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Toxopeus, Corike, Brian Jones, Jessica Brown, Mark Gurling, Cynthia Andjelic, and Cynthia L. Phillips. "422. Performance Evaluation of a Rapid and Easy-to-Use COVID-19 Test." Open Forum Infectious Diseases 7, Supplement_1 (October 1, 2020): S278. http://dx.doi.org/10.1093/ofid/ofaa439.616.
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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)
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Helm, Jared R., Brian Jones, Corike Toxopeus, David S. Rabiger, Mark Gurling, Madeline Veloz, Alex J. Kelley, et al. "1221. Evaluation of the FilmArray® Global Fever Panel." Open Forum Infectious Diseases 7, Supplement_1 (October 1, 2020): S631—S632. http://dx.doi.org/10.1093/ofid/ofaa439.1406.
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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)
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Green, Jeremy, Caitlin Carter, Craig Chandler, Angela Clark, and Stephanie Thatcher. "1015. Enhanced Detection of Bloodstream Pathogens From Positive Blood Culture Specimens With an Improved Multiplex PCR Molecular Diagnostic System." Open Forum Infectious Diseases 5, suppl_1 (November 2018): S302. http://dx.doi.org/10.1093/ofid/ofy210.852.
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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.
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Oberhettinger, Philipp, Jan Zieger, Ingo Autenrieth, Matthias Marschal, and Silke Peter. "Evaluation of two rapid molecular test systems to establish an algorithm for fast identification of bacterial pathogens from positive blood cultures." European Journal of Clinical Microbiology & Infectious Diseases 39, no. 6 (February 4, 2020): 1147–57. http://dx.doi.org/10.1007/s10096-020-03828-5.
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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.
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Liesman, Rachael M., Angela P. Strasburg, Angela K. Heitman, Elitza S. Theel, Robin Patel, and Matthew J. Binnicker. "Evaluation of a Commercial Multiplex Molecular Panel for Diagnosis of Infectious Meningitis and Encephalitis." Journal of Clinical Microbiology 56, no. 4 (February 7, 2018): e01927-17. http://dx.doi.org/10.1128/jcm.01927-17.
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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.
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Ruzante, Juliana M., Katherine Olin, Breda Munoz, Jeff Nawrocki, Rangaraj Selvarangan, and Lindsay Meyers. "Real-time gastrointestinal infection surveillance through a cloud-based network of clinical laboratories." PLOS ONE 16, no. 4 (April 30, 2021): e0250767. http://dx.doi.org/10.1371/journal.pone.0250767.
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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.
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Nguyen, Kiet, Lacie McKamey, and Sarah Green. "196. Impact of BioFire FilmArray® Blood Culture Identification on the Management of Staphylococcus aureus Bacteremia." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S117. http://dx.doi.org/10.1093/ofid/ofz360.271.
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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.
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Maves, Ryan, Derek Larson, Michael Dempsey, Benjamin Connors, James Baldwin, Richard Thomas, and Clarise Starr. "Feasibility and Validation of Viral Respiratory Disease Surveillance in a Combat Theater Using the Filmarray Respiratory Panel." Open Forum Infectious Diseases 4, suppl_1 (2017): S360. http://dx.doi.org/10.1093/ofid/ofx163.874.
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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.
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Chen, Lynette, Matthew Pettengill, Bryan Hess, and Joseph DeSimone. "866. Increased Diagnosis of Varicella-Zoster Virus Infection of the Central Nervous System With the BioFire FilmArray Meningitis/Encephalitis Panel." Open Forum Infectious Diseases 5, suppl_1 (November 2018): S22—S23. http://dx.doi.org/10.1093/ofid/ofy209.051.
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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.
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Salimnia, Hossein, Marilynn R. Fairfax, Paul R. Lephart, Paul Schreckenberger, Sharon M. DesJarlais, J. Kristie Johnson, Gwen Robinson, et al. "Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial." Journal of Clinical Microbiology 54, no. 3 (January 6, 2016): 687–98. http://dx.doi.org/10.1128/jcm.01679-15.
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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.
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Kirera, Ronald, Erick Kipkirui, Margaret Koech, Abigael Ombogo, Janet Ndonye, Mary Kirui, Cliff Odhiambo Philip, et al. "Identification of selected primary bloodstream infection pathogens in patients attending Kisii level five and Homa Bay county hospitals." F1000Research 9 (October 12, 2020): 1228. http://dx.doi.org/10.12688/f1000research.26300.1.
