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Journal of Clinical Microbiology

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https://www.readbyqxmd.com/read/28424254/a-european-multicentre-study-on-the-analytical-performance-of-the-veris-hiv-1-assay
#1
Patrick Braun, Rafael Delgado, Monica Drago, Diana Fanti, Hervé Fleury, Jörg Hofmann, Jacques Izopet, Ulrich Kalus, Alessandra Lombardi, MaAngeles Marcos, Davide Mileto, Karine Sauné, Siobhan O'Shea, Alfredo Pérez-Rivilla, John Ramble, Pascale Trimoulet, Jordi Vila, Duncan Whittaker, Alain Artus, Daniel Rhodes
The analytical performance of the VERIS HIV-1 Assay for use on the new, fully automated Beckman Coulter DxN VERIS Molecular Diagnostics System(¥) was evaluated at 10 European Virology laboratories. Precision, analytical sensitivity, performance with negative samples, linearity, and performance with HIV-1 Groups/Subtypes were evaluated. Precision for the 1 mL assay showed an SD of 0.14 log10 cp/mL or less and CV ≤6.1% for each level tested. The 0.175 mL assay showed an SD of 0.17 log10 cp/mL or less and CV ≤5...
April 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28424253/identification-of-acute-hiv-1-infection-by-hologic-aptima-hiv-1-rna-qualitative-assay
#2
Mark M Manak, Leigh Anne Eller, Jennifer Malia, Linda L Jagodzinski, Rapee Trichavaroj, Joseph Oundo, Cornelia Lueer, Fatim Cham, Mark de Souza, Nelson L Michael, Merlin L Robb, Sheila A Peel
The Hologic Aptima HIV-1 Qualitative RNA assay was used in a rigorous screening approach designed to identify individuals at the earliest stage of HIV-1 infection for enrollment into subsequent studies of cellular and viral events in early infection (RV217/Early Capture HIV Cohort - ECHO Study). Volunteers at high risk of HIV-1 infection were recruited from study sites in Thailand, Tanzania, Uganda and Kenya with high HIV-1 prevalence rates among the populations examined. Small volume blood samples were collected by finger-stick at twice-weekly intervals and tested by Aptima...
April 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28424252/comparison-of-saramis-4-12-and-ivd-3-0-vitek-ms-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-for-identification-of-mycobacteria-from-solid-and-liquid-culture-media
#3
Caroline Leyer, Guillaume Gregorowicz, Faiza Mougari, Laurent Raskine, Emmanuelle Cambau, Dominique de Briel
During the last decade, many publications studied the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for mycobacterial identification. Diverse and contradictory results indicated that optimal level for routine testing has not been reached yet. This work aimed to assess Vitek MS through two distinct versions, Saramis v4.12 RUO and the IVD v3.0, under conditions close to routine laboratory practice. Overall, 111 mycobacterial isolates were submitted to protein extraction and same spectra were matched against both databases...
