Fighting Mutations with Mutations: Evolutionarily Adapting a DNA Aptamer for High-Affinity Recognition of Mutated Spike Proteins of SARS-CoV-2.

An on-going challenge with COVID-19, which has huge implications for future pandemics, is the rapid emergence of viral variants that makes diagnostic tools less accurate, calling for rapid identification of recognition elements for detecting new variants caused by mutations. We hypothesize that we can fight mutations of the viruses with mutations of existing recognition elements. We demonstrate this concept via rapidly evolving an existing DNA aptamer originally selected for the spike protein (S-protein) of wildtype SARS-CoV-2 to enhance the interaction with the same protein of the Omicron variants.

Cerebrospinal fluid galactomannan detection for the diagnosis of central nervous system aspergillosis: a diagnostic test accuracy systematic review and meta-analysis.

Background: Cerebrospinal fluid (CSF) galactomannan is an adjunctive test for central nervous system (CNS) aspergillosis diagnosis with unclear diagnostic test characteristics.

Objectives: To evaluate the diagnostic test characteristics of CSF galactomannan in CNS aspergillosis.

Methods: Systematic review and meta-analysis.

Liquid NanoBiosensors Enable One-Pot Electrochemical Detection of Bacteria in Complex Matrices.

There is a need for point-of-care bacterial sensing and identification technologies that are rapid and simple to operate. Technologies that do not rely on growth cultures, nucleic acid amplification, step-wise reagent addition, and complex sample processing are the key for meeting this need. Herein, multiple materials technologies are integrated for overcoming the obstacles in creating rapid and one-pot bacterial sensing platforms.

Detection of Large Genomic RNA via DNAzyme-Mediated RNA Cleavage and Rolling Circle Amplification: SARS-CoV-2 as a Model.

A new method for the detection of genomic RNA combines RNA cleavage by the 10-23 DNAzyme and use of the cleavage fragments as primers to initiate rolling circle amplification (RCA). 230 different 10-23 DNAzyme variants were screened to identify those that target accessible RNA sites within the highly structured RNA transcripts of SARS-CoV-2. A total of 28 DNAzymes were identified with >20 % cleavage, 5 with >40 % cleavage and one with >60 % in 10 min.

Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer.

Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity.

Performance of saliva compared with nasopharyngeal swab for diagnosis of COVID-19 by NAAT in cross-sectional studies: Systematic review and meta-analysis.

Nucleic acid amplification testing (NAAT) is the preferred method to diagnose coronavirus disease 2019 (COVID-19). Saliva has been suggested as an alternative to nasopharyngeal swabs (NPS), but previous systematic reviews were limited by the number and types of studies available. The objective of this systematic review and meta-analysis was to assess the diagnostic performance of saliva compared with NPS for COVID-19.

A side-by-side comparison of the performance and time-and-motion data of VITEK MS.

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry systems are designed for rapid and reliable microbial identification. VITEK MS PRIME is the bioMérieux's new generation instrument equipped with a continuous load-and-go sample loading system, urgent slide prioritization for critical patient samples and new internal components for faster identification. The aim of this study was to assess the performance of VITEK MS PRIME and to compare it to that of the VITEK MS system.

Investigation of discordant SARS-CoV-2 RT-PCR results using minimally processed saliva.

Saliva is an attractive sample for coronavirus disease 2019 testing due its ease of collection and amenability to detect viral RNA with minimal processing. Using a direct-to-RT-PCR method with saliva self-collected from confirmed COVID-19 positive volunteers, we observed 32% false negative results. Confirmed negative and healthy volunteer samples spiked with 10 genome copies/mL of heat-inactivated severe acute respiratory syndrome coronavirus 2 showed false negative results of 10% and 13%, respectively.

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern.

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS-CoV-2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one-round SELEX experiments using five different trimeric spike proteins from variants, followed by high-throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments.

Methodological and reporting quality of non-inferiority randomized controlled trials comparing antifungal therapies: a systematic review.

Background: Detailed reporting is essential in non-inferiority randomized controlled trials (NI-RCTs) to assess evidence quality, as these trials inform standards of care.

Objectives: The primary objective was to evaluate the methodological and reporting quality of antifungal NI-RCTs.

Data Sources: Medline, EMBASE, the Cochrane CENTRAL and the United States Federal Drug Administration (FDA) drugs database were searched to 9 September 2020.

Secondary Analysis of a Systematic Review: Are Antifungal Noninferiority Trials at Risk of Eroding Effectiveness Because of Biocreep?

