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Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.

In February 2023, a 55-year-old man sought care at the emergency department of Vancouver General Hospital, Vancouver, British Columbia, Canada, for daily fevers, headache, and abdominal pain 5 days after [...]

BackgroundMetagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact as used in routine practice.MethodsWe performed a retrospective cohort study of all patients for whom plasma mNGS (Karius test) was performed for all indications at 5 United States institutions over 1.5 years. Comprehensive records review was performed, and standardized assessment of clinical impact of the mNGS based on the treating team's interpretation of Karius results and patient management was established.ResultsA total of 82 Karius tests were evaluated from 39 (47.6%) adults and 43 (52.4%) children and a total of 53 (64.6%) immunocompromised patients. Karius positivity rate was 50 of 82 (61.0%), with 25 (50.0%) showing 2 or more organisms (range, 2-8). The Karius test results led to positive impact in 6 (7.3%), negative impact in 3 (3.7%), and no impact in 71 (86.6%), and was indeterminate in 2 (2.4%). Cases with positive Karius result and clinical impact involved bacteria and/or fungi but not DNA viruses or parasites. In 10 patients who underwent 16 additional repeated tests, only 1 was associated with clinical impact.ConclusionsThe real-world impact of the Karius test as currently used in routine clinical practice is limited. Further studies are needed to identify high-yield patient populations, define the complementary role of mNGS to conventional microbiological methods, and discern how best to integrate mNGS into current testing algorithms.

Pathogen cell-free DNA (pcfDNA) in blood and urine is an attractive biomarker; however, the impact of preanalytical factors is not well understood. Blood and urine samples from healthy donors spiked with cfDNA from Mycobacterium tuberculosis, Salmonella enterica, Aspergillus fumigatus, and Epstein-Barr virus (EBV) and samples from tuberculosis patients were used to evaluate the impact of blood collection tube, urine preservative, processing delay, processing method, freezing and thawing, and sample volume on pcfDNA. The PCR cycle threshold (CT ) was used to measure amplifiable cfDNA. In spiked samples, the median CT values for M. tuberculosis, S. enterica, and EBV cfDNA were significantly lower in blood collected in K2EDTA tubes than those in Streck and PAXgene blood collection tubes, and they were was significantly lower in urine preserved with EDTA (EDTA-urine) than in urine preserved with Streck reagent (Streck-urine). Blood and urine samples from TB patients preserved with K2EDTA and Tris-EDTA, respectively, showed significantly lower median M. tuberculosis CT values than with the Streck blood collection tube and Streck urine preservative. Processing delay increased the median pathogen CT values for Streck and PAXgene but not K2EDTA blood samples and for urine preserved with Streck reagent but not EDTA. Double-spin compared with single-spin plasma separation increased the median pathogen CT regardless of blood collection tube. No differences were observed between whole urine and supernatant and between fresh and thawed plasma and urine after 24 weeks at -80°C. Larger plasma and urine volumes in contrived and patient samples showed a significantly lower median M. tuberculosis CT These findings suggest that large-volume single-spin K2EDTA-plasma and EDTA-whole urine with up to a 24-h processing delay may optimize pcfDNA detection.

