Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing [Virology]
LamPORE is a novel diagnostic platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining loop-mediated isothermal amplification with nanopore sequencing, which could potentially be used to analyze thousands of samples per day on a single instrument. We evaluated the performance of LamPORE against reverse transcriptase PCR (RT-PCR) using RNA extracted from spiked respiratory samples and stored nose and throat swabs collected at two UK hospitals. The limit of detection of LamPORE was 10 genome copies/μl of extracted RNA, which is above the limit achievable by RT-PCR, but was n...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Peto, L., Rodger, G., Carter, D. P., Osman, K. L., Yavuz, M., Johnson, K., Raza, M., Parker, M. D., Wyles, M. D., Andersson, M., Justice, A., Vaughan, A., Hoosdally, S., Stoesser, N., Matthews, P. C., Eyre, D. W., Peto, T. E. A., Carroll, M. W., de Silva, Tags: Virology Source Type: research

Evaluation of Diagnostic Accuracy of Eight Commercial Assays for the Detection of Measles Virus-Specific IgM Antibodies [Immunoassays]
The World Health Organization (WHO) has targeted measles for global eradication through mass immunization. For effective monitoring of eradication targets, high-quality surveillance is needed. The detection of IgM antibodies, specific to the measles virus, with the use of commercial enzyme-linked immunosorbent assays (ELISA or EIA) is broadly used within the WHO global measles and rubella laboratory network for laboratory confirmation, and in particular, ELISA kits manufactured by Siemens (Enzygnost kits) have been primarily used. Spurred by the discontinuation of these kits, this study aims to report on the clinical sensi...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Hiebert, J., Zubach, V., Charlton, C. L., Fenton, J., Tipples, G. A., Fonseca, K., Severini, A. Tags: Immunoassays Source Type: research

Analysis of Yersinia pseudotuberculosis Isolates Recovered from Deceased Mammals of a German Zoo Animal Collection [Clinical Veterinary Microbiology]
Yersinia pseudotuberculosis is an important pathogen for both humans and animals. It can infect livestock, as well as pets and wild animals. During recent years, a number of reports have described the isolation of Y. pseudotuberculosis from zoo animals, mainly birds and mammals, for which the infection was mostly lethal. Between 2005 and 2019, there were at least 17 cases of deceased mammals, belonging to five different species, which suffered from a Y. pseudotuberculosis infection at the Zoo Wuppertal, Germany. Since only scarce information exists on the properties of Y. pseudotuberculosis from zoo animals, we characteriz...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Hammerl, J. A., vom Ort, N., Barac, A., Jäckel, C., Grund, L., Dreyer, S., Heydel, C., Kuczka, A., Peters, H., Hertwig, S. Tags: Clinical Veterinary Microbiology Source Type: research

Rapid ResaImipenem/Acinetobacter NP Test for Detection of Carbapenem Susceptibility/Resistance in Acinetobacter baumannii [Bacteriology]
The rapid ResaImipenem/Acinetobacter NP test was developed for the identification of carbapenem resistance among Acinetobacter baumannii isolates. The principle of this test is based on the reduction of resazurin (a viability colorant) by metabolically active bacterial cells, hence detecting bacterial growth, in the presence of a defined concentration of imipenem chosen to be slightly above that defining imipenem resistance (6 μg/ml). Bacterial growth is visually detected by a color change from blue (resazurin) to purple or pink (resorufin product). A total of 110 A. baumannii isolates, among which 61 were imipenem resi...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Nordmann, P., Sadek, M., Tinguely, C., Poirel, L. Tags: Bacteriology Source Type: research

Four-Hour Immunochromatographic Detection of Intestinal Carriage of Carbapenemase-Producing Enterobacteriaceae: a Validation Study [Bacteriology]
The increasing incidence of carbapenemase-producing Gram-negative bacilli (C-PGNB) represents a major public health challenge. Rapid detection of digestive colonization with C-PGNB is fundamental to control their spread. We performed the validation of a rapid protocol for C-PGNB detection directly on rectal swabs. We developed a protocol combining enrichment by a rapid selective subculture of the rectal swab medium and realization of a Resist-4 O.K.N.V. K-SeT test on the bacterial pellet obtained. The limit of detection and performances of this protocol were validated in vitro on 52 C-PGNB strains spiked on a calibrated sa...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Gallah, S., Villageois-Tran, K., Godmer, A., Arlet, G., Rottman, M., Benzerara, Y., Garnier, M. Tags: Bacteriology Source Type: research

