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Performance and Implementation Evaluation of the Abbott BinaxNOW Rapid Antigen Test in a High-throughput Drive-through Community Testing Site in Massachusetts J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-23 Nira R. Pollock, Jesica R. Jacobs, Kristine Tran, Amber E. Cranston, Sita Smith, Claire Y. O’Kane, Tyler J. Roady, Anne Moran, Alison Scarry, Melissa Carroll, Leila Volinsky, Gloria Perez, Pinal Patel, Stacey Gabriel, Niall J. Lennon, Lawrence C. Madoff, Catherine Brown, Sandra C. Smole
Background: Rapid diagnostic tests (RDTs) for SARS-CoV-2 antigens (Ag) that can be performed at point-of-care (POC) can supplement molecular testing and help mitigate the COVID-19 pandemic. Deployment of an Ag RDT requires an understanding of its operational and performance characteristics under real-world conditions and in relevant subpopulations. We evaluated the Abbott BinaxNOW™ COVID-19 Ag Card
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Assessment of S1, S2 and NCP-specific IgM, IgA, and IgG antibody kinetics in acute SARS-CoV-2 infection by a microarray and twelve other immunoassays J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Georg Semmler, Marianna Theresia Traugott, Marianne Graninger, Wolfgang Hoepler, Tamara Seitz, Hasan Kelani, Mario Karolyi, Erich Pawelka, Sara Aragón de La Cruz, Elisabeth Puchhammer-Stöckl, Stephan Walter Aberle, Karin Stiasny, Alexander Zoufaly, Judith Helene Aberle, Lukas Weseslindtner
In this study, we comprehensively analyzed multispecific antibody kinetics of different immunoglobulins in hospitalized patients with acute SARS-CoV-2 infection. Three-hundred-fifty-four blood samples longitudinally obtained from 81 IgG seroconverting CoVID-19 patients were quantified for spike (S)1, S2, and nucleocapsid protein (NCP)- specific IgM, IgA, IgG, and total Ig antibodies using a microarray
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The Need for Dedicated Microbiology Leadership in the Clinical Microbiology Laboratory J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-17 Linoj P. Samuel, Glen T. Hansen, Colleen S. Kraft, Bobbi S. Pritt
Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, healthcare-acquired infections, antibiotic-resistant organisms and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed
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Mycoplasma hyopneumoniae surveillance in pig populations: Establishing sampling guidelines for detection in growing pigs J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-17 Maria Jose Clavijo, Dapeng Hu, Seth Krantz, Jean Paul Cano, Thairê Pereira Maróstica, Alexandra Henao-Diaz, Ana Paula S Poeta Silva, Deanne Hemker, Edgar Tapia, Silvia Zimmerman, Eduardo Fano, Dale Polson, Robert Fitzgerald, Alexander Tucker, Rodger Main, Chong Wang, Jeffrey J Zimmerman, Marisa L Rotolo
Ante-mortem detection of Mycoplasma hyopneumoniae (MHP) infection in swine production systems has relied on antibody testing, but the availability of tests based on DNA detection and novel diagnostic specimens, e.g., tracheal swabs and oral fluids, have the potential to improve MHP surveillance. A field study was performed over a 14-week period during which ten pigs in one pen at the center of a room
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Comparable specimen collection from both ends of at-home mid-turbinate swabs J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-17 Melissa Truong, Brian Pfau, Evan McDermot, Peter D. Han, Elisabeth Brandstetter, Matthew Richardson, Ashley E. Kim, Mark J. Rieder, Helen Y. Chu, Janet A. Englund, Deborah A. Nickerson, Jay Shendure, Christina M. Lockwood, Eric Q. Konnick, Lea M. Starita
At-home respiratory specimen collection for pathogen testing enables community sampling.…
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Multicenter Evaluation of Processing and Analysis of CAP Proficiency Testing Samples by Laboratory Automation J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-17 N. Esther Babady, Lori Bourassa, Carey-Ann D. Burnham, Mark Fisher, Erin McElvania, Christopher R. Polage, Julie Ribes
To maintain their Clinical Laboratory Improvement Amendment (CLIA) accreditation, clinical laboratories are expected to enroll in proficiency testing (PT) to confirm that all parts of the diagnostic testing process perform as expected (1).…
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Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Heba H. Mostafa, Karen C. Carroll, Rachel Hicken, Gregory J. Berry, Ryhana Manji, Elizabeth Smith, Jennifer L. Rakeman, Randal C. Fowler, Mindy Leelawong, Susan M. Butler-Wu, David Quintero, Minette Umali-Wilcox, Robert W. Kwiatkowski, David H. Persing, Fred Weir, Michael J. Loeffelholz, Alexander J. McAdam
With the approach of respiratory virus season in the Northern Hemisphere, clinical microbiology and public health laboratories will need rapid diagnostic assays to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from influenza virus and respiratory syncytial virus (RSV) infections for diagnosis and surveillance. In this study, the clinical performance of the Xpert Xpress SARS-CoV-2/Flu/RSV
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Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag Card J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Garrett A. Perchetti, Meei-Li Huang, Margaret G. Mills, Keith R. Jerome, Alexander L. Greninger, Michael J. Loeffelholz
