Auswahl der wissenschaftlichen Literatur zum Thema „BioFire® FilmArray® Torch System“

Abstract Background The BioFire® COVID-19 Test is a qualitative test for use on the FilmArray® 2.0 and Torch systems for the detection of SARS-CoV-2 RNA in nasopharyngeal swabs (NPS) in transport media. This test received Emergency Use Authorization from the FDA. A closed, disposable pouch contains all the necessary reagents for sample preparation, nucleic acid extraction, reverse transcription, polymerase chain reaction (PCR), and amplified nucleic acid detection to identify RNA from SARS-CoV-2 virus in an NPS specimen. Internal controls monitor all stages of the test process. Once an NPS sample (0.3 mL) is loaded into the system disposable pouch (Figure 1), the fully automated test returns results within an hour. As an additional resource, the BioFire® COVID-19 Test External Control Kit (+) includes positive external control material that may be used for quality control and laboratory verification. Figure 1. BioFire COVID-19 Test Disposable Pouch Methods The following were evaluated: • Limit of Detection (LoD) • Positive and Negative Percent Agreement (PPA and NPA, respectively) for clinical contrived samples and a limited number of clinical specimens • Exclusivity Results • LoD The LoD was evaluated using live SARS-CoV-2 virus (cultured from the USA_WA1/2020 strain obtained from World Reference Center for Emerging Viruses and Arboviruses (WRCEVA)). The LoD was determined to be 3.3E+02 GC/mL (2.2E-02 TCID50/mL). • Clinical Contrived Accurate detection of virus in clinical matrix was demonstrated at various LoD levels using thirty contrived individual unique clinical samples (PPA), and 66 individual unique negative clinical specimens (NPA). • Clinical Samples Positive samples were collected from patients presenting with signs or symptoms of COVID-19, and who were previously identified as positive for SARS-CoV-2 by another EUA test. Negative samples were collected in 2018, and therefore presumed negative for SARS-CoV-2. • Exclusivity The potential for cross-reactivity was evaluated for six viruses from the same genetic family as SARS- CoV-2, and for an additional 30 high priority organisms/viruses. No cross-reactivity was observed. Table 1. SARS-CoV-2 Virus Test Results at 1× and 0.1× LoD for the BioFire COVID-19 Test Table 2. Clinical Contrived and Negative Testing with the BioFire COVID-19 Test Table 3. BioFire COVID-19 Test Performance Summary Conclusion The BioFire COVID-19 Test reliably detects SARS-CoV-2 virus RNA in clinically relevant samples. Disclosures Corike Toxopeus, PhD, BioFire Defense, LLC. (Employee, stock owner) Brian Jones, PhD., BioFire Defense, LLC (Employee, own stock) Jessica Brown, BS, BioFire Defense (Employee, Stock owner) Mark Gurling, PhD, BioFire Defense, LLC (Employee) Cynthia Andjelic, PhD., BioFire Defense (Employee, Other Financial or Material Support, Own stocks) Cynthia L. Phillips, PhD, BioFire Defense (Employee, Scientific Research Study Investigator, Shareholder)BioFire Defense (Employee, Scientific Research Study Investigator, Shareholder)

