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Journal Diagn Microbiol Infect Dis

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Evaluation of the Abbott PanbioTM COVID-19 Ag Rapid Antigen Test for the Detection of SARS-CoV-2 in Asymptomatic Canadians

Julie L V Shaw, Vincent Deslandes, Jennifer Smith, Marc Desjardins,

<h4>Background</h4> Several rapid testing methodologies have been approved for testing of symptomatic individuals but have not been validated for asymptomatic screening. We evaluated performance of the Abbott PanbioTM COVID-19 rapid antigen assay in the asymptomatic setting. <h4>Methods</h4> We conducted a prospective study in an urban assessment center and in the ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Target Capture Sequencing of SARS-CoV-2 Genomes Using the ONETest Coronaviruses Plus

Shing H. Zhan, Sepideh M. Alamouti, Habib Daneshpajouh, Brian S. Kwok, Meng-Hsun Lee, Jaswinder Khattra, Herbert J. Houck, Kenneth H. Rand,

We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence SARS-CoV-2 genomes and select loci of other respiratory viruses. We applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a PCR assay. ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Algorithm for rational use of FilmArray Pneumonia Panel in bacterial coinfections of critically ill ventilated COVID-19 patients

Emmanuel Novy, Antoine Goury, Carine Thivilier, Thomas Guillard, Corentine Alauzet,

The FilmArray® Pneumonia Panel has proven to be an effective tool for rapid detection of main respiratory pathogens. However, its rational use needs appropriate knowledge and formation regarding its indication and interpretation. Herein, we provide some advices to help with success of its daily routine use, particularly in critically ill ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection

Juan Manuel Sánchez-Calvo, Juan Carlos Alados Arboledas, Luis Ros Vidal, José Luis de Francisco, María Dolores López Prieto,

<h4>Objectives</h4> : To compare the RT-PCR Allplex SARS-CoV-2/FluA/FluB/RSV Assay (Allplex assay) with other methods of detection of VOC B.1.1.7. <h4>Methods</h4> : Suspected and non-suspected cases of VOC B.1.1.7 were defined according to the VirSNiP assay, which detects N501Y and deletion H69-V70. For pre-screening, the Allplex™ and TaqPath assays were used. ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Evaluation of automated antigen detection test for detection of SARS-CoV-2

Gannon CK Mak, Stephen SY Lau, Kitty KY Wong, Nancy LS Chow, CS Lau, Ken HL Ng, Edman TK Lam, Rickjason CW Chan, Dominic NC Tsang,

Background and objective: RT-PCR is the gold standard to detect SARS-CoV-2, however, its capacity is limited. We evaluated an automated antigen detection (AAD) test, Elecsys SARS-CoV-2 Antigen (Roche, Germany), for detecting SARS-CoV-2. Results: We compared the limit of detection (LOD) between AAD, rapid antigen detection (RAD) test, SARS-CoV-2 Rapid Antigen ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Characterization of virulent Klebsiella variicola recovered from inpatients with intestinal and extraintestinal infections between 1987 and 1999.

Tiago Barcelos Valiatti, Fernanda Fernandes Santos, Pedro Henrique Soares Nunes, Rodrigo Cayô, Ana Cristina Gales, Tânia Aparecida Tardelli Gomes,

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115482]

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Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry.

Christian Salgård Jensen, Rimtas Dargis, Patricia Shewmaker, Xiaohui Chen Nielsen, Jens Jørgen Christensen,

This study evaluated the ability of the MALDI-ToF MS from Bruker Daltonics to identify clinical Mitis-Group-Streptococcus isolates with a focus on Streptococcus pseudopneumoniae. The results were analyzed using the standard log(score) and the previously published list(score). Importantly, using the log(score) no misidentifications occurred and 27 of 29 (93%) S. pneumoniae ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115487]

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Testing individual and pooled saliva samples for sars-cov-2 nucleic acid: a prospective study

M. Migueres, C. Vellas, F. Abravanel, I. Da Silva, C. Dimeglio, V. Ferrer, S. Raymond, JM. Mansuy, J. Izopet,

Control of the rapid spread of the SARS-CoV-2 virus requires efficient testing. We collected paired nasopharyngeal swab (NPs) and saliva samples from 303 subjects (52.8% symptomatic) at a drive-through testing center; 18% of whom tested positive. The NPs, salivas and five saliva pools were tested for SARS-CoV-2 RNA using the ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Activity of β-lactam plus β-lactam-enhancer combination cefepime/zidebactam against Klebsiella pneumoniae harbouring defective OmpK35/36 porins and carbapenemases.

Prashant Joshi, Rahul Shrivastava, Sachin Bhagwat, Mahesh Patel,

Cefepime/zidebactam is a β-lactam/β-lactam-enhancer based novel antibiotic which is in clinical development for treating infections caused by multidrug-resistant Gram-negative bacteria. Here, in vitro activity of cefepime/zidebactam was determined against multicentre Klebsiella pneumoniae clinical isolates co-expressing serine and/or metallo-carbapenemases and defective OmpK35 and OmpK36 porins. The MICs were determined using the ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115481]

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Assessment and utility of 2 Chlamydia trachomatis Pgp3 serological assays for seroprevalence studies among women in the United States.

