Erratum for Hashemi et al., "A Novel Platform Using RNA Signatures To Accelerate Antimicrobial Susceptibility Testing in Neisseria gonorrhoeae" [Errata]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Hashemi, M. M., Ram-Mohan, N., Yang, X., Andini, N., Gessner, N. R., Carroll, K. C., Wang, T.-H., Yang, S. Tags: Errata Source Type: research

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test [Virology]
In this study, the clinical performance of the Xpert Xpress SARS-CoV-2/Flu/RSV test (Cepheid, Sunnyvale, CA, USA) for nasopharyngeal swab specimens was evaluated in four centers: Johns Hopkins Medical Microbiology Laboratory, Northwell Health Laboratories, NYC Public Health Laboratory, and Los Angeles County/University of Southern California (LAC+USC) Medical Center. A total of 319 nasopharyngeal swab specimens, positive for SARS-CoV-2 (n = 75), influenza A virus (n = 65), influenza B virus (n = 50), or RSV (n = 38) or negative (n = 91) by the standard-of-care nucleic acid amplification tests at each site, were tested usin...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Mostafa, H. H., Carroll, K. C., Hicken, R., Berry, G. J., Manji, R., Smith, E., Rakeman, J. L., Fowler, R. C., Leelawong, M., Butler-Wu, S. M., Quintero, D., Umali-Wilcox, M., Kwiatkowski, R. W., Persing, D. H., Weir, F., Loeffelholz, M. J. Tags: Virology Source Type: research

Reply to Kidd et al., "New Names for Fungi of Medical Importance: Can We Have Our Cake and Eat It Too?" [Author Reply]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Borman, A. M., Johnson, E. M. Tags: Author Reply Source Type: research

Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag Card [Virology]
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 to reverse transcription-quantitative PCR (qRT-PCR) are currently lacking for many rapid antigen tests. Here, we evaluated the analytical sensitivity of the Abbott BinaxNOW COVID-19 Ag card using SARS-CoV-2-positive clinical sp...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Perchetti, G. A., Huang, M.-L., Mills, M. G., Jerome, K. R., Greninger, A. L. Tags: Virology Source Type: research

New Names for Fungi of Medical Importance: Can We Have Our Cake and Eat It Too? [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Kidd, S. E., Halliday, C. L., McMullan, B., Chen, S. C.- A., Elvy, J. Tags: Letter To The Editor Source Type: research

Variable Sensitivity of SARS-CoV-2 Molecular Detection in European Expert Laboratories: External Quality Assessment, June and July 2020 [Virology]
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 SARS-CoV-2 at different concentrations to evaluate sensitivity or other respiratory viruses to evaluate specificity of SARS-CoV-2 testing, was distributed to 68 laboratories in 35 countries. Specificity samples included seasonal ...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Fischer, C., Mögling, R., Melidou, A., Kühne, A., Oliveira-Filho, E. F., Wolff, T., Reiche, J., Broberg, E., Drosten, C., Meijer, A., Leitmeyer, K., Drexler, J. F., Reusken, C. B. E. M. Tags: Virology Source Type: research

Distribution of Novel Og Types in Shiga Toxin-Producing Escherichia coli Isolated from Healthy Cattle [Clinical Veterinary Microbiology]
In this study, we screened 366 STEC strains isolated from healthy cattle by using multiplex PCR kits including primers that targeted novel O-AGC types (Og types) found in OUT E. coli and Shigella strains in previous studies. Interestingly, 94 (25.7%) of these strains could be classified into 13 novel Og types. Genomic analysis revealed that the results of the in silico serotyping of novel Og-type strains were perfectly consistent with those of the PCR experiment. In addition, it was revealed that a dual Og8+OgSB17-type strain carried two types of O-AGCs from E. coli O8 and Shigella boydii type 17 tandemly inserted at the l...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Nguyen, T. T. H., Iguchi, A., Ohata, R., Kawai, H., Ooka, T., Nakajima, H., Iyoda, S. Tags: Clinical Veterinary Microbiology Source Type: research