Specificity of SARS-CoV-2 Real-Time PCR Improved by Deep Learning Analysis [Virology]
We describe how this model can be deployed as a quality assurance tool to monitor result interpretation in real time. The model’s performance with the TaqPath COVID19 Combo Kit assay, widely used for SARS-CoV-2 detection, is described. This model can be applied broadly for the primary interpretation of RT-PCR assays and potentially replace the CT interpretive paradigm. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Alouani, D. J., Rajapaksha, R. R. P., Jani, M., Rhoads, D. D., Sadri, N. Tags: Virology Source Type: research

Emergence of Parechovirus A3 as the Leading Cause of Central Nervous System Infection, Surpassing Any Single Enterovirus Type, in Children in Kansas City, Missouri, USA, from 2007 to 2016 [Epidemiology]
Picornaviruses, including Enterovirus species A to D (EV) and Parechovirus species A (PeV-A), are the leading reported causes of pediatric central nervous system infections in the United States. We investigated the molecular epidemiology of EV and PeV-A over 10 years in cerebrospinal fluid (CSF) collected from children seen at Children’s Mercy-Kansas City (CMKC) from 2007 through 2016. The overall prevalence for EV was 16% (862/5,362) and 7% (271/4,016) for PeV. Among all picornavirus CSF detections, EV was 76%, and PeV-A was 24%. Multiple EV types cocirculated each year, with a total of 31 EV types detected in the 1...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Sasidharan, A., Banerjee, D., Harrison, C. J., Selvarangan, R. Tags: Epidemiology Source Type: research

Antimicrobial Susceptibility Profiles To Predict the Presence of Carbapenemase Genes among Carbapenem-Resistant Pseudomonas aeruginosa Isolates [Bacteriology]
Detection of carbapenem-resistant Pseudomonas aeruginosa (CRPA) with carbapenemase-producing (CP) genes is critical for preventing transmission. Our objective was to assess whether certain antimicrobial susceptibility testing (AST) profiles can efficiently identify CP-CRPA. We defined CRPA as P. aeruginosa with imipenem or meropenem MICs of ≥8 μg/ml; CP-CRPA was CRPA with CP genes (blaKPC/blaIMP/blaNDM/blaOXA-48/blaVIM). We assessed the sensitivity and specificity of AST profiles to detect CP-CRPA among CRPA isolates collected by CDC’s Antibiotic Resistance Laboratory Network (AR Lab Network) and the Emerging I...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Vallabhaneni, S., Huang, J. Y., Grass, J. E., Bhatnagar, A., Sabour, S., Lutgring, J. D., Campbell, D., Karlsson, M., Kallen, A. J., Nazarian, E., Snavely, E. A., Morris, S., Wang, C., Lee, R., Koag, M., Lewis, R., Garcia, B., EIP Work Group, Brown, A. C. Tags: Bacteriology Source Type: research

Development of a Measles and Rubella Multiplex Bead Serological Assay for Assessing Population Immunity [Immunoassays]
Serosurveys are important tools for estimating population immunity and providing immunization activity guidance. The measles and rubella multiplex bead assay (MBA) offers multiple advantages over standard serological assays and was validated by comparison with the enzyme-linked immunosorbent assay (ELISA) and the measles plaque reduction neutralization (PRN) assay. Results from a laboratory-produced purified measles virus whole-virus antigen MBA (MeV WVAL) correlated better with ELISA and PRN than results from the baculovirus-expressed measles nucleoprotein (N) MBA. Therefore, a commercially produced whole-virus antigen (M...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Coughlin, M. M., Matson, Z., Sowers, S. B., Priest, J. W., Smits, G. P., van der Klis, F. R. M., Mitchell, A., Hickman, C. J., Scobie, H. M., Goodson, J. L., Alexander, J. P., Rota, P. A., Bankamp, B. Tags: Immunoassays Source Type: research

Driving Laboratory Standardization of Bacterial Culture and Antimicrobial Susceptibility Testing in Veterinary Clinical Microbiology in Europe and Beyond [Minireviews]
Globally, antimicrobial resistance is one of the most important public health challenges in which the clinical microbiology laboratory plays a critical role by providing guidance for antimicrobial treatment. Despite the recognition of its importance, there is still a real need for the standardized training of clinical microbiologists and harmonization of diagnostic procedures. This is particularly true for veterinary clinical microbiology, where additional challenges exist when microbiologists are trying to fulfill a professional role very similar to that of their colleagues working in human microbiology laboratories. The ...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Timofte, D., Broens, E. M., Guardabassi, L., Pomba, C., Allerton, F., Ikonomopoulos, J., Overesch, G., Damborg, P., on behalf of the European Network for Optimization of Veterinary Antimicrobial Treatment (ENOVAT), ESCMID Study Group for Veterinary Microb Tags: Minireviews Source Type: research