Multiple rapid antigen (Ag) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have recently received emergency-use authorization (EUA) from the U.S. Food and Drug Administration (FDA). Although less sensitive than molecular detection methods, rapid antigen testing offers the potential for inexpensive, quick, decentralized testing. Robust analytical sensitivity data in comparison
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Variable Sensitivity of SARS-CoV-2 Molecular Detection in European Expert Laboratories: External Quality Assessment, June and July 2020 J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Carlo Fischer, Ramona Mögling, Angeliki Melidou, Arne Kühne, Edmilson F. Oliveira-Filho, Thorsten Wolff, Janine Reiche, Eeva Broberg, Christian Drosten, Adam Meijer, Katrin Leitmeyer, Jan Felix Drexler, Chantal B. E. M. Reusken, Michael J. Loeffelholz
During the ongoing coronavirus disease 2019 (COVID-19) outbreak, robust detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key element for clinical management and to interrupt transmission chains. We organized an external quality assessment (EQA) of molecular detection of SARS-CoV-2 for European expert laboratories. An EQA panel composed of 12 samples, containing either
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Distribution of Novel Og Types in Shiga Toxin-Producing Escherichia coli Isolated from Healthy Cattle J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Thi Thu Huong Nguyen, Atsushi Iguchi, Ritsuko Ohata, Hisahiro Kawai, Tadasuke Ooka, Hiroshi Nakajima, Sunao Iyoda, Brad Fenwick
Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. Although most cases of STEC infection in humans are due to O157 and non-O157 serogroups, there are also reports of infection with STEC strains that cannot be serologically classified into any O serogroup (O-serogroup untypeable [OUT]). Recently, it has become clear that even OUT strains can be subclassified based on the
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Laboratory Automation in the Microbiology Laboratory: an Ongoing Journey, Not a Tale? J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Stefan Zimmermann, Erin McElvania
Clinical chemistry laboratories implemented fully automated devices decades before microbiologists started their subtle approaches to follow. Meanwhile several papers have been published about reduced time to reports, faster workflows, and increased sensitivity as results of lab automation. While the journey of automating microbiology workflows step by step was fascinating and beneficial, monetary
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Study To Evaluate the Performance of a Point-of-Care Whole-Blood HIV Viral Load Test (SAMBA II HIV-1 Semi-Q Whole Blood) J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Gary Brook, Tetiana Stepchenkova, Innocent M. Ali, Sandra Chipuka, Neha Goel, Helen Lee, Angela M. Caliendo
Remote areas of many low and middle income (LMI) countries have poor access to HIV viral load (HIV VL) testing. The SAMBA II (simple amplification-based assay) Semi-Q whole-blood test (Diagnostics for the Real World [DRW], Cambridge, UK) is a point-of-care assay, which uses leucodepletion technology to allow whole-blood testing in remote settings. A total of 1,540 consecutive HIV-positive clinic patients
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Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011 to 2019 J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Justine Schaeffer, Steliana Huhulescu, Anna Stoeger, Franz Allerberger, Werner Ruppitsch, John P. Dekker
Diphtheria is a vaccine-preventable disease with a high potential for reemergence. One of its causative agents is Corynebacterium diphtheriae, with some strains producing diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory tract or from skin infections. The aim of this study was to investigate the genetic diversity of these C
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Multicenter Evaluation of the Clinical Performance and the Neutralizing Antibody Activity Prediction Properties of 10 High-Throughput Serological Assays Used in Clinical Laboratories J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 C. Therrien, B. Serhir, M. Bélanger-Collard, J. Skrzypczak, D. K. Shank, C. Renaud, J. Girouard, V. Loungnarath, M. Carrier, G. Brochu, F. Tourangeau, B. Gilfix, A. Piche, R. Bazin, R. Guérin, M. Lavoie, V. Martel-Laferrière, C. Fortin, A. Benoit, D. Marcoux, N. Gauthier, A. M. Laumaea, R. Gasser, A. Finzi, M. Roger, Yi-Wei Tang
As the coronavirus disease 2019 (COVID-19) pandemic second wave is emerging, it is of the upmost importance to screen the population immunity in order to keep track of infected individuals. Consequently, immunoassays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high specificity and positive predictive values are needed to obtain an accurate epidemiological picture. As more
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Multicenter Evaluation of the Unyvero Platform for Testing Bronchoalveolar Lavage Fluid J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Matthias Klein, Johannes Bacher, Sandra Barth, Faranak Atrzadeh, Katja Siebenhaller, Inês Ferreira, Stephan Beisken, Andreas E. Posch, Karen C. Carroll, Richard G. Wunderink, Chao Qi, Fann Wu, Dwight J. Hardy, Robin Patel, Matthew D. Sims, Erin McElvania