Laboratory Automation in the Microbiology Laboratory: an Ongoing Journey, Not a Tale? [Commentary]
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 aspects were uncommon in most publications. In this issue of the Journal of Clinical Microbiology, K. Culbreath, H. Piwonka, J. Korver, and M. Noorbakhsh (J Clin Microbiol 59:e01969-20, https://doi.org/10.1128/JCM.01969-20) calcu...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Zimmermann, S. Tags: Commentary Source Type: research

Study To Evaluate the Performance of a Point-of-Care Whole-Blood HIV Viral Load Test (SAMBA II HIV-1 Semi-Q Whole Blood) [Virology]
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 in Cameroon (250), United Kingdom (633), Ukraine (412), and Zimbabwe (245) donated venous blood (all countries) and finger prick blood (all except UK) for testing on SAMBA II. SAMBA II results were compared with simultaneo...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Brook, G., Stepchenkova, T., Ali, I. M., Chipuka, S., Goel, N., Lee, H. Tags: Virology Source Type: research

Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011 to 2019 [Bacteriology]
This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistance more broadly, and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole-genome sequencing. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Schaeffer, J., Huhulescu, S., Stoeger, A., Allerberger, F., Ruppitsch, W. Tags: Bacteriology Source Type: research

Multicenter Evaluation of the Clinical Performance and the Neutralizing Antibody Activity Prediction Properties of 10 High-Throughput Serological Assays Used in Clinical Laboratories [Immunoassays]
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 data accumulate about the immune responses and the kinetics of neutralizing-antibody (nAb) production in SARS-CoV-2-infected individuals, new applications are forecast for serological assays such as nAb activity prediction in con...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Therrien, C., Serhir, B., Belanger-Collard, M., Skrzypczak, J., Shank, D. K., Renaud, C., Girouard, J., Loungnarath, V., Carrier, M., Brochu, G., Tourangeau, F., Gilfix, B., Piche, A., Bazin, R., Guerin, R., Lavoie, M., Martel-Laferriere, V., Fortin, C., Tags: Immunoassays Source Type: research

Multicenter Evaluation of the Unyvero Platform for Testing Bronchoalveolar Lavage Fluid [Bacteriology]
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 a multiplex molecular panel that detects 19 bacteria, 10 antibiotic resistance markers, and a fungus, Pneumocystis jirovecii, in BAL fluid in ~4.5 h. Its performance was evaluated using 1,016 prospectively collected and 392 arch...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Klein, M., Bacher, J., Barth, S., Atrzadeh, F., Siebenhaller, K., Ferreira, I., Beisken, S., Posch, A. E., Carroll, K. C., Wunderink, R. G., Qi, C., Wu, F., Hardy, D. J., Patel, R., Sims, M. D. Tags: Bacteriology Source Type: research

Pooled Saliva Specimens for SARS-CoV-2 Testing [Virology]
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 percentages of positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% confidence interval [CI], 65.8% to 90.5%) and 99.8% (95% CI, 98.7% to 100%), respectively. The percent positive agreement in...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Barat, B., Das, S., De Giorgi, V., Henderson, D. K., Kopka, S., Lau, A. F., Miller, T., Moriarty, T., Palmore, T. N., Sawney, S., Spalding, C., Tanjutco, P., Wortmann, G., Zelazny, A. M., Frank, K. M. Tags: Virology Source Type: research

Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium canis [Parasitology]
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 C. canis were analyzed using the new subtyping tool. Amplicons of the expected size were obtained from 49 isolates, and phylogenetic analysis identified 10 subtypes clustered into five distinct groups (XXa to XXe). The largest group, XXa, contained 43 isolates from four subtypes that differed slightly from each other at the nucleotide level, while groups XXb to XXe contain one to three isolates each. The similar distributions of subt...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Jiang, W., Roellig, D. M., Guo, Y., Li, N., Feng, Y., Xiao, L. Tags: Parasitology Source Type: research

