibiotic selection.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2807133-5
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  • 9
    In: Journal of Medical Virology, Wiley, Vol. 87, No. 3 ( 2015-03), p. 388-400
    Abstract: Occult hepatitis B is characterized by the absence of hepatitis B surface antigen (HBsAg) but the presence of HBV DNA. Because diagnosis of hepatitis B virus (HBV) typically includes HBsAg detection, occult HBV remains largely undiagnosed. Occult HBV is associated with increased risk of hepatocellular carcinoma, reactivation to chronic HBV during immune suppression, and transmission during blood transfusion and liver transplant. The mechanisms leading to occult HBV infection are unclear, although viral mutations are likely a significant factor. In this study, sera from 394 HIV‐positive South Africans were tested for HBV DNA and HBsAg. For patients with detectable HBV DNA, the overlapping surface and polymerase open reading frames (ORFs) were sequenced. Occult‐associated mutations—those mutations found exclusively in individuals with occult HBV infection but not in individuals with chronic HBV infection from the same cohort or GenBank references—were identified. Ninety patients (22.8%) had detectable HBV DNA. Of these, 37 had detectable HBsAg, while 53 lacked detectable surface antigen. The surface and polymerase ORFs were cloned successfully for 19 patients with chronic HBV and 30 patients with occult HBV. In total, 235 occult‐associated mutations were identified. Ten occult‐associated mutations were identified in more than one patient. Additionally, 15 amino acid positions had two distinct occult‐associated mutations at the same residue. Occult‐associated mutations were common and present in all regions of the surface and polymerase ORFs. Further study is underway to determine the effects of these mutations on viral replication and surface antigen expression in vitro. J. Med. Virol. 87:388–400, 2015 . © 2014 Wiley Periodicals, Inc.
    Type of Medium: Online Resource
    ISSN: 0146-6615 , 1096-9071
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 752392-0
    detail.hit.zdb_id: 1475090-9
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  • 10
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 3 ( 2022-06-29)
    Abstract: Because syphilis is a public health concern, new strategies and tools for detecting active syphilis cases should be evaluated for future implementation. We assessed the laboratory performance of the DPP Syphilis Screen & Confirm rapid immunodiagnostic test (Chembio Diagnostics, Medford, NY, USA), using visual reading and the manufacturer’s electronic test microreader, for detection of treponemal and nontreponemal antibodies in 383 fully characterized stored serum specimens. We used the Treponema pallidum particle agglutination (TPPA) test and rapid plasma reagin (RPR) test as reference tests for the DPP Syphilis Screen & Confirm assay treponemal and nontreponemal components, respectively. The sensitivity values for treponemal antibody detection by electronic reader and visual interpretation were 83.2% and 85.9%, respectively, with 100% specificity. For nontreponemal antibody detection, the sensitivity values were 65.7% and 69.0% and the specificity values were 88.7% and 89.4% for electronic reader and visual interpretation, respectively. There was excellent correlation between visual interpretation and the microreader for either component (kappa coefficient, 0.953). When restricting the analysis to RPR titers of ≥1:8, the sensitivity was 96.9% for either reading method; numerical microreader values showed good correlation with RPR titers (Spearman rho of 0.77). The DPP Syphilis Screen & Confirm assay showed good performance, compared to reference syphilis tests, using serum. Field evaluation studies should be done to validate its use for detection of active cases and for monitoring of treated syphilis patients. IMPORTANCE Syphilis remains a public health problem; therefore, health systems must incorporate screening tools that allow a rapid and accurate diagnosis to provide adequate treatment. The DPP Syphilis Screen & Confirm Assay simultaneously detects treponemal and nontreponemal antibodies, emerging as an alternative for identifying cases in situations in which there is no infrastructure to perform conventional syphilis testing, but it is necessary to generate evidence regarding the performance of this technology in various scenarios. We found that the test performs well, compared to TPPA and RPR tests, using stored samples from participants at high risk of acquiring syphilis. Additionally, when the Chembio microreader was incorporated, similar results are obtained by the device, compared to those reported by trained laboratory professionals, and correlated with the semiquantitative results of the RPR test. We think that the use of the DPP Syphilis Screen & Confirm Assay with the microreader might help in detecting active syphilis cases and perhaps in monitoring treatment responses in the field.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2807133-5
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