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Journal of Clinical Microbiology

James T Rudrik, Marty K Soehnlen, Michael J Perry, Maureen Sullivan, Wanda Reiter-Kintz, Philip A Lee, Denise Pettit, Anthony Tran, Erin Swaney
Matrix-assisted laser desorption ionization -- time of flight mass spectrometry (MALDI-TOF MS) sample preparation methods including the direct, on-plate formic acid, and ethanol/formic acid tube extraction were evaluated for their ability to render highly pathogenic organisms non-viable and safe for handling in a Biosafety Level-2 laboratory. Of these, the tube extraction procedure was the most successful, with none of the tested strains surviving this sample preparation method. Tube extracts from several agents of bioterrorism and their near neighbors were analyzed in an eight laboratory study to examine the utility of the Bruker Biotyper and Vitek MS MALDI-TOF MS systems and their IVD, research use only, and Security-Relevant databases, as applicable, to accurately identify these agents...
October 11, 2017: Journal of Clinical Microbiology
Mordechai Grupper, David P Nicolau, Jaber Aslanzadeh, Linda K Tanner, Joseph L Kuti
The effectiveness of antimicrobial binding resins present in blood culture (BC) bottles in removing meropenem, ceftolozane/tazobactam, and ceftazidime/avibactam is unknown. We assessed the time to detection (TTD) and growth of 2 Pseudomonas aeruginosa isolates in the presence of clinically meaningful concentrations of these antibiotics. BACTEC Plus Aerobic/F and BacT/ALERT FA Plus BC bottles were inoculated with one of two isolates (1 meropenem susceptible, 1 resistant), followed by fresh whole blood containing the peak, midpoint, or trough plasma concentrations for meropenem, ceftolozane/tazobactam, and ceftazidime/avibactam...
October 11, 2017: Journal of Clinical Microbiology
Remco P H Peters, Lindsey de Vos, Maduna Liteboho, Maanda Mudau, Jeffrey D Klausner, Marleen M Kock, Andrew Medina-Marino
The introduction of molecular diagnostic tests provides an important step to address the burden of sexually transmitted infections (STIs), especially Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV).….
October 11, 2017: Journal of Clinical Microbiology
Maan Hasso, Vanessa Porter, Andrew E Simor
Invasive infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are associated with considerable morbidity, mortality, and excess hospital costs (1-4).….
October 11, 2017: Journal of Clinical Microbiology
N J Polman, A Oštrbenk, L Xu, P J F Snijders, C J L M Meijer, M Poljak, D A M Heideman, M Arbyn
Human papillomavirus (HPV) testing is being increasingly incorporated into cervical cancer screening. VALGENT (VALidation of HPV GENotyping Tests) is a framework designed to evaluate the clinical performance of various HPV tests relative to the validated and accepted comparator test in a formalized and uniform manner. The aim of this study was to evaluate the clinical performance of the HPV-Risk assay within the VALGENT-3 panel, and to compare its performance to the clinically validated Hybrid Capture 2 assay (HC2)...
October 11, 2017: Journal of Clinical Microbiology
Jamie K Lemon, Pavel P Khil, Karen M Frank, John P Dekker
Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. Here, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection...
October 11, 2017: Journal of Clinical Microbiology
Virginia Balouz, Luciano J Melli, Romina Volcovich, Guillermo Moscatelli, Samanta Moroni, Nicolás González, Griselda Ballering, Margarita Bisio, Andrés Ciocchini, Carlos A Buscaglia, Jaime Altcheh
Chagas disease is caused by the protozoan parasite Trypanosoma cruzi. Assessment of parasitological cure upon treatment with available drugs relies on achieving consistent negative results in conventional parasitological and serological tests, which may take years to assess. Here, we evaluated the use of a recombinant T. cruzi antigen termed TSSA as an early serological marker of drug efficacy in T. cruzi-infected children. A cohort of 78 pediatric patients born to T. cruzi-infected mothers was included in this study...
October 4, 2017: Journal of Clinical Microbiology
Fernanda Esposito, Miriam R Fernandes, Ralf Lopes, Maria Muñoz, Caetano P Sabino, Marcos P Cunha, Ketrin C Silva, Rodrigo Cayô, Willames M Martins, Andrea M Moreno, Terezinha Knöbl, Ana C Gales, Nilton Lincopan
The emergence and rapid dissemination of colistin-resistant Escherichia coli carrying the plasmid-mediated mcr-1 gene has created an urgent need to develop specific screening methods. In this study, we evaluate four assays based on the inhibition of the MCR-1 activity by EDTA: i) a combined disk test (CDT) comparing the inhibition zones of colistin (10 μg) and colistin-plus-EDTA (10 μg-plus-100 mM); ii) reduction of colistin MIC (CMR) in the presence of EDTA (80 μg/mL); iii) a modified rapid polymyxin Nordmann/Poirel test (MPNP) and; iv) alteration of Zeta potential (RZP= ZP+EDTA/ZP-EDTA)...