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 [Clinical Veterinary Microbiology]
In this study, a multiepitope-based indirect chemiluminescence immunoassay (ME-CLIA) was developed for specifically detecting antibodies against FMDV serotype O in swine sera. The developed method presented high diagnostic sensitivity and excellent diagnostic specificity, and it could detect a broad spectrum of antibodies against FMDV serotype O. The diagnostic performance, accuracy rate, and analytical sensitivity of ME-CLIA were compared with those of three commercial kits. The immune protection value of multiple-epitope recombinant vaccine detected using ME-CLIA was preliminarily determined by observation of clinical sy...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Liu, W., Shao, J., Zhang, G., Chang, Y., Ge, S., Sun, Y., Gao, Z., Chang, H. Tags: Clinical Veterinary Microbiology Source Type: research

Evaluation of Optimal Blood Culture Incubation Time To Maximize Clinically Relevant Results from a Contemporary Blood Culture Instrument and Media System [Bacteriology]
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 (anaerobic) resin culture bottles in routine clinical use. Following institutional review board (IRB) approval, a retrospective review evaluated the outcomes of 158,710 bottles collected between November 2018 and October ...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Ransom, E. M., Alipour, Z., Wallace, M. A., Burnham, C.-A. D. Tags: Bacteriology Source Type: research

High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones [Epidemiology]
This study has been registered at ClinicalTrials.gov under registration no. NCT03374371.) (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Jamet, A., Guglielmini, J., Brancotte, B., Coureuil, M., Euphrasie, D., Meyer, J., Roux, J., Barnier, J.-P., Bille, E., Ferroni, A., Magny, J.-F., Bole-Feysot, C., Charbit, A., Nassif, X., Brisse, S. Tags: Epidemiology Source Type: research

Evaluation of the Dynamiker Cryptococcal Antigen Lateral Flow Assay for the Diagnosis of HIV-Associated Cryptococcosis [Mycology]
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 cerebrospinal fluid (CSF) samples from HIV patients with symptomatic meningitis and 113 serum samples from patients with suspected asymptomatic cryptococcal antigenemia. Compared to the IMMY CrAg LFA, sensitivity of Dynamiker Cr...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Kwizera, R., Omali, D., Tadeo, K., Kasibante, J., Rutakingirwa, M. K., Kagimu, E., Ssebambulidde, K., Williams, D. A., Rhein, J., Boulware, D., Meya, D. B. Tags: Mycology Source Type: research

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 [Epidemiology]
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 and molecular characterization was carried out using phenotypic methods, multilocus sequence typing (MLST), whole-genome sequencing (WGS), and core genome MLST (cgMLST). Thirty-nine isolates were analyzed. Twenty-one i...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Hoefer, A., Pampaka, D., Herrera-Leon, S., Peiro, S., Varona, S., Lopez-Perea, N., Masa-Calles, J., Herrera-Leon, L. Tags: Epidemiology Source Type: research

A Short-Tandem-Repeat Assay (MmySTR) for Studying Genetic Variation in Madurella mycetomatis [Mycology]
We describe the use of a short-tandem-repeat assay (MmySTR) for genotyping of M. mycetomatis isolates predominantly from Sudan. Eleven microsatellite markers (3 dinucleotides, 4 trinucleotide repeats, and 4 tetranucleotide repeats) were selected from the M. mycetomatis MM55 genome using the Tandem Repeats Finder software. PCR amplification primers were designed for each microsatellite marker using primer3 software and amplified in a multicolor multiplex PCR approach. To establish the extent of genetic variation within the population, a collection of 120 clinical isolates from different regions was genotyped with this assay...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Nyuykonge, B., Eadie, K., Zandijk, W. H. A., Ahmed, S. A., Desnos-Ollivier, M., Fahal, A. H., de Hoog, S., Verbon, A., van de Sande, W. W. J., Klaassen, C. H. W. Tags: Mycology Source Type: research