Phenotypic and Genomic Profiling of Staphylococcus argenteus in Canada and the United States and Recommendations for Clinical Result Reporting [Bacteriology]
We present phenotypic and genomic characteristics and provide recommendations for clinical reporting. Between 2017 and 2019, 22 isolates of S. argenteus were received at 2 large reference laboratories for identification. Identification with routine methods (biochemical, matrix-assisted laser desorption ionization–time of flight mass spectrometry [MALDI-TOF MS], 16S rRNA gene analysis) proved challenging to confidently distinguish these isolates from S. aureus. Whole-genome sequencing analysis was employed to confirm identifications. Using several different sequence-based analyses, all clinical isolates under investig...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Eshaghi, A., Bommersbach, C., Zittermann, S., Burnham, C.-A. D., Patel, R., Schuetz, A. N., Patel, S. N., Kus, J. V. Tags: Bacteriology Source Type: research

Predictive Value of Direct Disk Diffusion Testing from Positive Blood Cultures in a Childrens Hospital and Its Utility in Antimicrobial Stewardship [Bacteriology]
Accurate and early susceptibility results could reduce overuse of broad-spectrum antibiotics for empirical treatment of bacteremia. Direct disk diffusion testing (dDD) using nonstandardized inocula directly from blood cultures could facilitate earlier narrowing of antibiotics. To determine the predictive value of dDD compared with standardized antimicrobial susceptibility testing (AST), we performed a retrospective cohort study of 582 blood cultures from 495 pediatric patients with bacteremia. Positive and negative predictive value (PPV: number of isolates susceptible by both dDD and AST divided by the total number of isol...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Savage, T. J., Rao, S., Joerger, J., Ozonoff, A., McAdam, A. J., Sandora, T. J. Tags: Bacteriology Source Type: research

Closing the Brief Case: Disseminated Microsporidiosis with Intestinal Cryptosporidium Coinfection in a Patient with Kaposis Sarcoma and Castleman Disease Presenting with Acute Kidney Injury [Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Agarwal, A. N., Shieh, W.-J., Goldsmith, C. S., Qvarnstrom, Y., Ding, Y., Dallas, S. D., Mais, D. D. Tags: Brief Case Source Type: research

The Brief Case: Disseminated Microsporidiosis with Intestinal Cryptosporidium Coinfection in a Patient with Kaposis Sarcoma and Castleman Disease Presenting with Acute Kidney Injury [Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Agarwal, A. N., Shieh, W.-J., Goldsmith, C. S., Qvarnstrom, Y., Ding, Y., Dallas, S. D., Mais, D. D. Tags: Brief Case Source Type: research

Laboratory Diagnosis of 37 Cases of Bartonella Endocarditis Based on Enzyme Immunoassay and Real-Time PCR [Bacteriology]
In conclusion, EIA coupled with a novel real-time PCR assay can play an important role in Bartonella endocarditis diagnosis and expand the diagnostic arsenal at the disposal of the clinical microbiologist. Since serology remains a major diagnostic tool, recognizing its pitfalls is essential to avoid incorrect diagnosis. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Shapira, L., Rasis, M., Binsky Ehrenreich, I., Maor, Y., Katchman, E. A., Treves, A., Velan, A., Halutz, O., Graidy-Varon, M., Leibovitch, C., Maisler, N., Ephros, M., Giladi, M. Tags: Bacteriology Source Type: research

Precision Pandemic Preparedness: Improving Diagnostics with Metagenomics [Commentary]
The threat posed by novel pandemics in the future remains active. Equipping our routine laboratory with clinical metagenomics to detect unknown threats early on offers a considerable advantage and may be feasible and scalable with the ability to identify complicated infectious diseases in routine care. Though several technical and regulatory challenges still exist, clinical metagenomics may improve individual patient outcomes and provide earlier warning signs to improve pandemic preparedness. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Govender, K. N. Tags: Commentary Source Type: research

