Mycoplasma genitalium Detection in Urogenital Specimens from Symptomatic and Asymptomatic Men and Women by Use of the cobas TV/MG Test [Bacteriology]
This study demonstrated that the cobas assay was highly sensitive and specific in all relevant clinical samples for the detection of M. genitalium. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Van Der Pol, B., Waites, K. B., Xiao, L., Taylor, S. N., Rao, A., Nye, M., Chavoustie, S., Ermel, A., Kaplan, C., Eisenberg, D., Chan, P. A., Mena, L., Pacheco, S., Krishnamurthy, S., Mohan, R., Bertuzis, R., McGowin, C. L., Arcenas, R., Marlowe, E. M. Tags: Bacteriology Source Type: research

Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017 [Epidemiology]
This study provides an important baseline census of the standing pangenomic variation and drug resistance to aid the development of a statewide database for epidemiological studies and clinical decision making. Continued genomic surveillance will be necessary to accurately assess how the population of C. jejuni changes over the long term. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Park, C. J., Li, J., Zhang, X., Gao, F., Benton, C. S., Andam, C. P. Tags: Epidemiology Source Type: research

Detection of Intestinal Protozoa in Trichrome-Stained Stool Specimens by Use of a Deep Convolutional Neural Network [Parasitology]
Intestinal protozoa are responsible for relatively few infections in the developed world, but the testing volume is disproportionately high. Manual light microscopy of stool remains the gold standard but can be insensitive, time-consuming, and difficult to maintain competency. Artificial intelligence and digital slide scanning show promise for revolutionizing the clinical parasitology laboratory by augmenting the detection of parasites and slide interpretation using a convolutional neural network (CNN) model. The goal of this study was to develop a sensitive model that could screen out negative trichrome slides, while flag...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Mathison, B. A., Kohan, J. L., Walker, J. F., Smith, R. B., Ardon, O., Couturier, M. R. Tags: Parasitology Source Type: research

Evaluation of the EDTA-Modified Carbapenem Inactivation Method for Detecting Metallo-{beta}-Lactamase-Producing Pseudomonas aeruginosa [Bacteriology]
This study evaluated the performance of the EDTA-modified carbapenem inactivation method (eCIM) in tandem with the modified carbapenem inactivation method (mCIM) against a large collection of clinical P. aeruginosa isolates (n = 103) to provide clinicians a phenotypic test that not only identifies carbapenemase production but also distinguishes between metallo-β-lactamase and serine-carbapenemase production in P. aeruginosa. The mCIM test was performed according to Clinical and Laboratory Standards Institute guidelines, while the eCIM was conducted as previously described for Enterobacteriaceae. Test performance was c...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Gill, C. M., Lasko, M. J., Asempa, T. E., Nicolau, D. P. Tags: Bacteriology Source Type: research

Impact of the Beta-Glucan Test on Management of Intensive Care Unit Patients at Risk for Invasive Candidiasis [Mycology]
This study assessed the impact of BDG test results on therapeutic decisions. This was a single-center observational study conducted in an ICU over two 6-month periods. All BDG test requests for the diagnosis of IC were analyzed. Before the second period, the ICU physicians received a pocket card instruction (algorithm) for targeted BDG testing in high-risk patients. The performance of the BDG test for IC diagnosis was assessed, as well as its impact on antifungal (AF) prescription. Overall, 72 patients had ≥1 BDG test, and 14 (19%) patients had an IC diagnosis. The BDG test results influenced therapeutic decisions in 41...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Kritikos, A., Poissy, J., Croxatto, A., Bochud, P.-Y., Pagani, J.-L., Lamoth, F. Tags: Mycology Source Type: research

Ultrasensitive Clostridioides difficile Toxin Testing for Higher Diagnostic Accuracy [Minireviews]
Currently available diagnostic tests for Clostridioides difficile infection (CDI) lack specificity or sensitivity, which has led to guideline recommendations for multistep testing algorithms. Ultrasensitive assays for detection of C. difficile toxins provide measurements of disease-specific markers at very low concentrations. These assays may show improved accuracy compared to that of current testing methods and offer a potential standalone solution for CDI diagnosis, although large studies of clinical performance and accuracy are lacking. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Sandlund, J., Davies, K., Wilcox, M. H. Tags: Minireviews Source Type: research

Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens [Bacteriology]
This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. Most of the discrepant results have been observed in the low-pathogen-load samples. In addition, the QIAstat-Dx RP assay detected 19 additional targets in 19 respiratory samples that were not detected by the ePlex RPP assay. Nine of these...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Boers, S. A., Melchers, W. J. G., Peters, C. J. A., Toonen, M., McHugh, M. P., Templeton, K. E., Claas, E. C. J. Tags: Bacteriology Source Type: research

Closing the Brief Case: Tick-Borne Relapsing Fever in a Returned Traveler [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Snavely, E., Hymas, W., Couturier, M. R. Tags: The Brief Case Source Type: research

The Brief Case: Tick-Borne Relapsing Fever in a Returned Traveler [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Snavely, E., Hymas, W., Couturier, M. R. Tags: The Brief Case Source Type: research

Detection of Bovine Antibodies against a Conserved Capsid Epitope as the Basis of a Novel Universal Serological Test for Foot-and-Mouth Disease [Clinical Veterinary Microbiology]
In this study, a highly conserved region in the N terminus of FMDV capsid protein VP2 (VP2N) was characterized using a panel of intertype-reactive monoclonal antibodies. This revealed a universal epitope in VP2N which could be used as a peptide antigen to detect FMDV-specific antibodies against all types of the virus. A VP2-peptide enzyme-linked immunosorbent assay (VP2-ELISA) was optimized using experimental and reference antisera from immunized, convalescent, and naìˆve animals (n = 172). The VP2-ELISA is universal and simple and provided sensitive (99%) and specific (93%) detection of antibodies to all FMDV strains use...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Asfor, A. S., Howe, N., Grazioli, S., Berryman, S., Parekh, K., Wilsden, G., Ludi, A., King, D. P., Parida, S., Brocchi, E., Tuthill, T. J. Tags: Clinical Veterinary Microbiology Source Type: research

Group A Streptococcus Testing in Pediatrics: the Move to Point-of-Care Molecular Testing [Minireviews]
Each year, there are an estimated 11 million visits to ambulatory care centers for pharyngitis in children between the ages of 3 and 18 years. While there are many causes of pediatric pharyngitis, group A streptococcal pharyngitis represents 15 to 30% of infections and is the only cause for which treatment is recommended. Unfortunately, clinical suspicion is insufficient for the accurate diagnosis of group A streptococcal pharyngitis, and laboratory testing for confirmation of Streptococcus pyogenes infection is required to prevent complications of infection. Traditionally, throat swabs are inoculated onto agar plates for ...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Thompson, T. Z., McMullen, A. R. Tags: Minireviews Source Type: research

Updates in Laboratory Diagnostics for Invasive Fungal Infections [Minireviews]
Appropriate diagnosis of invasive fungal infections (IFIs) is critical due to the high rates of morbidity and mortality, as well as the substantial economic burden, associated with the management of these diseases. The recognition of IFI and differentiation from other infections with similar clinical presentations can be challenging, which can lead to diagnostic error that not only has an impact on individual patient health outcomes but also on antimicrobial drug usage and the growing threat of antimicrobial resistance in bacteria. Therefore, there is a significant need for improved stewardship related to diagnostic testin...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Terrero-Salcedo, D., Powers-Fletcher, M. V. Tags: Minireviews Source Type: research

Nasal Swab Sampling for SARS-CoV-2: a Convenient Alternative in Times of Nasopharyngeal Swab Shortage [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Pere, H., Podglajen, I., Wack, M., Flamarion, E., Mirault, T., Goudot, G., Hauw-Berlemont, C., Le, L., Caudron, E., Carrabin, S., Rodary, J., Ribeyre, T., Belec, L., Veyer, D. Tags: Letter To The Editor Source Type: research

Comparison of Copan ESwab and FLOQSwab for COVID-19 Diagnosis: Working around a Supply Shortage [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Vermeiren, C., Marchand-Senecal, X., Sheldrake, E., Bulir, D., Smieja, M., Chong, S., Forbes, J. D., Katz, K. Tags: Letter To The Editor Source Type: research

