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Journal of Clinical Microbiology

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https://www.readbyqxmd.com/read/29212705/update-from-a-twelve-year-nationwide-fungaemia-surveillance-increasing-intrinsic-and-acquired-resistance-causes-concern
#1
K M T Astvad, H K Johansen, B L Røder, F S Rosenvinge, J D Knudsen, L Lemming, H C Schønheyder, R K Hare, L Kristensen, L Nielsen, J B Gertsen, E Dzajic, M Pedersen, C Østergård, B Olesen, T S Søndergaard, M C Arendrup
New data from the Danish National Fungaemia Surveillance 2012-15 is reported and epidemiological trends are investigated in a 12-year perspective (2004-15). During 2012-15, 1900 out of 1939 (98%) fungal bloodstream isolates were included. The average incidence was 8.4/100,000 inhabitants and this appears to be stabilizing after the increase to 10.1/100,000 in 2011. The incidence was higher in males than females (10.0 vs 6.8) and in patients above 50 years, mainly driven by an increasing incidence among 80-89 years old males (65...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212704/performance-of-ceftolozane-tazobactam-etest-mic-test-strips-and-disk-diffusion-as-compared-to-reference-broth-microdilution-for-beta-lactam-resistant-pseudomonas-aeruginosa-isolates
#2
Romney M Humphries, Janet A Hindler, Paul Magnano, Annie Wong-Beringer, Robert Tibbetts, Shelley A Miller
The performance of ceftolozane-tazobactam Etest (bioMerieux, Marcy L'Etoile, France), MIC Test Strips (MTS, Liofilchem, Italy) and disk diffusion (Hardy, Santa Ana, CA) were evaluated for a collection of 308 beta-lactam resistant isolates of Pseudomonas aeruginosa recovered from three institutions in Los Angeles, CA. Reference testing was performed by reference broth microdilution (rBMD). MIC and disk results were interpreted using Clinical and Laboratory Standards Institute breakpoints. Overall, 72.5% of isolates were susceptible to C/T by rBMD...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212703/diagnostic-assay-development-for-poliovirus-eradication
#3
Nancy Gerloff, Hong Sun, Mark Mandelbaum, Chelsea Maher, W Allan Nix, Sohail Zaidi, Shahzad Shaukat, Lerato Seakamela, Uma P Nalavade, Deepa K Sharma, M Steven Oberste, Everardo Vega
With poliovirus eradication nearing, few pockets of active wild poliovirus (WPV) transmission remain in the world. Intratypic differentiation (ITD) plays a crucial part in laboratory surveillance as the molecular detection method that can identify and distinguish wild and vaccine-like polioviruses isolated from acute flaccid paralysis cases or environmental sources. The need to detect new variants of WPV serotype 1 (WPV1), and the containment of all serotype 2 polioviruses (PV2) in 2015 required changes to the previous version of the method...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212702/multicenter-clinical-validation-of-a-cartridge-based-real-time-pcr-system-for-detection-of-coccidioides-spp-in-lower-respiratory-specimens
#4
Michael A Saubolle, Bette R Wojack, Anne M Wertheimer, Atehkeng Z Fuayagem, Stephen Young, Brian A Koeneman
Available methods for the diagnosis of coccidioidomycosis have significant shortcomings relative to accuracy and timeliness. We retrospectively and prospectively evaluated the diagnostic performance and reproducibility of a new cartridge-based real-time PCR assay for Coccidioides spp. directly in lower respiratory secretions and compared them to today's gold standard fungal culture. The GeneSTAT® Coccidioides Assay uses a 106-bp target sequence repeated multiple times (∼60X) per genome, thus, lowering the limit of detection (LOD) for extracted DNA to 10 genome equivalents/ml...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212701/multicenter-evaluation-of-the-eplex%C3%A2-respiratory-pathogen-panel-for-the-detection-of-viral-and-bacterial-respiratory-tract-pathogens-in-nasopharyngeal-swabs
#5
N Esther Babady, Matthew R England, Kristen L Jurcic Smith, Taojun He, Dona Saumya Wijetunge, Yi-Wei Tang, Robin R Chamberland, Marilyn Menegus, Ella M Swierkosz, Robert C Jerris, Wallace Greene