April 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404684/the-immaculate-carbapenemase-study
#4
Kenneth S Thomson
Carbapenemase-producing organisms, or CPOs, are gram-negative pathogens that produce a transmissible carbapenemase and are typically resistant to most, sometimes all, antibiotics. We now face a global CPO pandemic of high mortality. In this issue of the Journal of Clinical Microbiology, J. A. Karlowsky et al (J. Clin Microbiol 55: xxxx-xxyy, 2017, https://doi.org/10.1128/JCM.02316-16) report the results of an extensive global surveillance study that provides much-needed information that enhances our understanding of carbapenemase-producing Enterobacteriaceae (CPE) and which will be valuable for the development of improved strategies for CPE control and therapy of infections...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404683/brain-eating-amoebae-predilection-sites-in-the-brain-and-disease-outcome
#5
Timothy Yu Yee Ong, Naveed Ahmed Khan, Ruqaiyyah Siddiqui
Acanthamoeba spp. and Balamuthia mandrillaris are causative agents of granulomatous amoebic encephalitis (GAE), while Naegleria fowleri causes primary amoebic meningoencephalitis (PAM). PAM is an acute infection lasting few days, while GAE is a chronic to subacute infection that can last up to several months. Here, we present a literature review of 86 case reports from 1968 to 2016 in order to explore affinity of these amoebae towards particular sites of the brain, diagnostic modalities, treatment options and the disease outcome in a comparative manner...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404682/comparison-of-the-eplex%C3%A2-respiratory-pathogen-panel-with-laboratory-developed-real-time-pcr-for-the-detection-of-respiratory-pathogens
#6
R H T Nijhuis, D Guerendiain, E C J Claas, K E Templeton
Infections of the respiratory tract can be caused by a diversity of pathogens, both viral and bacterial. Rapid microbiological diagnosis ensures appropriate antimicrobial therapy as well as effective implementation of isolation precautions. The ePlex® Respiratory Pathogen Panel (RP panel) is a novel molecular based assay, developed by GenMark Diagnostics Inc. (Carlsbad, California), to be performed within a single cartridge for the diagnosis of 25 respiratory pathogens (viral and bacterial). The objective of this study was to compare the performance of the RP panel with laboratory developed real-time PCR assays, using a variety of previously collected clinical respiratory specimens...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404681/non-pnca-gene-mutated-but-pyrazinamide-resistant-m-tuberculosis-why-is-that
#7
Jim Werngren, Erik Alm, Mikael Mansjö
Pyrazinamide (PZA) is a key component for the effective treatment of drug susceptible and PZA-susceptible MDR (MDR(PZA-S)) tuberculosis. pncA gene mutations are usually detected in a clear majority (>90%) of the PZA resistant strains but obviously not in all. Rapid and reliable PZA DST is critical whenever PZA will be used in the regimen, not least for the treatment of MDR(PZA-S) TB. In this study, we selected 26 PZA resistant isolates reported to carry a wildtype pncA gene. To confirm resistance, susceptibility testing was repeated to 100 mg/L and 200 mg/L PZA for all the 26 isolates and Sanger sequencing was repeated on the 18 isolates that remained PZA resistant...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404680/development-and-validation-of-a-lateral-flow-immunoassay-for-the-rapid-detection-of-ndm-producing-enterobacteriaceae
#8
Hervé Boutal, Thierry Naas, Karine Devilliers, Saoussen Oueslati, Laurent Dortet, Sandrine Bernabeu, Stéphanie Simon, Hervé Volland
The global spread of carbapenemase-producing Enterobacteriaceae (CPE) that are often resistant to most, if not all, classes of antibiotics is a major public health concern. NDM-1 carbapenemase is among the most worrisome carbapenemases given its rapid worldwide spread. We have developed and evaluated a lateral flow immunoassay (LFIA, called NDM LFIA) for rapid and reliable detection of NDM-like carbapenemase-producing Enterobacteriaceae from culture colonies.We evaluated the NDM LFIA using 175 reference enterobacterial isolates with characterized ß-lactamase gene content and 74 non-duplicate consecutive carbapenem-resistant clinical isolates referred for expertise to the French National Reference Center (NRC) for antibiotic resistance during a one-week period (in June 2016)...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404679/evaluation-of-taqman-array-card-tac-for-the-detection-of-central-nervous-system-infections-in-kenya
#9
Clayton O Onyango, Vladimir Loparev, Shirley Lidechi, Vinod Bhullar, D Scott Schmid, Kay Radford, Michael K Lo, Paul Rota, Barbara W Johnson, Jorge Munoz, Martina Oneko, Deron Burton, Carolyn M Black, John Neatherlin, Joel M Montgomery, Barry Fields