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 [Mycobacteriology and Aerobic Actinomycetes]
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 which are positive for Mycobacterium tuberculosis. The Xpert MTB/XDR assay simultaneously amplifies eight genes and promoter regions in M. tuberculosis and analyzes melting temperatures (Tms) using sloppy molecular beaco...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Cao, Y., Parmar, H., Gaur, R. L., Lieu, D., Raghunath, S., Via, N., Battaglia, S., Cirillo, D. M., Denkinger, C., Georghiou, S., Kwiatkowski, R., Persing, D., Alland, D., Chakravorty, S. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Closing The Brief Case: A Maggot Mystery--Ignatzschineria larvae Sepsis Secondary to an Infested Wound [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: DiFranza, L. T., Annavajhala, M. K., Uhlemann, A.-C., Green, D. A. Tags: The Brief Case Source Type: research

The Brief Case: A Maggot Mystery--Ignatzschineria larvae Sepsis Secondary to an Infested Wound [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: DiFranza, L. T., Annavajhala, M. K., Uhlemann, A.-C., Green, D. A. Tags: The Brief Case Source Type: research

Frequency of Positive Aspergillus Tests in COVID-19 Patients in Comparison to Other Patients with Pulmonary Infections Admitted to the Intensive Care Unit [Mycology]
In conclusion, in COVID-19 patients, the prevalence of a positive Aspergillus test was comparable to that in patients admitted for pneumococcal pneumonia but substantially lower than what we observed in patients with influenza. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Yusuf, E., Vonk, A., van den Akker, J. P. C., Bode, L., Sips, G. J., Rijnders, B. J. A., de Steenwinkel, J., Verkaik, N. J., Vogel, M., van der Eerden, M., van Westreenen, M. Tags: Mycology Source Type: research

Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany [Epidemiology]
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, and meropenem-vaborbactam), and remained susceptible to fosfomycin, colistin, and tigecycline. These isolates were assigned to different sequence types (STs) and indicated a predominance of isolates exhib...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Chakraborty, T., Sadek, M., Yao, Y., Imirzalioglu, C., Stephan, R., Poirel, L., Nordmann, P. Tags: Epidemiology Source Type: research

The Pediatric Endotracheal Aspirate Culture Survey (PETACS): Examining Practice Variation across Pediatric Microbiology Laboratories in the United States [Bacteriology]
This study serves as a pragmatic step in informing the development of robust clinical guidelines. Clinical outcome and implementation studies are necessary to determine the effectiveness of guidelines for TA cultures. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Prinzi, A. M., Parker, S. K., Curtis, D. J., Ziniel, S. I. Tags: Bacteriology Source Type: research

Comparative Analytical Evaluation of Four Centralized Platforms for the Detection of Mycobacterium tuberculosis Complex and Resistance to Rifampicin and Isoniazid [Mycobacteriology and Aerobic Actinomycetes]
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), and Roche cobas MTB and MTB-RIF/INH (Roche). We included Xpert MTB/RIF (Xpert) and GenoType MTBDRplus as comparators for TB and drug resistance detection, respectively. We assessed analytical sensitivity for the detection of...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: de Vos, M., Scott, L., David, A., Trollip, A., Hoffmann, H., Georghiou, S., Carmona, S., Ruhwald, M., Stevens, W., Denkinger, C. M., Schumacher, S. G. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

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) [Mycology]
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 (2005 to 2019) and primary clinical specimens from blastomycosis cases (2013 to 2019) from New York patients. We identified B. dermatitidis as the predominant pathogen in 38 cases of blastomycosis, while B. gilchristii was a mino...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Kaplan, M., Zhu, Y., Kus, J. V., McTaggart, L., Chaturvedi, V., Chaturvedi, S. Tags: Mycology Source Type: research

Establishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa [Epidemiology]
In conclusion, the highly reproducible novel P. aeruginosa cgMLST scheme facilitates outbreak investigations due to the publicly available cgMLST nomenclature. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Tönnies, H., Prior, K., Harmsen, D., Mellmann, A. Tags: Epidemiology Source Type: research