October 4, 2017: Journal of Clinical Microbiology
Stephen R Reichley, Cynthia Ware, James Steadman, Patricia S Gaunt, Julio C García, Benjamin R LaFrentz, Anil Thachil, Geoffrey C Waldbieser, Cynthia B Stine, Cova R Arias, Thomas Loch, Timothy J Welch, Rocco C Cipriano, Terrence E Greenway, Lester H Khoo, David J Wise, Mark L Lawrence, Matt J Griffin
Edwardsiella spp. are responsible for significant losses in important wild and cultured fish species worldwide. Recent phylogenomic investigations have determined bacteria historically classified as E. tarda actually represent three genetically distinct, yet phenotypically ambiguous taxa with varying degrees of pathogenicity in different hosts. Previous recognition of these taxa was hampered by the lack of a distinguishing phenotypic character. Commercial test panel configurations are relatively constant over time, and as new species are defined, appropriate discriminatory tests may not be present in current test panel arrangements...
October 4, 2017: Journal of Clinical Microbiology
Bin Zhou, Yi-Mo Deng, John R Barnes, October Sessions, Tsui-Wen Chou, Malania Wilson, Thomas J Stark, Michelle Volk, Natalie Spirason, Rebecca A Halpin, Uma Sangumathi Kamaraj, Tao Ding, Timothy B Stockwell, Mirella Salvatore, Elodie Ghedin, Ian G Barr, David E Wentworth
Influenza A and B viruses are the causative agents of annual influenza epidemics that can be severe; influenza A viruses intermittently cause pandemics. Sequence information from influenza genomes is instrumental in determining mechanisms underpinning antigenic evolution and antiviral resistance. However, due to sequence diversity and the dynamics of influenza evolution, rapid and high-throughput sequencing of influenza viruses remains a challenge. We developed a single-reaction FluA/B Multiplex RT-PCR method that amplifies the most critical genomic segments (HA, NA, and M) of seasonal influenza A and B viruses for next-generation sequencing, regardless of viral types, subtypes, or lineages...
October 4, 2017: Journal of Clinical Microbiology
André Kriegeskorte, Evgeny A Idelevich, Andreas Schlattmann, Franziska Layer, Birgit Strommenger, Olivier Denis, Gavin K Paterson, Mark A Holmes, Guido Werner, Karsten Becker
Similar to mecA, mecC confers resistance against beta-lactams, leading to the phenotype of a methicillin-resistant Staphylococcus aureus (MRSA). However, mecC-harboring MRSA pose special difficulties in their detection. The aim of this study was to assess and compare different phenotypic systems for screening, identification, and susceptibility testing of mecC-positive MRSA isolates. A well-characterized collection of mecC-positive S. aureus isolates (n = 111) was used for evaluation. Routinely used approaches were studied to determine their suitability to correctly identify mecC-harboring MRSA including three (semi-)automated antimicrobial susceptibility testing (AST) systems and five selective chromogenic agar plates...
October 4, 2017: Journal of Clinical Microbiology
Gina Thomson, David Turner, William Brasso, Susan Kircher, Thierry Guillet, Kenneth Thomson
There is an urgent need for rapid, accurate detection and classification of carbapenemases. The current study evaluated the automated BD Phoenix™ CPO Detect and the manual bioMérieux RAPIDEC® CARBA NP for meeting these needs. Both tests were challenged with 294 Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii chosen to provide extreme diagnostic difficulty. Carbapenemases such as KPC, NMC-A, IMI, SME, NDM, SPM, IMP, VIM, OXA-23, 40, 48, 58, 72, 181, and 232 were produced by 243 isolates and 51 carbapenemase-negative isolates included porin mutants and producers of ESBLs, AmpCs, K1, and broad spectrum β-lactamases...
October 4, 2017: Journal of Clinical Microbiology
D Nikolic, S S Richter, K Asamoto, R Wyllie, R Tuttle, G W Procop
Background: There is substantial evidence that stool culture and parasitological examinations are of minimal-to-no value after three days of hospitalization. We implemented and studied the impact of a clinical decision support tool (CDST) to decrease unnecessary stool cultures (STCUL), ova/parasite (O&P) exams and Giardia/Cryptosporidium enzyme immunoassay screens (GC-EIA) for patients hospitalized > 3 days.Methods: We studied the frequency of these stool studies ordered ≤ 3days and > 3 days of hospitalization (i...