Infections of the central nervous system (CNS) are often acute with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan Array Card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid (CSF). The 21-pathogen TAC assays include two parasites (Balamuthia mandrillaris and Acanthamoeba), six bacterial pathogens (Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Mycoplasma pneumoniae, Mycobacterium tuberculosis, and Bartonella) and 13 viruses (parechovirus, dengue, nipah, varicella zoster, mumps, measles, lyssa, herpes simplex virus 1 and 2, Epstein Barr virus, enterovirus, cytomegalovirus and chikungunya)...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404678/antifungal-susceptibility-testing-of-aspergillus-spp-by-using-a-cci-based-maldi-tof-ms-method-appears-to-not-offer-benefit-over-the-traditional-broth-microdilution-testing
#10
Melissa R Gitman, Lisa McTaggart, Joanna Spinato, Rahgavi Poopalarajah, Erin Lister, Shahid Husain, Julianne V Kus
Aspergillus spp. cause serious invasive lung infections and Aspergillus fumigatus is the most commonly encountered clinically significant species. Voriconazole is considered to be the drug of choice for A. fumigatus infections, however rising resistance rates have been reported. We evaluated a MALDI-ToF MS-based method for the differentiation between wild type and non-wild type isolates of 20 Aspergillus spp. (including 3 isolates 2 A. ustus, and 1 A. calidoustus that were used as controls due their intrinsic low azole susceptibility with respect to the in vitro response to voriconazole)...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404677/comparison-of-two-whole-genome-sequencing-methods-for-analysis-of-three-methicillin-resistant-staphylococcus-aureus-outbreaks
#11
Scott A Cunningham, Nicholas Chia, Patricio R Jeraldo, Daniel J Quest, Julie A Johnson, Dave J Boxrud, Angela J Taylor, Jun Chen, Gregory D Jenkins, Travis M Drucker, Heidi Nelson, Robin Patel
Whole genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404676/multicenter-performance-assessment-of-the-carba-np-test
#12
Scott A Cunningham, Brandi Limbago, Maria Traczewski, Karen Anderson, Meredith Hackel, Janet Hindler, Dan Sahm, Efe Alyanak, Adrian Lawsin, Christopher A Gulvik, Tom J B de Man, Jayawant N Mandrekar, Audrey N Schuetz, Stephen Jenkins, Romney Humphries, Elizabeth Palavecino, Shawn Vasoo, Robin Patel
Eighty Gram-negative bacilli (54 Enterobacteriaceae and 26 non-fermenting Gram-negative bacilli), obtained from multiple institutions in the United States were distributed in a blinded manner to seven testing laboratories to compare the performance of a test for detection of carbapenemase production, the Carba NP test. The Carba NP test was performed by all laboratories, following the Clinical and Laboratory Standards Institute (CLSI) procedure. Site-versus-site comparisons demonstrated a high level of consistency for the Carba NP assay with just 3/21 site comparisons yielding a difference in sensitivity (p<0...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404675/nucleic-acid-extraction-from-residual-aptima-clinical-samples-evaluation-of-automated-platform-to-enhance-workflow
#13
Julia Mayes, Nadika Liyanarachchy, Michelle N D Balm
Transcription mediated amplification with the Aptima Combo 2 (AC2) assay (Hologic) is a highly sensitive and specific method for detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) from clinical samples collected in Aptima collection systems (1).….
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404674/laboratory-diagnosis-of-lassa-fever
#14
Vanessa Raabe, Jeffrey Koehler
Lassa virus remains an important cause of illness in West Africa and among travelers returning from this region with an acute febrile illness. The symptoms of Lassa fever can be non-specific and mimic those of other endemic infections, especially early in illness, making a clinical diagnosis difficult; therefore, laboratory testing is needed to confirm the diagnosis. Early identification of Lassa fever is crucial for maximizing the benefit of available antiviral therapy as treatment efficacy rapidly decreases following clinical onset of disease...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404673/update-on-malaria-diagnostics-and-test-utilization
#15
Blaine A Mathison, Bobbi S Pritt
Malaria is a potentially life-threatening disease requiring rapid diagnosis and treatment. Although microscopic examination of thick and thin blood films remains the gold standard for laboratory diagnosis, rapid antigen tests and nucleic acid amplification methods may also play a useful role for detection of acute infection. This review discusses the advantages and disadvantages of the commonly-used diagnostic methods and provides important practice points for optimal malaria test utilization.