Importance: The COVID-19 pandemic has led to 775 million documented cases and over 7 million deaths worldwide as of March 2024 and is an ongoing health crisis. To limit viral spread within households and in the community, public health officials have recommended self-isolation, self-quarantine of exposed household contacts, and mask use. Yet, risk of household transmission (HHT) may be underestimated due to low frequency of sampling, and risk factors for HHT are not well understood. Objectives: To estimate the secondary attack rate of SARS-CoV-2 within households and to define the risk factors for new infections in household members who are in close contact with the index case. Design, setting, and participants: In this prospective cohort study, from March 2020—December 2021 we enrolled 60 households with index cases who tested positive for SARS-CoV-2. All household contacts and index cases were tested daily for SARS-CoV-2 via reverse transcription polymerase chain reaction (RT-PCR) using self-collected anterior nares specimens. Households were followed until all study participants in the household tested negative for SARS-CoV-2 for seven consecutive days. We collected sex, age, race/ethnicity, comorbidities, and relationship to index case for secondary contacts, household level characteristics including primary income, household density, and square feet per person on property. We compared the sociodemographic variables between COVID-19 positive and negative household members and between households where secondary transmission did and did not occur. Main outcomes and measures: Daily anterior nares swabs were tested for SARS-CoV-2 using RT-PCR, in order to assess duration of nasal shedding of SARS-CoV-2, as well as risk of transmission to secondary household contacts. Results: Of the 163 participants in this study, 84 (51.5%) were women; median age (IQR) was 36.0 (17.0–54.0) years of age; 78 (47.8%) were white and 48 (29.5%) were Hispanic/LatinX. Of the fifty households with household contacts, at least one secondary case occurred in twenty-six households (52.0%) and forty-five household contacts (43.7%) were infected. Secondary attack rate was lowest among children of index cases (6/23, 26.1%). Modified Poisson regression identified that the risk of transmission to household contacts increases significantly with age (Risk ratio for each increase in years of age = 1.01, 95% CI = 1.00–1.02). Mixed effects regression models identified that participants with chronic diseases, such as asthma, diabetes, cancer, or cardiac disease, had higher Cts at baseline when compared to participants without chronic diseases (6.62, 95% CI: 1.46–11.77, p = 0.02) and show a slower rate of increase in Ct over time (-0.43, 95% CI: -0.77 to -0.09, p = 0.02) Conclusions and relevance: This study suggests that HHT represents a key source of community-based infection of SARS-CoV-2. Allocation of resources for contact investigations and prevention interventions should focus on the individuals at highest risk of infection in households, especially those with higher density homes. [ABSTRACT FROM AUTHOR]

Characterizing mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome has led to the identification of variants of concern (VOCs) on the basis of such criteria as increased [...]

Real-time reverse transcription PCR (rRT-PCR) is the standard diagnostic method for coronavirus disease 2019, but it cannot differentiate between actively replicating and inactive virus. Active replication is a critical factor [...]

Healthcare personnel (HCP) represent a unique group of concern for transmission of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), the causative agent of coronavirus disease (COVID-19), because of their increased [...]

The ability of clinical laboratories to meet the demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing is critical for reducing coronavirus disease (COVID-19)-related illness, death, and economic impact. [...]

This study found 0.7% olopatadine (Pataday Once Daily Relief Extra Strength) eye drops to provide better initial comfort than 0.3% pheniramine maleate/0.025% naphazoline hydrochloride (VISINE® Allergy Eye Relief Multi-Action Antihistamine and Redness Reliever) eye drops suggesting that patients may comply better with the Pataday than VISINE. To compare the ocular comfort at instillation of Pataday and VISINE allergy eye drops. Minimally symptomatic participants were recruited based upon Standard Patient Evaluation of Eye Dryness (SPEED) questionnaire scores (≤3 units); they also had minimal between-eye inter-ocular comfort differences as judged by visual analogue scale scores (VAS; ≤7 units). Baseline comfort was evaluated by eye with a VAS. One drop of Pataday or VISINE was then applied to the right eye with the alternative drop being applied to the left eye. The same VAS evaluated comfort by eye at drop instillation, and then at 30 seconds, 1 minute, and 2 minutes post-instillation. Drop experience was also evaluated with Likert questions. LogMAR visual acuities and bulbar conjunctival redness were evaluated pre- and post-drop instillation. A total of 159 participants were recruited (mean ± SD age = 26.2 ± 7.5). The VAS found that eyes treated with Pataday were significantly more comfortable at instillation than eyes treated with VISINE. Likert questions indicated that participants significantly preferred Pataday drops compared to the VISINE drops at instillation with regards to overall eye comfort, eye stinging, eye burning, and foreign body sensation. There were no between drop differences in visual acuity, though eyes treated with VISINE were less red than eyes treated with Pataday. Topically applied Pataday drops were more comfortable than VISINE drops. [ABSTRACT FROM AUTHOR]

The article describes the case of a 55-year old man diagnosed with Plasmodium knowlesi infection after returning to Canada from the Philippines. The patient had taken malaria chemoprophylaxis and recovered following treatment with atovaquone/proguanil. Results were observed from his abdominal computed tomography, peripheral blood thin smear and loop-mediated isothermal amplification testing. A background on documented P. knowlesi malaria cases in Palawan Island, Philippines is provided.