Benefits Derived from Full Laboratory Automation in Microbiology: a Tale of Four Laboratories [Bacteriology]
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. This is the first large, multicenter study in North America to report on the benefits derived from automation measured in full-time equivalents (FTE), FTE reallocation, productivity, cost per specimen, and cost avoidance. Pre- an...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Culbreath, K., Piwonka, H., Korver, J., Noorbakhsh, M. Tags: Bacteriology Source Type: research

Multicenter Evaluation of Ceftazidime-Avibactam Susceptibility Testing of Enterobacterales and Pseudomonas aeruginosa on the Vitek 2 System [Bacteriology]
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 following FDA/ISO performance criteria using the FDA-recognized CLSI/EUCAST breakpoints (sensitive [S], ≤8/4 μg/ml; resistant [R], ≥16/4 μg/ml). The overall EA was 94.5% (1,014/1,073) and CA was 98.7% (1,059/1,073). ...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Humphries, R., Campeau, S., Davis, T. E., Nagaro, K. J., LaBombardi, V. J., Franklin, S., Heimbach, L., Dwivedi, H. P. Tags: Bacteriology Source Type: research

Potential Contributions of Anaerobes in Cystic Fibrosis Airways [Minireviews]
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 has demonstrated a polymicrobial lower respiratory community compromised of facultative and obligate anaerobes. Despite the understanding of a complex bacterial milieu in CF patient airways, specific roles of anaerobes in ...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Thornton, C. S., Surette, M. G. Tags: Minireviews Source Type: research

Tuberculous Meningitis: Pathogenesis, Immune Responses, Diagnostic Challenges, and the Potential of Biomarker-Based Approaches [Minireviews]
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 the disease and guide us toward the identification of targets that may be useful for vaccines or host-directed therapeutics. In this review, we summarize the current knowledge about the immunology and pathogenesis of TBM and su...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Manyelo, C. M., Solomons, R. S., Walzl, G., Chegou, N. N. Tags: Minireviews Source Type: research

Comparison of ZMAC and MARC-145 Cell Lines for Improving Porcine Reproductive and Respiratory Syndrome Virus Isolation from Clinical Samples [Virology]
This study compared PRRSV VI results in ZMAC and MARC-145 cells from 375 clinical samples (including 104 lung, 140 serum, 90 oral fluid, and 41 processing fluid samples). The PRRSV VI success rate was very low in oral fluids and processing fluids regardless of whether ZMAC cells or MARC-145 cells were used. Success rates of PRRSV VI from lung and serum samples were significantly higher in ZMAC than in MARC-145 cells. Lung and serum samples with threshold cycle (CT) values of
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Yim-im, W., Huang, H., Park, J., Wang, C., Calzada, G., Gauger, P., Harmon, K., Main, R., Zhang, J. Tags: Virology Source Type: research

Diagnostic Accuracy Study of a Novel Blood-Based Assay for Identification of Tuberculosis in People Living with HIV [Mycobacteriology and Aerobic Actinomycetes]
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 with HIV (PLHIV) against a comprehensive microbiological reference standard (CMRS) and against Xpert MTB/RIF on the first sputum sample alone. We depict results based on performance targets set by the WHO in comparis...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Södersten, E., Ongarello, S., Mantsoki, A., Wyss, R., Persing, D. H., Banderby, S., Strömqvist Meuzelaar, L., Prieto, J., Gnanashanmugam, D., Khatri, P., Schumacher, S. G., Denkinger, C. M. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases [Minireviews]
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. Nucleic acid pathogen detection methods, typically PCR, have numerous limitations, such as highly sophisticated equipment requirements, reagents, and trained personnel relying on well-established laboratories, beside...
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Mustafa, M. I., Makhawi, A. M. Tags: Minireviews Source Type: research

Answer to March 2021 Photo Quiz [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Adler, H., Cruise, J., Yong, J., Patel, A., Mikhail, M., Beadsworth, M. B. J., Beeching, N. J. Tags: Photo Quiz Source Type: research

Photo Quiz: Disseminated Violaceous Skin Lesions following Allogeneic Stem Cell Transplant [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Authors: Adler, H., Cruise, J., Yong, J., Patel, A., Mikhail, M., Beadsworth, M. B. J., Beeching, N. J. Tags: Photo Quiz Source Type: research