Abstract Background Acute Febrile Illness (AFI) is caused by a diverse set of pathogens. The FilmArray Global Fever (GF) Panel, developed by BioFire Defense in collaboration with the U.S. Department of Defense and NIAID, uses an automated, multiplex nested PCR system to evaluate whole blood samples for multiple pathogens simultaneously in under an hour. Methods BioFire Defense conducted analytical performance studies to show sensitivity (LoD), inclusivity, and specificity (exclusivity), and a prospective clinical study to evaluate the positive percent agreement (PPA) and negative percent agreement (NPA) of the GF Panel. The results of these studies will be reported in two submissions to the US FDA. Results The analytical performance demonstrated the ability to accurately detect multiple pathogens, including Category A biothreat pathogens. Eleven locations around the world tested 1,865 specimens on the GF Panel. The rate of positive detections was 35% (652/1865), with Plasmodium spp. accounting for the majority of positives (53.4%, 348/652) and dengue virus the second most (40.5%, 264/652). Other detected pathogens include Leptospira spp., West Nile virus, Zika virus, Leishmania spp., Crimean-Congo hemorrhagic fever virus, and chikungunya virus. Twenty-eight (28) specimens had more than one detected pathogen (4.3% of positive specimens). Comparator testing consisted of in-house developed PCR assays followed by bidirectional sequencing. PPA between GF Panel and comparator testing ranged between 92.7-100%, and the NPA ranged between 99.3-100%. In all cases, discrepancies coincided with analytes that were near the limit of detection of the GF Panel and comparator assays. When the GF Panel result was compared to site-specific malaria testing, the PPA ranged between 94.7-100% and the NPA ranged between 43.3-100%. Analysis of the NPA suggests that the GF Panel is more sensitive than microscopy, producing “discrepancies” for this comparison. The wide range in NPA between sites could be due to variation in microscopy technique; the GF Panel eliminates such variation because it is fully automated. Conclusion The results show that the FilmArray GF Panel could aid in rapid and actionable AFI diagnosis caused by multiple, sometimes co-occurring, pathogens. Disclosures Jared R. Helm, PhD, BioFire Defense (Employee) Brian Jones, PhD, BioFire Defense, LLC (Employee, own stock) Corike Toxopeus, PhD, BioFire Defense, LLC. (Employee, stock owner) David S. Rabiger, PhD, BioFire Defense (Employee) Mark Gurling, PhD, BioFire Defense, LLC (Employee) Olivia Jackson, n/a, BioFire Defense (Employee) Marissa Burton, BS Biology, Biomerieux, Inc. (Shareholder) Cynthia Andjelic, PhD, BioFire Defense (Employee, Other Financial or Material Support, Own stocks) Cynthia L. Phillips, PhD, BioFire Defense (Employee, Scientific Research Study Investigator, Shareholder)BioFire Defense (Employee, Scientific Research Study Investigator, Shareholder)

Abstract Background Timely bloodstream infection (BSI) pathogen identification requires robust sample purification and testing methods that can accommodate the wide variety of blood culture media used for growing positive blood culture (PBC) specimens. Sensitive molecular methods are needed for identification of all organisms present in PBD, especially polymicrobial cultures which can be difficult to identify with standard methods. Multiple types of BD and BioMérieux blood culture media commonly used in hospital laboratories were used to evaluate the performance of a prototype BioFire® FilmArray® Blood Culture Identification 2 (BCID2) Panel with PBCs. Methods Fungi (seven) and bacteria (19) were independently seeded in blood samples, inoculated into as many as eight different types of blood culture bottles, and incubated on the recommended instrument. Time to positivity (TTP) was recorded for all PBCs. Subsets of PBCs were enumerated and tested on the BioFire BCID2 Panel and BioFire® FilmArray® Blood Culture Identification (BCID) panel. Polymicrobial testing was performed by seeding fast and slow growing organisms into the same bottles. Results Over 750 PBCs were enumerated; ~500 PBCs were tested on the BioFire BCID2, and over 200 were also tested on the BioFire BCID. 100% of seeded PBCs tested on the BioFire Panels resulted in correct pathogen identification. Across all bottle types, fungi grew to levels ranging from 8E+05 to 5E+07 CFU/mL, Gram-positive bacteria titers ranged from 7E+06 to 2E+09, and Gram-negative bacteria titers ranged from 9E+07 to 3E+09. Polymicrobial PBCs (30) had reduced titers of slow growing organisms when seeded with fast growing organisms but were detected by both BioFire BCID Panels at a rate of 99%. Conclusion This study demonstrates that a prototype BioFire BCID2 Panel, and the BioFire BCID Panel, robustly detect and identify (100%) BSI pathogens over a multitude of common blood culture media and systems. Results confirm PBC (single and polymicrobial) titers are above the levels of sensitivity for both BioFire panels. An expanded menu of targets (organism and resistance) and faster run time with the BioFire BCID2 Panel will offer a flexible and comprehensive aid in the diagnosis of BSIs. The BioFire® BCID2 Panel has not yet been evaluated by the FDA or other regulatory agencies for in vitro diagnostic use. Disclosures J. Green, BioFire Diagnostics, LLC: Employee, Salary. C. Carter, BioFire Diagnostics, LLC: Employee, Salary. C. Chandler, BioFire Diagnostics, LLC: Employee, Salary. A. Clark, BioFire Diagnostics, LLC: Employee, Salary. S. Thatcher, BioFire Diagnostics, LLC: Employee, Salary.

