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 coinfection 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 1058-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 and LOS 19.9 days. 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 did not suggest acute bacterial or fungal infection in 73 (45%) of 165 individuals sampled within 24 h of intubation. Cultures ≥ 1 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 prior to/around the time of intubation correlated with no culture growth or recovery of normal oral flora ± yeast. Discontinuation of empiric antibacterials should be considered in these patients aided by other clinical findings, history of prior antimicrobials, laboratory testing, and overall clinical course. 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.

Bacterial and Fungal Co-Infections and Superinfections in a Cohort of COVID-19 Patients: Real-Life Data from an Italian Third Level Hospital

“…To fight the inflammatory syndrome, many immunomodulant agents are used, such as corticosteroids, anti-interleukin-1 (IL-1), anti-interleukin-6 (IL-6), and inhibitors of the JAK-STAT pathway [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. The use of immune suppressive drugs, combined with the natural immune suppression caused by the virus, can lead to a surge of secondary bacterial and fungal infections [ 8 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ].…”

Secondary bacterial infection in Adult Patients with COVID-19 in Iraq

“…To the contrary, Tang (2021) found that only about 6% of bacterial infections were caused by a single organism (30). Results from sputum cultures showed a mixed infection type in 8.7% of 165 patients in one study (Liu HH et al, 2021). (19).…”

“…This finding may be explained by the fact that patients in this age range are more likely to have other predisposing diseases, such as diabetes mellitus, hypertension, liver dysfunction, or kidney failure. The research was conducted in the United States (Liu HH et al, 2021) (19). People between the ages of 56 and 80 had the highest infection rate (43%).…”

The RALE Score Versus the CT Severity Score in Invasively Ventilated COVID-19 Patients—A Retrospective Study Comparing Their Prognostic Capacities

“…Pulmonary vascular dysfunctions described in COVID-19 ARDS are not captured by the CTSS and RALE score [ 29 , 30 , 31 , 32 , 33 , 34 ]. Aside from thrombo-embolic complications, mortality may be also driven by other factors, such as bacterial and fungal infections complications [ 35 , 36 ] and ICU-acquired weakness. The initial ventilator management was also shown to moderate the prognostic value of other predictive parameters [ 37 ].…”