Background: The performance of the new ePlex® Respiratory Pathogen (RP) Panel (GenMark Diagnostics) for the simultaneous detection of 19 viruses (influenza A, influenza A H1, influenza A 2009 H1, influenza A H3, influenza B, adenovirus, coronaviruses [HKU1, OC43, NL63, 229E], human rhinovirus/enterovirus, human metapneumovirus, parainfluenza viruses 1, 2, 3 and 4, respiratory syncytial virus (RSV) [RSVA and RSV B]) and two bacteria (Mycoplasma pneumoniae and Chlamydia pneumoniae) was evaluated.Methods: Prospectively and retrospectively collected nasopharyngeal swab (NPS) specimens (n =2,908) were evaluated using the ePlex RP Panel with the bioMérieux/BioFire FilmArray® Respiratory Panel (BF RP) as the comparator method...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212700/the-alere%C3%A2-binaxnow%C3%A2-pneumococcal-urinary-antigen-test-diagnostic-sensitivity-for-adult-pneumococcal-pneumonia-and-relationship-to-specific-serotypes
#6
Hisashi Shoji, Arnau Domenech, Antonella Francesca Simonetti, Aida González, Dolores García, Meritxell Cubero, Sara Martí, Masayuki Maeda, Fe Tubau, Josefina Liñares, Maria Angeles Domínguez, Jordi Carratalà, Carmen Ardanuy
Little is known about the sensitivity of the BinaxNOW® pneumococcal urinary antigen (PUA) test for adult pneumococcal pneumonia caused by different serotypes. In this study, we aimed to analyze the trends in the sensitivity of the PUA test over a 15-year period (2001-2015), and to analyze its sensitivity for pneumococcal pneumonia caused by different serotypes. In total, we analyzed 1096 pneumococcal isolates from adults with pneumococcal pneumonia that had a PUA test performed at the onset of the episode...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212699/rapid-microarray-based-detection-of-rifampicin-isoniazid-and-fluoroquinolone-resistance-in-mycobacterium-tuberculosis-using-a-single-cartridge
#7
Juliane Havlicek, Beatrice Dachsel, Peter Slickers, Sönke Andres, Patrick Beckert, Silke Feuerriegel, Stefan Niemann, Matthias Merker, Ines Labugger
Rapid and robust identification of mutations in Mycobacterium tuberculosis complex (MTBC) strains mediating multidrug and extensively drug-resistant (M/XDR) phenotypes is crucial to combat the MDR tuberculosis (TB) epidemic. Currently available molecular TB drug susceptibility tests are either restricted to single targets/drugs (i.e. Xpert MTB/RIF) or aid the risk of cross-contaminations due to the design limitations of the open platform (i.e. line probe assays).With a good understanding of the technical and commercial boundaries we designed a test cartridge with an introduction of dried reagents, based on an oligonucleotide array, which has the ability to identify MTBC strains resistant to isoniazid, rifampicin and the fluoroquinolones...
December 6, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29187565/clinical-and-laboratory-standards-institute-clsi-evaluation-of-oxacillin-and-cefoxitin-disk-diffusion-and-minimum-inhibitory-concentration-breakpoints-for-detection-of-meca-mediated-oxacillin-resistance-in-staphylococcus-schleiferi
#8
H K Huse, S A Miller, S Chandrasekaran, J A Hindler, S D Lawhon, D A Bemis, L F Westblade, R M Humphries
Staphylococcus schleiferi is a beta-hemolytic, coagulase-variable colonizer of small animals that can cause opportunistic infections in humans. In veterinary isolates, mecA-mediated oxacillin resistance is significant, with reported resistance rates of >39%. The goal of this study was to evaluate oxacillin and cefoxitin disk diffusion (DD) and minimum inhibitory concentration (MIC) breakpoints for detection of mecA-mediated oxacillin resistance in 52 human and 38 veterinary isolates of S. schleiferi Isolates were tested on multiple brands of commercial media following Clinical and Laboratory Standards Institute (CLSI) methods...
November 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29187564/a-comparison-of-aspergillus-and-mucorales-pcr-testing-of-different-bal-fractions-from-patients-with-suspected-invasive-pulmonary-fungal-disease
#9
Jan Springer, P Lewis White, Johanna Kessel, Imke Wieters, Daniel Teschner, Daniel Korczynski, Tobias Liebregts, Oliver A Cornely, Stefan Schwartz, Thomas Elgeti, Lisa Meintker, Stefan W Krause, Raquel B Posso, Werner J Heinz, Sandra Fuhrmann, Jörg Janne Vehreschild, Hermann Einsele, Volker Rickerts, Juergen Loeffler
In patients with haematological malignancies, bronchoalveolar lavage fluid specimens (BALF) are commonly used for the diagnosis of mould infections. However, it is not clear whether the cellular pellet (P) or the supernatant fraction (S) of the BALF is optimal for molecular diagnostic testing. Thus, 99 BALF specimens from 96 haematology patients with or without allogeneic hematopoietic stem cell transplant were collected. Pellets and supernatants were processed alone and in combination (S/P) by two fungal-specific real-time PCR assays compliant with international recommendations...
