Assessment of Respiratory Bacterial Coinfections Among Severe Acute Respiratory Syndrome Coronavirus 2-Positive Patients Hospitalized in Intensive Care Units Using Conventional Culture and BioFire, FilmArray Pneumonia Panel Plus Assay

Abstract

Up to 15% of patients infected by SARS-CoV-2 present severe forms requiring hospitalisation in intensive care units and which are associated with high mortality. The prevalence of bacterial infections in these patients is not well established and more data are needed to guide empiric antibiotic therapy and improve patient outcomes. In this prospective multicenter study, we assessed bacterial co-infections identified in culture from 99 French patients infected by SARS-Cov-2 and hospitalized in intensive care units. We concomitantly evaluated the value of the use of an innovative molecular diagnostic technologies, the BioFire® FilmArray® Pneumonia Panel plus (FA-pneumo) assay, to early identify these co-infections in these patients and the concordance with conventional culture. We showed that a bacterial co-infection was detected in 15% of patients based on conventional culture. S. aureus and H. influenzae were the most prevalent pathogens. The sensitivity of FA-pneumo compared to culture was 100%. Conversely, the specificity varied between 88.4 and 100% according to the pathogen and our results highlighted that 60.5% of bacterial targets reported using this assay were not recovered by culture; 76.9% of discordant results corresponded to bacteria belonging to commensal oral flora and/or reported with ≤ 10 5 copies/mL of bacterial nucleic acids. Based on its excellent sensitivity, the FA-pneumo assay is useful to rule out bacterial co-infections in the context of severe SARS-CoV-2 infection and avoid the inappropriate prescription of antibiotics. However, positive tests should be interpreted carefully taking into consideration DNA bacterial load, all clinical and biological signs.

Respiratory bacterial co-infections in intensive care unit-hospitalized COVID-19 patients: Conventional culture vs BioFire FilmArray pneumonia Plus panel

“…The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) is a major threat for global health, worldwide. Approximately 15% of patients develop a severe respiratory failure requiring hospitalization in intensive care units (ICUs) ( Kolenda et al, 2020 ).…”

The Complexity of Co-Infections in the Era of COVID-19

“…Furthermore, such detection does not guarantee live bacterium analogous to the issue of viable versus non-viable virus with similar technology. Kolenda et al [ 129 ] tactfully address this issue with corroborative evidence. They found that up to 60% of bacteria found by amplification assay could not be corroborated with culture results.…”

“…Some patients may have carriage of high numbers of potentially pathogenic bacteria in either the respiratory tract or at the endotracheal site during intubation without infection. The potential for such ambiguity is illustrated by several studies in which molecular amplification studies have been used for secondary bacterial diagnosis [100,[125][126][127][128][129]. Although there is a correlation of amplification Ct values with bacterial load, even such quantitative assessment does not necessarily imply infection.…”

“…The type of proposed co-pathogen changes during the course of COVID-19 [49,76,118,128,[134][135][136][137][138][139][140]. Common respiratory bacteria more often cause infection in early stages of the illness [75,125,129,133,[141][142][143]. Nosocomial infections can be common as the viral illness progresses albeit the institutional rate is quite variable [49,118,119,123,131,[135][136][137][138][139][140][144][145][146][147].…”

Ceftobiprole Perspective: Current and Potential Future Indications

“…Data are increasing regarding bacterial co-infections in the severe disease caused by SARS-CoV-2, but the subject is not yet fully understood [ 21 , 22 ]. GPB are the most common pathogens that cause community-acquired pneumonia co-infections in COVID-19 subjects, although there is an increasing ratio of infections with GNB among hospital-acquired lung superinfections [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. Ceftobiprole may fit within a monotherapy stewardship intervention in patients with CAP or HAP at risk for MRSA or Pseudomonas aeruginosa [ 29 ], with or without subsequent de-escalation ( Figure 1 ).…”