ABSTRACT
Background Stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, long COVID is incompletely understood and characterised by a wide range of manifestations that are difficult to analyse computationally. Additionally, the generalisability of machine learning classification of COVID-19 clinical outcomes has rarely been tested.Methods We present a method for computationally modelling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning.Findings We found six clusters of PASC patients, each with distinct profiles of phenotypic abnormalities, including clusters with distinct pulmonary, neuropsychiatric, and cardiovascular abnormalities, and a cluster associated with broad, severe manifestations and increased mortality. There was significant association of cluster membership with a range of pre-existing conditions and measures of severity during acute COVID-19. We assigned new patients from other healthcare centres to clusters by maximum semantic similarity to the original patients, and showed that the clusters were generalisable across different hospital systems. The increased mortality rate originally identified in one cluster was consistently observed in patients assigned to that cluster in other hospital systems. Interpretation Semantic phenotypic clustering provides a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.
ABSTRACT
We evaluate whether biases found in the 2007 Associated Press poll have persisted. Data from the 2018 and 2019 pre-COVID Football Bowl Subdivision seasons show that geographic and recency biases have diminished. However, AP pollsters during 2018–19 appear to have favoured even more disproportionately Notre Dame and the teams from the five so-called Power-5 conferences than they did in 2007. © 2023 Informa UK Limited, trading as Taylor & Francis Group.
ABSTRACT
Background. The spread of carbapenemase-producing Enterobacterales (CPE) is global threat. Numerous outbreaks of CPE have been reported during the COVID-19 pandemic. We describe the impact of of the SARS-CoV-2 pandemic on the emergence of CPE in south-central Ontario, Canada. Incidence of clinical isolates of CPE and isolates with different CPE genes in Toronto/Peel region, 2017-2021. The upper panel shows the incidence of patients with clinical isolates of CPE by year and quarter from q4 2007 to q1 2022. The lower panel shows the incidence of patients with clinical isolates with different carbapenemase genes by fiscal year during the same period. Methods. TIBDN has performed population-based surveillance for CPE in Toronto/Peel region (pop 4.5M) from first identified isolate in 2007. All laboratories test/refer all carbapenem non-susceptible Enterobacterial isolates for identification of CPE. Hospital charts are reviewed and patients/physicians interviewed. Population data are obtained from Statistics Canada. Results. From 10/2007 to 3/31/2022, 1367 persons colonized or infected with CPE were identified. Theirmedian age was 68.7yrs (IQR 54-78yrs);761 (56%) weremale. 772 (56%) were colonized when first identified;115 (8.4%) were bacteremic at identification or subsequently developed bacteremia. The most common organisms were E. coli (651, 48%), K. pneumoniae (436, 32%), Enterobacter spp. (146, 11%), Citrobacter spp (62, 5%);the most common genes were NDM+/-OXA-48 (722, 53%), OXA-48-like (341, 25%), KPC (225, 16%), VIM(44, 3%). The incidence of CPE infections increased steadily until 3/2020 then declined by 61%and remained stable until 3/2022 (Figure, upper panel). The declinewas greater for E. coli (56%decrease), K. pneumoniae (62%) than for Enterobacter spp. (30%) and other species (19%). It occurred in all genes in 2020;however, KPC containing organisms increased again in 2021 (Figure, lower panel). Conclusion. The advent of the COVID-19 pandemic was associated with an immediate, substantial decline in the incidence of patients with CPE in our population area. This decline occurred in both isolates with genes usually occurring in cases imported from other countries, and in those usually occurring in cases associated with transmission within Canadian hospitals. Decreased travel and enhanced infection prevention and control in hospitals may both have contributed to reductions in CPE during the pandemic. (Figure Presented).
Subject(s)
COVID-19 , Neoplasms , COVID-19 Vaccines , Humans , Neoplasms/drug therapy , SARS-CoV-2 , Vaccination/adverse effectsABSTRACT
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and associated coronavirus disease 19 (COVID-19) began ravaging most of the globe in November 2019. In the United States more than 25 million people have been infected with SARS-CoV-2. To date, COVID-19 has killed close to 400,000 U.S. citizens. In the face of limited pharmacotherapies, the current burden of SARS-CoV-2 and COVID-19 signals overwhelming sickness and trillions in healthcare costs ahead. The need to expeditiously identify safe and efficacious prophylaxis and treatment options is critical. Drug repositioning may be a promising strategy toward mitigating the impact of SARS-CoV-2 and COVID-19. This rapid review appraises available evidence on the viability of vintage antimalarial drugs chloroquine (CHQ) and its analog hydroxychloroquine (HCQ) repositioned for SARS-CoV-2 prophylaxis and COVID-19 treatment. Findings suggest neither the use of CHQ nor HCQ singularly, or concomitantly, with azithromycin and/or zinc provide definitive benefits for use against SARS-CoV-2 infection or COVID-19 illness. Moreover, administration of these medications was linked to significant and sometimes fatal complications.