Abstract Fast identification of pathogens directly from positive blood cultures is of highest importance to supply an adequate therapy of bloodstream infections (BSI). There are several platforms providing molecular-based identification, detection of antimicrobial resistance genes, or even a full antimicrobial susceptibility testing (AST). Two of such test systems allowing rapid diagnostics were assessed in this study: The Biofire FilmArray® and the Genmark ePlex®, both fully automated test system with a minimum of hands-on time. Overall 137 BSI episodes were included in our study and compared to conventional culture–based reference methods. The FilmArray® is using one catridge including a panel for the most common bacterial and fungal BSI pathogens as well as selected resistance markers. The ePlex® offers three different cartridges for detection of Gram-positives, Gram-negatives, and fungi resulting in a broader panel including also rare pathogens, putative contaminants, and more genetic resistance markers. The FilmArray® and ePlex® were evaluated for all 137 BSI episodes with FilmArray® detecting 119 and ePlex® detecting 128 of these. For targets on the respective panel of the system, the FilmArray® generated a sensitivity of 98.9% with 100% specificity on Gram-positive isolates. The ePlex® system generated a sensitivity of 94.7% and a specificity of 90.7% on Gram-positive isolates. In each case, the two systems performed with 100% sensitivity and specificity for the detection of Gram-negative specimens covered by each panel. In summary, both evaluated test systems showed a satisfying overall performance for fast pathogen identification and are beneficial tools for accelerating blood culture diagnostics of sepsis patients.

ABSTRACT Rapid and accurate laboratory tests are important for the timely diagnosis and treatment of central nervous system infections. The FilmArray meningitis/encephalitis (ME) panel (BioFire Diagnostics, Salt Lake City, UT) is an FDA-cleared, multiplex molecular panel that allows the detection of 14 pathogens (bacterial [n = 6], viral [n = 7], and fungal [n = 1] pathogens) from cerebrospinal fluid (CSF). In this study, we evaluated the performance characteristics of the FilmArray ME panel using clinical, residual CSF samples (n = 291) that tested positive by a routine method(s) (e.g., bacterial culture, individual real-time PCR assay) for a pathogen represented on the ME panel. Of note, a subset (n = 76) of the CSF specimens was collected during the prevaccine era and had been characterized as positive for a bacterial pathogen. The FilmArray ME panel demonstrated an overall percent positive agreement (PPA) of 97.5% (78/80) for bacterial pathogens, 90.1% (145/161) for viruses, and 52% (26/50) for Cryptococcus neoformans/C. gattii. Despite the low overall agreement (52%) between the ME panel and antigen testing for detection of C. neoformans/C. gattii, the percent positive agreement of the FilmArray assay for C. neoformans/C. gattii was 92.3% (12/13) when the results were compared directly to the results of routine fungal smear or culture. The FilmArray ME panel offers a rapid (∼60-min), syndrome-based approach for the detection of select meningitis and encephalitis pathogens.

Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its causes. The use of novel multiplex molecular assays for pathogen detection and identification provides a unique opportunity to improve pathogen detection, and better understand risk factors and burden associated with AGI in the community. In this study, de-identified results from BioFire® FilmArray® Gastrointestinal (GI) Panel were obtained from January 01, 2016 to October 31, 2018 through BioFire® Syndromic Trends (Trend), a cloud database. Data was analyzed to describe the occurrence of pathogens causing AGI across United States sites and the relative rankings of pathogens monitored by FoodNet, a CDC surveillance system were compared. During the period of the study, the number of tests performed increased 10-fold and overall, 42.6% were positive for one or more pathogens. Seventy percent of the detections were bacteria, 25% viruses, and 4% parasites. Clostridium difficile, enteropathogenic Escherichia coli (EPEC) and norovirus were the most frequently detected pathogens. Seasonality was observed for several pathogens including astrovirus, rotavirus, and norovirus, EPEC, and Campylobacter. The co-detection rate was 10.2%. Enterotoxigenic E. coli (ETEC), Plesiomonas shigelloides, enteroaggregative E. coli (EAEC), and Entamoeba histolytica were detected with another pathogen over 60% of the time, while less than 30% of C. difficile and Cyclospora cayetanensis were detected with another pathogen. Positive correlations among co-detections were found between Shigella/Enteroinvasive E. coli with E. histolytica, and ETEC with EAEC. Overall, the relative ranking of detections for the eight GI pathogens monitored by FoodNet and BioFire Trend were similar for five of them. AGI data from BioFire Trend is available in near real-time and represents a rich data source for the study of disease burden and GI pathogen circulation in the community, especially for those pathogens not often targeted by surveillance.