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Background: Bloodstream infection (BSI) contributes to a substantial proportion of mortality in sub-Saharan Africa and is marked by the presence of bacterial and/or fungal microorganisms in the blood. Because BSI can be life threatening, it requires a timely, reliable and accurate diagnosis. This study retrospectively analyzed data of identified BSI pathogens and compared the performance of the different diagnostic technologies used in terms of accuracy, sensitivity, turnaround time (TAT) and cost. Methods: Currently, culture followed by analytical profile index biochemical strips (API), (BioMerieux) are used as the conventional standard diagnostics in Kenyan public hospitals and labs. We compared the results of this standard to that of the BioFire FilmArray (FA) (BioFire Diagnostics) and MicroScan WalkAway-40 plus System (MS) (Beckman Coulter) used in diagnosis of BSI. The FA technology was able to identify 150/152 bacterial and yeast isolates with an overall accuracy of 99.04% (95% CI: 96.59-99.88%), sensitivity of 98.68% (95% CI: 95.33-99.84%), mean TAT of 8 hours 40 minutes per eight samples and running cost per sample of USD 140.11. The MS identified 150/152 isolates with an overall accuracy of 98.56% (95% CI: 95.86-99.70%), sensitivity of 98.68% (95% CI: 95.30-99.84%), mean TAT per sample was 42 hours and running cost per sample of USD 28.05. API detected 150/152 isolates, with an overall accuracy of 99.04% (95% CI: 96.59-99.88%), sensitivity of 98.68% (95% CI: 95.33-99.84%) and the mean TAT per sample was 53 and 103 hours for bacterial and yeast samples, respectively, with a running cost per sample of USD 28.05.Conclusions: The findings in this paper suggest that the FA and MS platforms should be able to perform adequately in Kenya referral hospitals and medical clinics as a rapid diagnostic tool.
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O’Neal, Melissa, Hanna Murray, Sangita Dash, Majdi N. Al-Hasan, Julie Ann Justo, and P. Brandon Bookstaver. "Evaluating appropriateness and diagnostic stewardship opportunities of multiplex polymerase chain reaction gastrointestinal testing within a hospital system." Therapeutic Advances in Infectious Disease 7 (January 2020): 204993612095956. http://dx.doi.org/10.1177/2049936120959561.
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Objective: This single-center, retrospective, observational cohort study evaluates the appropriateness of the BioFire® FilmArray® Gastrointestinal (GI) multiplex PCR panel testing at a community-teaching hospital. Methods: All adult, hospitalized patients at Prisma Health Richland Hospital with a documented GI multiplex PCR panel from 1 April 2015 through 28 February 2018 were included in the analysis. Inappropriate use of the GI panel was defined as a test obtained without documented diarrhea, greater than 2 days of hospitalization, redundant use with other diagnostic tests (e.g. Clostridioides difficile PCR), or laxative use in the preceding 48 h. Antibiotic use and host variables were compared between groups with positive and negative results. Results: During the study period, 442 GI panels were obtained, among which 268 (61%) were deemed inappropriate. Primary reasons for inappropriate testing were lack of documented diarrhea ( n = 92), greater than 2 days of hospitalization ( n = 116), having a duplicate C. difficile PCR test ordered ( n = 118), or laxative use in the 48 h before testing ( n = 36). A total of 141 (32%) GI panels were positive. The most frequently identified pathogens were C. difficile (51.1%, n = 72), Enteropathogenic Escherichia coli (17.7%, n = 25), and Norovirus GI/GII (12.1%, n = 17). Patients with negative GI panel results were initiated on antibiotics significantly less frequently than those with positive GI panels (62.5% versus 80.2%, p < 0.00001). Conclusion: Stewardship opportunities exist to optimize the diagnostic application of the GI multiplex PCR panel.
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Moffa, Matthew A., Derek N. Bremmer, Dustin Carr, Carley Buchanan, Nathan R. Shively, Rawiya Elrufay, and Thomas L. Walsh. "Impact of a Multiplex Polymerase Chain Reaction Assay on the Clinical Management of Adults Undergoing a Lumbar Puncture for Suspected Community-Onset Central Nervous System Infections." Antibiotics 9, no. 6 (May 26, 2020): 282. http://dx.doi.org/10.3390/antibiotics9060282.
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Patients admitted from the community with a suspected central nervous system (CNS) infection require prompt diagnostic evaluation and correct antimicrobial treatment. A retrospective, multicenter, pre/post intervention study was performed to evaluate the impact that the BioFire® FilmArray® meningitis/encephalitis (ME) panel run in-house had on the clinical management of adult patients admitted from the community with a lumbar puncture (LP) performed for a suspected CNS infection. The primary outcome was the effect that this intervention had on herpes simplex virus (HSV) polymerase chain reaction (PCR) turnaround time (TAT). Secondary outcomes included the effect that this intervention had on antiviral days of therapy (DOT), total antimicrobial DOT, and hospital length of stay (LOS). A total of 81 and 79 patients were included in the pre-intervention and post-intervention cohorts, respectively. The median HSV PCR TAT was significantly longer in the pre-intervention group (85 vs. 4.1 h, p < 0.001). Total antiviral DOT was significantly greater in the pre-intervention group (3 vs. 1, p < 0.001), as was total antimicrobial DOT (7 vs. 5, p < 0.001). Pre-intervention hospital LOS was also significantly longer (6.6 vs. 4.4 days, p = 0.02). Implementing the ME panel in-house for adults undergoing an LP for a suspected community-onset CNS infection significantly reduced the HSV PCR TAT, antiviral DOT, total antimicrobial DOT, and hospital LOS.