Bronchoalveolar lavage (BAL) culture is a standard, though time-consuming, approach for identifying microorganisms in patients with severe lower respiratory tract (LRT) infections. The sensitivity of BAL culture is relatively low, and prior antimicrobial therapy decreases the sensitivity further, leading to overuse of empirical antibiotics. The Unyvero LRT BAL Application (Curetis GmbH, Germany) is
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Pooled Saliva Specimens for SARS-CoV-2 Testing J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Bidisha Barat, Sanchita Das, Valeria De Giorgi, David K. Henderson, Stacy Kopka, Anna F. Lau, Tracey Miller, Theresa Moriarty, Tara N. Palmore, Shari Sawney, Chris Spalding, Patricia Tanjutco, Glenn Wortmann, Adrian M. Zelazny, Karen M. Frank, Alexander J. McAdam
We evaluated saliva (SAL) specimens for SARS-CoV-2 reverse transcriptase PCR (RT-PCR) testing by comparison of 459 prospectively paired nasopharyngeal (NP) or midturbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (n = 380) and in the emergency department (ED) (n = 69). The
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Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium canis J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Wen Jiang, Dawn M. Roellig, Yaqiong Guo, Na Li, Yaoyu Feng, Lihua Xiao, Bobbi S. Pritt
Cryptosporidium canis is an important cause of cryptosporidiosis in canines and humans. Studies of the transmission characteristics of C. canis are currently hampered by the lack of suitable subtyping tools. In this study, we conducted a genomic survey of the pathogen and developed a subtyping tool targeting the partial 60-kDa glycoprotein gene (gp60). Seventy-six isolates previously identified as
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Development of an Indirect Chemiluminescence Immunoassay Using a Multiepitope Recombinant Protein To Specifically Detect Antibodies against Foot-and-Mouth Disease Virus Serotype O in Swine J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Wei Liu, Junjun Shao, Guanglei Zhang, Yanyan Chang, Sudan Ge, Yue Sun, Zhan Gao, Huiyun Chang, Brad Fenwick
Foot-and-mouth disease virus (FMDV) has led to serious losses in animal husbandry worldwide. Seromonitoring of FMDV postvaccination is important for the control and eradication of foot-and-mouth disease (FMD) in regions and countries where vaccination is widespread. However, many commercial kits present high false-positive rates. In this study, a multiepitope-based indirect chemiluminescence immunoassay
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Evaluation of Optimal Blood Culture Incubation Time To Maximize Clinically Relevant Results from a Contemporary Blood Culture Instrument and Media System J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Eric M. Ransom, Zahra Alipour, Meghan A. Wallace, Carey-Ann D. Burnham, Patricia J. Simner
Timely diagnosis of microorganisms in blood cultures is necessary to optimize therapy. Although blood culture media and systems have evolved for decades, the standard interval for incubation prior to being discarded as negative has remained 5 days. Here, we evaluated the optimal incubation time for the BacT/Alert Virtuo blood culture detection system (bioMérieux) using FA Plus (aerobic) and FN Plus
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High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Anne Jamet, Julien Guglielmini, Bryan Brancotte, Mathieu Coureuil, Daniel Euphrasie, Julie Meyer, Johanna Roux, Jean-Philippe Barnier, Emmanuelle Bille, Agnès Ferroni, Jean-François Magny, Christine Bôle-Feysot, Alain Charbit, Xavier Nassif, Sylvain Brisse, Alexander Mellmann
Staphylococcus epidermidis is a pathogen emerging worldwide as a leading cause of health care-associated infections. A standardized high-resolution typing method to document transmission and dissemination of multidrug-resistant S. epidermidis strains is needed. Our aim was to provide a core genome multilocus sequence typing (cgMLST) scheme for S. epidermidis to improve the international surveillance
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Evaluation of the Dynamiker Cryptococcal Antigen Lateral Flow Assay for the Diagnosis of HIV-Associated Cryptococcosis J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Richard Kwizera, Denis Omali, Kiiza Tadeo, John Kasibante, Morris K. Rutakingirwa, Enock Kagimu, Kenneth Ssebambulidde, Darlisha A. Williams, Joshua Rhein, David Boulware, David B. Meya, Kimberly E. Hanson
Cryptococcal meningitis is a leading cause of meningitis in sub-Saharan Africa. Given the need for rapid point-of-care testing, we evaluated the diagnostic performance of the Dynamiker cryptococcal antigen (CrAg) lateral flow assay (LFA). We assessed the diagnostic performance of the Dynamiker CrAg LFA compared to the IMMY CrAg LFA as the reference standard. We tested 150 serum, 115 plasma, and 100
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Molecular and Epidemiological Characterization of Toxigenic and Nontoxigenic Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, and Corynebacterium ulcerans Isolates Identified in Spain from 2014 to 2019 J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Andreas Hoefer, Despina Pampaka, Silvia Herrera-León, Sonia Peiró, Sarai Varona, Noemí López-Perea, Josefa Masa-Calles, Laura Herrera-León, Daniel J. Diekema
