Journal: Microbiology Spectrum

Article Title: Diagnosis and Treatment of Bacterial Pneumonia in Critically Ill Patients with COVID-19 Using a Multiplex PCR Assay: A Large Italian Hospital’s Five-Month Experience

doi: 10.1128/Spectrum.00695-21

Figure Lengend Snippet: Comparison between the FilmArray pneumonia plus panel and standard-of-care reference testing results for LRT samples from COVID-19 patients with bacterial pneumonia ^a

Article Snippet: In September 2020, when the second wave of the SARS-CoV-2 pandemic was raging in Italy, we implemented the multiplexed, semiquantitative FilmArray pneumonia plus (FA-PP) panel (BioFire, Salt Lake City, UT, USA) assay ( ) for routine clinical use at our institution (a large Italian university hospital).

Techniques: Comparison

Journal: Microbiology Spectrum

Article Title: Diagnosis and Treatment of Bacterial Pneumonia in Critically Ill Patients with COVID-19 Using a Multiplex PCR Assay: A Large Italian Hospital’s Five-Month Experience

doi: 10.1128/Spectrum.00695-21

Figure Lengend Snippet: Quantitative result agreement between the FilmArray pneumonia plus (FA-PP) panel and standard-of-care (SoC) culture testing methods for 202 bacterial organisms detected in bronchoalveolar lavage (BAL) fluid or endotracheal aspirate (ETA) samples from ICU patients. All but 22 (which did not grow in culture) organisms were detected at or above the 1 × 10 4 CFU/ml (BAL fluid sample) or 1 × 10 5 CFU/ml (ETA sample) thresholds for clinically relevant quantification by both methods. The diagonal dashed line connects dots that represent bacterial organisms with fully concordant results (71/202; 35.1%), whereas dots above or below the line represent bacterial organisms with SoC culture loads that exceeded (18/202, 8.9%) or did not exceed (113/202, 56.0%), respectively, those of the FA-PP panel by ≥1 log 10 . Shades of gray are used to depict the different numbers of samples corresponding to each dot.

Article Snippet: In September 2020, when the second wave of the SARS-CoV-2 pandemic was raging in Italy, we implemented the multiplexed, semiquantitative FilmArray pneumonia plus (FA-PP) panel (BioFire, Salt Lake City, UT, USA) assay ( ) for routine clinical use at our institution (a large Italian university hospital).

Techniques:

Journal: Microbiology Spectrum

Article Title: Diagnosis and Treatment of Bacterial Pneumonia in Critically Ill Patients with COVID-19 Using a Multiplex PCR Assay: A Large Italian Hospital’s Five-Month Experience

doi: 10.1128/Spectrum.00695-21

Figure Lengend Snippet: Overview of antimicrobial therapy interventions performed according to FilmArray pneumonia plus (FA-PP) panel results. Interventions were stratified into three relevant groups based on the full concordance of positive (A) or negative (B) FA-PP testing results or the partial or full discordance (C) of FA-PP testing results, respectively, with the results by standard-of-care (SoC) culture for the lower respiratory tract (LRT) samples tested. For each LRT sample, the type(s) of interventions and the antibiotics involved (one or more per intervention) are reported, together with whether the interventions resulted in appropriate antimicrobial escalations/initiations (93 in panel A and 22 in panel C) or deescalations (10 in panel A and 6 in panel C), appropriate antimicrobial discontinuations (5 in panel B), and inappropriate antimicrobial escalations/initiations (4 in panel C). Cases with no antimicrobial therapy interventions (5 in panel A, 85 in panel B, and 4 in panel C) are reported as well.

Article Snippet: In September 2020, when the second wave of the SARS-CoV-2 pandemic was raging in Italy, we implemented the multiplexed, semiquantitative FilmArray pneumonia plus (FA-PP) panel (BioFire, Salt Lake City, UT, USA) assay ( ) for routine clinical use at our institution (a large Italian university hospital).

Techniques:

Journal: Microbiology Spectrum

Article Title: Diagnosis and Treatment of Bacterial Pneumonia in Critically Ill Patients with COVID-19 Using a Multiplex PCR Assay: A Large Italian Hospital’s Five-Month Experience

doi: 10.1128/Spectrum.00695-21

Figure Lengend Snippet: Characteristics of bacterial pneumonia episodes detected or not detected by the FilmArray pneumonia plus panel in 97 mechanically ventilated patients with COVID-19 ^a

Article Snippet: In September 2020, when the second wave of the SARS-CoV-2 pandemic was raging in Italy, we implemented the multiplexed, semiquantitative FilmArray pneumonia plus (FA-PP) panel (BioFire, Salt Lake City, UT, USA) assay ( ) for routine clinical use at our institution (a large Italian university hospital).