Editorial Board [Masthead]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - February 18, 2021 Category: Microbiology Tags: Masthead Source Type: research

Clinical Performance of the Point-of-Care cobas Liat for Detection of SARS-CoV-2 in 20 Minutes: a Multicenter Study [Virology]
Highly accurate testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the point of care (POC) is an unmet diagnostic need in emergency care and time-sensitive outpatient care settings. Reverse transcription-PCR (RT-PCR) technology is the gold standard for SARS-CoV-2 diagnostics. We performed a multisite U.S. study comparing the clinical performance of the first U.S. Food and Drug Administration (FDA)-authorized POC RT-PCR for detection of SARS-CoV-2 in 20 min, the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test, to the most widely used RT-PCR laboratory test, the cobas 68/8800 SARS-CoV-2 tes...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Hansen, G., Marino, J., Wang, Z.-X., Beavis, K. G., Rodrigo, J., Labog, K., Westblade, L. F., Jin, R., Love, N., Ding, K., Garg, S., Huang, A., Sickler, J., Tran, N. K. Tags: Virology Source Type: research

Too Slow, Less Dough for SARS-CoV-2 Tests? A Micro-Comic Strip [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: McAdam, A. J. Tags: Editorial Source Type: research

Comparison of the Quidel Sofia SARS FIA Test to the Hologic Aptima SARS-CoV-2 TMA Test for Diagnosis of COVID-19 in Symptomatic Outpatients [Virology]
The Quidel Sofia severe acute respiratory syndrome (SARS) fluorescent immunoassay (FIA) test (SOFIA) is a rapid antigen immunoassay for the detection of SARS coronavirus 2 (SARS-CoV-2) proteins from nasal or nasopharyngeal swab specimens. The purpose of this study was to compare the results of the SOFIA test to those of the Hologic Aptima SARS-CoV-2 TMA test (APTIMA TMA), a high-throughput molecular diagnostic test that uses transcription-mediated amplification (TMA) for the detection of SARS-CoV-2 nucleic acid from upper respiratory tract specimens. Three hundred forty-seven symptomatic patients from an urgent care center...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Beck, E. T., Paar, W., Fojut, L., Serwe, J., Jahnke, R. R. Tags: Virology Source Type: research

Saliva Is a Promising Alternative Specimen for the Detection of SARS-CoV-2 in Children and Adults [Virology]
Testing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been burdened by the scarcity of testing materials and personal protective equipment for health care workers. The simple and painless process of saliva collection allows for widespread testing, but enthusiasm is hampered by variable performance compared to that of nasopharyngeal swab (NPS) samples. We prospectively collected paired NPS and saliva samples from a total of 300 unique adult and pediatric patients. SARS-CoV-2 RNA was detected in 32.2% (97/300) of the individuals using the TaqPath COVID-19 Combo kit (Thermo Fisher). Performance...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Yee, R., Truong, T. T., Pannaraj, P. S., Eubanks, N., Gai, E., Jumarang, J., Turner, L., Peralta, A., Lee, Y., Dien Bard, J. Tags: Virology Source Type: research

Extraction-Free Methods for the Detection of SARS-CoV-2 by Reverse Transcription-PCR: a Comparison with the Cepheid Xpert Xpress SARS-CoV-2 Assay across Two Medical Centers [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Cameron, A., Pecora, N. D., Pettengill, M. A. Tags: Letter To The Editor Source Type: research

Evaluation of the Panbio COVID-19 Rapid Antigen Detection Test Device for the Screening of Patients with COVID-19 [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Fenollar, F., Bouam, A., Ballouche, M., Fuster, L., Prudent, E., Colson, P., Tissot-Dupont, H., Million, M., Drancourt, M., Raoult, D., Fournier, P.-E. Tags: Letter To The Editor Source Type: research

Biographical Feature: Fred C. Tenover, Ph.D., D(ABMM), F(AAM), FIDSA [Biographical Feature]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Tang, Y.-W. Tags: Biographical Feature Source Type: research