Answer to June 2021 Photo Quiz [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Nath, R., Rashid, M. M., Nath, P., Akter, D., Mondal, D., Basher, A. Tags: Photo Quiz Source Type: research

Photo Quiz: Significant Inclusions in Polymorphonuclear Leukocytes [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Nath, R., Rashid, M. M., Nath, P., Akter, D., Mondal, D., Basher, A. Tags: Photo Quiz Source Type: research

Correction for Khan et al., "A Multicenter Study To Evaluate Ceftaroline Breakpoints: Performance in an Area with High Prevalence of Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Lineage" [Author Correction]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Khan, A., Rivas, L. M., Spencer, M., Martinez, R., Lam, M., Rojas, P., Porte, L., Silva, F., Braun, S., Valdivieso, F., M{upsilon}̈lhauser, M., Lafourcade, M., Miller, W. R., Garcia, P., Arias, C. A., Munita, J. M. Tags: Author Correction Source Type: research

Correction for Cutts et al., "Inactivating Zaire Ebolavirus in Whole-Blood Thin Smears Used for Malaria Diagnosis" [Author Correction]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Cutts, T. A., Cook, B. W. M., Poliquin, P. G., Strong, J. E., Theriault, S. S. Tags: Author Correction Source Type: research

False Immunological Detection of CTX-M Enzymes in Klebsiella oxytoca [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Ortiz de la Rosa, J. M., Demord, A., Poirel, L., Greub, G., Blanc, D., Nordmann, P. Tags: Letter To The Editor Source Type: research

Evaluations of SARS-CoV-2 Serological Assay Performance Need Inclusion of Long-Term Samples [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Favresse, J., Douxfils, J. Tags: Letter To The Editor Source Type: research

Development and Validation of a Multiplex Microsphere Immunoassay Using Dried Blood Spots for SARS-CoV-2 Seroprevalence: Application in First Responders in Colorado, USA [Immunoassays]
In this study, a high-throughput SARS-CoV-2 multiplex microsphere immunoassay (MMIA) was developed for the receptor binding domain (RBD) and nucleocapsid (N) that was more sensitive than enzyme-linked immunosorbent assay (ELISA) (98% versus 87%). The MMIA was then applied and validated in 264 first responders in Colorado using serum and dried blood spot (DBS) eluates, compared to ELISA, and evaluated for neutralizing antibodies. Four percent (11/264) of first responders were seropositive in July to August 2020. Serum and DBS were highly correlated for anti-RBD and anti-N antibodies (R = 0.83, P
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Schultz, J. S., McCarthy, M. K., Rester, C., Sabourin, K. R., Annen, K., DomBourian, M., Eisenmesser, E., Frazer-Abel, A., Knight, V., Jaenisch, T., Morrison, T. E., Rochford, R., Kedl, R. M. Tags: Immunoassays Source Type: research

Clinical and Analytical Evaluation of the Alinity m HR HPV Assay within the VALGENT-3 Framework [Virology]
In conclusion, Alinity m fulfills the international accuracy requirements for use in cervical cancer screening and shows excellent HPV genotype-specific concordance with three clinically validated HPV tests. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Dhillon, S. K., Ostrbenk Valencak, A., Xu, L., Poljak, M., Arbyn, M. Tags: Virology Source Type: research

A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches [Mycobacteriology and Aerobic Actinomycetes]
The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow f...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Bogaerts, B., Delcourt, T., Soetaert, K., Boarbi, S., Ceyssens, P.-J., Winand, R., Van Braekel, J., De Keersmaecker, S. C. J., Roosens, N. H. C., Marchal, K., Mathys, V., Vanneste, K. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Comparative Performance of Latest-Generation and FDA-Cleared Serology Tests for the Diagnosis of Chagas Disease [Parasitology]
This study provides a direct comparison of the latest-generation IgG serology assays with four previously assessed FDA-cleared tests. Seven hundred ten blood donor plasma specimens were evaluated by Wiener Lisado and Wiener v.4.0 enzyme-linked immunosorbent assays (ELISAs) and Abbott PRISM Chagas chemiluminescent assay (ChLIA). Sensitivity and specificity were assessed relative to infection status as determined by the original blood donation testing algorithm. All three latest-generation assays demonstrated 100% specificity (95% confidence interval [CI], 98.6 to 100.0). Wiener Lisado, Wiener v.4.0, and Abbott PRISM had sen...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Kelly, E. A., Bulman, C. A., Gunderson, E. L., Irish, A. M., Townsend, R. L., Sakanari, J. A., Stramer, S. L., Bern, C., Whitman, J. D. Tags: Parasitology Source Type: research