This study examines the microbiological and epidemiological characteristics of toxigenic and nontoxigenic Corynebacterium isolates submitted to the national reference laboratory in Spain, between 2014 and 2019, in order to describe the current situation and improve our knowledge regarding these emerging pathogens. Epidemiological information was extracted from the Spanish Surveillance System. Microbiological
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A Short-Tandem-Repeat Assay (MmySTR) for Studying Genetic Variation in Madurella mycetomatis J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Bertrand Nyuykonge, Kimberly Eadie, Willemien H. A. Zandijk, Sarah A. Ahmed, Marie Desnos-Ollivier, Ahmed H. Fahal, Sybren de Hoog, Annelies Verbon, Wendy W. J. van de Sande, Corné H. W. Klaassen, Kimberly E. Hanson
Madurella mycetomatis is the major causative agent of eumycetoma, a neglected tropical infection characterized by painless subcutaneous lesions, inflammation, and grains draining from multiple sinuses. To study the epidemiology of mycetoma, a robust discriminatory typing technique is needed. We describe the use of a short-tandem-repeat assay (MmySTR) for genotyping of M. mycetomatis isolates predominantly
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Xpert MTB/XDR: a 10-Color Reflex Assay Suitable for Point-of-Care Settings To Detect Isoniazid, Fluoroquinolone, and Second-Line-Injectable-Drug Resistance Directly from Mycobacterium tuberculosis-Positive Sputum J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Yuan Cao, Heta Parmar, Rajiv L. Gaur, Deanna Lieu, Shobana Raghunath, Nova Via, Simone Battaglia, Daniela M. Cirillo, Claudia Denkinger, Sophia Georghiou, Robert Kwiatkowski, David Persing, David Alland, Soumitesh Chakravorty, Christine Y. Turenne
We describe the design, development, analytical performance, and a limited clinical evaluation of the 10-color Xpert MTB/XDR assay (CE-IVD only, not for sale in the United States). This assay is intended as a reflex test to detect resistance to isoniazid (INH), fluoroquinolones (FLQ), ethionamide (ETH), and second-line injectable drugs (SLIDs) in unprocessed sputum samples and concentrated sputum sediments
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Frequency of Positive Aspergillus Tests in COVID-19 Patients in Comparison to Other Patients with Pulmonary Infections Admitted to the Intensive Care Unit J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Erlangga Yusuf, Alieke Vonk, Johannes P. C. van den Akker, Lonneke Bode, Gregorius J. Sips, Bart J. A. Rijnders, Jurriaan de Steenwinkel, Nelianne J. Verkaik, Marius Vogel, Menno van der Eerden, Mireille van Westreenen, Kimberly E. Hanson
The aim of this study was to describe the frequency of positive Aspergillus tests in COVID-19 patients and investigate the association between COVID-19 and a positive Aspergillus test result. We compared the proportion of positive Aspergillus tests in COVID-19 patients admitted to the intensive care unit (ICU) for >24 h with two control groups: patients with community-acquired pneumonia with (i) a
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Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Trinad Chakraborty, Mustafa Sadek, Yancheng Yao, Can Imirzalioglu, Roger Stephan, Laurent Poirel, Patrice Nordmann, Daniel J. Diekema
A series of clinical NDM-5-producing Escherichia coli isolates obtained from two surveillance networks for carbapenem-producing Enterobacterales from 2018 to 2019, namely, Switzerland (NARA) and Germany (SurvCARE), were analyzed. The 33 NDM-5-producing E. coli isolates were highly resistant to β-lactams, including novel β-lactam/β-lactamase inhibitor combinations (ceftazidime-avibactam, imipenem-relebactam
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The Pediatric Endotracheal Aspirate Culture Survey (PETACS): Examining Practice Variation across Pediatric Microbiology Laboratories in the United States J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Andrea M. Prinzi, Sarah K. Parker, Donna J. Curtis, Sonja I. Ziniel, Christine Y. Turenne
In the absence of evidence-based laboratory guidelines, the workup and interpretation of tracheal aspirate (TA) cultures remains controversial and confusing within the fields of clinical microbiology, infectious diseases, and critical care. Between 22 January and 24 February 2020, we conducted a national, web-based survey of microbiology laboratory personnel in free-standing pediatric hospitals and
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Comparative Analytical Evaluation of Four Centralized Platforms for the Detection of Mycobacterium tuberculosis Complex and Resistance to Rifampicin and Isoniazid J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Margaretha de Vos, Lesley Scott, Anura David, Andre Trollip, Harald Hoffmann, Sophia Georghiou, Sergio Carmona, Morten Ruhwald, Wendy Stevens, Claudia M. Denkinger, Samuel G. Schumacher, Melissa B. Miller