Abstract Background Staphylococcus aureus bacteremia (SAB) is associated with 30-day mortality rates that are as high as 20 to 40%. In order to reduce mortality and treatment failures, SAB management should include prompt infectious diseases (ID) consult, repeat blood cultures, source control, intravenous antibiotics for the entirety of treatment, and optimal treatment duration. The objective of this study was to determine the impact of BioFire FilmArray® Blood Culture Identification (BCID) on the implementation of these standard of care measures in the management of SAB across a large health system. Methods This study was an IRB approved, retrospective chart review evaluating the impact of rapid diagnostics on the management of SAB before and after implementation of BCID. The composite endpoint consisted of mortality at 30 days, persistent SAB (≥7 days), and recurrence of S. aureus infection within 30 days. Patients were included if they were ≥18 years old and at least one blood culture was positive with S. aureus. The pre-BCID period was between September 1, 2016 and March 31, 2017. The post-BCID period was between April 1, 2017 and July 31, 2018. Fisher’s exact test, student’s t-test, and descriptive statistics were used in the analysis. Results A total of 200 patients met eligibility (pre-BCID, n = 102; post-BCID, n = 98). The composite endpoint was met in 34% of patients in the pre-BCID group and 29% in the post-BCID group (P = 0.45). Mortality at 30 days (17% vs. 17%, P = 1.00), persistent SAB (16% vs. 13%, P = 0.69), and rates of recurrence within 30 days (4% vs. 1%, P = 0.37) were similar between groups. ID consult increased after BCID implementation (83% vs. 92%, P = 0.001). More patients in the post-BCID received appropriate durations of antibiotics (75% vs. 86%, P = 0.04) and had decreased time, in hours, to definitive therapy (7 ± 17 vs. 1 ± 5, P ≤ 0.05). Conclusion The management of SAB after implementation of BCID did not show a decrease in the primary outcome but did show an improved time to appropriate therapy. A larger study is needed to determine whether improved time to appropriate therapy translates to an improvement in patient outcomes. Disclosures All authors: No reported disclosures.

Abstract Background Viral respiratory infections are a significant threat to deployed military units. Pathogen-based surveillance may be hampered by limitations in trained personnel in theater, difficulty with specimen shipment, and technical issues with equipment maintenance. In this project, we evaluated the performance of the FilmArray respiratory panel at military clinics in Afghanistan and compare results to testing performed in the United States. Methods Participants were recruited after presenting at military clinics at Bagram Airfield (BAF), Afghanistan, in 2013–2014 with fever (≥38° C) and respiratory symptoms (cough, dyspnea, chest pain, and/or sore throat). General medical laboratory staff at BAF were trained to operate the FilmArray; nasopharyngeal swabs were obtained and tested in-theater using the FilmArray respiratory panel (Biofire Diagnostics, Salt Lake City, UT). Samples were then shipped to the USAFSAM Applied Technology Center in 50% RNALater (Qiagen, Valencia, CA) without dry ice and then retested using the same panel. Selected influenza isolates then underwent sequencing to evaluate for potential novel circulating strains. Results 29 specimens underwent testing. A virus was identified on FilmArray in 22/29 specimens at BAF and 24/29 specimens at USAFSAM, of whom 17/29 had influenza A. Positive results between BAF and USAFSAM were concordant in all cases; 2 of the negative results at BAF were identified as having influenza A and rhinovirus, respectively. Among those with influenza A, all but one had undergone seasonal influenza vaccination. 5 influenza isolates then underwent sequencing; 2 were A(H1N1pdm09) consistent with the predominant 2012–2013 strain, while 3 were A(H3N2) viruses with HA mutations that differed from those in the 2013–2014 vaccine strain. No resistance-associated neuraminidase mutations were identified. Conclusion Surveillance using the FilmArray system is effective and feasible in theater by general laboratory staff. H1N1 and H3N2 influenza A viruses predominated in this sample of acute respiratory infections in a deployed military setting despite high vaccination rates. The use of the RNALater preservative is an effective method for specimen transport without requiring a cold chain and may facilitate biosurveillance in remote settings. Disclosures All authors: No reported disclosures.

