High Rates of Bacterial Pulmonary Co-Infections and Superinfections Identified by Multiplex PCR among Critically Ill COVID-19 Patients

Regev Cohen; Frida Babushkin; Talya Finn; Keren Geller; Hanna Alexander; Candice Datnow; Martina Uda; Maurice Shapiro; Svetlana Paikin; Jonathan Lellouche

doi:10.3390/microorganisms9122483

High Rates of Bacterial Pulmonary Co-Infections and Superinfections Identified by Multiplex PCR among Critically Ill COVID-19 Patients

Microorganisms. 2021 Nov 30;9(12):2483. doi: 10.3390/microorganisms9122483.

Authors

Regev Cohen^{1

2}, Frida Babushkin², Talya Finn^{1

2}, Keren Geller², Hanna Alexander², Candice Datnow², Martina Uda³, Maurice Shapiro³, Svetlana Paikin⁴, Jonathan Lellouche^{1

4}

Affiliations

¹ Adelson School of Medicine, Ariel University, Ariel 4077625, Israel.
² Infectious Diseases Unit, Sanz Medical Center, Laniado Hospital, Netanya 4244915, Israel.
³ Intensive Care Unit, Sanz Medical Center, Laniado Hospital, Netanya 4244915, Israel.
⁴ Clinical Microbiology Laboratory, Sanz Medical Center, Laniado Hospital, Netanya 4244915, Israel.

Abstract

Background: The role of bacterial co-infection and superinfection among critically ill COVID-19 patients remains unclear. The aim of this study was to assess the rates and characteristics of pulmonary infections, and associated outcomes of ventilated patients in our facility.

Methods: This was a retrospective study of ventilated COVID-19 patients between March 2020 and March 2021 that underwent BioFire^®, FilmArray^® Pneumonia Panel, testing. Community-acquired pneumonia (CAP) was defined when identified during the first 72 h of hospitalization, and ventilator-associated pneumonia (VAP) when later.

Results: 148 FilmArray tests were obtained from 93 patients. With FilmArray, 17% of patients had CAP (16/93) and 68% had VAP (64/93). Patients with VAP were older than those with CAP or those with no infection (68.5 vs. 57-59 years), had longer length of stay and higher mortality (51% vs. 10%). The most commonly identified FilmArray target organisms were H. influenzae, S. pneumoniae, M. catarrhalis and E. cloacae for CAP and P. aeruginosa and S. aureus for VAP. FilmArray tests had high negative predictive values (99.6%) and lower positive predictive values (~60%).

Conclusions: We found high rates of both CAP and VAP among the critically ill, caused by the typical and expected organisms for both conditions. VAP diagnosis was associated with poor patient outcomes.

Keywords: COVID-19; FimArray; PCR; co-infection; community-acquired pneumonia; critically ill; intensive-care unit; superinfection; ventilator-associated pneumonia.