By Margie Morgan, PhD, D (ABMM), Medical Director Microbiology, Cedars Sinai Medical Center, Los Angeles, CA
Accelerate Diagnostics, Inc., a diagnostics company dedicated to providing solutions for the challenge of antibiotic resistance and hospital-acquired infections, recently announced the FDA registration of an automated module that concentrates organisms recovered in positive blood cultures (PBC) for direct testing on Matrix-assisted laser desorption/ionization-time of flight (MALDI–TOF).
Over the last four decades, clinical microbiology laboratories have utilized a variety of methods to biochemically identify organisms, beginning with tubed media, advancing to biochemical test strips and spot tests then automated biochemical panels. But these pale in comparison to the advance made in organism identification offered by MALDI-TOF, offering a rapid (<10 minutes), accurate (>95%) and less expensive alternative for the identification of organisms growing on solid media. It eliminated the need for most other identification methods, identifying species with similar phenotypic, genotypic, and biochemical properties that was not previously possible, and correctly recognizing organisms that previously went unidentified or misidentified. This has led to the emergence of previously under recognized pathogens and improved infectious disease diagnosis and patient care.
Expanding the ways to use MALDI-TOF beyond identification from agar plates became the next frontier, with a new application being the identification of organisms directly from PBC. This application has the potential to decrease time to organism identification by 18 – 36 hours compared to routine methods. There were numerous publications, beginning in 2011 describing manual methods for washing, centrifugation, filtration, and extraction to purify and concentrate a PBC suitable for MALDI-TOF testing. (1) In 2021 Bruker launched the MBT Sepsityper® IVD kit which provides reagents and standardized guidance through a multi-step manual process for concentrate preparation, requiring an approximate hands-on time of 20-30 min. When paired with the Bruker MALDI Biotyper® it enabled the rapid identification of 425 gram-negative and gram-positive bacterial species and yeast. This workflow would be far less costly and identify far more organisms compared to testing PBC on multi-plex molecular panels. Our experience agreed with published data demonstrating a high rate (>=90%) of gram-negative bacteria and gram-positive (>85%) bacteria identified. Yeasts were identified with a lower rate of approximately 40% in our experience. Overall, the no organism identification rate for all organisms tested was approximately 20%. We reasoned our verification of the MBT Sepsityper® to be successful, however our staff resisted implementation due to the disruption it caused on a busy blood culture processing bench due to the numerous manual manipulation steps and hands-on time required.
So why try the Accelerate Arc™ Module and Blood Culture Kit?
The Arc module provides an automated option with decreased hands-on time (2-3 min), minimal manual manipulations, and better staff acceptance for organism concentration compared to manual methods and our experience with the MBT Sepsityper®. An individual PBC specimen could be prepared without major disruption to the blood culture processing bench and the rapid identification of the organism could supply real time information to assist with antimicrobial stewardship and patient care. In addition, data presented at ECCMID 2022 on the Arc Module performance and MALDI identification looked quite promising and compared favorably with manual methods including the MBT Sepsityper®. (2,3)
Processing PBC on the Arc Module is described in the below illustration.
This illustration demonstrates the simple workflow and limited hands-on-time necessary to prepare an organism concentrate. The Arc module software provides helpful prompts to guide you through the process.
Our experience with the Arc™ Module and BC Kit
The Arc module is a reliable instrument, and organism concentration supplies adequate biomass in a cloudy 200uL suspension to deliver an identification with good accuracy when tested on the Bruker MALDI Biotyper®. Rarely the concentrate is pinkish in color due to residual red blood cells which may lead to the organism not being identifiable. Two spots on the MALDI target for gram-negative organisms was quite adequate and identified >=90% of organisms with a score >2. Gram-positive organisms most often required at least 3 spots and required the addition of formic acid and identified >=80% or organisms with a score between 1.7-2. The identification of yeast has been problematic and immediate Arc Module concentration of the PBC after removal from the blood culture instrument identified <=50% of yeast with scores of 1.7 – 2.0. Preliminary data in our laboratory suggests that extending the incubation time of the PBC an additional 6-8 hours before concentration preparation provides an increased rate of identification to approximately 70%.
There are many ways the Arc module concentrate can be used. In our laboratory we investigated using the Arc/MALDI workflow to supplement existing systems in our laboratory that fail to provide an identification, such as gram-negative bacilli that are not identified by the Accelerate Pheno® system or gram-positive organisms that fail to identify using a molecular multiplex panel. We have also studied workflows to replace the initial set-up of expensive molecular identification and resistance marker panels where there is no benefit over just providing an identification. For example, PBC with gram-positive cocci in pairs and chains (potential Streptococcus) could be directly identified by MALDI supplying valuable information for antimicrobial stewardship without the expense of a molecular panel and only perform molecular resistance testing on certain organisms when beneficial.
Expanded use of the Arc concentrate
There is also the ability to use of the Arc concentrate in testing other than MALDI-TOF. The organism concentrate is non-viable but may be suitable for molecular assays to search out resistance mechanisms such as PBP2a to detect methicillin resistance in Staphylococcus aureus or lateral flow assays to detect Carbapenemase resistance in gram-negative bacilli. Other specimen types cultured in blood culture vials could be concentrated using the Arc module, such as identification of organisms growing from sterile body fluids. Please note that these uses of the Arc output for lateral flow molecular assays or processing of sterile body fluids with the Arc BC kit are outside of the indications and instructions for use provided by Accelerate Diagnostics and would need proper validation.
In conclusion: Introduction of the Accelerate Arc™ Module and BC Kit supplies an automated option for the cleanup of positive blood cultures for rapid identification by MALDI-TOF. Arc concentrate/MALDI workflows could be developed to meet your laboratory needs in supplying rapid organism identification from PBC, including potential reduction of costs by decreasing the use of expensive molecular panels. The rapid identification of PBC pathogens will enhance antimicrobial stewardship efforts to improve patient care.
1. Comparison of the MALDI Biotyper system using Sepsityper specimen processing to routine microbiological methods for identification of bacteria from positive blood culture bottles
Blake W Buchan, Katherine M Riebe, Nathan A Ledeboer PMID 22162549, J. Clin Micro, 2012
2. Analytical Performance of the Automated Accelerate Arc BC kit and Module for Direct Identification from Positive Blood Cultures using MALDI – ECCMID 2022
Ana Campos-Alvarez, Sarah Bolanos, Katy Lank, Richard Nyberg, Shelley, Campeau, Carlos Michel (Accelerate Diagnostics)
3. Comparison of the Accelerate Arc module and BC kit for isolation of microorganisms from positive blood culture broths and suitability for MALDI-ToF analysis – ECCMID 2022
Brian Mesich, Derek Gerstbrein, Amorina Cruz, Matthew L. Faron, Shelley Campeau, and Blake W. Buchan (Medical College of Wisconsin, Accelerate Diagnostics)