Noninferiority randomized controlled trial (RCT) effectiveness may erode when results favor the active control over time and when a decreasingly effective control arm is used in serial trials. We analyzed 32 antifungal noninferiority RCTs (NI-RCTs) for these scenarios in this secondary analysis of a systematic review. Our exploratory analysis suggests that the erosion risk in the effectiveness of antifungal noninferiority trials is uncommon.

High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva.

We report a simple and rapid saliva-based SARS-CoV-2 antigen test that utilizes a newly developed dimeric DNA aptamer, denoted as DSA1N5, that specifically recognizes the spike proteins of the wildtype virus and its Alpha and Delta variants with dissociation constants of 120, 290 and 480 pM, respectively, and binds pseudotyped lentiviruses expressing the wildtype and alpha trimeric spike proteins with affinity constants of 2.1 pM and 2.3 pM, respectively.

Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library.

We performed in vitro selection experiments to identify DNA aptamers for the S1 subunit of the SARS-CoV-2 spike protein (S1 protein). Using a pool of pre-structured random DNA sequences, we obtained over 100 candidate aptamers after 13 cycles of enrichment under progressively more stringent selection pressure. The top 10 sequences all exhibited strong binding to the S1 protein.

Update on Pulmonary Cryptococcosis.

Pulmonary cryptococcosis is a common but underdiagnosed opportunistic fungal infection in both immunocompromised and immunocompetent patients. The causal agents include at least eight evolutionary distinct haploid lineages as well as their hybrids of the human pathogenic Cryptococcus complex. In this update, we review recent advances in epidemiology, mode of transmission, risk factors, diagnostic methods, and therapy of pulmonary cryptococcosis.

Cryptococcemia presenting as an opportunistic infection due to chronic visceral leishmaniasis.

We present a case of visceral leishmaniasis (VL) in a previously immunocompetent patient. At the time of presentation, he was co-infected with . This case demonstrates how infectious diseases besides human immunodeficiency virus can lead to immunosuppression for patients, placing them at risk of opportunistic infections.

Widespread amphotericin B-resistant strains of in Hamilton, Canada.

Purpose: Amphotericin B (AMB) is one of the major antifungal drugs used in the management of aspergillosis and is especially recommended for treating triazole-resistant strains of . However, relatively little is known about the AMB susceptibility patterns of in many parts of the world. This study aims to describe the AMB susceptibility patterns in Hamilton, Ontario, Canada.

Sputum plug selection under inverted microscopy improves microbial identification during exacerbations of airway diseases.

Background: Salivary contamination decreases the yield of identifying potential airway bacterial and fungal pathogens in routine cultures of spontaneous or induced sputum during exacerbations of airway diseases. We investigated the utility of selecting out the squamous cells from sputum using inverted microscopy.

Methods: Sputum was obtained from fifty subjects, then divided to facilitate parallel processing of paired samples for gram-stain and semi-quantitative cultures, and quantitative cytometry.

Limited evidence of fungicide-driven triazole-resistant Aspergillus fumigatus in Hamilton, Canada.

Aspergillus fumigatus is a ubiquitous opportunistic fungal pathogen that can cause aspergillosis in humans. Over the last decade there have been increasing global reports of treatment failure due to triazole resistance. An emerging hypothesis states that agricultural triazole fungicide use causes clinical triazole resistance.

Process Mapping in a Pediatric Emergency Department to Minimize Missed Urinary Tract Infections.

Urinary tract infections (UTIs) are common in young children and are seen in emergency departments (EDs) frequently. Left untreated, UTIs can lead to more severe conditions. Our goal was to undertake a quality improvement (QI) initiative to help minimize the number of children with missed UTIs in a newly established tertiary care pediatric emergency department (PED).

Impact of the combination of daptomycin and trimethoprim-sulfamethoxazole on clinical outcomes in methicillin-resistant Staphylococcus aureus infections.

Complicated Staphylococcus aureus infections, including bacteremia, are often associated with treatment failures, prolonged hospital stays, and the emergence of resistance to primary and even secondary therapies. Daptomycin is commonly used as salvage therapy after vancomycin failure for the treatment of methicillin-resistant S. aureus (MRSA) infections.

Characterization of methicillin-resistant Staphylococcus aureus isolates from patients with persistent or recurrent bacteremia.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) are associated with considerable morbidity and mortality, especially with persistent (PB) or recurrent bacteremia (RB).

Objective: To determine the frequency of PB and RB in patients with MRSA BSI, and to characterize the isolates from these patients.

Methods: Surveillance for MRSA BSI was performed for one year in 13 Canadian hospitals.