Abstract Background Varicella-zoster virus (VZV) infection of the central nervous system (CNS) is relatively uncommon. Diagnostic tests historically utilized culture, serologies, and targeted PCR methods. In April 2016, our institution began using the BioFire FilmArray meningitis/encephalitis (BFME) panel for cerebrospinal fluid (CSF) specimen analysis. We hypothesized that the diagnosis of VZV CNS infection increased at our institution with the implementation of this diagnostic panel. Methods We conducted chart reviews of patients from 2 time periods. In the first period, April 2013–March 2016, BFME was not available for CSF analysis (pre-BFME period). We reviewed all positive CSF VZV PCR results during this period. Medical charts of these patients were reviewed for epidemiology, clinical presentation, treatment course, and outcome. In the second period, April 2016–March 2018, BFME was performed on all CSF specimens obtained by lumbar puncture (BFME period). Patients with a positive VZV result on BFME underwent similar chart review. Results In the 3-year pre-BFME period, 292 VZV PCR tests were performed. Six patients were diagnosed with VZV CNS infection; median age 61 years. Five of the 6 patients (83%) had cutaneous zoster. All 6 patients received antiviral therapy. Five of the 6 patients clinically improved; 1 patient with VZV encephalitis died. In the 2-year BFME period, 1,113 CSF samples were evaluated, and 18 of these were positive for VZV (1.6%); median age 55 years. Only 7 of the 18 (39%) had cutaneous zoster at the time of hospitalization. All 18 received antiviral therapy with clinical improvement. Conclusion Prior to implementation of the BFME panel at our institution, VZV CNS infection was rarely diagnosed. Diagnosis at that time relied on physicians’ requests for a targeted CSF VZV PCR. The majority of the patients during that period had a concurrent zoster rash. In a shorter period utilizing syndromic testing (BFME) on CSF specimens, we diagnosed 3 times as many cases of VZV CNS disease. Only a minority of these patients presented with a concurrent zoster rash. The use of syndromic testing of CSF will likely identify more cases of VZV CNS disease. Disclosures All authors: No reported disclosures.

Sepsis is a major cause of morbidity, mortality, and increased medical expense. Rapid diagnosis improves outcomes and reduces costs. The FilmArray blood culture identification panel (BioFire Diagnostics LLC, Salt Lake City, UT), a highly multiplexed PCR assay, can identify 24 etiologic agents of sepsis (8 Gram-positive, 11 Gram-negative, and 5 yeast species) and three antimicrobial resistance genes (mecA,vanA/B, andblaKPC) from positive blood culture bottles. It provides results in about 1 h with 2 min for assay setup. We present the results of an eight-center trial comparing the sensitivity and specificity of the panel with those of the laboratories' standard phenotypic identification techniques, as well as with molecular methods used to distinguishAcinetobacter baumanniifrom other members of theA. calcoaceticus-A. baumanniicomplex and to detect antimicrobial resistance genes. Testing included 2,207 positive aerobic blood culture samples, 1,568 clinical and 639 seeded. Samples were tested fresh or were frozen for later testing within 8 h after the bottles were flagged as positive by an automated blood culture system. At least one organism was detected by the panel in 1,382 (88.1%) of the positive clinical specimens. The others contained primarily off-panel organisms. The panel reported multiple organisms in 81 (5.86%) positive clinical specimens. The unresolved blood culture identification sensitivity for all target detections exceeded 96%, except forKlebsiella oxytoca(92.2%), which achieved 98.3% sensitivity after resolution of an unavoidable phenotypic error. The sensitivity and specificity forvanA/BandblaKPCwere 100%; those formecAwere 98.4 and 98.3%, respectively.