Damien C Danavall, Sarah Gwyn, Gloria E Anyalechi, Katherine E Bowden, Jaeyoung Hong, Robert D Kirkcaldy, Kyle T Bernstein, Ellen N Kersh, Diana Martin, Brian H Raphael,

Two plasmid gene protein (Pgp3)-based serological assays, the Pgp3-ELISA and multiplex bead assay (Pgp3-MBA), were compared and used to estimate seropositivity of Chlamydia trachomatis (CT) among females 14 to 39 years old participating in the National Health and Nutrition Examination Survey between 2013-2016. Of the 2,201 specimens tested, 502 (29.5%, ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115480]

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The potential impact of discrepancies between automated susceptibility platforms and other testing metho`dologies for cefazolin in the treatment of Enterobacterales bloodstream infections.

Mandee Noval, Emily L Heil, Paula Williams, J Kristie Johnson, Kimberly C Claeys,

Revised breakpoints for cefazolin (CFZ) against Enterobacterales may be difficult to implement with current automated susceptibility testing platforms and could falsely report organisms as susceptible, leading to inappropriate treatment for bloodstream infections (BSI). This was a retrospective cohort of adult patients with Enterobacterales BSI reported CFZ susceptible per Vitek®2. The ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115483]

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Serological response in health care workers after a single dose of SARS-CoV-2 vaccine using six automated SARS-CoV-2 antibody assays.

Matthias Cuykx, Olivier Mortelé, Hilde Jansens, Sofie Schouwers, Anissa Meskal, Ilse Hoffbauer, Bart Peeters,

Spike (S)- and nucleocapsid (N)-specific serological assay responses were determined before and/or after first dose SARS-CoV-2 vaccination in 22 individuals. S-specific assays quantified antibodies after vaccination with significant higher levels in participants with a previous infection. Be cautious combining N-/S-specific assay results, potentially differentiating post-infection/vaccination immunization as assay-specific N-antibody waning ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115486]

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SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: Reports in two cities in the United States

Mindy Leelawong, Stephanie L. Mitchell, Randal C. Fowler, Scott Hughes, Marissa P. Griffith, Jane W. Marsh, Lee H. Harrison, Jennifer L. Rakeman,

Nasal and nasopharyngeal swab specimens tested by the Cepheid Xpert Xpress SARS-CoV-2 were analyzed by whole-genome sequencing based on impaired detection of the N2 target. Each viral genome had at least one mutation in the N gene, which likely arose independently in the New York City and Pittsburgh study sites. ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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BACTERIAL CO-INFECTIONS IN COVID-19 PNEUMONIA IN A TERTIARY CARE HOSPITAL: SURFING THE FIRST WAVE

Mario Ruiz-Bastián, Iker Falces-Romero, Juan Carlos Ramos-Ramos, Manuela de Pablos, Julio García-Rodríguez, SARS-CoV-2 Working Group,

The aim of this study is to review bacterial isolates from respiratory samples of patients with severe COVID-19 disease during the first two months of the first wave of in our hospital. A single-centre retrospective observational study in critically ill adult patients was performed. A total of 1251 respiratory samples ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, :]

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Identification of bacterial co-detections in COVID-19 critically Ill patients by BioFire® FilmArray® pneumonia panel: a systematic review and meta-analysis.

Tristan T Timbrook, Kyle D Hueth, Christine C Ginocchio,

Among critically ill COVID-19 patients, bacterial coinfections may occur, and timely appropriate therapy may be limited with culture-based microbiology due to turnaround time and diagnostic yield challenges (e.g. antibiotic pre-exposure). We performed a systematic review and meta-analysis of the impact of BioFire® FilmArray® Pneumonia Panel in detecting bacteria and clinical ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115476]

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Comparison of outcomes in urinary tract infections caused by AmpC-harboring organisms treated with AmpC stable versus AmpC susceptible agents.

Julia Sapozhnikov, Angela Huang, Kelsey Zeeck, Allison Gibble,

There is minimal data on the optimal treatment of lower inoculum infections such as urinary tract infections (UTIs) caused by SPICE organisms which encode the betalactamase enzyme, AmpC. This single-center, retrospective review of adult hospitalized patients with UTIs caused by a SPICE organism compared outcomes amongst patients treated with drugs ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115472]

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Anti-staphylococcal lysin, LSVT-1701, activity: In vitro susceptibility of Staphylococcus aureus and coagulase-negative staphylococci (CoNS) clinical isolates from around the world collected from 2002 to 2019.

David B Huang, Helio S Sader, Paul R Rhomberg, Eric Gaukel, Katyna Borroto-Esoda,

LSVT-1701 (previously known as SAL200), is a novel, recombinantly-produced, bacteriophage-encoded lysin that specifically targets staphylococci via cell wall enzymatic hydrolysis. In vitro activities of LSVT-1701 and comparators were tested against 415 Staphylococcus aureus and coagulase-negative staphylococci (CoNS) clinical isolates expressing various resistance phenotypes. The isolates were collected worldwide from 2002 ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115471]

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Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings.

