Impact of rapid multiplex PCR on management of antibiotic therapy in COVID-19-positive patients hospitalized in intensive care unit

Abstract

Because the diagnosis of co/superinfection in COVID-19 patients is challenging, empirical antibiotic therapy is frequently initiated until microbiological analysis results. We evaluated the performance and the impact of the BioFire® FilmArray® Pneumonia plus Panel on 112 respiratory samples from 67 COVID-19 ICU patients suspected of co/superinfections. Globally, the sensitivity and specificity of the test were 89.3% and 99.1%, respectively. Positive tests led to antibiotic initiation or adaptation in 15% of episodes and de-escalation in 4%. When negative, 28% of episodes remained antibiotic-free (14% no initiation, 14% withdrawal). Rapid multiplex PCRs can help to improve antibiotic stewardship by administering appropriate antibiotics earlier and avoiding unnecessary prescriptions. Supplementary Information The online version contains supplementary material available at 10.1007/s10096-021-04213-6.

Identification of bacterial co-detections in COVID-19 critically Ill patients by BioFire® FilmArray® pneumonia panel: a systematic review and meta-analysis

“…Excluded studies were comprised of 12 duplicates studies, 96 non-PN/PN plus Panel studies, 18 review articles or position statements, 17 non-clinical or non-human studies, two commentaries, three non-SARS-CoV-2 study, and one study due to insufficient data for evaluating incidence of co-detections related to PN Panel [Khurana et al, 2021] . After removing duplicate and non-applicable studies, seven studies with 558 patients were included for the systematic review and meta-analyses ( Table 1 , Supplementary Table 2) [ Camelena et al, 2021 , Kolenda et al, 2020 , Verroken et al, 2020 , Kreitmann et al, 2020 , Contou et al, 2020 , Foschi et al, 2021 , Maataoui et al, 2021 ]. Studies included a study from Belgium, Italy, and five studies from France occurring from January to December, 2020 and all used the PN plus panel version.…”

“…at ICU admit, upon intubation, within 48h of intubation, etc.). Four studies reported on timing of specimen collection including two studies noting an average collection 1 and 5 days after ICU admission, one study reporting an average of 3 hours after intubation, and one study with 33% of PN Panel testing within 48 hours of ICU admission [ Verroken et al, 2020 , Kreitmann et al, 2020 , Contou et al, 2020 , Maataoui et al, 2021 ]. Antibiotic use occurred in 28.1% to 79% of patients before respiratory specimens were obtained.…”

“…In contrast, culture-based detections yielded a pooled incidence of 18% (95% CI 0.02 to 0.45; I 2 =93%, Cochran's Q p<.01, Egger's test p=.87; Supplementary Figure 2) [ Camelena et al, 2021 , Kolenda et al, 2020 , Kreitmann et al, 2020 ]. Two additional PN plus Panel studies only reported co-detections per specimen, indicating many patients had multiple specimens collected, and noted 33% and 40% bacterial co-detections, respectively [ Foschi et al, 2021 , Maataoui et al, 2021 ]. Finally, one study did not report out bacterial co-detection attributed specifically to PN plus Panel per patient or per specimen, but noted overall 28% co-detections by either culture or PN plus Panel [Contou et al, 2020] .…”

“…Bacteria detected by PN plus Panel among all evaluated specimens resulted in 302 positive organism results for non-atypical bacteria among six studies [ Camelena et al, 2021 , Kolenda et al, 2020 , Verroken et al, 2020 , Contou et al, 2020 , Foschi et al, 2021 , Maataoui et al, 2021 ]. One study was excluded as individual organisms could not specifically be delineated to the PN plus Panel [Kreitmann et al, 2020] .…”

“…Atypical bacteria were detected in two studies reflecting M. pneumoniae and L. pneumophila [ Kolenda et al, 2020 , Foschi et al, 2021 ] . Viral results were noted in two studies which reported a human rhinovirus/enterovirus and an adenovirus [ Kolenda et al, 2020 , Maataoui et al, 2021 ]. Isolates with resistant gene detection were noted in 4 of 7 studies, including bla CTX-M extended-spectrum β-lactamases (ESBLs), bla NDM and bla VIM carbapenemase, and S. aureus methicillin-resistance genes [ Camelena et al, 2021 , Kolenda et al, 2020 , Verroken et al, 2020 , Foschi et al, 2021 , Maataoui et al, 2021 ].…”