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

Regev Cohen; Talya Finn; Frida Babushkin; Keren Geller; Hanna Alexander; Maurice Shapiro; Martina Uda; Abdol R Mostrchy; Rabia Amash; Zvi Shimoni; Svetlana Paikin; Adi Ilani; Jonathan Lellouche

doi:10.1080/23744235.2021.1985732

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

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

Authors

Regev Cohen^{1

2}, Talya Finn^{1

2}, Frida Babushkin¹, Keren Geller¹, Hanna Alexander¹, Maurice Shapiro³, Martina Uda³, Abdol R Mostrchy⁴, Rabia Amash⁴, Zvi Shimoni⁵, Svetlana Paikin⁶, Adi Ilani⁶, Jonathan Lellouche⁶

Affiliations

¹ Infectious Diseases Unit, Sanz Medical Center, Laniado Hospital, Netanya, Israel.
² Ruth and Bruce Rappaport Faculty of Medicine, Technion University, Haifa, Israel.
³ Intensive Care Unit, Sanz Medical Center, Laniado Hospital, Netanya, Israel.
⁴ Corona Ward, Sanz Medical Center, Laniado Hospital, Netanya, Israel.
⁵ Department of Internal Medicine B, Sanz Medical Center, Laniado Hospital, Netanya, Israel.
⁶ Department of Clinical Laboratories, Sanz Medical Center, Laniado Hospital, Netanya, Israel.

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.

MeSH terms

COVID-19*
Coinfection* / epidemiology
Humans
Multiplex Polymerase Chain Reaction
Pandemics
Respiratory System
Retrospective Studies
SARS-CoV-2