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An Introduction to Antimicrobial Rapid Diagnostic Testing

To initiate appropriate antimicrobial therapy, it is imperative to identify the causative pathogens and select agent(s) that have adequate activity against the pathogens. However, the time it takes to deliver antimicrobial susceptibility test data ranges from 24 to 72 hours with an average of approximately 40 hours. Delay in initiation of appropriate antibiotic therapy has long been recognized as a risk factor for mortality. A study by Kumar et al has demonstrated each hour of delay in appropriate antibiotic therapy in patients with septic shock can result in 7.6% reduction in survival.

With the recent technology innovations, rapid “point-of-care” diagnostic tests are made available. Rapid diagnostic testing (RDT) can be utilized in faster identification of causative pathogens, reducing time to appropriate antimicrobial therapy, minimizing antibiotic resistance, decreasing costs associated to inappropriate antibiotic use and improving patient outcomes.

PNA-FISH (Peptide Nucleic Acid Fluorescent In Situ Hybridization Molecular Strains)

The PNA-FISH technology employs the use of fluorescent-labeled probes to target species specific rRNA sequences. The fluorescent-labeled probes allow the visualization of target microorganism. The turnaround time for PNA-FISH is approximately 90 minutes. Refer to the summary table for list of organisms that each RDT identifies.  PNA-FISH does not detect resistance markers.

rPCR (Random Polymerase Chain Reaction) (GeneXpert)

The real-time polymerase chain reaction technology is built into the GeneXpert system, allowing the automation and integration of sample preparation, nucleic acid amplification and detection of target sequence. The turnaround time is approximately less than or equal to 60 minutes for identification of select organisms.

Nucleic Acid (Verigene)

The nucleic acid microarray assay allows identification of pathogens and resistance markers with a turnaround time of 120 to 150 minutes (gram positive organisms: 150 minutes; gram negative organisms: 120 minutes). The system utilizes a single use cartridge to process nucleic acid extraction, array hybridization and reading to provide results.

MALDI-TOF (Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectroscopy)

The MALDI-TOF is an innovative mass spectroscopy technology to identify microorganisms. Specimen sample is converted into charged particles and separated to measure travel time “time of flight” to mass analyzer. The unique time of flight signature is then used to identify the individual organisms. MALDI-TOF provides a rapid turnaround time of 10 to 30 minutes for identification of pathogen and a large cost for the device itself. A wide selection of pathogen can be detected using MALDI-TOF but resistance marker is still in development.

Summary table of Rapid Diagnostic Tests*


Trade Name



Resistance Marker

Detection Time


(Peptide Nucleic Acid Fluorescence In Situ Hybridization)



Staph spp . ,Enterococcus spp. E. coli, K. Pneumoniae, P. aeruginosa

Candida spp.


1.5 hours

rPCR (random polymerase chain reaction)



CoNS (Coag negative Staphylococcus), MSSA, MRSA


mecA, vanA

<1 hour

Nucleic acid



Gram Positive: Staph spp. Strep spp. Enterococcus spp.

Gram Negative: E. coli, Klebsiella spp.,  P. aeruginosa , Serratia spp., Acinetobacter spp., Proteus spp, Citrobacter spp, Enterobacter spp.


mecA, vanA, vanB


2 – 2.5 hours

MALDI-TOF ( Matrix-assisted laser desorption/ionization time of flight)



Gram positive,  gram negative, yeast, fungi, mycobacteria

In development

10 – 30 minutes

*Disclaimer for potential omission/update; refer to individual rapid diagnostic test manufacturer website for further information

As technology advances, various rapid diagnostic tests are available for the timely detection of causative pathogens. Rapid diagnostic testing technology is another opportunity for collaboration between microbiologists, pharmacists and physicians that can improve patient outcomes. While numerous studies have been conducted to investigate patient and associated financial outcomes for the use of RDT in patients with bacteremia, RDT are of little value if the results are not reviewed and acted upon in a timely manner. Holtzman et al examined the impact of PNA-FISH in identification of S. aureus vs. Coagulase-negative S. aureus in blood cultures in the absence of active antimicrobial stewardship program (ASP) associated intervention. Results revealed PNA-FISH assays without active reporting of results or support from ASP team, did not reduce length of stay or vancomycin use. Similar results were reported by Carver et al in another study.  

