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

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.

SARS-CoV-2–Legionella Co-Infections: A Systematic Review and Meta-Analysis (2020–2021)

“…After applying the inclusion and exclusion criteria ( Figure 1 ), a total of 38 articles were included in the qualitative synthesis [ 23 , 24 , 26 , 28 , 29 , 35 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 ]. More precisely, 27 observational studies (see Table 1 for details), 1 case series, and 10 case reports (see Appendix A for details) were included.…”

“…In other words, the available studies presumptively oversampled patients with more severe COVID-19. In such a setting, bacterial co-infection and a poor prognosis are probably more common than in the majority of SARS-CoV-2 cases from the general population [ 13 , 47 , 75 ]. Not coincidentally, the risk factors associated with more severe SARS-CoV-2 cases, such as male gender and older age, were identified as significant effectors for new diagnoses of co-infections.…”

“…First, the reported observational studies were not specifically designed for addressing the specific topic of SARS-CoV-2– Legionella co-infections, and only a small fraction was designed to assess the occurrence of atypical pathogens [ 42 ]. In most cases, the diagnoses were obtained as a consequence of a larger screening, and particularly among reports based on PCR [ 23 , 47 , 49 ], presumptively as a part of larger differential diagnosis approach.…”

Respiratory viruses: their importance and lessons learned from COVID-19

“…should always be considered, especially in critically ill patients. Recent reports showed a higher incidence of co-infections and superinfection in patients with COVID-19, especially in severe cases requiring mechanical ventilation [104][105][106][107][108][109].…”

Prevention and treatment of ventilator-associated pneumonia in COVID-19

“…The widespread use of new molecular technology effectively alleviates this problem and contributes to the increasing incidence of VAP. Tools based on multiplex polymerase chain reaction make it possible to diagnose early VAP and identify VAP usually underdiagnosed by conventional culture-based methods ( Cohen et al, 2021 ; Wicky et al, 2022 ). It has been reported in the literature, the combination of sequential PCR and electrospray ionization mass spectrometry was a potential rapid technique to diagnose VAP within 6 h ( Hou et al, 2020 ).…”