High rate of bacterial respiratory tract co-infections upon admission amongst moderate to severe COVID-19 patients
Creators: name: Cohen, Regev
name: Finn, Talya
name: Babushkin, Frida
name: Geller, Keren
name: Alexander, Hanna
name: Shapiro, Maurice
name: Uda, Martina
name: Mostrchy, Abdol R.
name: Amash, Rabia
name: Shimoni, Zvi
name: Paikin, Svetlana
name: Ilani, Adi
name: Lellouche, Jonathan
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: The role of bacterial and viral co-infection in the current COVID-19 pandemic remains elusive. The aim of this study was to describe the rates and features of co-infection on admission of COVID-19 patients, based on molecular and routine laboratory methods. A retrospective study of COVID-19 and non-COVID-19 patients undergoing Biofire<sup>®</sup>, FilmArray<sup>®</sup> Pneumonia Panel, bioMérieux, and routine cultures during the first 3 days from admission, between June 2019 and March 2021. FilmArray tests were performed in 115 COVID-19 and in 61 non-COVID-19 patients. Most (&gt;99%) COVID-19 patients had moderate-critical illness, 37% required mechanical ventilation. Sputa and endotracheal aspirates were the main samples analyzed. Positive FilmArray tests were found in 60% (70/116) of the tests amongst COVID-19 patients and 62.5% (40/64) amongst non-COVID-19 patients. All 70 cases were positive for bacterial targets, while one concomitant virus (<i>Rhinovirus/Enterovirus</i>) and one <i>Legionella</i> spp. were detected. The most common bacterial targets were <i>Haemophilus influenzae</i> (36%), <i>Staphylococcus aureus</i> (23%), <i>Streptococcus pneumoniae</i> (10%) and <i>Enterobacter cloacae</i> (10%). Correlation between FilmArray and cultures was found in 81% and 44% of negative and positive FA tests, respectively. Positive FilmArray results typically (81%) triggered the administration of antibiotic therapy and negative results resulted in antimicrobials to be withheld in 56% of cases and stopped in 8%. Bacterial cultures of COVID-19 patients were positive in 30/88 (34%) of cases. Bacterial co-infection is common amongst moderate-critical COVID-19 patients on admission while viral and atypical bacteria were exceedingly rare. Positive FilmArray results could trigger potentially unnecessary antibiotic treatment.KEY POINTWe found high rates of on-admission bacterial co-infection amongst hospitalized moderate to severe COVID-19 patients. Molecular tests (Biofire, FilmArray) and routine microbiological tests revealed 60% and 34% bacterial co-infection, respectively, while viral and fungal co-infections were rare. We found high rates of on-admission bacterial co-infection amongst hospitalized moderate to severe COVID-19 patients. Molecular tests (Biofire, FilmArray) and routine microbiological tests revealed 60% and 34% bacterial co-infection, respectively, while viral and fungal co-infections were rare.