The Genotype-to-Phenotype Dilemma: How Should Laboratories Approach Discordant Susceptibility Results? [Minireviews]
Traditional culture-based methods for identification and antimicrobial susceptibility testing (AST) of bacteria take 2 to 3 days on average. Syndromic molecular diagnostic panels have revolutionized clinical microbiology laboratories as they can simultaneously identify an organism and detect some of the most significant antimicrobial resistance (AMR) genes directly from positive blood culture broth or from various specimen types (e.g., whole blood, cerebrospinal fluid, and respiratory specimens). The presence or absence of an AMR marker associated with a particular organism can be used to predict the phenotypic AST results...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Yee, R., Dien Bard, J., Simner, P. J. Tags: Minireviews Source Type: research

Prevalence of blaCTX-M Genes in Gram-Negative Bloodstream Isolates across 66 Hospitals in the United States [Epidemiology]
Understanding bacterial species at greatest risk for harboring blaCTX-M genes is necessary to guide antibiotic treatment. We identified the species-specific prevalence of blaCTX-M genes in Gram-negative clinical isolates from the United States. Twenty-four microbiology laboratories representing 66 hospitals using the GenMark Dx ePlex blood culture identification Gram-negative (BCID-GN) panel extracted blood culture results from April 2019 to July 2020. The BCID-GN panel includes 21 Gram-negative targets. Along with identifying blaCTX-M genes, it detects major carbapenemase gene families. A total of 4,209 Gram-negative bloo...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Tamma, P. D., Smith, T. T., Adebayo, A., Karaba, S. M., Jacobs, E., Wakefield, T., Nguyen, K., Whitfield, N. N., Simner, P. J. Tags: Epidemiology Source Type: research

Performance of Three Commercial Molecular Diagnostic Assays for the Simultaneous Detection of Mycoplasma genitalium and Macrolide Resistance [Bacteriology]
The increasing frequency of macrolide resistance is an emerging issue in the treatment of Mycoplasma genitalium infection. Because evaluation of new commercial kits detecting M. genitalium and macrolide resistance is needed, we evaluated the performance and handling characteristics of the Allplex MG & AziR (Seegene), the Macrolide-R/MG ELITe MGB (ELITechGroup), and the ResistancePlus MG FleXible (SpeeDx-Cepheid) kits in comparison with those of an in-house real-time PCR and 23S rRNA gene sequencing used as the reference. A total of 239 urogenital specimens (135 M. genitalium-positive and 104 M. genitalium-negative spec...
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Authors: Le Roy, C., Bebear, C., Pereyre, S. Tags: Bacteriology Source Type: research

Editorial Board [Masthead]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - May 19, 2021 Category: Microbiology Tags: Masthead Source Type: research

Multicenter Evaluation of Processing and Analysis of College of American Pathologists (CAP) Proficiency Testing Samples by Laboratory Automation [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Babady, N. E., Bourassa, L., Burnham, C.-A. D., Fisher, M., McElvania, E., Polage, C. R., Ribes, J. Tags: Letter To The Editor Source Type: research

Anti-Human T-Cell Leukemia Virus Type 1 (HTLV-1) Antibody Assays in Cerebrospinal Fluid for the Diagnosis of HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis [Virology]
The anti-human T-cell leukemia virus type 1 (HTLV-1) antibody assay in common use has changed from the particle agglutination (PA) method to chemiluminescent immunoassay (CLIA) and chemiluminescent enzyme immunoassay (CLEIA). These assays were validated in serum but not in cerebrospinal fluid (CSF). However, anti-HTLV-1 antibody positivity in CSF is a requisite for diagnosing HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). We qualitatively compared the assays in CSF from 47 HAM/TSP patients diagnosed using PA, 15 HTLV-1 carriers (HCs), and 18 negative controls. In determining the positivity or negativi...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Kodama, D., Tanaka, M., Matsuzaki, T., Nozuma, S., Matsuura, E., Takashima, H., Izumo, S., Kubota, R. Tags: Virology Source Type: research

Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations [Bacteriology]
In this study, 28 H. pylori strains isolated from gastric biopsy specimens from a high-gastric-cancer-risk (HGCR) population living in the Andes Mountains in Túquerres, Colombia and 31 strains from a low-gastric-cancer-risk (LGCR) population residing on the Pacific coast in Tumaco, Colombia were subjected to antibiotic susceptibility testing for amoxicillin, clarithromycin, levofloxacin, metronidazole, rifampin, and tetracycline. Resistance-associated genes were amplified by PCR for all isolates, and 29 isolates were whole-genome sequenced (WGS). No strains were resistant to amoxicillin, clarithromycin, or rifampin....
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Mannion, A., Dzink-Fox, J., Shen, Z., Piazuelo, M. B., Wilson, K. T., Correa, P., Peek, R. M., Camargo, M. C., Fox, J. G. Tags: Bacteriology Source Type: research

Deciphering an Adenovirus F41 Outbreak in Pediatric Hematopoietic Stem Cell Transplant Recipients by Whole-Genome Sequencing [Virology]
We report here the clinical course of HAdV-F41 infection and the phylogenetic investigation to identify interpatient transmission. HAdV DNA was quantified in stool and plasma samples by real-time PCR. HAdV type was determined by sequencing of the fiber and hexon genes. Phylogenetic investigation was done with whole-genome sequences obtained by next-generation sequencing. HAdV loads in stool samples ranged from 6.60 to 10.10 log10 copies/ml. HAdV-F41 detection in plasma was observed in four patients, but no disseminated disease was reported. Two patients died, but neither death was attributed to HAdV. While sequencing limit...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Lefeuvre, C., Salmona, M., Feghoul, L., Ranger, N., Mercier-Delarue, S., Nizery, L., Alimi, A., Dalle, J.-H., LeGoff, J. Tags: Virology Source Type: research

Detection of Tick-Borne Bacteria from Whole Blood Using 16S Ribosomal RNA Gene PCR Followed by Next-Generation Sequencing [Bacteriology]
Reported cases of tick-borne diseases have steadily increased for more than a decade. In the United States, a majority of tick-borne infections are caused by bacteria. Clinical diagnosis may be challenging, as tick-borne diseases can present with similar symptoms. Laboratory diagnosis has historically relied on serologic methods, which have limited utility during the acute phase of disease. Pathogen-specific molecular methods have improved early diagnosis, but can be expensive when bundled together and may miss unexpected or novel pathogens. To address these shortcomings, we developed a 16S rRNA gene PCR with a next-genera...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Rodino, K. G., Wolf, M. J., Sheldon, S., Kingry, L. C., Petersen, J. M., Patel, R., Pritt, B. S. Tags: Bacteriology Source Type: research

Verification and Validation of SARS-CoV-2 Assay Performance on the Abbott m2000 and Alinity m Systems [Virology]
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 Thermo Fisher 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, and commercially available controls were used for the analytical verification to confirm the limit of detection, linearity, and reproducibility. We used nasopharyngeal (NP) swab specimens collected in saline for the clinica...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Hirschhorn, J. W., Kegl, A., Dickerson, T., Glen, W. B., Xu, G., Alden, J., Nolte, F. S. Tags: Virology Source Type: research

Comparable Specimen Collection from Both Ends of At-Home Midturbinate Swabs [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Truong, M., Pfau, B., McDermot, E., Han, P. D., Brandstetter, E., Richardson, M., Kim, A. E., Rieder, M. J., Chu, H. Y., Englund, J. A., Nickerson, D. A., Shendure, J., Lockwood, C. M., Konnick, E. Q., Starita, L. M., on behalf of the Seattle Flu Study In Tags: Letter To The Editor Source Type: research

Mycoplasma hyopneumoniae Surveillance in Pig Populations: Establishing Sampling Guidelines for Detection in Growing Pigs [Epidemiology]
Antemortem detection of Mycoplasma hyopneumoniae 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, has the potential to improve M. hyopneumoniae surveillance. A field study was performed over a 14-week period during which 10 pigs in one pen at the center of a room with 1,250 6-week-old pigs housed in 46 pens were intratracheally inoculated with M. hyopneumoniae. Thereafter, one tracheal sample, four serum samples, and one oral fluid sample were collected from every pen at 2-week int...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Clavijo, M. J., Hu, D., Krantz, S., Cano, J. P., Pereira Marostica, T., Henao-Diaz, A., Poeta Silva, A. P. S., Hemker, D., Tapia, E., Zimmerman, S., Fano, E., Polson, D., Fitzgerald, R., Tucker, A., Main, R., Wang, C., Zimmerman, J. J., Rotolo, M. L. Tags: Epidemiology Source Type: research

Clinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from Stool [Bacteriology]
Helicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high clarithromycin-based therapy failure rates, are seen worldwide, but U.S. data are limited. We developed a real-time PCR assay for simultaneous detection of H. pylori and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an H. pylori stool ...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Marrero Rolon, R., Cunningham, S. A., Mandrekar, J. N., Polo, E. T., Patel, R. Tags: Bacteriology Source Type: research

Portable RT-PCR System: a Rapid and Scalable Diagnostic Tool for COVID-19 Testing [Virology]
This study assessed the agreement and accuracy of the portable Biomeme SARS-CoV-2 system against the gold standard tests. Nasopharyngeal and nasal swabs were used. Of the 192 samples tested using the Biomeme SARS-CoV-2 system, the results from 189 samples (98.4%) were in agreement with the reference standard-of-care RT-PCR testing for SARS-CoV-2. The portable system generated simultaneous results for nine samples in 80 min with high positive and negative percent agreements of 99.0% and 97.8%, respectively. We performed separate testing in a sealed glove box, offering complete biosafety containment. Thus, the Biomeme SARS-C...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Zowawi, H. M., Alenazi, T. H., AlOmaim, W. S., Wazzan, A., Alsufayan, A., Hasanain, R. A., Aldibasi, O. S., Althawadi, S., Altamimi, S. A., Mutabagani, M., Alamri, M., Almaghrabi, R. S., Al-Abdely, H. M., Memish, Z. A., Alqahtani, S. A. Tags: Virology Source Type: research

Evaluation of the Roche cobas MTB and MTB-RIF/INH Assays in Samples from Germany and Sierra Leone [Mycobacteriology and Aerobic Actinomycetes]
In conclusion, cobas MTB and MTB-RIF/INH assays provide accurate detection of MTBC DNA and resistance-associated mutations in respiratory samples. The influence of regional variations in the prevalence of resistance-conferring mutations requires further investigation. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Nadarajan, D., Hillemann, D., Kamara, R., Foray, L., Conteh, O. S., Merker, M., Niemann, S., Lau, J., Njoya, M., Kranzer, K., Somoskovi, A., Maurer, F. P. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study [Epidemiology]
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. From October 2019 to March 2020, we conducted a home-based cross-sectional study in the greater Seattle, WA, area, utilizing electronic consent and data collection instruments. Participants received nasal swab collection kits via rapid delivery within 24 hours of self-reporting respiratory symptoms. S...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Kim, A. E., Brandstetter, E., Wilcox, N., Heimonen, J., Graham, C., Han, P. D., Starita, L. M., McCulloch, D. J., Casto, A. M., Nickerson, D. A., Van de Loo, M. M., Mooney, J., Ilcisin, M., Fay, K. A., Lee, J., Sibley, T. R., Lyon, V., Geyer, R. E., Thomp Tags: Epidemiology Source Type: research

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 [Immunoassays]
In this study, we comprehensively analyzed multispecific antibody kinetics of different immunoglobulins in hospitalized patients with acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Three hundred fifty-four blood samples longitudinally obtained from 81 IgG-seroconverting progressed coronavirus disease 2019 (CoVID-19) patients were quantified for spike 1 (S1), S2, and nucleocapsid protein (NCP)-specific IgM, IgA, IgG, and total Ig antibodies using a microarray, 11 different enzyme-linked immunosorbent assays (ELISAs)/chemiluminescence immunoassays (CLIAs), and 1 rapid test by seven manufacturer...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Semmler, G., Traugott, M. T., Graninger, M., Hoepler, W., Seitz, T., Kelani, H., Karolyi, M., Pawelka, E., Aragon de La Cruz, S., Puchhammer-Stöckl, E., Aberle, S. W., Stiasny, K., Zoufaly, A., Aberle, J. H., Weseslindtner, L. Tags: Immunoassays Source Type: research

Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis [Minireviews]
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (sal...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Lee, R. A., Herigon, J. C., Benedetti, A., Pollock, N. R., Denkinger, C. M. Tags: Minireviews Source Type: research