The Clinical Microbiology Laboratory Response to COVID-19: a Micro-Comic Strip [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: McAdam, A. J. Tags: Editorial Source Type: research

Clinical Evaluation of the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the COVID-19 Pandemic [Virology]
Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To meet diagnostic needs as the pandemic grows, the U.S. Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed the first manufacturer-independent evaluation of the fully automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roch...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Poljak, M., Korva, M., Knap Gasper, N., Fujs Komlos, K., Sagadin, M., Ursic, T., Avsic Zupanc, T., Petrovec, M. Tags: Virology Source Type: research

Evaluation of Saline, Phosphate-Buffered Saline, and Minimum Essential Medium as Potential Alternatives to Viral Transport Media for SARS-CoV-2 Testing [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Rodino, K. G., Espy, M. J., Buckwalter, S. P., Walchak, R. C., Germer, J. J., Fernholz, E., Boerger, A., Schuetz, A. N., Yao, J. D., Binnicker, M. J. Tags: Letter To The Editor Source Type: research

A Pandemic in Times of Global Tourism: Superspreading and Exportation of COVID-19 Cases from a Ski Area in Austria [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Correa-Martinez, C. L., Kampmeier, S., Kümpers, P., Schwierzeck, V., Hennies, M., Hafezi, W., Kühn, J., Pavenstädt, H., Ludwig, S., Mellmann, A. Tags: Letter To The Editor Source Type: research

Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit [Virology]
Nearly 400,000 people worldwide are known to have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) beginning in December 2019. The virus has now spread to over 168 countries including the United States, where the first cluster of cases was observed in the Seattle metropolitan area in Washington. Given the rapid increase in the number of cases in many localities, the availability of accurate, high-throughput SARS-CoV-2 testing is vital to efforts to manage the current public health crisis. In the course of optimizing SARS-CoV-2 testing performed by the University of Washington Clinical Virolog...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Nalla, A. K., Casto, A. M., Huang, M.-L. W., Perchetti, G. A., Sampoleo, R., Shrestha, L., Wei, Y., Zhu, H., Jerome, K. R., Greninger, A. L. Tags: Virology Source Type: research

Laboratory Diagnosis of COVID-19: Current Issues and Challenges [Commentary]
The COVID-19 outbreak has had a major impact on clinical microbiology laboratories in the past several months. This commentary covers current issues and challenges for the laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the preanalytical stage, collecting the proper respiratory tract specimen at the right time from the right anatomic site is essential for a prompt and accurate molecular diagnosis of COVID-19. Appropriate measures are required to keep laboratory staff safe while producing reliable test results. In the analytic stage, real-time reverse transcripti...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Tang, Y.-W., Schmitz, J. E., Persing, D. H., Stratton, C. W. Tags: Commentary Source Type: research

Computer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical Microbiologist [Commentary]
Artificial intelligence (AI) is increasingly becoming an important component of clinical microbiology informatics. Researchers, microbiologists, laboratorians, and diagnosticians are interested in AI-based testing because these solutions have the potential to improve a test’s turnaround time, quality, and cost. A study by Mathison et al. used computer vision AI (B. A. Mathison, J. L. Kohan, J. F. Walker, R. B. Smith, et al., J Clin Microbiol 58:e02053-19, 2020, https://doi.org/10.1128/JCM.02053-19), but additional opportunities for AI applications exist within the clinical microbiology laboratory. Large data sets wit...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Rhoads, D. D. Tags: Commentary Source Type: research

Evaluation of Nucleocapsid and Spike Protein-Based Enzyme-Linked Immunosorbent Assays for Detecting Antibodies against SARS-CoV-2 [Immunoassays]
At present, PCR-based nucleic acid detection cannot meet the demands for coronavirus infectious disease (COVID-19) diagnosis. Two hundred fourteen confirmed COVID-19 patients who were hospitalized in the General Hospital of Central Theater Command of the People’s Liberation Army between 18 January and 26 February 2020 were recruited. Two enzyme-linked immunosorbent assay (ELISA) kits based on recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (rN) and spike protein (rS) were used for detecting IgM and IgG antibodies, and their diagnostic feasibility was evaluated. Among the ...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Liu, W., Liu, L., Kou, G., Zheng, Y., Ding, Y., Ni, W., Wang, Q., Tan, L., Wu, W., Tang, S., Xiong, Z., Zheng, S. Tags: Immunoassays Source Type: research