Failure to rapidly identify drug-resistant tuberculosis (TB) increases the risk of patient mismanagement, the amplification of drug resistance, and ongoing transmission. We generated comparative analytical data for four automated assays for the detection of TB and multidrug-resistant TB (MDR-TB): Abbott RealTime MTB and MTB RIF/INH (Abbott), Hain Lifescience FluoroType MTBDR (Hain), BD Max MDR-TB (BD)
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Development of a Duplex Real-Time PCR Assay for the Differentiation of Blastomyces dermatitidis and Blastomyces gilchristii and a Retrospective Analysis of Culture and Primary Specimens from Blastomycosis Cases from New York (2005 to 2019) J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Mitchell Kaplan, YanChun Zhu, Julianne V. Kus, Lisa McTaggart, Vishnu Chaturvedi, Sudha Chaturvedi, Kimberly E. Hanson
Blastomycosis due to Blastomyces dermatitidis and Blastomyces gilchristii is a significant cause of respiratory mycoses in North America with occasional reported outbreaks. We developed a highly sensitive, specific, and reproducible TaqMan duplex real-time PCR assay for the differentiation of B. dermatitidis and B. gilchristii. The new assay permitted retrospective analysis of Blastomyces cultures
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Establishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Hauke Tönnies, Karola Prior, Dag Harmsen, Alexander Mellmann, John P. Dekker
The environmental bacterium Pseudomonas aeruginosa, particularly multidrug-resistant clones, is often associated with nosocomial infections and outbreaks. Today, core genome multilocus sequence typing (cgMLST) is frequently applied to delineate sporadic cases from nosocomial transmissions. However, until recently, no cgMLST scheme for a standardized typing of P. aeruginosa was available. To establish
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Benefits Derived from Full Laboratory Automation in Microbiology: a Tale of Four Laboratories J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Karissa Culbreath, Heather Piwonka, John Korver, Mir Noorbakhsh, Erin McElvania
Automation in clinical microbiology is starting to become more commonplace and reportedly offers several advantages over the manual laboratory. Most studies have reported on the rapid turnaround times for culture results, including times for identification of pathogens and their respective antimicrobial susceptibilities, but few have studied the benefits from a laboratory efficiency point of view.
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Multicenter Evaluation of Ceftazidime-Avibactam Susceptibility Testing of Enterobacterales and Pseudomonas aeruginosa on the Vitek 2 System J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Romney Humphries, Shelley Campeau, Thomas E. Davis, Kristin J. Nagaro, Vincent J. LaBombardi, Simone Franklin, Lisa Heimbach, Hari P. Dwivedi, Patricia J. Simner
In this multisite study, Vitek 2 AST-Gram-Negative Ceftazidime/Avibactam test results for 1,073 isolates (866 Enterobacterales and 207 Pseudomonas aeruginosa) were compared to the Clinical and Laboratory Standards Institute (CLSI) broth microdilution (BMD) reference method. The results were analyzed for essential agreement (EA), category agreement (CA), major error rates, and very major error rates
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Potential Contributions of Anaerobes in Cystic Fibrosis Airways J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Christina S. Thornton, Michael G. Surette, Colleen Suzanne Kraft
Cystic fibrosis (CF) is the most common, lethal genetic disease among the Caucasian population. The leading cause of mortality is recurrent acute exacerbations resulting in chronic airway inflammation and subsequent downward progression of pulmonary function. Traditionally, these periods of clinical deterioration have been associated with several principal pathogens. However, a growing body of literature
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Tuberculous Meningitis: Pathogenesis, Immune Responses, Diagnostic Challenges, and the Potential of Biomarker-Based Approaches J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Charles M. Manyelo, Regan S. Solomons, Gerhard Walzl, Novel N. Chegou, Colleen Suzanne Kraft
Tuberculous meningitis (TBM) is the most devastating form of tuberculosis (TB), causing high mortality or disability. Clinical management of the disease is challenging due to limitations of the existing diagnostic approaches. Our knowledge on the immunology and pathogenesis of the disease is currently limited. More research is urgently needed to enhance our understanding of the immunopathogenesis of
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Comparison of ZMAC and MARC-145 Cell Lines for Improving Porcine Reproductive and Respiratory Syndrome Virus Isolation from Clinical Samples J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Wannarat Yim-im, Haiyan Huang, Jie Park, Chong Wang, Gabriela Calzada, Phillip Gauger, Karen Harmon, Rodger Main, Jianqiang Zhang, Brad Fenwick
The MARC-145 cell line is commonly used to isolate porcine reproductive and respiratory syndrome virus (PRRSV) for diagnostics, research, and vaccine production, but it yields frustratingly low success rates of virus isolation (VI). The ZMAC cell line, derived from porcine alveolar macrophages, has become available, but its utilization for PRRSV VI from clinical samples has not been evaluated. This