November 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29187563/automated-interpretation-of-blood-culture-gram-stains-using-a-deep-convolutional-neural-network
#10
Kenneth P Smith, Anthony D Kang, James E Kirby
Microscopic interpretation of stained smears is one of the most operator-dependent and time intensive activities in the clinical microbiology laboratory. Here, we investigated application of an automated image acquisition and convolutional neural network (CNN)-based approach for automated Gram stain classification. Using an automated microscopy platform, uncoverslipped slides were scanned with a 40x dry objective, generating images of sufficient resolution for interpretation. We collected 25,488 images from positive blood culture Gram stains prepared during routine clinical workup...
November 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29187562/development-and-validation-of-a-real-time-pcr-assay-for-rapid-detection-of-candida-auris-from-surveillance-samples
#11
L Leach, Y Zhu, S Chaturvedi
Candida auris is an emerging multidrug-resistant yeast causing invasive healthcare-associated infection with high mortality worldwide. Rapid identification of C. auris is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan based real-time PCR assay targeting the internal transcribed spacer 2 (ITS2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive with the detection limit of one C...
November 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29187561/a-real-pain-diagnostic-quandaries-and-septic-arthritis
#12
Cristina Costales, Susan M Butler-Wu
Rapid diagnosis and treatment of an infected joint is paramount in preserving orthopedic function. Here, we present a brief review of the many challenges associated with the diagnosis of both septic arthritis and prosthetic joint infections. We will also discuss the many laboratory tests currently available to aid in accurate diagnosis of joint infection as well as emerging diagnostics that may have future utility in the diagnosis of these challenging clinical entities.
November 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167294/verification-of-ceftazidime-avibactam-and-ceftolozane-tazobactam-susceptibility-testing-methods-against-carbapenem-resistant-enterobacteriaceae-and-pseudomonas-aeruginosa
#13
Ryan K Shields, Cornelius J Clancy, A William Pasculle, Ellen G Press, Ghady Haidar, Binghua Hao, Liang Chen, Barry N Kreiswirth, M Hong Nguyen
Ceftazidime-avibactam and ceftolozane-tazobactam are newly approved agents for the treatment of infections caused by multidrug-resistant Gram negative bacteria. Resistance to both agents has been described clinically. Susceptibility testing for either agent is unavailable on automated systems. Our objective was to compare disk diffusion and Etest against standard broth microdilution (BMD) methods for testing ceftazidime-avibactam and ceftolozane-tazobactam against a diverse collection of carbapenem-resistant Enterobacteriaceae (CRE) and Pseudomonas aeruginosa (CRP), respectively...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167293/perioperative-antibiotic-prophylaxis-has-no-effect-on-time-to-positivity-and-proportion-of-positive-samples-a-cohort-study-of-64-cutibacterium-acnes-bone-and-joint-infections
#14
Alexia Anagnostopoulos, Daniel A Bossard, Bruno Ledergerber, Patrick O Zingg, Annelies S Zinkernagel, Christian Gerber, Yvonne Achermann
If a bone or joint infection is suspected, perioperative antibiotic prophylaxis is frequently withheld until the intraoperative microbiological sampling has been performed. This practice builds upon the hypothesis that perioperative antibiotics could render culture results negative and thus impede tailored antibiotic treatment of infections. We aimed to assess the influence of antibiotic prophylaxis within 30 to 60 minutes before surgery on time to positivity of microbiological samples and proportion of positive samples in Cutibacterium acnes bone and joint infections...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167292/clinical-evaluation-of-the-cepheid-xpert%C3%A2-tv-assay-for-detection-of-trichomonas-vaginalis-with-prospectively-collected-female-and-male-specimens
#15
Jane R Schwebke, C A Gaydos, T Davis, J Marrazzo, D Furgerson, S N Taylor, B Smith, L H Bachmann, R Ackerman, T Spurrell, D Ferris, C A Burnham, H Reno, J Lebed, D Eisenberg, P Kerndt, S Philip, J Jordan, N Quigley
Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and acquisition/transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA-cleared in the United States for detection of Trichomonas vaginalis (TV) in specimens from both women and men. This current study reports the results of a multicenter study recently conducted using the Xpert TV Assay to test specimens from both men and women. On-demand results were available in as little as 40 minutes for positive specimens...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167291/candida-auris-an-emerging-fungal-pathogen