September 27, 2017: Journal of Clinical Microbiology
Lance R Peterson, Stephen A Young, Thomas E Davis, Zi-Xuam Wang, John Duncan, Christopher Noutsios, Oliver Liesenfeld, John C Osiecki, Michael A Lewinski
Nucleic acid amplification tests are reliable tools for the detection of toxigenic Clostridium difficile from unformed (liquid or soft) stool samples. The objective of this study was to evaluate performance of the cobas® Cdiff Test on the cobas® 4800 System using prospectively collected stool specimens from patients suspected of C. difficile infection (CDI). Performance of the cobas® Cdiff Test was compared to the combined results of direct and broth enriched toxigenic culture in a large, multicenter clinical trial...
September 27, 2017: Journal of Clinical Microbiology
Linda D Stewart, Lyanne McCallan, James McNair, Adrian McGoldrick, Rowan Morris, Jean-Louis Moyen, Lucía De Juan Ferré, Beatriz Romero, Elena Alonso, Sven D C Parsons, Paul Van Helden, Flábio R Araújo, Irene R Grant
A novel lateral flow immunochromatographic device (LFD) was evaluated in several veterinary diagnostic laboratories. It was confirmed to be specific for Mycobacterium bovis and M. caprae cells. The performance of the novel LFD was assessed relative to the confirmatory tests routinely applied after culture (spoligotyping or qPCR) in each laboratory; liquid (MGIT or BacT/Alert) and/or solid (Stonebrink, Coletsos or Lowenstein-Jensen) cultures were tested. In comparison to spoligotyping of acid-fast positive MGIT cultures, percentage agreement between positive LFD and spoligotyping results was excellent in two UK laboratories (97...
September 27, 2017: Journal of Clinical Microbiology
Bobbi S Pritt
Optimal laboratory test utilization is important for providing high quality clinical care and efficiently using limited health care resources. While microbiologists have long been advocates for appropriate laboratory test utilization, the wide-spread availability of electronic medical records capable of supporting clinician order entry and clinical decision support tools (CDSTs) have provided expanded opportunities for implementing effective, automated test stewardship protocols. In this issue of the Journal of Clinical Microbiology, D...
September 27, 2017: Journal of Clinical Microbiology
Kohei Uechi, Tatsuya Tada, Kayo Shimada, Kyoko Kuwahara-Arai, Momoko Arakaki, Takaaki Tome, Isamu Nakasone, Shiro Maeda, Teruo Kirikae, Jiro Fujita
The carbapenem inactivation method (CIM) and modified CIM (mCIM) are simple and economical phenotypic screening methods for detecting carbapenemase production in Gram-negative bacteria. Although the mCIM has been recommended by the Clinical and Laboratory Standards Institute, both the CIM and mCIM have limitations. This study describes another modified CIM. called the CIMTris, in which carbapenemase was extracted from bacteria with 0.5 M Tris-HCl (pH 7.6) buffer. The ability of the CIMTris to detect carbapenemase production was examined in Acinetobacter and Pseudomonas species...
September 27, 2017: Journal of Clinical Microbiology
Caroline Mahinc, Pierre Flori, Edouard Delaunay, Cécile Guillerme, Sana Charaoui, Hélène Raberin, Jamal Hafid, Coralie L'Ollivier
A study comparing the ICT (immunochromatography technology) Toxoplasma® IgG and IgM rapid diagnostic test (LDBIO Diagnostics, France) with the fully automated system, Architect, was performed on samples from university hospitals of Marseille and Saint-Etienne. A total of 767 prospective sera and 235 selected sera were collected. The panels were selected to test various IgG and IgM parameters. The reference technique Toxoplasma IgGII Western Blot (LDBIO Diagnostics) was used to confirm the IgG results and commercial kits Platelia Toxo IgM (Biorad) and Toxo-ISAgA (bioMérieux) were used in Saint-Etienne and Marseille respectively, as the IgM reference technique...
September 27, 2017: Journal of Clinical Microbiology
Lauren A Darling, Ann M Evans, Kathleen A Stellrecht, Seela M Nattanmai, Clemente I Montero
The global emergence of carbapenem resistant Enterobacteriaceae (CRE) is a major concern for public health.….
September 20, 2017: Journal of Clinical Microbiology
Edith Erika Machowski, Bavesh Davandra Kana
Molecular diagnostics have revolutionized the management of health care through enhanced detection of disease or infection and effective engagement into care. In recognition of this, the World Health Organization approved the rollout out of nucleic acid amplification technologies for identification of Mycobacterium tuberculosis using platforms such as GeneXpert MTB/RIF, the GenoType MTBDRplus Line Probe Assay and more recently, GeneXpert MTB/RIF Ultra. These assays can simultaneously detect tuberculosis infection and assess rifampicin resistance...
September 20, 2017: Journal of Clinical Microbiology
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