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Diagnostic Accuracy Study of a Novel Blood-Based Assay for Identification of Tuberculosis in People Living with HIV J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Erik Södersten, Stefano Ongarello, Anna Mantsoki, Romain Wyss, David H. Persing, Sara Banderby, Linda Strömqvist Meuzelaar, Jacqueline Prieto, Devasena Gnanashanmugam, Purvesh Khatri, Samuel G. Schumacher, Claudia M. Denkinger, Melissa B. Miller
A nonsputum triage test to rule out tuberculosis (TB) disease is a WHO high-priority diagnostic, and a combinatory score based on a 3-gene host signature has shown promise in discriminating TB from other illnesses. We evaluated the accuracy of an early-prototype cartridge assay (“Xpert MTB Host Response” or Xpert-MTB-HR-Prototype) of this 3-gene signature on biobanked blood samples from people living
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SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-18 Mujahed I. Mustafa, Abdelrafie M. Makhawi, Colleen Suzanne Kraft
Infectious diseases are one of the most intimidating threats to human race, responsible for an immense burden of disabilities and deaths. Rapid diagnosis and treatment of infectious diseases offers a better understanding of their pathogenesis. According to the World Health Organization, the ideal approach for detecting foreign pathogens should be rapid, specific, sensitive, instrument-free, and cost-effective
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Copan eNAT Transport System to Address Challenges in COVID-19 Diagnostics in Regions with Limited Testing Access J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-12 Melissa Richard-Greenblatt, Courtney E. Comar, Laurence Flevaud, Marina Berti, Rebecca M. Harris, Susan R. Weiss, Laurel Glaser
Community-based healthcare clinics and hospital outreach services have the potential to expand coronavirus disease 2019 (COVID-19) diagnostics to rural areas. However, reduced specimen stability during extended transport, the absence of cold chain to centralized laboratories, and biosafety concerns surrounding specimen handling has limited this expansion. In the following study, we evaluated eNAT (Copan
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Comparison of sixteen serological SARS-CoV-2 immunoassays in sixteen clinical laboratories J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-11 Lene H. Harritshøj, Mikkel Gybel-Brask, Shoaib Afzal, Pia R. Kamstrup, Charlotte S. Jørgensen, Marianne Kragh Thomsen, Linda Hilsted, Lennart Friis-Hansen, Pal B. Szecsi, Lise Pedersen, Lene Nielsen, Cecilie B. Hansen, Peter Garred, Trine-Line Korsholm, Susan Mikkelsen, Kirstine O. Nielsen, Bjarne K. Møller, Anne T. Hansen, Kasper K. Iversen, Pernille B. Nielsen, Rasmus B. Hasselbalch, Kamille Fogh
Serological SARS-CoV-2 assays are needed to support clinical diagnosis and epidemiological investigations. Recently, assays for large-scale detection of total antibodies (total-Ab) and immunoglobulin (Ig) G and M against SARS-CoV-2 antigens have been developed, but there are limited data on the diagnostic accuracy of these assays. This study was a Danish national collaboration and evaluated fifteen
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Clinical Implications of Multiplex Pathogen Panels for the Diagnosis of Acute Viral Gastroenteritis J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 Eli Wilber, Julia M Baker, Paulina Rebolledo
Acute gastroenteritis remains a significant cause of morbidity and mortality both in high and low-resource settings. The development of nucleic acid based testing has demonstrated that viruses are a common, yet often undetected, cause of acute gastroenteritis. The development of multiplex pathogen PCR panels makes it possible to detect these viral pathogens with greater sensitivity and rapidity than
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On the consequences of poorly defined breakpoints for rifampin susceptibility testing of Mycobacterium tuberculosis complex J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 Claudio U. Köser, Sophia B. Georghiou, Thomas Schön, Max Salfinger
In a recent report of a systematic review of critical concentrations (CCs), the World Health Organization (WHO) lowered the rifampin (RIF) CC for antimicrobial susceptibility testing (AST) of the Mycobacterium tuberculosis complex using Middlebrook 7H10 medium and the BACTEC Mycobacterial Growth Indicator Tube (MGIT) 960 system from 1 to 0.5 μg/mL. The previous RIF CC for 7H10 had been in use for over
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Antibody responses to two recombinant treponemal antigens (rp17 and TmpA) before and after azithromycin treatment for yaws in Ghana and Papua New Guinea. J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 Nishanth Parameswaran, Oriol Mitjà, Christian Bottomley, Cynthia Kwakye, Wendy Houinei, Allan Pillay, Damien Danavall, Kai-Hua Chi, Ronald C Ballard, Anthony W Solomon, Cheng Y Chen, Sibauk V. Bieb, Yaw Adu-Sarkodie, David CW Mabey, Kingsley Asiedu, Michael Marks, Diana Martin
WHO and its partners aim to interrupt yaws transmission in endemic countries and to certify others as being yaws-free. Transmission can be assessed using rapid plasma reagin (RPR) tests, reflecting current or recent infection, but RPR is operationally impractical.
