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

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

doi:10.3390/microorganisms9122483

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Journal: Microorganisms	Publication Date: Nov 30, 2021
Citations: 19	License type: CC BY 4.0

Affiliation: Ariel University, Laniado Hospital

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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.

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Patients hospitalized in intensive care units (ICUs) with critical novel coronavirus disease 2019 (COVID-19) have a high mortality rate, reaching ~50% [1,2].The causes contributing to mortality are respiratory failure with severe hypoxemia and its immediate consequences, multiorgan failure, thromboembolism, hemorrhage, and healthcare-associated infections (HAIs) associated with bacteria and filamentous fungi.Bacterial co-infections, diagnosed around the time of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, appear to be uncommon, occurring in 0.6 to 3.2%of patients [3], some studies reported higher rates, reaching 26–28% [4,5,6] or more [7]
Between March 2020 and March 2021, 887 COVID-19 patients were hospitalized in our facility, of which 132 (15%) needed mechanical ventilation at some point during their hospital stay and, of these, 93 (70%) were tested for secondary bacterial infection using the FA pneumonia panel
Of the 62 positive FA tests performed for ventilator-associated pneumonia (VAP), the most common targets found were: P. aeruginosa (26/62, 42%), S. aureus

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Introduction

Patients hospitalized in intensive care units (ICUs) with critical novel coronavirus disease 2019 (COVID-19) have a high mortality rate, reaching ~50% (range 16–78%) [1,2].The causes contributing to mortality are respiratory failure with severe hypoxemia and its immediate consequences, multiorgan failure, thromboembolism, hemorrhage, and healthcare-associated infections (HAIs) associated with bacteria and filamentous fungi.Bacterial co-infections, diagnosed around the time of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, appear to be uncommon, occurring in 0.6 to 3.2%of patients [3], some studies reported higher rates, reaching 26–28% [4,5,6] or more [7]. Patients hospitalized in intensive care units (ICUs) with critical novel coronavirus disease 2019 (COVID-19) have a high mortality rate, reaching ~50% (range 16–78%) [1,2]. The causes contributing to mortality are respiratory failure with severe hypoxemia and its immediate consequences, multiorgan failure, thromboembolism, hemorrhage, and healthcare-associated infections (HAIs) associated with bacteria and filamentous fungi. Bacterial co-infections, diagnosed around the time of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, appear to be uncommon, occurring in 0.6 to 3.2%. Of patients [3], some studies reported higher rates, reaching 26–28% [4,5,6] or more [7]. The co-infection rates in COVID-19 seem to be lower than those reported for influenza pandemics [8,9].

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