Expanding Access to Biospecimens for Lyme Disease Test Development [Commentary]
The laboratory diagnosis of Lyme disease relies upon serologic testing. A standard or modified two-tiered testing algorithm is used to enhance the accuracy of antibody detection. However, this approach suffers from a lack of sensitivity in early Lyme disease. Ongoing efforts to develop more sensitive antibody detection technologies and other diagnostic approaches are dependent upon the availability of quality-assured biospecimens linked to reliable clinical data. In this issue of the Journal of Clinical Microbiology, Horn et al. (E. J. Horn, G. Dempsey, A. M. Schotthoefer, U. L. Prisco, et al., J Clin Microbiol 58:e00032-2...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Schmitz, J. L. Tags: Commentary Source Type: research

Identification of Mycobacterium tuberculosis Peptides in Serum Extracellular Vesicles from Persons with Latent Tuberculosis Infection [Mycobacteriology and Aerobic Actinomycetes]
Identification of biomarkers for latent Mycobacterium tuberculosis infection and risk of progression to tuberculosis (TB) disease are needed to better identify individuals to target for preventive therapy, predict disease risk, and potentially predict preventive therapy efficacy. Our group developed multiple reaction monitoring mass spectrometry (MRM-MS) assays that detected M. tuberculosis peptides in serum extracellular vesicles from TB patients. We subsequently optimized this MRM-MS assay to selectively identify 40 M. tuberculosis peptides from 19 proteins that most commonly copurify with serum vesicles of patients with...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Mehaffy, C., Kruh-Garcia, N. A., Graham, B., Jarlsberg, L. G., Willyerd, C. E., Borisov, A., Sterling, T. R., Nahid, P., Dobos, K. M. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Answer to June 2020 Photo Quiz [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Kim, J. J., Luethy, P. M., Stashek, K. M., Koka, R., Mathur, P. Tags: Photo Quiz Source Type: research

Photo Quiz: An Elderly Leukemia Patient with Jaw Pain and Swelling and Subjective Fevers [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Kim, J. J., Luethy, P. M., Stashek, K. M., Koka, R., Mathur, P. Tags: Photo Quiz Source Type: research

A Method To Prevent SARS-CoV-2 IgM False Positives in Gold Immunochromatography and Enzyme-Linked Immunosorbent Assays [Immunoassays]
We set out to investigate the interference factors that led to false-positive novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgM detection results using gold immunochromatography assay (GICA) and enzyme-linked immunosorbent assay (ELISA) and the corresponding solutions. GICA and ELISA were used to detect SARS-CoV-2 IgM in 86 serum samples, including 5 influenza A virus (Flu A) IgM-positive sera, 5 influenza B virus (Flu B) IgM-positive sera, 5 Mycoplasma pneumoniae IgM-positive sera, 5 Legionella pneumophila IgM-positive sera, 6 sera of HIV infection patients, 36 rheumatoid factor IgM (RF-IgM)-positive ...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Wang, Q., Du, Q., Guo, B., Mu, D., Lu, X., Ma, Q., Guo, Y., Fang, L., Zhang, B., Zhang, G., Guo, X. Tags: Immunoassays Source Type: research

Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting [Bacteriology]
Applying digital PCR (dPCR) technology to challenging clinical and industrial detection tasks has become more prevalent because of its capability for absolute quantification and rare target detection. However, practices learned from quantitative PCR (qPCR) that promote assay robustness and wide-ranging utility are not readily applied in dPCR. These include internal amplification controls to account for false-negative reactions and amplicon high-resolution melt (HRM) analysis to distinguish true positives from false positives. Incorporation of internal amplification controls in dPCR is challenging because of the limited flu...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Aralar, A., Yuan, Y., Chen, K., Geng, Y., Ortiz Velez, D., Sinha, M., Lawrence, S. M., Fraley, S. I. Tags: Bacteriology Source Type: research