Each RDT system has its own pros and cons. There is no single RDT shown to be superior to others; rather the choice of RDT should be based on facility workflow and needs. Items to consider include purchase price or leasing agreement for the RDT device, purchase price of testing cartridges, microbiology laboratory working space, anticipated volume of cultures for microbiology laboratory testing, complexity of the test(s), education and training required for the select RDT, microbiology technician skills to perform RDT, use of RDT within the clinical workflow including the testing done by microbiology technicians, pharmacists review and communications of results to prescribers. Whereas the procurement of RDT may increase expense for the microbiology laboratory, cost savings can be derived by reducing unnecessary diagnostic tests, pharmacy drug costs from reducing inappropriate antibiotic therapy, infection control savings for decreased infections due to reductions in transmission of organisms and reduced length of stay. A multidisciplinary team approach is needed to assess the clinical workflow for integration of RDT as well as to determine the interdepartmental return of investment for RDT. The key to successful RDT integration is the collaboration of ASP team with all other clinical care providers in delivering timely communication of RDT results.

I would highly encourage you to explore and learn more about the existing RDT options. Most importantly, I advise you to share the knowledge you have on RDT and start discussions with your facility microbiologists, pharmacists and physicians about the use of RDT and how it may be used at your facility to improve patient outcomes.


Bauer KA, West JE, Balada-Llasat JM, et al. An Antimicrobial Stewardship Program’s Impact with Rapid Polymerase Chain Reaction Methicillin-Resistant Staphylococcus aureus/S. aureus Blood Culture Test in Patients with S. aureus Bacteremia. Clin Infect Dis. 2010; 51(9):1074-1080. 

Bauer KA, Perez KK, Forrest GN, et al. Review of Rapid Diagnostic Tests Used by Antimicrobial Stewardship Programs. Clin Infect Dis. 2014;59(S3) S134-145.

Carver PL, Lin SW, DePestel DD, et al. Impact of mecA Gene Testing and Intervention by Infectious Disease Clinical Pharmacists on Time to Optimal Antimicrobial Therapy for Staphylococcus aureus Bacteremia at a University Hospital. J of Clin Microbiology 2008; 46(7):2381-2383. 

Goff DG, Karam GH. (18 Feb. 2014) Antimicrobial Stewardship and Rapid Diagnostic Testing. [Webinar]. In ASHP Advantage Continuing Education Series. Accessed at

Goff D, Karam GH. (2013, Dec. 26). Still Talking about Antimicrobial Stewardship? Get started! [Webinar]. In ASHP Advantage Continuing Education Series. Accessed at

Goff DA, Jankowski C, Tenover FC. Using Rapid Diagnostic Tests to Optimize Antimicrobial Selection in Antimicrobial Stewardship Programs. Pharmacotherapy 2012; 32(8):677-687.

Holtzman C, Whitney D, Barlam T, et al. Assessment of Impact of Peptide Nucleic Acid Fluorescence In Situ Hybridization for Rapid Identification of Coagulase-Negative Staphylococci in Absence of Antimicrobial Stewardship Intervention. J of Clin Microbiology 2011; 49(4):1581-82.

Kumar A, Roberts D, Wood KE, et al. Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock. Crit Care Med 2006; 34:1589-1596.

Lodise TP, McKinnon PS, Swiderski L, et al. Outcomes Analysis of Delayed Antibiotic Treatment for Hospital-Acquired Staphylococcus aureus Bacteremia. Clin Infect Dis. 2003; 36:1418-1423.

Rice LB. Rapid Diagnostics and Appropriate Antibiotic Use. Clin Infect Dis. 2011;52(S4):S357-S360.

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