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404672/increased-tuberculosis-patient-mortality-associated-with-mycobacterium-tuberculosis-mutations-conferring-resistance-to-second-line-antituberculous-drugs
#16
Sophia B Georghiou, Marva Seifert, Donald G Catanzaro, Richard S Garfein, Timothy C Rodwell
Rapid molecular diagnostics have great potential to limit the spread of multi- and extensively drug-resistant tuberculosis (M/XDR-TB). These technologies detect mutations in the Mycobacterium tuberculosis (Mtb) genome that confer phenotypic drug resistance. However, there is little data published regarding the relationships between the detected Mtb resistance mutations and M/XDR-TB treatment outcomes, limiting our current ability to exploit the full potential of molecular diagnostics. We analyzed clinical, microbiological and sequencing data for 451 patients and their clinical isolates collected in a multinational, observational cohort study to determine if there was an association between Mtb resistance mutations and patient mortality...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404671/an-update-on-antimicrobial-resistance-in-clostridium-difficile-resistance-mechanisms-and-antimicrobial-susceptibility-testing
#17
Zhong Peng, Dazhi Jin, Hyeun Bum Kim, Charles W Stratton, Bin Wu, Yi-Wei Tang, Xingmin Sun
Oral antibiotics such as metronidazole, vancomycin and fidaxomicin are therapies of choice for CDI. Several important mechanisms for C. difficile antibiotic resistance have been described; these include the acquisition of antibiotic resistance genes via transfer of mobile genetic elements, selective pressure in vivo resulting in gene mutations, altered expression of redox-active proteins, iron metabolism and DNA repair, as well as biofilm formation. This update summarizes new information published since 2010 on phenotypic and genotypic resistance mechanisms in C...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28381611/prospective-evaluation-of-resistanceplus%C3%A2-mg-a-new-multiplex-qpcr-assay-for-the-detection-of-mycoplasma-genitalium-and-macrolide-resistance
#18
S N Tabrizi, J Su, C S Bradshaw, C K Fairley, S Walker, L Y Tan, E Mokany, S M Garland
Mycoplasma genitalium is a significant pathogen for which first-line treatment is becoming less effective due to increased resistance to macrolides. As conventional culture and antimicrobial susceptibility testing is not feasible for routine detection of this pathogen, molecular markers such as detection of mutations in the 23S rRNA gene have been described to predict resistance. Recently a novel multiplex qPCR assay, ResistancePlus™ MG, has been described for the simultaneous detection of Mycoplasma genitalium and macrolide resistance...
April 5, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28381610/-identification-of-virulent-capnocytophaga-canimorsus-isolates-by-capsular-typing
#19
Estelle Hess, Francesco Renzi, Dunia Koudad, Mélanie Dol, Guy R Cornelis
Capnocytophaga canimorsus is a dog oral commensal that causes rare but severe infections in humans. C. canimorsus was recently shown to be endowed with a capsular polysaccharide implicated in the resistance to the innate immune system of the host. Here we developed the first C. canimorsus capsular serotyping scheme. We describe nine different serovars (A to I), which allowed to type 25/25 isolates from human infections but only 18/52 isolates from dog mouths, indicating that the repertoire of capsules in the species is vast...
April 5, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28381609/the-modified-carbapenem-inactivation-method-mcim-for-phenotypic-detection-of-carbapenemase-production-among-enterobacteriaceae
#20
Virginia M Pierce, Patricia J Simner, David R Lonsway, Darcie E Roe-Carpenter, J Kristie Johnson, William B Brasso, April M Bobenchik, Zabrina C Lockett, Angella Charnot-Katsikas, Mary Jane Ferraro, Richard B Thomson, Stephen G Jenkins, Brandi M Limbago, Sanchita Das
The ability of clinical microbiology laboratories to reliably detect carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is an important element of the effort to prevent and contain the spread of these pathogens and an integral part of antimicrobial stewardship. Existing methods each have limitations. A new, straightforward, inexpensive, and specific phenotypic method for the detection of carbapenemase production, the carbapenem inactivation method (CIM), was recently described. Here we describe a two-stage evaluation of a modified carbapenem inactivation method (mCIM), in which tryptic soy broth was substituted for water during the inactivation step and the length of this incubation was extended...
April 5, 2017: Journal of Clinical Microbiology
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