Development of a Multiplex PCR-Based Assay for Rapid Serotyping of Erysipelothrix Species [Clinical Veterinary Microbiology]
The Gram-positive bacterium Erysipelothrix rhusiopathiae is a zoonotic pathogen that causes erysipelas in a wide range of mammalian and avian species. Historically, E. rhusiopathiae has been differentiated from other Erysipelothrix species by serotyping. Among 28 serovars of Erysipelothrix species, specific serovars, namely, 1a, 1b, and 2 of E. rhusiopathiae, are associated mainly with the disease in pigs, poultry, and humans; however, other serovar strains are often simultaneously isolated from diseased and healthy animals, indicating the importance of isolate serotyping for epidemiology. The traditional serotyping protoc...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Shimoji, Y., Shiraiwa, K., Tominaga, H., Nishikawa, S., Eguchi, M., Hikono, H., Ogawa, Y. Tags: Clinical Veterinary Microbiology Source Type: research

Comparison of Two Multilocus Sequence Typing Schemes for Mycoplasma bovis and Revision of the PubMLST Reference Method [Clinical Veterinary Microbiology]
Mycoplasma bovis causes pneumonia, pharyngitis, otitis, arthritis, mastitis, and reproductive disorders in cattle and bison. Two multilocus sequence typing (MLST) schemes have been developed for M. bovis, with one serving as the PubMLST reference method, but no comparison of the schemes has been undertaken. Although the PubMLST scheme has proven to be highly discriminatory and informative, the recent discovery of isolates missing one of the typing loci, adh-1, raises concern about its suitability for continued use. The goal of our study was to compare the performance of the two MLST schemes and identify a new reference sch...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Register, K. B., Lysnyansky, I., Jelinski, M. D., Boatwright, W. D., Waldner, M., Bayles, D. O., Pilo, P., Alt, D. P. Tags: Clinical Veterinary Microbiology Source Type: research

Accuracy of QuantiFERON-TB Gold Plus Test for Diagnosis of Mycobacterium tuberculosis Infection in Children [Mycobacteriology and Aerobic Actinomycetes]
Compared to its predecessor QuantiFERON-TB Gold In Tube (QFT-IT), QuantiFERON-TB Gold Plus (QFT-Plus) contains an additional antigen tube (TB2), stimulating both CD4+ and CD8+ T cells. The ability to discriminate CD4+ and CD8+ responses is suggested to be useful in differentiating stages of Mycobacterium tuberculosis infection. While QFT-Plus has already been evaluated in adults, there are not enough data in children evaluated for suspected active tuberculosis (TB) or latent TB infection (LTBI). A prospective cross-sectional study was conducted among children aged 0 to 17 years who were evaluated for suspected active TB or...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Buonsenso, D., Delogu, G., Perricone, C., Grossi, R., Careddu, A., De Maio, F., Palucci, I., Sanguinetti, M., Valentini, P., Sali, M. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Qualitative Variation among Commercial Immunoassays for Detection of Measles-Specific IgG [Immunoassays]
Measurement of measles virus-specific IgG is used to assess presumptive evidence of immunity among immunocompetent individuals with uncertain immune or vaccination status. False-negative test results may lead to unnecessary quarantine and exclusion from activities such as employment, education, and travel or result in unnecessary revaccination. In contrast, false-positive results may fail to identify susceptible individuals and promote spread of disease by those who are exposed and unprotected. To better understand the performance characteristics of tests to detect measles IgG, we compared five widely used, commercially av...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Latner, D. R., Sowers, S. B., Anthony, K., Colley, H., Badeau, C., Coates, J., Wong, P., Fakile, Y., Interiano, C., Pannell, K. B., Leung-Pineda, V., Patel, M. M., Rota, P. A., Limbago, B. M., Hickman, C. J. Tags: Immunoassays Source Type: research

Comparable Detections of Viral Pathogens in Lower Respiratory Tract Specimens with the BioFire Respiratory Panel 2 and the BioFire Pneumonia Panel [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Hughes, A. E. O., Webber, D. M., Wallace, M. A., Johnson, C., Burnham, C.-A. D., Anderson, N. W. Tags: Letter To The Editor Source Type: research