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Evaluation of the Accelerate PhenoTM system for rapid identification and antimicrobial susceptibility testing of positive blood culture bottles inoculated with primary sterile specimens from patients with suspected severe infections J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 V Chapot, L Effenberg, J Dohmen-Ruetten, J Buer, J Kehrmann
The Accelerate PhenoTM system (APS, Accelerate Diagnostics) is approved for the rapid identification and phenotypic antimicrobial susceptibility testing (AST) of microorganisms grown from positive blood cultures inoculated with blood from septic patients. We evaluated the performance for identification and AST from positive blood culture bottles inoculated with primary sterile non-blood specimens from
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Molecular Amplification Assays Accuracy for Diagnosis of Staphylococcal Pneumonia: a Systematic Review and Meta-analysis J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 Ke Chen, Sarfraz Ahmed, Changfeng Sun, Yun-Jian Sheng, Gang Wu, Cun-Liang Deng, Suvash Chandra Ojha
Rapid and accurate identification of staphylococcal pneumonia is crucial for effective antimicrobial stewardship. We performed a meta-analysis to evaluate the diagnostic value of nucleic acid amplification tests (NAAT) from lower respiratory tract (LRT) samples of suspected pneumonia patients for avoiding superfluous empirical methicillin-resistant Staphylococcus aureus (MRSA) treatment. PubMed, Scopus
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Verification and Validation of SARS-CoV-2 Assay Performance on the Abbott m2000 and Alinity m Systems J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 Julie W. Hirschhorn, April Kegl, Tanisha Dickerson, W. Bailey Glen, Gang Xu, Jay Alden, Frederick S. Nolte
We verified the analytical performance of the Abbott RealTime SARS-CoV-2 assay on the m2000 system and compared its clinical performance to the CDC 2019-nCoV Real-Time PCR Diagnostic Panel and the ThermoFisher TaqPath RT-PCR COVID-19 kit. We also performed a bridging study comparing the RealTime SARS-CoV-2 assay with the new Abbott Alinity m SARS-CoV-2 assay. A number of standards, reference materials
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Deciphering an Adenovirus F41 outbreak in hematopoietic stem cell transplant paediatric recipients by whole genome sequencing J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-10 Caroline Lefeuvre, Maud Salmona, Linda Feghoul, Noémie Ranger, Séverine Mercier-Delarue, Laure Nizery, Aurélia Alimi, Jean-Hugues Dalle, Jérôme LeGoff
Human adenovirus (HAdV) represent a major cause of mortality and morbidity in pediatric recipients of allogeneic hematopoietic stem cells transplantation (HSCT). HAdV F type 41 (HAdV-F41) infections in HSCT patients are scarce whereas HAdV-F41 circulates commonly in healthy individuals. Between March and July 2018, HAdV-F41 infections were identified in four children (A, B, C and E) with allogeneic
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Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-09 Ashley E. Kim, Elisabeth Brandstetter, Naomi Wilcox, Jessica Heimonen, Chelsey Graham, Peter D. Han, Lea M. Starita, Denise J. McCulloch, Amanda M. Casto, Deborah A. Nickerson, Margaret M. Van de Loo, Jennifer Mooney, Misja Ilcisin, Kairsten A. Fay, Jover Lee, Thomas R. Sibley, Victoria Lyon, Rachel E. Geyer, Matthew Thompson, Barry R. Lutz, Mark J. Rieder, Trevor Bedford, Michael Boeckh, Janet A.
Introduction. While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure.