Detection of SARS-CoV-2 Antibodies in Oral Fluid Obtained Using a Rapid Collection Device [Immunoassays]
Current commercially available methods for reliably detecting antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain expensive and inaccessible due to the need for whole-blood collection by highly trained phlebotomists using personal protective equipment (PPE). We have evaluated an antibody detection approach using the OraSure Technologies oral antibody collection device (OACD) and their proprietary SARS-CoV-2 total antibody detection enzyme-linked immunosorbent assay (ELISA). We found that the OraSure test for total antibody detection in oral fluid had comparable sensitivity and specificity...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: MacMullan, M. A., Chellamuthu, P., Mades, A., Das, S., Turner, F., Slepnev, V. I., Ibrayeva, A. Tags: Immunoassays Source Type: research

Evaluation of a SARS-CoV-2 Surrogate Virus Neutralization Test for Detection of Antibody in Human, Canine, Cat, and Hamster Sera [Immunoassays]
Surrogate neutralization assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be done without biosafety level 3 containment and in multiple species are desirable. We evaluate a recently developed surrogate virus neutralization test (sVNT) in comparison to 90% plaque reduction neutralization tests (PRNT90) in human, canine, cat, and hamster sera. With PRNT90 as the reference, sVNT had sensitivity of 98.9% and specificity of 98.8%. Using a panel of immune sera corresponding to other coronaviruses, we confirm the lack of cross-reactivity to other coronaviruses in SARS-CoV-2 sVNT and PRNT90, except ...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Perera, R. A. P. M., Ko, R., Tsang, O. T. Y., Hui, D. S. C., Kwan, M. Y. M., Brackman, C. J., To, E. M. W., Yen, H.-l., Leung, K., Cheng, S. M. S., Chan, K. H., Chan, K. C. K., Li, K.-C., Saif, L., Barrs, V. R., Wu, J. T., Sit, T. H. C., Poon, L. L. M., P Tags: Immunoassays Source Type: research

Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods [Bacteriology]
In this study, we used 64 S. pseudopneumoniae strains, 59 S. pneumoniae strains, 22 S. mitis strains, 24 S. oralis strains, 6 S. infantis strains, and 1 S. peroris strain to test the capability of three single genes (rpoB, gyrB, and recA), two multilocus sequence analysis (MLSA) schemes, the single nucleotide polymorphism (SNP)-based phylogeny tool CSI phylogeny, a k-mer-based identification method (KmerFinder), average nucleotide identity (ANI) using fastANI, and core genome analysis to identify S. pseudopneumoniae. Core genome analysis and CSI phylogeny were able to cluster all strains into distinct clusters related to t...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Jensen, C. S., Iversen, K. H., Dargis, R., Shewmaker, P., Rasmussen, S., Christensen, J. J., Nielsen, X. C. Tags: Bacteriology Source Type: research

A Multiplex Microsphere IgG Assay for SARS-CoV-2 Using ACE2-Mediated Inhibition as a Surrogate for Neutralization [Immunoassays]
The coronavirus disease 2019 (COVID-19) pandemic has highlighted the challenges inherent to the serological detection of a novel pathogen such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Serological tests can be used diagnostically and for surveillance, but their usefulness depends on their throughput, sensitivity, and specificity. Here, we describe a multiplex fluorescent microsphere-based assay, 3Flex, that can detect antibodies to three major SARS-CoV-2 antigens—spike (S) protein, the spike ACE2 receptor-binding domain (RBD), and nucleocapsid (NP). Specificity was assessed using 213 prepandemi...
Source: Journal of Clinical Microbiology - January 21, 2021 Category: Microbiology Authors: Cameron, A., Porterfield, C. A., Byron, L. D., Wang, J., Pearson, Z., Bohrhunter, J. L., Cardillo, A. B., Ryan-Muntz, L., Sorensen, R. A., Caserta, M. T., Angeloni, S., Hardy, D. J., Zand, M. S., Pecora, N. D. Tags: Immunoassays Source Type: research