Development of an RNA Strand-Specific Hybridization Assay To Differentiate Replicating versus Nonreplicating Influenza A Viruses [Virology]
Replication of influenza A virus (IAV) from negative-sense viral RNA (vRNA) requires the generation of positive-sense RNA (+RNA). Most molecular assays, such as conventional real-time reverse transcriptase PCR (rRT-PCR), detect total RNA in a sample without differentiating vRNA from +RNA. These assays are not designed to distinguish IAV infection versus exposure of an individual to an environment enriched with IAVs but wherein no viral replication occurs. We therefore developed a strand-specific hybridization (SSH) assay that differentiates between vRNA and +RNA and quantifies relative levels of each RNA species. The SSH a...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Yang, G., Hodges, E. N., Winter, J., Zanders, N., Shcherbik, S., Bousse, T., Murray, J. R., Muraduzzaman, A. K. M., Rahman, M., Alamgir, A. S. M., Flora, M. S., Blanton, L., Barnes, J. R., Wentworth, D. E., Davis, C. T. Tags: Virology Source Type: research

Evaluation of Commercial Molecular Diagnostic Methods for Detection and Determination of Macrolide Resistance in Mycoplasma pneumoniae [Bacteriology]
We evaluated six commercial molecular tests targeting Mycoplasma pneumoniae, namely, the BioFire FilmArray respiratory panel (RP), the Meridian Alethia Mycoplasma Direct, the GenMark ePlex respiratory pathogen panel (RPP), the Luminex NxTAG RPP, the ELITech ELITe InGenius Mycoplasma MGB research use only (RUO) PCR, and the SpeeDx Resistance Plus MP assays. Laboratory-developed PCR assays at the University of Alabama at Birmingham and the Centers for Disease Control and Prevention were used as reference standards. Among 428 specimens, 212 were designated confirmed positives for M. pneumoniae. The highest clinical sensitivit...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Leal, S. M., Totten, A. H., Xiao, L., Crabb, D. M., Ratliff, A., Duffy, L. B., Fowler, K. B., Mixon, E., Winchell, J. M., Diaz, M. H., Benitez, A. J., Wolff, B. J., Qin, X., Tang, Y.- W., Gonzalez, M., Selvarangan, R., Hong, T., Brooks, E., Dallas, S., At Tags: Bacteriology Source Type: research

Evaluation and Optimization of the Clinical Accuracy of Hybribio's 14 High-Risk HPV with 16/18 Genotyping Assay within the VALGENT-3 Framework [Virology]
Hybribio’s 14 High-Risk HPV with 16/18 genotyping real-time PCR (HBRT-H14) is a human papillomavirus (HPV) assay with approval from the China Food and Drug Administration that is widely used in China. VALGENT (VALidation of HPV GENotyping Tests) is an established framework for evaluating HPV tests’ clinical performance relative to validated comparators. The aim of this study was to assess the clinical accuracy of HBRT-H14 following international validation criteria. Within VALGENT-3, clinical performance of HBRT-H14 was compared with Hybrid Capture 2 (HC2), Linear Array HPV genotyping test (Linear Array), and C...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Xu, L., Ostrbenk Valencak, A., Poljak, M., Arbyn, M. Tags: Virology Source Type: research

The Panther Fusion System with Open Access Functionality for Laboratory-Developed Tests for Influenza A Virus Subtyping [Virology]
In conclusion, either FluA virus typing assay would be a valuable complement to the Panther Fusion respiratory menu given the performance of these LDTs, the system’s full automation, and the ability to split eluates for both IVD and LDT testing. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Stellrecht, K. A., Cimino, J. L., Maceira, V. P. Tags: Virology Source Type: research

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing [Bacteriology]
Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turn...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Neuenschwander, S. M., Terrazos Miani, M. A., Amlang, H., Perroulaz, C., Bittel, P., Casanova, C., Droz, S., Flandrois, J.-P., Leib, S. L., Suter-Riniker, F., Ramette, A. Tags: Bacteriology Source Type: research

Evaluation of the Performance of the IMMY sona Aspergillus Galactomannan Lateral Flow Assay When Testing Serum To Aid in Diagnosis of Invasive Aspergillosis [Mycology]
The objective of this study was to determine the performance of the recently released IMMY sona Aspergillus LFA when testing serum samples. The study took the form of a retrospective, anonymous case/control study comprising 179 serum samples from 136 patients with invasive fungal disease, previously documented using recently revised internationally accepted definitions. The LFA was performed following the manufacturer’s instructions using a cube reader to generate a galactomannan index (GMI). Performance parameters were determined, and receiver operator characteristic (ROC) analysis was used to identify an optimal th...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: White, P. L., Price, J. S., Posso, R., Cutlan-Vaughan, M., Vale, L., Backx, M. Tags: Mycology Source Type: research

