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. 2022 Feb;54(2):134-144.
doi: 10.1080/23744235.2021.1985732. Epub 2021 Oct 4.

High rate of bacterial respiratory tract co-infections upon admission amongst moderate to severe COVID-19 patients

Regev Cohen  1   2 , Talya Finn  1   2 , Frida Babushkin  1 , Keren Geller  1 , Hanna Alexander  1 , Maurice Shapiro  3 , Martina Uda  3 , Abdol R Mostrchy  4 , Rabia Amash  4 , Zvi Shimoni  5 , Svetlana Paikin  6 , Adi Ilani  6 , Jonathan Lellouche  6
Affiliations

High rate of bacterial respiratory tract co-infections upon admission amongst moderate to severe COVID-19 patients

Regev Cohen et al. Infect Dis (Lond). 2022 Feb.

Abstract

Background: 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.

Methods: A retrospective study of COVID-19 and non-COVID-19 patients undergoing Biofire®, FilmArray® Pneumonia Panel, bioMérieux, and routine cultures during the first 3 days from admission, between June 2019 and March 2021.

Results: FilmArray tests were performed in 115 COVID-19 and in 61 non-COVID-19 patients. Most (>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 (Rhinovirus/Enterovirus) and one Legionella spp. were detected. The most common bacterial targets were Haemophilus influenzae (36%), Staphylococcus aureus (23%), Streptococcus pneumoniae (10%) and Enterobacter cloacae (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.

Conclusions: 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.

Keywords: Biofire; COVID-19; FilmArray; co-infection; multiplex polymerase chain rection (PCR); respiratory infection.

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Conflict of interest statement

The authors declare no conflict of interests.

Figures

Figure 1.
Figure 1.
FilmArray and routine cultures from COVID-19 and non-COVID-19 patients that were included in the study.
Figure 2.
Figure 2.
Positive early FilmArray tests amongst COVID-19 patients according to the sample type.
See this image and copyright information in PMC

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