Syndromic Testing for Infectious Diseases: Multiplex Panels for Positive Blood Culture Bottles

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Robin Patel, M.D.

Elizabeth P. and Robert E. Allen Professor of Individualized Medicine
Professor of Medicine and Professor of Microbiology
Director, Infectious Diseases Research Laboratory
Co-Director, Bacteriology Laboratory
Vice Chair of Education
Division of Clinical Microbiology
Mayo Clinic, Rochester, Minnesota



Hello. My name is Robin Patel. I am the Elizabeth P. and Robert E. Allen Professor of Individualized Medicine, professor of Medicine, professor of Microbiology, director of the Infectious Diseases Research Laboratory, co-director of the Bacteriology Laboratory, and vice chair of Education in the Department of Laboratory Medicine and Pathology at Mayo Clinic in Rochester, Minnesota. In this presentation, I will be discussing syndromic testing for infectious diseases, multiplex panels for testing positive blood culture bottles. 


My disclosures are shown on this slide.


Bacteremia is a major cause of morbidity and mortality. In patients with septic shock, delays in administration of active antimicrobial therapy are associated with increased mortality. Early administration of active ‘empiric’ antimicrobial treatment may, however, be compromised by antibacterial drug resistance. Conversely, ‘empiric’ therapy is oftentimes unnecessarily broad spectrum, addressing the possibility of underlying antibacterial drug resistance, but resulting in unneeded selection of antibacterial resistance, cost, toxicity and/or microbiome disturbances.

Conventional blood culture practices 

Though the introduction of automated, continuous monitoring blood culture systems in the last century improved the diagnosis of bacteremia, there remain delays in identification of pathogens and antimicrobial susceptibility testing, and in the designation of contaminants when conventional approaches are used. This is because all that has been historically available when a bottle signals positive is a Gram stain, with identification and susceptibility testing not conventionally occurring until after subcultures regrow the organism. This can impact patient management decisions, contribute to morbidity and mortality, and potentially lead to adverse outcomes, such as Clostridioides difficile-associated diarrhea.

FDA-approved multiplex panels for detection of gram-positive bacteria in positive blood cultures1

There are now several FDA-approved/cleared, multiplex assays that simultaneously detect several microorganisms, as well as select resistance genes, from positive blood culture bottles. These include the FilmArray Blood Culture Identification or BCID2 panel from BioFire Diagnostics, which has been available since 2013 (originally as the BCID panel); the Verigene Gram-Positive Blood Culture Test, or BC-GP, and Gram-Negative Blood Culture Test, or BC-GN from Luminex, which have been available since 2012 and 2014, respectively; and the GenMarkDx, ePlex BCID-GP and BCID-GN panels and ePlex BCID Fungal Pathogen, or BCID-FP panel, which have been available since 2018, 2019, and 2018, respectively. Gram-positive organisms on these panels are shown on this slide.

FDA-approved multiplex panels for detection of gram-negative bacteria in positive blood cultures,1 continued

Gram-negative organisms on these panels are shown on this slide.

FDA-approved multiplex panels for detection of select resistance genes in positive blood cultures,1 continued

Resistance genes on these panels are shown on this slide.

FDA-approved multiplex panels for detection of fungi in positive blood cultures,1 continued

And finally, fungal organisms on these panels are shown on this slide.

FilmArray® Blood Culture Identification Panel (BioFire)

These tests are largely “add-on” tests and are quite expensive. Therefore, when they first became available, their value needed to be assessed. Most studies evaluating the impact of these tests have been pre- and post-intervention studies, in other words, studies using historical controls. Results of such studies can be confounded by changes in practice occurring over time, aside from the test itself. To overcome this limitation, our group performed a randomized controlled clinical trial evaluating the clinical impact of BCID testing of positive blood culture bottles along with simultaneous antimicrobial stewardship guidance. This study was done with an earlier version of the BioFire panel than is available today.

Randomized Controlled Clinical Trial, Mayo Clinic 2013-20142

617 patients were randomized to one of three arms: standard blood culture processing, or our control arm, which included organism identification using MALDI-TOF mass spectrometry; the BCID test reported with templated comments; or the BCID test reported with templated comments and real-time audit with feedback by an antimicrobial stewardship team.

Supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number UM1AI104681 (Antibacterial Resistance Leadership Group)

The study was performed at Mayo Clinic Rochester and was supported by BioFire, Mayo Clinic, and the Antibacterial Resistance Leadership Group of the National Institute of Allergy and Infectious Diseases of the National Institutes of Health.

Clinical outcomes2

There was no effect on length of stay, mortality, 30-day readmissions with the same organism, toxicity or adverse drug reactions, time to blood culture clearance, development of Clostridioides difficile-associated diarrhea, or acquisition of drug-resistant organisms between the study groups.

Comparison of time to identification, susceptibility results, and antibiotic modifications2

However, antibiotic escalation occurred sooner in both BCID groups compared to the control group, and time to de-escalation to appropriate antibiotics was notably shortest in the BCID group with concomitant antimicrobial stewardship intervention.


Molecular panels for testing positive blood culture bottles have several limitations. They are largely “add-on” tests, because conventional subcultures and antimicrobial susceptibility testing are still required, although re-identification of isolated colonies may be avoided if the colony morphology in question is consistent with the molecularly detected organism. To realize maximal benefits, these assays should be performed 24/7, adding logistical hurdles for both the laboratory and the stewardship system.

In addition, the available panels do not cover all causes of bloodstream infection and may not be capable of identifying all pathogens in mixed infections, even if the organisms are included on the panel. False positive results may occur. In our clinical practice, we have observed that the BCID or BCID2 panels may detect organisms not visualized on Gram stain or recovered in culture in 1.7% of positive BD BACTEC blood culture bottles, with Candida parapsilosis and tropicalisProteus species, Acinetobacter calcoaceticus-baumannii complex, and Pseudomonas aeruginosa being some commonly involved organisms. The presence of nucleic acids from nonviable organisms in blood culture bottles likely explains this. It is therefore important to correlate the results of these panels with Gram stain.

Additionally, rare instances of species-level misidentification have been reported. While the other two commercially available assays offer customized ordering of different panels based on the Gram stain, this option is not available with the BCID2 panel. Lastly, a narrow spectrum of genes associated with drug resistance in Gram-negative bacilli is included in these panels, and therefore, their ability to fully recapitulate phenotypic susceptibility results of Gram-negative bacilli is limited. 

It is important when using these panels to think about how results are reported. This slide shows what the instrument reports in the left-hand column, and what we report in the middle and right-hand columns. We provide an interpretation as to what has been found and how the patient should be managed.


Overall, multiplex panels for testing positive blood culture bottles offer minimal hands-on time and sample preparation and are highly automated. They have rapid turnaround times, enabling identification of select pathogens within one to three hours, depending on the platform, allowing for early optimization of antimicrobial therapy, as well as implementation of appropriate infection prevention and control measures. Our randomized controlled clinical trial shows that these panels add value in clinical practice. In order to enable rapid escalation or de-escalation of antimicrobial therapy, results should be reported to providers as rapidly and directly as possible and should also ideally be communicated to an expert in antimicrobial stewardship who can work with providers to optimize therapy. 


  1. Ramanan P, Bryson A, Binnicker M, et al. Syndromic panel-based testing in clinical microbiology. Clin Microbiol Rev. 2018 Jan 31(1):e00024-17. 
  2. Banerjee R, Teng CB, Cunningham SA, et al. Randomized multiplex polymerase chain reaction-based blood culture identification and susceptibility testing. Clin Infect Dis. 2015 Oct 1;61(7):1071-80.


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