The Lyme Disease Biobank: Characterization of 550 Patient and Control Samples from the East Coast and Upper Midwest of the United States [Immunoassays]
Lyme disease (LD) is an increasing public health problem. Current laboratory testing is insensitive in early infection, the stage at which appropriate treatment is most effective in preventing disease sequelae. The Lyme Disease Biobank (LDB) collects samples from individuals with symptoms consistent with early LD presenting with or without erythema migrans (EM) or an annular, expanding skin lesion and uninfected individuals from areas of endemicity. Samples were collected from 550 participants (298 cases and 252 controls) according to institutional review board-approved protocols and shipped to a centralized biorepository....
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Horn, E. J., Dempsey, G., Schotthoefer, A. M., Prisco, U. L., McArdle, M., Gervasi, S. S., Golightly, M., De Luca, C., Evans, M., Pritt, B. S., Theel, E. S., Iyer, R., Liveris, D., Wang, G., Goldstein, D., Schwartz, I. Tags: Immunoassays Source Type: research

Editorial Board [Masthead]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Tags: Masthead Source Type: research

Rapid Identification of Mycoplasma bovis Strains from Bovine Bronchoalveolar Lavage Fluid with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry after Enrichment Procedure [Clinical Veterinary Microbiology]
Mycoplasma bovis is a leading cause of pneumonia in modern calf rearing. Fast identification is essential to ensure appropriate antimicrobial therapy. Therefore, the objective of this study was to develop a protocol to identify M. bovis from bronchoalveolar lavage fluid (BALf) with matrix-assisted laser desorption ionization–time of flight mass spectrometry MALDI-TOF MS and to determine the diagnostic accuracy in comparison with other techniques. BALf was obtained from 104 cattle, and the presence of M. bovis was determined in the following three ways: (i) rapid identification of M. bovis with MALDI-TOF MS (RIMM) (BA...
Source: Journal of Clinical Microbiology - May 26, 2020 Category: Microbiology Authors: Bokma, J., Van Driessche, L., Deprez, P., Haesebrouck, F., Vahl, M., Weesendorp, E., Deurenberg, R. H., Pardon, B., Boyen, F. Tags: Clinical Veterinary Microbiology Source Type: research

Fluorescent Hybridization of Mycobacterium leprae in Skin Samples Collected in Burkina Faso [Mycobacteriology and Aerobic Actinomycetes]
Leprosy is caused by Mycobacterium leprae, and it remains underdiagnosed in Burkina Faso. We investigated the use of fluorescent in situ hybridization (FISH) for detecting M. leprae in 27 skin samples (skin biopsy samples, slit skin samples, and skin lesion swabs) collected from 21 patients from Burkina Faso and three from Côte d’Ivoire who were suspected of having cutaneous leprosy. In all seven Ziehl-Neelsen-positive skin samples (four skin biopsy samples and three skin swabs collected from the same patient), FISH specifically identified M. leprae, including one FISH-positive skin biopsy sample that remained ...
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Millogo, A., Loukil, A., Fellag, M., Diallo, B., Ouedraogo, A. S., Godreuil, S., Drancourt, M. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Nanopore Sequencing Reveals Novel Targets for Detection and Surveillance of Human and Avian Influenza A Viruses [Virology]
In conclusion, we have shown that PB2 or NS gene RT-PCRs are suitable alternatives to the recommended M gene RT-PCR for diagnosis of IAV. Long-read nanopore sequencing facilitates the identification of novel diagnostic targets. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Yip, C. C.-Y., Chan, W.-M., Ip, J. D., Seng, C. W.-M., Leung, K.-H., Poon, R. W.-S., Ng, A. C.-K., Wu, W.-L., Zhao, H., Chan, K.-H., Siu, G. K.-H., Ng, T. T.-L., Cheng, V. C.-C., Kok, K.-H., Yuen, K.-Y., To, K. K.-W. Tags: Virology Source Type: research