Techniques:

Journal: Microorganisms

Article Title: Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays

doi: 10.3390/microorganisms10091856

Figure Lengend Snippet: The most relevant FDA-approved syndromic panels for the diagnosis of respiratory illnesses for both the upper and the lower respiratory tracts.

Article Snippet: The FilmArray ® system (BioFireDiagnostics) can identify, in a semi-quantitative mode, both virus- and bacteria-associated pneumonia, as well as determining seven resistance markers (e.g., methicillin- and carbapenem-resistance genes) in 1 h. The extraction, purification of the nucleic acids from the respiratory sample, and nested multiplex PCR are performed in the same cartridge.

Techniques: Biomarker Discovery, Amplification, Multiplex Assay, Quantitative RT-PCR, Microarray, DNA Hybridization, Hybridization

Journal: Clinical Microbiology Newsletter

Article Title: Why Can't We Just Use PCR? The Role of Genotypic versus Phenotypic Testing for Antimicrobial Resistance Testing

doi: 10.1016/j.clinmicnews.2018.05.003

Figure Lengend Snippet: Commercial diagnostic panels with genotypic resistance detection a

Article Snippet: The FilmArray pneumonia panel will be the next test offered by BioFire Diagnostics, offering the first semi-quantitative multiplex panel for detection of bacteria, as well as qualitative detection of viruses and atypical bacteria.

Techniques: Diagnostic Assay, Luminex, Microarray, Nested PCR, Bacteria, DNA Hybridization, Virus, Hybridization

Journal: European Journal of Immunology

Article Title: Type‐I Interferon assessment in 45 minutes using the FilmArray ® PCR platform in SARS‐CoV‐2 and other viral infections

doi: 10.1002/eji.202048978

Figure Lengend Snippet: Type‐I Interferon quantification using FilmArray ® platform. (A) Spearman correlation [IC95%] between ISG score as defined by a 6‐interferon stimulated gene transcriptional signature using Nanostring ® platform and ISG score as defined by a 4‐interferon stimulated gene transcriptional signature using FilmArray ® technology, obtained from whole blood from (i) febrile infants (n = 86 patients from one experiment, green circle) with proven infections attending pediatric emergency departments, (ii) patients with severe infection caused by SARS‐CoV2 hospitalized in the ICU (n = 26 patients from one experiment, red square), and (iii) healthcare workers with COVID‐19 with mild symptoms (n = 7 patients from one experiment, blue triangle) (ρ = 0.991). (B) Spearman correlation between ISG score as defined by a 4‐interferon stimulated gene transcriptional signature using FilmArray ® technology and IFN‐α2 concentrations measured by SIMOA ® platform, obtained from whole blood from (i) febrile infants (n = 56 patients from one experiment, green circle) with proven infections attending pediatric emergency departments, (ii) patients with severe infection caused by SARS‐CoV2 hospitalized in the ICU (n = 16 patients from one experiment, red square), and (iii) healthcare workers with COVID‐19 with mild symptoms (n = 7 patients from one experiment, blue triangle) (ρ = 0.832). Patients are represented by different forms and nonlinear regression (second order polynomial, quadratic) is represented by a black line. IFN (Interferon), ISG (Interferon Stimulated Genes).

Article Snippet: The aim of this proof‐of‐concept study is to evaluate a prototype multiplex interferon transcription profiling panel for its ability to semiquantify four interferon‐related mRNA markers directly from blood, using the BioFire FilmArray ® PCR System.

Techniques: Infection

Journal: European Journal of Immunology

Article Title: Type‐I Interferon assessment in 45 minutes using the FilmArray ® PCR platform in SARS‐CoV‐2 and other viral infections

doi: 10.1002/eji.202048978

Figure Lengend Snippet: Type‐I IFN assessment in COVID‐19 critically ill patients using FilmArray ® platform. ISG score as defined by a 4 interferon stimulated gene transcriptional signature was determined by IFN pouch FilmArray ® panel, obtained from whole blood from selected patients severely infected by SARS‐CoV‐2 at ±5 days after admission in the ICU (n = 16 patients from one experiment) and healthy volunteers (n = 10 donors from one experiment). COVID‐19 critically‐ill patients are represented by a black dot, and these samples are stratified according to their impairment of IFN response. The healthy volunteers (n = 10 donors from one experiment) are represented by a black dot also. The dashed line represents the arbitrary threshold of the ISG score set to separate patients with a positive (n = 4 patients from one experiment) or negative (n = 12 patients from one experiment) IFN response. The box‐and‐whisker plots represent the median and min‐max; Mann–Whitney U test ** p < 0.01; **** p < 0.0001. IFN (Interferon), ISG (Interferon Stimulated Genes).

Article Snippet: The aim of this proof‐of‐concept study is to evaluate a prototype multiplex interferon transcription profiling panel for its ability to semiquantify four interferon‐related mRNA markers directly from blood, using the BioFire FilmArray ® PCR System.

Techniques: Infection, Whisker Assay, MANN-WHITNEY