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Posnakoglou, Lamprini, Vasiliki Syriopoulou, Tania Siahanidou, Eleni Atmatzidou, Triantafyllos Syriopoulos, and Athanasios Michos. "1399. A Prospective Cohort Study Regarding the Impact of Biofire® FilmArray® Meningitis/Encephalitis (FA) Panel in Children with Suspected Central Nervous System Infection." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S509. http://dx.doi.org/10.1093/ofid/ofz360.1263.
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Abstract Background Rapid detection of pathogens involved in central nervous system (CNS) infections could be important for the optimal patient management and overall hospitalization cost. The aim of the study was to evaluate the possible benefits with the use of BioFire® FilmArray® meningitis/encephalitis (FA) panel in children with suspected CNS infection. Methods A prospective cohort study, was performed on children admitted to a tertiary pediatric hospital, over a period of 1 year (April 2018–April 2019), with possible CNS infection and cerebrospinal fluid (CSF) pleocytosis (>15 cells/mm3). For each child that FA was used for the diagnosis, an age-matched control was selected, and separate molecular CSF microbiological tests were sent according to pediatrician’s discretion. Conventional microbiological procedures were performed in all children. Length of hospital stay, duration of antimicrobials, and total cost of hospitalization were compared between groups. FA enables rapid automated cerebrospinal fluid testing for 14 common viral, bacterial and yeast pathogens that cause CNS infections. The cost was estimated according to ICD-10 diagnosis standard cost, adding additional daily hospitalization cost, FA or other molecular microbiological tests costs. Results A total of 142 children were included in the study (71 cases). The median age of cases and controls was 2.5 months (IQR: 1–72) and 2 months (IQR: 0.7–36) respectively (P = 0.157). A pathogen was detected in 38/71 (53.5%) children with the use of FA and in 16/71 (22.5%) in the control group (P < 0.001). In aseptic meningitis cases a virus was detected in 27/60 (45%) and in 11/64 (16.4%) controls (P < 0.001). Length of stay in cases and controls with aseptic meningitis was 5 days (IQR: 4–8) and 8 (IQR: 6–10) respectively (P < 0.001). The median duration of antimicrobials in cases was 4 days (IQR: 2–5.7) and 7 (IQR: 5–10) respectively (P < 0.001). The hospitalization cost was calculated in cases and controls 1,042 (IQR: 932–1372€) and 1,522 (IQR: 1,302–1,742€) respectively (P < 0.001). Conclusion The use of FA was able to reduce significantly the hospitalization days and the total cost comparing to the control group in children with suspected CNS infection. Disclosures All authors: No reported disclosures.
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Lu, Yang, Joseph Hatch, Kristen Holmberg, Anna Hurlock, Daria Drobysheva, Usha Spaulding, Sophia Vourli, et al. "651. Multi-Center Evaluation of the BioFire® FilmArray® Blood Culture Identification 2 Panel for the Detection of Microorganisms and Resistance Markers in Positive Blood Cultures." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S299—S300. http://dx.doi.org/10.1093/ofid/ofz360.719.
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Abstract Background The BioFire® FilmArray® Blood Culture Identification 2 (BCID2) Panel is a diagnostic test that provides results for 26 bacterial, 7 fungal pathogens and 10 antimicrobial resistance (AMR) genes from positive blood culture (PBC) specimens in about an hour. The BCID2 Panel builds upon the existing BCID Panel with several additional assays that include Candida auris and an expanded AMR gene menu that provides methicillin-resistant Staphylococcus aureus (MRSA) results plus detection for mcr-1, carbapenem resistance, and ESBL. Here, we summarize studies conducted to establish clinical performance using an Investigational Use Only version of the BCID2 Panel. Methods Three studies were performed. The first involves prospective collection and testing of an expected ~1,000 residual PBCs at 7 US and 2 EU sites, which began in October 2018 and will conclude in June 2019. BCID2 Panel performance is compared with reference methods of microbial culture as well as PCR/sequencing for AMR genes. In addition, BCID2 Panel MRSA results are compared with the FDA-cleared Xpert MRSA/SA BC system (Cepheid, Inc). Relevant bacterial isolates recovered from PBCs are also evaluated by various phenotypic antimicrobial susceptibility testing (AST) methods. The prospective evaluation is supplemented with a second study that involves testing of ~300 pre-selected, archived PBCs containing rare organisms. The third study includes over 500 seeded blood cultures containing very rare organisms with an evaluation of co-spiked samples. Results With over 1,200 samples tested to date (out of an anticipated 1,800 total), the BCID2 Panel has demonstrated an overall sensitivity of >98% and specificity of >99% for identification of microorganisms compared with culture. Concordance between the BCID2 Panel and the Xpert MRSA/SA BC test is >99% for identification of MRSA. Evaluation of BCID2 Panel AMR gene detection relative to AST and PCR is ongoing. Conclusion The FilmArray® BCID2 Panel appears to be a sensitive, specific, and robust test for rapid detection of microorganisms and MRSA in PBCs. With the use of this comprehensive test, improved antimicrobial stewardship is anticipated. Disclosures All authors: No reported disclosures
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Sieling, William, Matthew Oberhardt, Philip Zachariah, Celibell Vargas, Angela Barrett, Matthew R. Phillips, Lyn Finelli, and Lisa Saiman. "2220. Comparative Incidence and Burden of Respiratory Viruses Associated with Hospitalization in Adults." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S757—S758. http://dx.doi.org/10.1093/ofid/ofz360.1898.
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Abstract Background The population-based incidence and burden of community-onset non-influenza respiratory viruses associated with hospitalization in adults has not been systematically assessed. Methods On admission, patients with respiratory symptoms are tested for respiratory viruses by multiplex polymerase chain reaction (BioFire FilmArray Respiratory Panel) as per standard of care at our university teaching hospital (1160 beds). A retrospective study was performed to identify adults who had influenza, parainfluenza virus (PIV), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), or adenovirus (AV) detected within 3 days of admission from October 2017 to October 2018. To calculate population-based incidence per 100,000 persons (using 2010 US Census data), the number of cases was adjusted by the hospital’s percent market share for zip codes as determined by New York State’s all payer data reporting system. To improve the incidence estimate’s reliability, only cases living in zip codes for which the hospital had ≥ 60% market share were included. We compared median length of stay (LOS), ICU admission, and in-hospital mortality associated with each virus. Results Influenza A (H3) had the highest overall incidence followed by Influenza B and RSV. For each virus, the highest incidence was observed in adults ≥ 65 years old (figure). Overall, 12.9% of cases were hospitalized in the ICU and 4.7% died during hospitalization (table). AV, hMPV, and RSV were associated with the longest LOS. AV, PIV, and RSV were associated with the largest proportion of ICU admissions and deaths. Conclusion While Influenza A (H3) and Influenza B were associated with the highest population-based incidence, non-influenza respiratory viruses caused substantial morbidity in older adults. Compared with influenza viruses, AV, PIV, and RSV were associated with greater severity determined by ICU admissions and death. Disclosures All authors: No reported disclosures.
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Dave, Gipshu, Phoebe Katzenbach, Johanna Sandlund, Joel Estis, Ali Mukherjee, Niamh Nolan, Anna Almazan, et al. "645. Singulex Clarity Norovirus Assay (In Development) Provides Ultrasensitive Detection of Norovirus Genogroups I and II." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S297—S298. http://dx.doi.org/10.1093/ofid/ofz360.713.
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Abstract Background Commercially available enzyme immunoassays (EIAs) for detection of norovirus antigen have poor sensitivity and are limited to use in investigations of a gastroenteritis outbreak. Hence, there remains a need for a standalone high-sensitivity assay that enables rapid and accurate detection of norovirus antigen. Methods The Singulex Clarity norovirus assay is currently in development for use on the Singulex Clarity® system (Singulex Inc., Alameda, CA, USA), a fully-automated platform powered by Single Molecule Counting technology (registered with the FDA and CE marked). The assay uses paramagnetic microparticles bound to capture antibody and a fluorescently labeled reporter antibody to detect virion capsid protein of norovirus genogroups I (GI) and II (GII) in the stool. For the development of Clarity Norovirus assay, diagnostic performance of 4 antibody pairs (as Capture and Detection reagent) were evaluated by testing 137 stool samples from patients with suspected norovirus infection. Samples were sourced from three providers: (1) 90 genotyped samples of which 75 were positive (19 different genotypes) and 15 were negative by the CDC assay, (2) 3 samples positive and 5 samples negative by the BioFire® FilmArray® Gastrointestinal Panel, and (3) 39 samples negative by a lab-developed test using Cepheid reagents (SmartCycler®). Results From all the antibody pairs tested, one of the pairs had best performance with the area under the receiver operating characteristic (AuROC) curve demonstrating a C-Statistic of 0.959 (95% CI 0.921–0.997), compared with AuROC C-statistic of 0.943 (95% CI 0.896–0.990), 0.871 (95% CI 0.807–0.936), and 0.914 (95% CI 0.863–0.964) for the three other pairs. The Clarity assay detected all 19 different genotypes tested (figures). Conclusion The ultrasensitive and rapid Clarity norovirus assay (in development) for detection of GI and GII demonstrated excellent performance with one of the antibody pairs tested and detected all 19 tested genotypes. The Clarity assay may offer a standalone solution for norovirus diagnostics. Disclosures All authors: No reported disclosures.
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Claeys, Kimberly C., Kathryn Schlaffer, Zegbeh Kpadeh-Rogers, Yunyun Jiang, Scott R. Evans, J. Kristie Johnson, and Surbhi Leekha. "151. Comparing the Clinical Utility of Rapid Diagnostic Tests for Gram-Negative Bloodstream Infection Using a Desirability of Outcomes Ranking." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S102. http://dx.doi.org/10.1093/ofid/ofz360.226.
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Abstract Background Rapid diagnostic testing (RDT) technology in bloodstream infections (BSI) has outpaced provider understanding of how to effectively use it. To optimize the use of RDT platforms and antibiotic therapy, decision makers must determine which RDTs to implement at their institutions. A thorough understanding of which platform to choose extends beyond simple analytic measures of sensitivities and specificities and should include a robust analysis of how these RDTs could impact clinical decisions. Methods Retrospective study of adult patients with Gram-negative (GN) BSI from at University of Maryland Medical Center. The clinical microbiology laboratory used Verigene® BC-GN in clinical practice. Discarded blood samples were run on BioFire® FilmArray BCID. Final organism identification/susceptibility, antibiotic exposures, and clinical outcomes were reviewed. DOOR was applied to theoretical therapy decisions based on both actual prescribing adherence to institutional algorithm recommendations; 1 being most and 6 being least desirable (Table 1). A partial credit scoring system was applied to DOOR from most (100) to least desirable (0) outcome. Comparisons were made in a paired manner. Results 77 patients met inclusion. The median age was 58 (IQR 47, 68), 44.2% were in the ICU, and 75.3% had ID consult within 24 hours of BSI. Organism identification included: E. coli (35.1%), K. pneumoniae (23.4%), P. mirabilis (10.4%), S. marcescens (10.4%), Enterobacter spp. (9.4%), P. aeruginosa (3.9%). The only resistance determinant was CTX-M (11.6%). An antibiotic change occurred in 26.2% of cases, divided between antibiotic escalation and de-escalation. Based on the actual utilization of RDT results, median DOOR was not different between BC-GN and BCID (3 [IQR 3.4] vs. 4 [IQR 3.4], P = 0.44). Using a partial credit scoring system, the mean score was not different between platforms (49.8 [SD 26.8] vs. 47.7 [SD 20.3], P = 0.44). Through pairwise comparisons, BC-GN would have resulted in an optimal outcome of 15.3% (95% CI 4.7% to 19.3%) more often than BCID. Conclusion Based on the actual use of RDTs for GN BSI there was no difference in potential clinical outcomes between platforms in this relatively small sample. DOOR is a novel mechanism to quantitate clinical utility and compare RDTs. Disclosures All authors: No reported disclosures.
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Abu Sitta, Emad, Nicole Hubbard, and Geehan Suleyman. "643. Comparison of Multiplex Polymerase Chain Reaction (PCR) and Routine Culture for the Detection of Respiratory Pathogens in Pneumonia Patients." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S297. http://dx.doi.org/10.1093/ofid/ofz360.711.
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Abstract Background The identification of causative pathogens in pneumonia can be challenging, and conventional culture methods can take up to 72 hours. However, rapid microbiologic tests identify organisms within hours. The Biofire®Filmarray ((bioMérieux, North Carolina) Pneumonia Panel was recently approved by the FDA. The multiplex PCR system identifies 33 targets from sputum and bronchoalveolar (BAL) samples, which include 18 bacteria, 8 viruses, and 7 antibiotic resistance genes. The purpose is to compare the panel to routine culture methods for the detection of respiratory pathogens in patients with pneumonia in a 794-bed teaching hospital in northwest Ohio. Methods We retrospectively screened all hospitalized intensive care unit patients who met clinical and radiological criteria of pneumonia using electronic medical records between November 2018 and February 2019. Adult patients who had respiratory cultures collected within 7 days were included. Repeat specimens were excluded. Routine cultures were performed using the laboratory’s standard procedure, and Pneumonia Panel testing was performed according to manufacturer instructions. Results Fifty-nine respiratory or 13 BAL and 46 sputum specimens were evaluated. There was no discrepancy between culture and PCR in 63% (37/59) samples. One (8%) BAL and 10 (22%) sputum specimens had additional pathogens detected by PCR. There was a discrepancy between culture and PCR in four (31%) BAL and seven (15%) sputum samples. The largest discrepancy was noted amongst Serratia marcescens (4/59 or 7%) and Haemophilus influenzae (6/59 or 10%) species. Only one sputum culture had Legionella detected by PCR. Additionally, 17 specimens had a virus detected either alone or with another bacterial pathogen by PCR. For the resistance genes, KPC was detected by PCR but not by Modified Carbapenem Inactivation Method (mCIM) test. The mecA gene was detected in six of seven (86%) of methicillin-resistant Staphylococcus aureus (MRSA) isolates. CTX-M was detected in Serratia and Klebsiella pneunomiae in two samples; however, the organisms were not isolated in culture. Conclusion The Pneumonia Panel can identify additional bacteria that did not grow in culture. This panel can rapidly identify pathogens and potentially reduce unnecessary antibiotic use. Disclosures All authors: No reported disclosures
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Chiasson, Jordan, James B. Cutrell, James B. Cutrell, Jodlowski Tomasz, Winter Smith, and Marcus Kouma. "2001. Assessment of Real-world Effectiveness of a Rapid Blood Culture Diagnostic Panel at a Veterans Affairs Medical Center." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S671. http://dx.doi.org/10.1093/ofid/ofz360.1681.
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Abstract Background Rapid blood culture diagnostics can improve patient outcomes, particularly when paired with robust interventions such as 24/7 stewardship coverage. We sought to determine the clinical impact of a rapid blood culture identification (BCID) panel (BioFire® FilmArray Multiplex PCR) in an established antimicrobial stewardship program (ASP). In addition to clinician education, BCID results were reviewed by the ASP team during weekday business hours, for an average of 2 hours daily based on availability. Methods Data on demographics, blood cultures, antimicrobial use, length of stay and mortality were collected on inpatients at the VA North Texas Health Care System with at least one positive blood culture for bacterial or yeast isolates from March 2017 to June 2017 (pre-BCID) and from March 2018 to June 2018 (post-BCID). The primary outcome was a composite of time to optimal therapy from blood culture collection, defined as escalation, de-escalation, discontinuation, or optimization of antimicrobials retrospectively adjudicated based on final culture results. Secondary outcomes included time to effective therapy, total days of therapy (DOT), length of stay, and 30-day mortality and readmission rates. Results 195 patients were screened with 130 patients included in the study. No significant differences in baseline characteristics were observed between groups (Table 1). Sixty-one patients were included in the pre-BCID arm and 69 in the post-BCID arm. Median time to optimal therapy was 82.9 hours (IQR; 12.8–99.8) in the pre-BCID arm and 33.9 hours (IQR; 11.2–64.8) in the post-BCID arm (P = 0.005) (Table 2). No significant change in 30-day mortality or 30-day readmission rates was noted. Vancomycin DOT was 4 days (IQR; 2–5) and 3 days (IQR; 1–4) (P = 0.024), and piperacillin–tazobactam DOT was 4 (IQR; 0–5) and 2 (IQR; 0–4) (P = 0.043), in the pre-BCID and post-BCID groups, respectively (Figure 1). Conclusion Introduction of BCID into the daily workflow of our ASP resulted in a significant reduction in time to optimal therapy for bloodstream infections. DOT for select broad-spectrum antibiotics were also significantly reduced. This study highlights the potential benefit of rapid diagnostics without negative impact to patient care even in settings without resources for 24/7 ASP review. Disclosures All authors: No reported disclosures.
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Montgomery, Jesse, Neil Draper, Andrew Hemmert, and Robert Crisp. "Rapid Detection and Genotyping of Antimicrobial Resistance Determinants with the BioFire FilmArray® System." Open Forum Infectious Diseases 3, suppl_1 (2016). http://dx.doi.org/10.1093/ofid/ofw172.1547.
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Fhooblall, Mokshanand, Fikile Nkwanyana, and Koleka P. Mlisana. "Evaluation of the BioFire® FilmArray® Blood Culture Identification Panel on positive blood cultures in a regional hospital laboratory in KwaZulu-Natal." African Journal of Laboratory Medicine 5, no. 1 (February 1, 2016). http://dx.doi.org/10.4102/ajlm.v5i1.411.
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Background: There are presently many non-culture-based methods commercially available to identify organisms and antimicrobial susceptibility from blood culture bottles. Each platform has its benefits and limitations. However, there is a need for an improved system with minimal hands-on requirements and short run times.Objectives: In this study, the performance characteristics of the FilmArray® BCID Panel kit were evaluated to assess the efficiency of the kit against an existing system used for identification and antimicrobial susceptibility of organisms from blood cultures.Methods: Positive blood cultures that had initially been received from hospitalised patients of a large quaternary referral hospital in Durban, South Africa were processed as per routine protocol at its Medical Microbiology Laboratory. Positive blood cultures were processed on the FilmArray BCID Panel kit in parallel with the routine sample processing. Inferences were then drawn from results obtained.Results: Organism detection by the FilmArray BCID panel was accurate at 92.6% when organisms that were on the repertoire of the kit were considered, compared to the combination methods (reference method used in the study laboratory). Detection of the antimicrobial resistance markers provided by the panel and reference method demonstrated 100% consistency. Blood cultures with a single organism were accurately identified at 93.8% by FilmArray, while blood cultures with more than one organism were identified at 85.7%.Conclusion: The FilmArray BCID Panel kit is valuable for detection of organisms and markers of antibiotic resistance for an extensive range of organisms.
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Holma, Tanja, Jukka Torvikoski, Nathalie Friberg, Annika Nevalainen, Eveliina Tarkka, Jenni Antikainen, and Jari J. Martelin. "Rapid molecular detection of pathogenic microorganisms and antimicrobial resistance markers in blood cultures: evaluation and utility of the next-generation FilmArray Blood Culture Identification 2 panel." European Journal of Clinical Microbiology & Infectious Diseases, August 5, 2021. http://dx.doi.org/10.1007/s10096-021-04314-2.
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AbstractRapid detection of pathogens causing bloodstream infections (BSI) directly from positive blood cultures is of highest importance in order to enable an adequate and timely antimicrobial therapy. In this study, the utility and performance of a recently launched next-generation fully automated test system, the Biofire FilmArray® Blood Culture Identification 2 (BCID2) panel, was evaluated using a set of 103 well-characterized microbial isolates including 29 antimicrobial resistance genes and 80 signal-positive and 23 signal-negative clinical blood culture samples. The results were compared to culture-based reference methods, MALDI-TOF, and/or 16S rDNA sequencing. Of the clinical blood culture samples, 68 were monomicrobial (85.0%) and 12 polymicrobial (15.0%). Six samples contained ESBL (blaCTX-M), two MRSA (mecA), and three MRSE (mecA) isolates. In overall, the FilmArray BCID2 panel detected well on-panel targets and resistance markers from mono- and polymicrobial samples. However, one Klebsiella aerogenes and one Bacteroides ovatus were undetected, and the assay falsely reported one Shigella flexneri as Escherichia coli. Hence, the sensitivity and specificity for detecting microbial species were 98.8% (95%CI, 95.8–99.9%) and 99.9% (95%CI, 99.8–99.9%), respectively. The sensitivity and specificity for detecting of resistance gene markers were 100%. The results were available within 70 min from signal-positive blood cultures with minimal hands-on time. In conclusion, the BCID2 test allows reliable and simplified detection of a vast variety of clinically relevant microbes causing BSI and the most common antimicrobial resistance markers present among these isolates.
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DiDiodato, Giulio, and Nellie Bradbury. "Cerebrospinal Fluid Analysis With the BioFire FilmArray Meningitis/Encephalitis Molecular Panel Reduces Length of Hospital Stay in Patients With Suspected Central Nervous System Infections." Open Forum Infectious Diseases 6, no. 4 (March 5, 2019). http://dx.doi.org/10.1093/ofid/ofz119.
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Waldrop, Greer, Jason Zucker, Alexandra Boubour, Sara Radmard, Daniel A. Green, and Kiran T. Thakur. "Clinical Significance of Positive Results of the BioFire Cerebrospinal Fluid FilmArray Meningitis/Encephalitis Panel at a Tertiary Medical Center in the United States." Archives of Pathology & Laboratory Medicine, June 4, 2021. http://dx.doi.org/10.5858/arpa.2020-0380-oa.
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Context.— The FilmArray Meningitis/Encephalitis (ME) panel is the first US Food and Drug Administration–cleared multiplex polymerase chain reaction panel for the detection of central nervous system infections. While the assay's performance characteristics have been described, the real-world significance of positive results has not been fully characterized. Objective.— To evaluate the clinical significance of positive ME panel results in a tertiary care medical center in New York, New York. Design.— Four physicians independently performed retrospective clinical assessments of all positive ME panel results at Columbia University Irving Medical Center, including the Children's Hospital of New York, during an 18-month period. Each reviewer determined the likelihood of central nervous system infection for all cases and whether cases fit Brighton diagnostic criteria for meningitis, encephalitis, or meningoencephalitis. Results.— Among 119 cases, there was 75% positive agreement (95% CI, 54%–89%) between ME panel results and clinical consensus, which varied among panel targets. Conclusions.— The ME panel showed good agreement with expert clinical consensus for patients presenting with acute meningitis/encephalitis. Factors contributing to clinically insignificant ME positive results included low pretest probability, traumatic lumbar puncture, specimen contamination, and detection of incidental viral targets such as human herpesvirus 6. Notably, the ME panel detected more than twice the number of cases of bacterial meningitis detected by culture alone, particularly among patients receiving empiric antimicrobial therapy before lumbar puncture. Appropriate test use and contextual interpretation of results are critical to leveraging the advantages of the platform while avoiding potential pitfalls.
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Dien Bard, Jennifer, and Kevin Alby. "Point-Counterpoint: Meningitis/Encephalitis Syndromic Testing in the Clinical Laboratory." Journal of Clinical Microbiology 56, no. 4 (January 17, 2018). http://dx.doi.org/10.1128/jcm.00018-18.
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INTRODUCTION Syndromic panels were first FDA cleared for detection of respiratory pathogens in 2008. Since then, other panels have been approved by the FDA, and most recently, the FilmArray meningitis/encephalitis panel (BioFire, Salt Lake City, UT) has become available. This assay detects 14 targets within 1 h and includes pathogens that typically cause different manifestations of infection, although they infect the same organ system. Several studies have reported both false-positive and false-negative results with this test, and all agree that the cost is significant. As with other panels, health care systems have adopted different strategies for offering this assay. Some have implemented strategies to limit the use of the test to certain patient populations, others have elected not to offer the test, and others have elected not to offer the test and instead request that providers order specific PCRs for the pathogens that best fit the patient's symptoms. In this Point-Counterpoint, Jennifer Dien Bard of the Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, and of the Keck School of Medicine at the University of Southern California explains why laboratories should offer these assays without restriction. Kevin Alby of the University of Pennsylvania explains the concerns about the use of these assays as first-line tests and why some limitations on their use might be appropriate.
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Aldriweesh, Mohammed A., Edi A. Shafaay, Saud M. Alwatban, Obeid M. Alkethami, Faisal N. Aljuraisi, Mohammad Bosaeed, and Naif Khalaf Alharbi. "Viruses Causing Aseptic Meningitis: A Tertiary Medical Center Experience With a Multiplex PCR Assay." Frontiers in Neurology 11 (December 7, 2020). http://dx.doi.org/10.3389/fneur.2020.602267.
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Background: Central nervous system (CNS) infection is associated with high rates of morbidity and mortality, and despite advancements in molecular testing, aseptic meningitis remains challenging to diagnose. Aseptic meningitis cases are often underreported worldwide, which impacts the quality of patient care. Therefore, we aimed to assess the results of BioFire® FilmArray® meningitis/encephalitis (ME) PCR panel, clinical characteristics, and etiologies of aseptic meningitis patients.Methods: From January 2018 to January 2020, all pediatric and adult patients in a large tertiary medical center who underwent lumbar puncture and cerebrospinal fluid (CSF) testing by a ME multiplex PCR panel and who fit the aseptic meningitis definition were retrospectively reviewed.Results: Data were reviewed from 1,607 patients; 240 met the inclusion criteria (54.6% males; 68.8% <4 years of age). The rate of detected viral causes of aseptic meningitis was 40.4%; therefore, 59.6% of the patients remained with unidentified etiology. Among the identified viral meningitis, enterovirus and human herpesvirus 6 (HHV-6) were the most common (25 and 7.9%, respectively). The median length of hospital stay was 6 days, and it was longer in patients with unidentifiable aseptic meningitis (p < 0.0001).Conclusion: Aseptic meningitis is common among suspected meningitis patients, but most cases remained of unknown etiology. The most common identified viruses were enterovirus followed by HHV-6, and there is predominance in males and the pediatric age group. These results highlight that further research is needed to identify other etiologies and possible additional viral pathogens for aseptic meningitis in the current diagnostic methods.
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Keske, Şiran, Burak Zabun, Kahraman Aksoy, Füsun Can, Erhan Palaoğlu, and Önder Ergönül. "Rapid Molecular Detection of Gastrointestinal Pathogens and Its Role in Antimicrobial Stewardship." Journal of Clinical Microbiology 56, no. 5 (March 7, 2018). http://dx.doi.org/10.1128/jcm.00148-18.
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ABSTRACT We aimed to detect the etiological agents of acute diarrhea by a molecular gastrointestinal pathogen test (MGPT) and to assess the impact of MGPT on antimicrobial stewardship programs (ASP). This is a prospective observational study and was conducted between 1 January 2015 and 30 June 2017. We included consequent patients who had acute diarrhea. At the end of 2015, we implemented ASP in acute diarrhea cases and compared the outcomes in the pre-ASP and post-ASP periods. An FDA-cleared multiplexed gastrointestinal PCR panel system, the BioFire FilmArray (Idaho Technology, Salt Lake City, UT), which detects 20 pathogens in stool, was used. In 499 out of 699 patients (71%), at least one pathogen was detected. Among 314 adults with positive MGPT, 101 (32%) enteropathogenic Escherichia coli (EPEC), 71 (23%) enteroaggregative E. coli (EAEC), 68 (22%) enterotoxigenic E. coli (ETEC), 55 (18%) Shiga toxin-producing E. coli (STEC) (17%) Norovirus , 48 (15%) Campylobacter , 21 (7%) Salmonella , and 20 (6%) Clostridium difficile strains were detected. Among 185 children, 55 (30%) EPEC, 37 (20%) C. difficile , 32 (17%) Norovirus , 29 (16%) EAEC, 22 (12%) STEC, 21 (11%) ETEC, 21 (11%) Campylobacter , 20 (11%) Salmonella , and 16 (5%) Rotavirus strains were detected. Inappropriate antibiotic use decreased in the post-ASP period compared with the pre-ASP period among inpatients (42.9% and 25.8%, respectively; P = 0.023). Using MGPT in clinical practice significantly decreased the unnecessary use of antibiotics. Detection of high rates of C. difficile in children and Salmonella spp., as well as relatively high rates of Campylobacter spp., which were hard to isolate by routine stool culture, were remarkable.