Multicenter Evaluation of a PCR-Based Digital Microfluidics and Electrochemical Detection System for the Rapid Identification of 15 Fungal Pathogens Directly from Positive Blood Cultures [Mycology]
Routine identification of fungal pathogens from positive blood cultures by culture-based methods can be time-consuming, delaying treatment with appropriate antifungal agents. The GenMark Dx ePlex investigational use only blood culture identification fungal pathogen panel (BCID-FP) rapidly detects 15 fungal targets simultaneously in blood culture samples positive for fungi by Gram staining. We aimed to determine the performance of the BCID-FP in a multicenter clinical study. Blood culture samples collected at 10 United States sites and tested with BCID-FP at 4 sites were compared to the standard-of-care microbiological and ...
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Zhang, S. X., Carroll, K. C., Lewis, S., Totten, M., Mead, P., Samuel, L., Steed, L. L., Nolte, F. S., Thornberg, A., Reid, J. L., Whitfield, N. N., Babady, N. E. Tags: Mycology Source Type: research

Differentiation of Community-Associated and Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates and Identification of spa Types by Use of PCR and High-Resolution Melt Curve Analysis [Clinical Veterinary Microbiology]
Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are present worldwide and represent a major public health concern. The capability of PCR followed by high-resolution melt (HRM) curve analysis for the detection of community-associated and livestock-associated MRSA strains and the identification of staphylococcal protein A (spa) locus was evaluated in 74 MRSA samples which were isolated from the environment, humans, and pigs on a single piggery. PCR-HRM curve analysis identified four spa types among MRSA samples and differentiated MRSA strains accordingly. A nonsubjective differentiation model was develop...
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Ghorashi, S. A., Heller, J., Zhang, Q., Sahibzada, S. Tags: Clinical Veterinary Microbiology Source Type: research

High-Content Screening, a Reliable System for Coxiella burnetii Isolation from Clinical Samples [Bacteriology]
Q fever, caused by Coxiella burnetii, is a worldwide zoonotic disease that may cause severe forms in humans and requires a specific and prolonged antibiotic treatment. Although current serological and molecular detection tools allow a reliable diagnosis of the disease, culture of C. burnetii strains is mandatory to assess their susceptibility to antibiotics and sequence their genome in order to optimize patient management and epidemiological studies. However, cultivating this fastidious microorganism is difficult and restricted to reference centers, as it requires biosafety level 3 laboratories and relies on cell culture p...
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Francis, R., Mioulane, M., Le Bideau, M., Mati, M.-C., Fournier, P.-E., Raoult, D., Bou Khalil, J. Y., La Scola, B. Tags: Bacteriology Source Type: research

Evaluation of a Novel Multiplex PCR Panel Compared to Quantitative Bacterial Culture for Diagnosis of Lower Respiratory Tract Infections [Bacteriology]
Quantitative bacterial culture of bronchoalveolar lavage fluids (BALF) is labor-intensive, and the delay involved in performing culture, definitive identification, and susceptibility testing often results in prolonged use of broad-spectrum antibiotics. The Unyvero lower respiratory tract (LRT) panel (Curetis, Holzgerlingen, Germany) allows the multiplexed rapid detection and identification of 20 potential etiologic agents of pneumonia within 5 h of collection. In addition, the assay includes detection of gene sequences that confer antimicrobial resistance. We retrospectively compared the performance of the molecular panel ...
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Collins, M. E., Popowitch, E. B., Miller, M. B. Tags: Bacteriology Source Type: research

Photo Quiz: A 55-Year-Old-Man with Rectal Bleeding and a Rectal Mass [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Poon, Y. C., Choy, C. Y., Bundele, M. M., Sadarangani, S. P. Tags: Photo Quiz Source Type: research

Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-{beta}-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit [Bacteriology]
We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total ...
Source: Journal of Clinical Microbiology - April 23, 2020 Category: Microbiology Authors: Chapman, P., Forde, B. M., Roberts, L. W., Bergh, H., Vesey, D., Jennison, A. V., Moss, S., Paterson, D. L., Beatson, S. A., Harris, P. N. A. Tags: Bacteriology Source Type: research