#16
Emily S Spivak, Kimberly E Hanson
Candida auris has emerged globally as a multidrug resistant, healthcare-associated fungal pathogen. Recent reports highlight ongoing challenges due to organism misidentification, high rates of antifungal drug resistance and significant patient mortality. The predilection for intra and inter-healthcare facility transmission possibly promoted by virulence factors that facilitate skin colonization and environmental persistence is unique among Candida species. This minireview details the global emergence of C. auris and discusses issues relevant to clinical microbiology laboratories, hospital infection control and antimicrobial stewardship efforts...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167290/evaluation-of-whole-genome-sequencing-for-mycobacterial-species-identification-and-drug-susceptibility-testing-in-a-clinical-setting-a-large-scale-prospective-assessment-of-performance-against-line-probe-assays-and-phenotyping
#17
T Phuong Quan, Zharain Bawa, Dona Foster, Tim Walker, Carlos Del Ojo Elias, Priti Rathod, Zamin Iqbal, Phelim Bradley, Janet Mowbray, A Sarah Walker, Derrick W Crook, David H Wyllie, Timothy E A Peto, E Grace Smith
Use of whole genome sequencing (WGS) for routine Mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared performance of WGS and standard laboratory workflows prospectively, by parallel processing at a major Mycobacterial Reference Service over one year, for species identification, first-line Mycobacterium tuberculosis (TB) resistance prediction, and turnaround time. Of 2039 isolates with line-probe results for species identification, 74 (3.6%) failed sequencing or WGS species identification...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167289/evaluation-of-copan-eswab-transport-system-for-viability-of-pathogenic-fungi-using-modification-of-clinical-and-laboratory-standards-institute-m40-a2-document
#18
Bharat Gandhi, Richard Summerbell, Tony Mazzulli
The Copan ESwab system was evaluated for its ability to maintain viability of pathogenic fungi. Tests followed the Clinical and Laboratory Standards Institute (CLSI) M40 -A2 roll plate method at both room and refrigerator temperatures. A system was devised for standardizing homogeneous inoculum suspensions of variously sized conidia and sporangiospores of filamentous fungi. A total of 19 clinical and reference strains were standardized to 0.5 McFarland turbidity standard with a simple photometer. Corresponding optical densities were measured with a spectrophotometer...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167288/a-predominant-vntr-cluster-of-mycobacterium-tuberculosis-isolates-among-asylum-seekers-in-the-netherlands-and-denmark-deciphered-by-whole-genome-sequencing
#19
Rana Jajou, Albert de Neeling, Erik Michael Rasmussen, Anders Norman, Arnout Mulder, Rianne van Hunen, Gerard de Vries, Walid Haddad, Richard Anthony, Troels Lillebaek, Wim van der Hoek, Dick van Soolingen
Background: In many countries, Mycobacterium tuberculosis (Mtb) isolates are routinely subjected to VNTR typing to investigate Mtb transmission. Unexpectedly, cross border clusters have been identified among African refugees in the Netherlands and Denmark, although transmission in these countries was unlikely. Whole genome sequencing (WGS) was applied to analyse in depth transmission and assess the precision of VNTR typing.Methods: WGS was applied to 40 Mtb isolates from refugees in the Netherlands and Denmark, mostly from the Horn of Africa, sharing the exact same VNTR profile...
November 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29167287/u-s-high-level-isolation-unit-clinical-laboratory-capabilities-update
#20
Jocelyn J Herstein, Peter C Iwen, Katelyn C Jelden, Paul D Biddinger, Shawn G Gibbs, Aurora B Le, Angela Hewlett, John J Lowe
In late 2014, fifty-six hospitals in the US were designated by state and federal public health authorities as specially-designed high-level isolation units (HLIUs) equipped with advanced infrastructure, laboratory capabilities, and trained staff to care for patients with highly hazardous communicable diseases (HHCDs), such as Ebola. This survey describes clinical laboratory support capabilities of U.S. HLIUs, including the specific test menus that HLIUs have identified to safely manage HHCD patients, and the locations where such testing would be performed...
November 22, 2017: Journal of Clinical Microbiology
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