First Open Task: Fighting Secondary Effects of COVID-19

Bacteria like Streptococcus pneumoniae complicate viral infections like the flu, H1N1, and Covid-19. CDC

Severely ill patients with COVID-19 can succumb to bacterial pneumonia as a secondary infection. Today we release a new dataset that can be leveraged to help develop new antibiotics. This is the focus of the first open task we announce today. The dataset was curated by Dr. Jonathan Stokes. A recent report in The Lancet by Fei Zhou and colleagues has shed important light on the risk factors for mortality of adult patients with COVID-19 in Wuhan, China. Their analyses showed that increased odds of in-hospital death were associated with older age, a higher Sequential Organ Failure Assessment (SOFA) score, and d-dimer (a small peptide present in the blood) greater than 1 µg/ml. However, an additional alarming observation from this study is the high proportion of non-surviving patients who developed a secondary infection. Indeed, Of the 54 non-survivors observed, 27 of these patients had a secondary infection (50%). Contrarily, only one of the 137 surviving patients tracked in this paper had a secondary infection (~0.7%). In total 53 of 54 non-survivors (98%) were administered antibiotics, as were 128 of 137 survivors (93%). There is a possibility that severely ill patients with COVID-19 are developing secondary bacterial pneumonia infections as a result of significantly depleted lung function. Bacterial pneumonia can be caused by a wide array of bacterial species, including Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and others. Worryingly, multidrug-resistant strains of these species are seen in clinical settings. In addition to using our tools to discover potential therapeutics against SARS-CoV-2, efforts are underway to identify new antibiotics that can effectively eradicate those antibiotic-resistant bacteria that often cause bacterial pneumonia. Through this additional work, our goal is to decrease the healthcare burden of secondary infections and increase the likelihood of survival of critically ill patients with COVID-19.

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