Translating Microbiome Research From and To the Clinic.

Extensive research has elucidated the influence of the gut microbiota on human health and disease susceptibility and resistance. We review recent clinical and laboratory-based experimental studies associating the gut microbiota with certain human diseases. We also highlight ongoing translational advances that manipulate the gut microbiota to treat human diseases and discuss opportunities and challenges in translating microbiome research from and to the bedside.

Possible Predictors of Coinfection in COVID-19: Making a Difficult Diagnosis

Background Coinfection with COVID-19 and a secondary pathogen contributes to morbidity and mortality. Despite its contribution to outcomes, diagnosing coinfection is challenging and no predictive tools have been established. To better assess risk factors for coinfection, we performed a review of all patients hospitalized for COVID-19 in our institution and evaluated them for candidate predictors of coinfection. Methods Medical records were reviewed in all patients admitted with COVID-19 at University of Chicago Medical Center between March 1, 2020 and April 18, 2020. Those identified as having coinfection were compared to those without coinfection. Secondary review was performed for characteristics of the coinfection, including diagnosis, microbiology, drug resistance, and nosocomial acquisition. Results 401 patients were included in the study, the mean age was 60 years (SD-17), 29% had severe disease, and 13% died. At least one test for coinfection was performed in 99% of patients. Coinfection was identified in 15% (72/401) of patients. Coinfection was associated with older age, disease severity, and hospital complications, such as DVT/PE, AKI, and delirium. [Table 1] No symptom, non-microbiologic test, radiograph, or preexisting condition was associated with coinfection. Dyspnea, chest pain, and obesity were more common in those without coinfection. 74% received antibiotics. The most common sites for coinfection were urinary 33%, lower respiratory 26%, and blood 24%. [Table2] Bacteria were most frequently recovered (82%). The most commonly recovered pathogens were Enterobacterales (42%), Staphylococcus aureus (12%), and Pseudomonas (4%). 42% of the infections were hospital acquired, 16% caused by MDRO, and 13% were catheter or ventilator associated. Table 1. Clinical Characteristics Associated with Coinfection Abbreviations: sd, standard deviation;WBC, white blood cell count;CRP, C-reactive protein;COPD, chronic obstructive pulmonary disease;ARDS, acute respiratory distress syndrome;DVT, deep venous thrombosis;PE, pulmonary embolism;MI, myocardial infarction;AKI, acute kidney injury Table 2. Characteristics of Coinfection Abbreviations: Cath, catheter;Vent, ventilator;Assoc, Associated;MDRO, Multiple Drug Resistant Organism Conclusion Coinfection in COVID-19 was most closely associated with age, COVID-19 disease severity, and complicated hospitalization. No presenting symptoms, non-microbiologic test, or radiograph was associated with coinfection, underscoring the challenge in diagnosing coinfection. A remarkable number of infections were hospital acquired, MDRO, and catheter/ventilator associated. Further prospective study on coinfection in COVID-19 is needed to guide diagnosis and treatment. Disclosures Renslow Sherer, MD, Gilead Sciences, Inc (Grant/Research Support)

Cancer, transplant, and immunocompromising conditions were not significantly associated with severe illness or death in hospitalized COVID-19 patients.

OBJECTIVE: Patients with cancer, transplant, and other immunocompromising conditions are at uncertain risk of severe COVID-19 illness. This study aimed to clarify whether patients with immunocompromising conditions were more likely to develop severe COVID-19 illness in a single urban academic medical center. METHODS: A retrospective chart review and electronic data extraction of the first 401 patients at the University of Chicago Hospitals with SARS-CoV-2 infection was performed. Patients met criteria for severe COVID-19 illness if they required ICU level care, high flow oxygen, positive pressure support, helmet non-invasive ventilation, mechanical ventilation, or ECMO, developed ARDS, or died. RESULTS: The mean age was 60 years, 52% were women, 90% were African American, and mortality at 30 days post discharge was 13%. Severe COVID-19 illness was found in 168 (40%) patients. Of the 56 patients with past or current cancer, 25 (45%) had severe illness (p=0.76). Of the 55 patients with other immunocompromised conditions, 24 (44%) had severe illness (p=0.89) After controlling for age, sex, and race, neither cancer (p=0.73) nor immunocompromised conditions (p=0.64) were associated with severe illness. CONCLUSION: No association was found between severe COVID-19 illness and cancer, transplant, and other immunocompromising conditions in a cohort of mostly African American patients.

Community-acquired Coinfection in Coronavirus Disease 2019: A Retrospective Observational Experience.

Community-acquired coinfection in coronavirus disease 2019 (COVID-19) is not well defined. Current literature describes coinfection in 0-40% of COVID-19 patients. In this retrospective report, coinfection was identified in 3.7% of patients and 41% of patients admitted to intensive care (P < .005). Despite infrequent coinfection, antibiotics were used in 69% of patients.