Bacterial and Fungal Growth in Sputum Cultures from 165 COVID-19 Pneumonia Patients Requiring Intubation: Evidence for Antimicrobial Resistance Development and Analysis of Risk Factors

Abstract

Background: Coronavirus SARS-CoV-2 causes COVID-19 illness which can progress to severe pneumonia. Empiric antibacterials are often employed though frequency of bacterial superinfection is debated and concerns raised about selection of bacterial antimicrobial resistance. We evaluated sputum bacterial and fungal growth from 165 intubated COVID-19 pneumonia patients. Objectives were to determine frequency of culture positivity, risk factors for and outcomes of positive cultures, and timing of antimicrobial resistance development. Methods: Retrospective reviews were conducted of COVID-19 pneumonia patients requiring intubation admitted to a 1,058-bed four community hospital system on the east coast United States, March 1 to May 1, 2020. Length of stay (LOS) was expressed as mean (standard deviation); 95% confidence interval (95% CI) was computed for overall mortality rate using the exact binomial method, and overall mortality was compared across each level of a potential risk factor using a Chi-Square Test of Independence. All tests were two-sided, and significance level was set to 0.05.Results: Average patient age was 68.7 years. Eighty-three patients (50.3% of total) originated from home, 10 from group homes (6.1% of total), and 72 from nursing facilities (43.6% of total). Mortality was 62.4%, highest for nursing home residents (80.6%). Findings from 253 sputum cultures overall were evaluated and did not suggest acute bacterial or fungal infection in 89 (54%) of 165 individuals sampled within 24 hours of intubation. Cultures > one week following intubation did grow potential pathogens in 72 (64.9%) of 111 cases with 70.8% consistent with late pneumonia and 29.2% suggesting colonization. Twelve (10.8% of total) of these late post-intubation cultures revealed worsened antimicrobial resistance predominantly in Pseudomonas, Enterobacter, or Staphylococcus aureus.Conclusions: In severe COVID-19 pneumonia, a radiographic ground glass interstitial pattern and lack of purulent sputum suggest antibacterials are not needed. Discontinuation of empiric antibacterials should be considered after 48 hours in absence of sputum to culture or results reported "without growth" or "normal flora." Continuing longterm hospitalisation and antibiotics are associated with sputum cultures reflective of hospital-acquired microbes and increasing antimicrobial resistance.Trial registration: Not applicable as this was a retrospective chart review study without interventional arm.