Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19

Caméléna, François; Moy, Anne Clotilde; Dudoignon, Emmanuel; Poncin, Thibaut; Deniau, Benjamin; Guillemet, Lucie; Goff, Jérôme Le; Budoo, Mélissa; Benyamina, Mourad; Chaussard, Maïté; Coutrot, Maxime; Lafaurie, Matthieu; Plaud, Benoît; Mebazaa, Alexandre; Dépret, François; Berçot, Béatrice

doi:10.1016/j.diagmicrobio.2020.115183

Cited by 36 publications

(43 citation statements)

References 11 publications

(20 reference statements)

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“…In line with previous works, we found that respiratory bacterial co-infections are quite common in critically ill COVID-19 patients (more than 30% of positive cultures), with Pseudomonas aeruginosa (14.7%), Klebsiella pneumoniae (6.9%) and Staphylococcus aureus (6.5%) the most detected pathogens ( Caméléna et al, 2021 ; Maes et al, 2021 ; Hughes et al, 2020 ).…”

Section: Discussionsupporting

confidence: 92%

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

Foschi

Zignoli

Gaibani

et al. 2021

Journal of Microbiological Methods

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The prevalence and microbiology of concomitant respiratory bacterial infections in patients with SARS-CoV-2 infection are not yet fully understood. In this retrospective study, we assessed respiratory bacterial co-infections in lower respiratory tract samples taken from intensive care unit-hospitalized COVID-19 patients, by comparing the conventional culture approach to an innovative molecular diagnostic technology. A total of 230 lower respiratory tract samples (i.e., bronchial aspirates or bronchoalveolar lavages) were taken from 178 critically ill COVID-19 patients. Each sample was processed by a semi-quantitative culture and by a multiplex PCR panel (FilmArray Pneumonia Plus panel), allowing rapid detection of a wide range of clinically relevant pathogens and a limited number of antimicrobial resistance markers. More than 30% of samples showed a positive bacterial culture, with Pseudomonas aeruginosa , Klebsiella pneumoniae and Staphylococcus aureus the most detected pathogens. FilmArray showed an overall sensitivity and specificity of 89.6% and 98.3%, respectively, with a negative predictive value of 99.7%. The molecular test significantly reduced the turn-around-time (TAT) and increased the rates of microbial detection. Most cases missed by culture were characterized by low bacterial loads (10 4 –10 5 copies/mL). FilmArray missed a list of pathogens not included in the molecular panel, especially Stenotrophomonas maltophilia (8 cases). FilmArray can be useful to detect bacterial pathogens in lower respiratory tract specimens of COVID-19 patients, with a significant decrease of TAT. The test is particularly useful to rule out bacterial co-infections and avoid the inappropriate prescription of antibiotics.

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Section: Discussionsupporting

confidence: 92%

“…Besides culture, only a few data are available about the use of molecular techniques for the identification of bacterial pathogens in the respiratory tract of COVID-19 patients ( Kolenda et al, 2020 ; Caméléna et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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

Foschi

Zignoli

Gaibani

et al. 2021

Journal of Microbiological Methods

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“…However, molecular detection methods might be an important tool in future studies. 33,34 So far, only few studies have investigated fungal superinfections in COVID-19 patients. [13][14][15]17,[35][36][37] The significance of viral reactivation remains unclear.…”

Section: Discussionmentioning

confidence: 99%

Bacterial pulmonary superinfections are associated with longer duration of ventilation in critically ill COVID-19 patients

Buehler

Zinkernagel

Hofmaenner

et al. 2021

Cell Reports Medicine

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The impact of secondary bacterial infections (superinfections) in COVID-19 is not well understood. In this prospective, monocentric cohort study we aim to investigate the impact of superinfections in COVID-19 patients with acute respiratory distress syndrome. Patients are assessed for concomitant microbial infections by longitudinal analysis of tracheobronchial secretions, bronchoalveolar lavages and blood cultures. In 45 critically ill patients, we identify 19 patients with superinfections (42.2%). Superinfections are detected on day 10 after intensive care admission. The proportion of participants alive and off invasive mechanical ventilation at study day 28 (ventilator-free days (VFDs) at 28 days) is substantially lower in patients with superinfection (subhazard ratio 0.37, 95%-CI 0.15-0.90, p=0.028). Patients with pulmonary superinfections have a higher incidence of bacteraemia, virus reactivations, yeast colonization, and required intensive care treatment for a longer time. Superinfections are frequent and associated with reduced VFDs at 28 days despite a high rate of empirical antibiotic therapy.

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“…The slightly higher prevalence rate of VAP is likely attributable to the use of the multiplex PCR technology. 31 We are aware of no other reports of the incidence of VAP in severe SARS-CoV-2 pneumonia.…”

Section: Discussionmentioning

confidence: 97%

“…The slightly higher prevalence rate of VAP is likely attributable to the use of the multiplex PCR technology. 31…”

Section: Discussionmentioning

confidence: 99%

Bacterial superinfection pneumonia in SARS-CoV-2 respiratory failure

Pickens¹,

Gao²,

Cuttica³

et al. 2021

Preprint

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BackgroundSevere community-acquired pneumonia secondary to SARS-CoV-2 is a leading cause of death. Current guidelines recommend patients with SARS-CoV-2 pneumonia receive empirical antibiotic therapy for suspected bacterial superinfection, but little evidence supports these recommendations.MethodsWe obtained bronchoscopic bronchoalveolar lavage (BAL) samples from patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. We analyzed BAL samples with multiplex PCR and quantitative culture to determine the prevalence of superinfecting pathogens at the time of intubation and identify episodes of ventilator-associated pneumonia (VAP) over the course of mechanical ventilation. We compared antibiotic use with guideline-recommended care.ResultsThe 179 ventilated patients with severe SARS-CoV-2 pneumonia discharged from our hospital by June 30, 2020 were analyzed. 162 (90.5%) patients had at least one BAL procedure; 133 (74.3%) within 48 hours after intubation and 112 (62.6%) had at least one subsequent BAL during their hospitalization. A superinfecting pathogen was identified within 48 hours of intubation in 28/133 (21%) patients, most commonly methicillin-sensitive Staphylococcus aureus or Streptococcus species (21/28, 75%). BAL-based treatment reduced antibiotic use compared with guideline-recommended care. 72 patients (44.4%) developed at least one VAP episode. Only 15/72 (20.8%) of initial VAPs were attributable to multidrug-resistant pathogens. The incidence rate of VAP was 45.2/1000 ventilator days.ConclusionsWith use of sensitive diagnostic tools, bacterial superinfection at the time of intubation is infrequent in patients with severe SARS-CoV-2 pneumonia. Treatment based on current guidelines would result in substantial antibiotic overuse. The incidence rate of VAP in ventilated patients with SARS-CoV-2 pneumonia are higher than historically reported.

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Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19

Cited by 36 publications

References 11 publications

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

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

Bacterial pulmonary superinfections are associated with longer duration of ventilation in critically ill COVID-19 patients

Bacterial superinfection pneumonia in SARS-CoV-2 respiratory failure

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