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Point-Counterpoint: Should Clinical Microbiology Laboratories Report Vancomycin Minimum Inhibitory Concentrations? J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-03 Sara L. Revolinski, Christopher D. Doern
With numerous reported challenges to reporting minimum inhibitory concentrations (MIC) for vancomycin, clinical laboratories are attempting to identify accurate methods for MIC testing. However, the issues of poor reproducibility, accuracy, and clinical utility remain a challenge. In this Point-Counter Point, Dr. Sara Revolinski discusses the pros of reporting MICs for vancomycin while Dr. Christopher
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Applications of machine learning to the problem of antimicrobial resistance: An emerging model for translational research J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-03 Melis N. Anahtar, Jason H. Yang, Sanjat Kanjilal
Antimicrobial resistance (AMR) remains one of the most challenging phenomena of modern medicine. Machine learning (ML) is a subfield of artificial intelligence that focuses on the development of algorithms that learn how to accurately predict outcome variables using large sets of predictor variables that are typically not hand selected and are minimally curated. Models are parameterized using a training
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A Test For The Rapid Detection of the Cefazolin Inoculum Effect in Methicillin-Susceptible Staphylococcus aureus J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-03 Sandra Rincon, Lina P. Carvajal, Sara I. Gomez-Villegas, Aura M. Echeverri, Rafael Rios, An Dinh, Claudia Pedroza, Karen M. Ordoñez, Esteban Nannini, Zhizeng Sun, Vance G. Fowler, Barbara E. Murray, William R. Miller, Timothy Palzkill, Lorena Diaz, Cesar A. Arias, Jinnethe Reyes
The cefazolin inoculum effect (CzIE) has been associated with therapeutic failures and mortality in invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections. A diagnostic test to detect the CzIE is not currently available. We developed a rapid (∼3 h) CzIE colorimetric test to detect staphylococcal-β-lactamase (BlaZ) activity in supernatants after ampicillin induction. The test was validated
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Mycobactericidal effect of different regimens measured by molecular bacterial load assay among people treated for multidrug-resistant tuberculosis in Tanzania J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-03 Peter M. Mbelele, Emmanuel A. Mpolya, Elingarami Sauli, Bariki Mtafya, Nyanda E. Ntinginya, Kennedy K. Addo, Katharina Kreppel, Sayoki Mfinanga, Patrick P.J. Phillips, Stephen H. Gillespie, Scott K. Heysell, Wilber Sabiiti, Stellah G. Mpagama
Background: Rifampicin or multidrug-resistant-tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis (Mtb) killing rates measured by molecular bacterial load assay (TB-MBLA) in sputa correlate with composition of the
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Clinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from Stool J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-03 Rebecca Marrero Rolon, Scott A Cunningham, Jayawant N Mandrekar, Erin T Polo, Robin Patel
Helicobacter pylori infection is mainly diagnosed non-invasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empiric, with clarithromycin triple therapy recommended where resistance rates are below 15%. Rising clarithromycin resistance resulting in high therapy failure rates is seen worldwide but United States data is limited. We developed a real-time PCR assay for
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The performance of two novel chromogenic media for the identification of multi-drug resistant Candida auris compared with other commercially available formulations J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-02-03 Auke W. de Jong, Chendo Dieleman, Mauricio Carbia, Ratna Mohd Tap, Ferry Hagen
Non-albicans Candida species are emerging in the nosocomial environment, with the multidrug-resistant species Candida auris being the most notorious example. Consequently, rapid and accurate species identification has become essential. The objective of this study was to evaluate five commercially available chromogenic media for the presumptive identification of C. auris.
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Self-collected Saline Gargle Samples as an Alternative to Healthcare Worker Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-01-29 David M. Goldfarb, Peter Tilley, Ghada N. Al-Rawahi, Jocelyn A. Srigley, Geoffrey Ford, Heather Pedersen, Abhilasha Pabbi, Stephanie Hannam-Clark, Marthe Charles, Michelle Dittrick, Vijay J. Gadkar, Jeffrey M. Pernica, Linda M. N. Hoang
Background: We assessed the performance, stability, and user acceptability of swab-independent self-collected saliva and saline mouth rinse/gargle sample types for the molecular detection of SARS-CoV-2 in adults and school-aged children. Methods: Outpatients who had recently been diagnosed with COVID-19 or were presenting with suspected COVID-19 were asked to have a nasopharyngeal swab collected and
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Performance Characteristics of BinaxNOW COVID-19 Antigen Card for Screening Asymptomatic Individuals in a University Setting J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-01-28 Nkemakonam C Okoye, Adam P Barker, Kenneth Curtis, Richard R Orlandi, Emily A Snavely, Cameron Wright, Kimberly E Hanson, Lauren N Pearson
We compared the performance of the Abbott BinaxNOW COVID-19 Antigen Card to a standard RT-PCR assay (ThermoFisher TaqPath COVID-19 Combo Kit) for the detection of SARS-CoV-2 in 2,645 asymptomatic students presenting for screening at the University of Utah. SARS-CoV-2 RNA was detected in 1.7% of the study participants by RT-PCR. BinaxNOW identified 24 infections but missed 21 infections that were detected
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Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC) J. Clin. Microbiol. (IF 5.897) Pub Date : 2021-01-27 Sean X. Zhang, N. Esther Babady, Kimberly E. Hanson, Amanda T. Harrington, Paige M.K. Larkin, Sixto M. Leal, Paul M. Luethy, Isabella W. Martin, Preeti Pancholi, Gary W. Procop, Stefan Riedel, Seyedmojtaba Seyedmousavi, Kaede V. Sullivan, Thomas J. Walsh, Shawn R. Lockhart
Fungal infections are a rising threat to our immunocompromised patient population as well as other non-immunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories