scholarly journals 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

2021 ◽  
Author(s):  
Tanja Holma ◽  
Jukka Torvikoski ◽  
Nathalie Friberg ◽  
Annika Nevalainen ◽  
Eveliina Tarkka ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Blood Culture ◽  
Sensitivity And Specificity ◽  
Blood Cultures ◽  
Next Generation ◽  
Gene Markers ◽  
Rdna Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Resistance Markers ◽  
Culture Identification

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.

scholarly journals Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial

2016 ◽  
Vol 54 (3) ◽  
pp. 687-698 ◽  
Author(s):  
Hossein Salimnia ◽  
Marilynn R. Fairfax ◽  
Paul R. Lephart ◽  
Paul Schreckenberger ◽  
Sharon M. DesJarlais ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Blood Culture ◽  
Sensitivity And Specificity ◽  
Resistance Genes ◽  
Salt Lake ◽  
Klebsiella Oxytoca ◽  
Content Type ◽  
Clinical Specimens ◽  
Antimicrobial Resistance Genes ◽  
Culture Identification

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.

scholarly journals 300. Pediatric Center Evaluation of the BioFire® Blood Culture Identification 2 Panel Versus the Original BioFire®FilmArray® Blood Culture Identification Panel for the Detection of Microorganisms and Resistance Markers in Positive Blood Cultures

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S148-S149
Author(s):  
Kristina B Pierce ◽  
Rebecca Barr ◽  
Aubrie Hopper ◽  
Charlotte Bowerbank ◽  
Anne Shaw ◽  
...  
Keyword(s):  
Blood Culture ◽  
False Negative ◽  
Bloodstream Infections ◽  
Turnaround Time ◽  
Rapid Identification ◽  
Blood Cultures ◽  
Species Level ◽  
Genus Level ◽  
Antimicrobial Resistance Genes ◽  
Culture Identification

Abstract Background Studies show a rising annual incidence of severe sepsis, with bloodstream infections continuing to impact children. Rapid identification of causative agents and timely administration of targeted therapy can positively impact patient outcomes and improve antibiotic stewardship. The BioFire® Blood Culture Identification 2 (BCID2) Panel (BioFire Diagnostics, LLC), an updated version of the FDA-cleared BioFire® FilmArray® Blood Culture Identification (BCID) Panel, designed for use on positive blood cultures (PBCs), assesses 43 analytes, including 17 novel analytes (8 bacterial, 2 fungal, and 7 antimicrobial resistance genes), with a similar turnaround time. Methods De-identified residual PBCs for which clinician-ordered testing per standard of care (SoC) had been performed were enrolled and tested with an Investigation-Use-Only version of the BCID2 Panel. Only one positive bottle per patient was enrolled. Results of BCID2 and BCID were compared. Results 116 PBCs (48 aerobic and 68 anaerobic) were evaluated using the BioFire BCID2 Panel and results were compared to the BioFire BCID Panel. Of the 116 cases, 103 were positive on both the BioFire BCID2 Panel and the BioFire BCID Panel. Ten cases were negative on both tests. While the two panels showed 97% agreement, three cases were discrepant. Using culture (SoC) as the tiebreaker, two cases were false positive and one case was false negative on the BioFire BCID Panel. In all three cases, results from culture and the BioFire BCID2 Panel were in agreement. As expected, no organisms were detected on the BioFire BCID2 Panel in PBCs from 10% (12/116) of PBC bottles where culture identified only organisms that are not part of the panel menu. With the BioFire BCID2 Panel’s expanded platform, two cases identified as Enterobacteriaceae on the BioFire BCID Panel were identified to the genus level on the BioFire BCID2 Panel; 31 cases detected to the genus level on the BioFire BCID Panel were identified to the species level on the BioFire BCID2 Panel. Conclusion Overall, the BioFire BCID2 Panel performed well against the BioFire BCID Panel for identification of bloodstream pathogens and provided additional discrimination of some pathogens to the genus or species level. Data presented are from assays that have not been cleared or approved for diagnostic use. Disclosures All Authors: No reported disclosures

scholarly journals Benefits of Adding a Rapid PCR-Based Blood Culture Identification Panel to an Established Antimicrobial Stewardship Program

2016 ◽  
Vol 54 (10) ◽  
pp. 2455-2463 ◽  
Author(s):  
Shawn H. MacVane ◽  
Frederick S. Nolte
Keyword(s):  
Antimicrobial Resistance ◽  
Blood Culture ◽  
Antimicrobial Stewardship ◽  
Bacterial Species ◽  
Effective Therapy ◽  
Control Group ◽  
Stewardship Program ◽  
Antimicrobial Resistance Genes ◽  
Culture Identification ◽  
Organism Identification

Studies have demonstrated that the combination of antimicrobial stewardship programs (ASP) and rapid organism identification improves outcomes in bloodstream infections (BSI) but have not controlled for the incremental contribution of the individual components. Hospitalized adult patients with blood culture pathogens on a rapid, multiplex PCR-based blood culture identification panel (BCID) that included 19 bacterial species, 5Candidaspp., and 4 antimicrobial resistance genes were studied over sequential time periods in a pre-post quasiexperimental study in 3 groups in the following categories: conventional organism identification (controls), conventional organism identification with ASP (AS), and BCID with ASP (BCID). Clinical and economic outcomes were compared between groups. There were 783 patients with positive blood cultures; of those patients, 364 (115 control, 104 AS, and 145 BCID) met inclusion criteria. The time from blood culture collection to organism identification was shorter in the BCID group (17 h;P< 0.001) than in the control group (57 h) or the AS group (54 h). The BCID group had a shorter time to effective therapy (5 h;P< 0.001) than the control group (15 h) or AS group (13 h). The AS (57%) and BCID (52%) groups had higher rates of antimicrobial de-escalation than the control group (34%), with de-escalation occurring sooner in the BCID group (48 h;P= 0.034) than in the AS group (61 h) or the control group (63 h). No difference between the control group, AS group, and BCID group was seen with respect to mortality, 30-day readmission, intensive care unit length of stay (LOS), postculture LOS, or costs. In patients with BSI, ASP alone improved antimicrobial utilization. Addition of BCID to an established ASP shortened the time to effective therapy and further improved antimicrobial use compared to ASP alone, even in a setting of low antimicrobial resistance rates.

scholarly journals 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

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S299-S300
Author(s):  
Yang Lu ◽  
Joseph Hatch ◽  
Kristen Holmberg ◽  
Anna Hurlock ◽  
Daria Drobysheva ◽  
...  
Keyword(s):  
Blood Culture ◽  
Fungal Pathogens ◽  
Clinical Performance ◽  
Carbapenem Resistance ◽  
Blood Cultures ◽  
Microbial Culture ◽  
Candida Auris ◽  
Comprehensive Test ◽  
Resistance Markers ◽  
Culture Identification

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

scholarly journals A Multi-Center Clinical Study to Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex ® Blood Culture Identification Gram-Negative Panel

2021 ◽  
Author(s):  
Donna M. Wolk ◽  
Stephen Young ◽  
Natalie N. Whitfield ◽  
Jennifer L. Reid ◽  
Adam Thornberg ◽  
...  
Keyword(s):  
Clinical Study ◽  
Antimicrobial Resistance ◽  
Blood Culture ◽  
Resistance Genes ◽  
Limit Of Detection ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Gram Negative ◽  
Antimicrobial Resistance Genes ◽  
Culture Identification

Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex ® Investigational Use Only Blood Culture Identification Gram-Negative Panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard of care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with gram-negative Gram stain results. Of these, 109 samples had false negative and/or positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and post-discordant resolution sample accuracy excludes 37 gram-negative organisms representing 20 uncommon genera, 10 gram-positive organisms, and 1 Candida sp. present in 5% of samples that are not targeted by the BCID-GN. The overall weighted PPA, which averages the individual PPAs from the 27 targets (gram-negative and ARG), was 94.9%. The limit of detection ranged from 10 4 to 10 7 CFU/mL, except for one strain of Fusobacterium necrophorum at 10 8 CFU/mL.

scholarly journals Evaluation of the BioFire® FilmArray® Blood Culture Identification Panel on positive blood cultures in a regional hospital laboratory in KwaZulu-Natal

2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Mokshanand Fhooblall ◽  
Fikile Nkwanyana ◽  
Koleka P. Mlisana
Keyword(s):  
Blood Culture ◽  
Antimicrobial Susceptibility ◽  
Reference Method ◽  
Blood Cultures ◽  
Combination Methods ◽  
Single Organism ◽  
Hospitalised Patients ◽  
Short Run ◽  
Culture Identification ◽  
Study Laboratory

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.

scholarly journals Clinical Evaluation of the iCubate iC-GPC Assay for Detection of Gram-Positive Bacteria and Resistance Markers from Positive Blood Cultures

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Paul A. Granato ◽  
Melissa M. Unz ◽  
Raymond H. Widen ◽  
Suzane Silbert ◽  
Stephen Young ◽  
...  
Keyword(s):  
Blood Culture ◽  
Staphylococcus Epidermidis ◽  
Bloodstream Infections ◽  
Blood Cultures ◽  
Gram Positive ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Sequencing Method ◽  
Resistance Markers ◽  
Gram Positive Cocci

ABSTRACT The iC-GPC Assay (iCubate, Huntsville, AL) is a qualitative multiplex test for the detection of five of the most common Gram-positive bacteria (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Enterococcus faecalis, and Enterococcus faecium) responsible for bacterial bloodstream infections, performed directly from positive blood cultures. The assay also detects the presence of the mecA, vanA, and vanB resistance determinants. This study comparatively evaluated the performance of the iC-GPC Assay against the Verigene Gram-positive blood culture (BC-GP) assay (Luminex Corp., Austin, TX) for 1,134 patient blood culture specimens positive for Gram-positive cocci. The iC-GPC Assay had an overall percent agreement with the BC-GP assay of 95.5%. Discordant specimens were further analyzed by PCR and a bidirectional sequencing method. The results indicate that the iC-GPC Assay together with the iCubate system is an accurate and reliable tool for the detection of the five most common Gram-positive bacteria and their resistance markers responsible for bloodstream infections.

scholarly journals Antimicrobial Resistance Patterns of Bacterial Isolates from Blood Culture among HIV/AIDS Patients at Felege Hiwot Referral Hospital, Northwest Ethiopia

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Mohabaw Jemal ◽  
Teshiwal Deress ◽  
Teshome Belachew ◽  
Yesuf Adem
Keyword(s):  
Antimicrobial Resistance ◽  
Blood Culture ◽  
Agar Plate ◽  
Blood Cultures ◽  
Resistant Bacteria ◽  
Bacterial Isolates ◽  
Aids Patients ◽  
Gram Positive ◽  
Gram Negative ◽  
Hiv Aids

Background. The emergence and spread of antimicrobial resistance in bacteria is recognized as a global public health problem. Bloodstream infection with antimicrobial-resistant bacteria in HIV/AIDS patients makes the problem more challenging. So, regular and periodic diagnosis and use of the appropriate antimicrobial susceptibility pattern determination is the only option for decreasing the prevalence and development of drug-resistant bacteria. Methods. An institution-based cross-sectional study was conducted among 384 HIV/AIDS patients. Sociodemographic data of patients were recorded using structured questionnaires. Blood cultures were collected with BACTEC aerobic blood culture bottles. A pair of samples was collected from each patient aseptically and incubated at 37°. If samples are positive for bacterial agents, they were subcultured to solid media such as blood agar plate, chocolate agar plate, and MacConkey agar plates. Identification was performed using colony characteristics and standard biochemical techniques. The antimicrobial susceptibility test was determined by the Kirby–Bauer disc diffusion method. Data entry and analysis were performed while using SPSS version 20. Descriptive statistics were performed to calculate frequencies. Results. Altogether, 384 patients were included, and 123 blood cultures were positive, so that the yield was thus 32%. About 46 (37.4%) of Gram-negative and 77 (62.6%) of Gram-positive bacterial species were identified. Among Gram-negative bacterial isolates, K. pneumoniae was the leading pathogen, 19 (41.3%), whereas S. aureus, 38 (49.4%), was predominant among Gram-positive isolates. In his study, the majority of Gram-positive isolates showed high level of resistance to penicillin, 72 (95.5%), tetracycline, 55 (71.4%), and cotrimoxazole, 45 (58.4%). About 28 (73.6%) of S. aureus isolates were also methicillin-resistant. Gram-negative bacterial isolates also showed a high resistance to ampicillin (91.3%), tetracycline (91.3%), and gentamicin (47.8%). Overall, about 78% of multidrug resistance was observed. Conclusion. Several pathogens were resistant to greater than five antimicrobial agents, so that proper management of patients with bacteremia is needed, and a careful selection of effective antibiotics should be practiced.

scholarly journals Metagenomics: aid to combat antimicrobial resistance in diarrhea

Gut Pathogens ◽  
2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Rituparna De
Keyword(s):  
Antimicrobial Resistance ◽  
Antimicrobial Agents ◽  
Genetic Recombination ◽  
Molecular Taxonomy ◽  
Ecological Niches ◽  
Next Generation ◽  
Genetic Determinants ◽  
Antimicrobial Resistance Genes ◽  
And Function ◽  
Generation Sequencing

Abstract Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.

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