Rapid High-Throughput Whole-Genome Sequencing of SARS-CoV-2 by Using One-Step Reverse Transcription-PCR Amplification with an Integrated Microfluidic System and Next-Generation Sequencing [Virology]
The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here, we report a simple and efficient workflow for whole-genome sequencing utilizing one-step reverse transcription-PCR (RT-PCR) amplification on a microfluidic platform, followed by MiSeq amplicon sequencing. The method uses Fluidigm integrated fluidic circuit (IFC) and instruments to amplify 48 samples with 39 pairs of primers, including 35 custom-designed primer pairs and four additional primer pairs from the ARTIC network protocol v3. Application of this method on RNA samples from both viral isolates and clinical spec...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Li, T., Chung, H. K., Pireku, P. K., Beitzel, B. F., Sanborn, M. A., Tang, C. Y., Hammer, R. D., Ritter, D., Wan, X.-F., Maljkovic Berry, I., Hang, J. Tags: Virology Source Type: research

Genomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST [Bacteriology]
Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve the discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 225 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% ...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Weigand, M. R., Peng, Y., Pouseele, H., Kania, D., Bowden, K. E., Williams, M. M., Tondella, M. L. Tags: Bacteriology Source Type: research

Evaluation of the Accelerate Pheno System for Rapid Identification and Antimicrobial Susceptibility Testing of Positive Blood Culture Bottles Inoculated with Primary Sterile Specimens from Patients with Suspected Severe Infections [Bacteriology]
The Accelerate Pheno system is approved for 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 of the system for identification and AST from positive blood culture bottles inoculated with primary sterile nonblood specimens from patients with suspected severe infections. One hundred positive blood culture bottles with primary sterile specimens (63 cerebrospinal fluids, 16 ascites, 7 pleural fluids, 4 vitreous fluids, 5 joint aspirates, and 5 other aspirates) from 100 patie...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Chapot, V., Effenberg, L., Dohmen-Ruetten, J., Buer, J., Kehrmann, J. Tags: Bacteriology Source Type: research

Comparison of 16 Serological SARS-CoV-2 Immunoassays in 16 Clinical Laboratories [Virology]
This study was a Danish national collaboration and evaluated 15 commercial and one in-house anti-SARS-CoV-2 assays in 16 laboratories. Sensitivity was evaluated using 150 samples from individuals with asymptomatic, mild, or moderate COVID-19, nonhospitalized or hospitalized, confirmed by nucleic acid amplification tests (NAAT); samples were collected 13 to 73 days either from symptom onset or from positive NAAT (patients without symptoms). Specificity and cross-reactivity were evaluated in samples collected prior to the SARS-CoV-2 epidemic from>586 blood donors and patients with autoimmune diseases, cytomegalovirus or E...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Harritshoj, L. H., Gybel-Brask, M., Afzal, S., Kamstrup, P. R., Jorgensen, C. S., Thomsen, M. K., Hilsted, L., Friis-Hansen, L., Szecsi, P. B., Pedersen, L., Nielsen, L., Hansen, C. B., Garred, P., Korsholm, T.-L., Mikkelsen, S., Nielsen, K. O., Moller, B Tags: Virology Source Type: research

Antibody Responses to Two Recombinant Treponemal Antigens (rp17 and TmpA) before and after Azithromycin Treatment for Yaws in Ghana and Papua New Guinea [Epidemiology]
WHO and its partners aim to interrupt yaws transmission in countries of endemicity 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. We evaluated changes in antibody levels against two recombinant treponemal antigens, rp17 (also known as Tp17) and TmpA, after antibiotic treatment given as part of a randomized controlled trial for yaws in Ghana and Papua New Guinea. Paired serum samples from children aged 6 to 15 years with confirmed yaws, collected before and after treatment, were tested...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Parameswaran, N., Mitja, O., Bottomley, C., Kwakye, C., Houinei, W., Pillay, A., Danavall, D., Chi, K.-H., Ballard, R. C., Solomon, A. W., Chen, C. Y., Bieb, S. V., Adu-Sarkodie, Y., Mabey, D. C. W., Asiedu, K., Marks, M., Martin, D. L. Tags: Epidemiology Source Type: research

Immunologic Testing for SARS-CoV-2 Infection from the Antigen Perspective [Minireviews]
Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally as a severe pandemic. SARS-CoV-2 infection stimulates antigen-specific antibody responses. Multiple serologic tests have been developed for SARS-CoV-2. However, which antigens are most suitable for serological testing remains poorly understood. Specifically, which antigens have the highest sensitivity and specificity for serological testing and which have the least cross-reactivity with other coronaviruses are currently unknown. Previous studies have shown that the S1 domain...
Source: Journal of Clinical Microbiology - April 20, 2021 Category: Microbiology Authors: Li, D., Li, J. Tags: Minireviews Source Type: research