Meredith S Muller, Srijana B Chhetri, Christopher Basham, Tyler Rapp, Feng-Chang Lin, Kelly Lin, Daniel Westreich, Carla Cerami, Jonathan J Juliano, Jessica T Lin,

Alternatives to nasopharyngeal sampling are needed to increase capacity for SARS-CoV-2 testing. Among 275 participants, we piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including polyester flocked swabs as well as 3D-printed plastic lattice swabs, placed into viral transport media or an RNA stabilization agent. Flocked nasal swabs ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115469]

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Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens.

Floriana Bonura, Chiara Mascarella, Chiara Filizzolo, Celestino Bonura, Donatella Ferraro, Francesca Di Bernardo, Antonella Collura, Vito Martella, Giovanni M Giammanco, Simona De Grazia,

The performance of 2 antigenic commercial assays for enteric adenovirus (AdV) infection, bioNexia Rota-Adeno ImmunoChromatographic Tests (ICT) and LIAISON® Adenovirus ChemiLuminescence Immuno Assays (CLIA), was evaluated on 321 stools from children hospitalized for acute gastroenteritis in Palermo, Italy, using a Real time-PCR (Rt-PCR) as reference method. The CLIA showed higher ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115459]

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A comparison of cotton-tipped and nylon flocked swabs for culture of Neisseria gonorrhoeae from oropharyngeal samples.

Tiffany R Phillips, Marjan Tabesh, Christopher K Fairley, Kate Maddaford, Shivani Pasricha, Rebecca Wigan, Vesna De Petra, Deborah A Williamson, Eric P F Chow,

Our aim was to determine if there was a difference in culture positivity for oropharyngeal gonorrhoea when sampling using a nylon-flocked versus cotton-tipped swab. We collected FLOQSwabs and cotton-tipped swabs from individuals aged ≥ 18 years who had untreated oropharyngeal gonorrhoea detected by NAAT between November 2019-June 2020.Of 78 participants, ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115455]

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Predictors and usefulness of targeted therapy for pneumococcal community-acquired pneumonia diagnosed by the urinary antigen test: a prospective, observational cohort study.

Akihiro Ito, Tadashi Ishida, Hiromasa Tachibana, Yosuke Nakanishi, Akio Yamazaki, Yasuyoshi Washio,

The aim of the present study was to investigate the predictors of targeted therapy (TT) for pneumococcal community-acquired pneumonia (PCAP) with a positive urinary antigen test (UAT) and compare the outcomes with those of nontargeted therapy. This prospective cohort study enrolled consecutive PCAP patients with a positive UAT who were ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(1):115457]

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Impact of Chronic Hepatitis C virus co-infection on outcomes of infective endocarditis in people who inject drugs.

Chloe Tom, Glen Huang, Alexander J Kovalic, Kyle A Davis, James E Peacock,

Injection drug use (IDU) is a risk factor for infective endocarditis (IE) and hepatitis C virus (HCV) infection. This retrospective cohort study assessed HCV's impact on outcomes of adult people who inject drugs (PWID). Those admitted due to IE using modified Duke criteria from January 2012 through May 2018 were ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115453]

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Emergence of GES-19-producing Pseudomonas aeruginosa exoU+ belonging to the global high-risk clone ST235 in cystic fibrosis infection.

Roberto Rosales-Reyes, Fernanda Esposito, Herrison Fontana, José Luis Lezana-Fernández, Ricardo Lascurain, Miguel A De la Cruz, Bruna Fuga, Nilton Lincopan, José Ignacio Santos-Preciado,

The emergence of high-risk clones of priority pathogens exhibiting convergence of antimicrobial resistance and virulence is a critical issue worldwide. In a previous study, an extensively drug-resistant Pseudomonas aeruginosa was isolated from a chronically colonized pediatric patient with cystic fibrosis (CF). In this study, we analyzed genomic data of this ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(1):115454]

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Diagnostic Performance of Ion 16S Metagenomics Kit and Ion Reporter Metagenomics Workflow for Bacterial Pathogen Detection in Culture-Negative Clinical Specimens From Sterile Sources.

Michael Malczynski, Alex Zhu, Teresa Zembower, Chao Qi,

PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(2):115451]

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The reliability of saliva for the detection of SARS-CoV-2 in symptomatic and asymptomatic patients: Insights on the diagnostic performance and utility for COVID-19 screening.

Khaled J Alkhateeb, Meredith N Cahill, Adam S Ross, Forest W Arnold, James W Snyder,

Current literature has focused on testing saliva in symptomatic patients, and little information is available regarding saliva performance in asymptomatic severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. We compared paired saliva and nasopharyngeal swabs (NPS) collected from 33 symptomatic and 12 asymptomatic known SARS-CoV-2-positive patients. Saliva had an overall sensitivity of ... Read more >>

Diagn Microbiol Infect Dis (Diagnostic microbiology and infectious disease)
[2021, 101(3):115450]

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