Rapid Microbiology Testing

Vol. 22 • Issue 1 • Page 17


So many rapid microbial tests, so little time. Rapid microbiology testing is no longer a dream of the future; it is, indeed, the present and has the promise to only continue to grow.

Faster methodologies and emerging technologies have revolutionized microbial testing over the past several years. During its infancy enzyme immunoassay/antigen/antibody (EIA) tests slashed traditional culture testing times from days to hours to minutes. Newer methodologies are not only promising the same, but significantly increasing sensitivity and specificity of tested pathogens.

Rapid microbiology diagnostics is also no longer limited to just large laboratories with a large cash flow. With a menu of available tests that multiplies and grows every year, many companies are dedicating themselves to producing affordable and easily performable assays that laboratories of all sizes can integrate into their daily workflow and yearly budget.

Available assays range from having the ability to identify hospital-acquired infections (HAIs) to critical infectious diseases such as the influenza virus in fewer than two hours. Many tests are CLIA approved, allowing medical laboratory scientists of all levels to perform the test. These easy-to-use, quick identifying systems are improving healthcare one rapid test at a time.


There are several advantages to starting a menu of available rapid microbiological diagnostics in a lab. Increased turnaround time may be one of the most appealing features. By definition, a laboratory’s turnaround time (TAT) is one of the most noticeable signs of laboratory service and is often used as a key performance indicator.1 These assays also allow the capability of offering testing 24 hours a day, 7 days a week. With healthcare providers having results in hours or some cases minutes and any time of the day and/or week, they are given the option of completing the diagnostic picture they developed for the patient in a much shorter time frame than when only having the option of utilizing conventional microbiology.

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Limited training and skill are required to successfully setup one of these tests. Many rapid molecular assays do not require much more than a quick squeeze of a reagent ampule into a designated space followed by a vortex and pipette of patient specimen into its own designated well. Advanced pipetting skills and challenging reagent preparation are limited to PCR methodologies such as ASRs, which typically take several hours to perform by a designated technologist. Rapid methodologies can also be assigned to an area of the laboratory or as part of technologist’s tasks for that day; it does not require one specialized personnel.

As well, laboratories have the option with many companies to run multiple platforms on a single instrument. This allows laboratories to purchase one piece of equipment but offer and perform many different diagnostic tests. This means assays such as MRSA, Influenza, Enterovirus and Clostridium difficile can be resulted in less than one day on the same patient all while utilizing one, single instrument.

Being able to offer rapid molecular microbiology testing in-house allows a laboratory to be more cost effective for the hospital. In a 2007 article,2 Dan M. Hyder, MD, medical director of the core laboratory, flow cytometry, and molecular diagnostics at Southwest Washington Medical Center, Vancouver, Wash., was asked if bringing molecular testing in house was cost-effective. “Absolutely,” Hyder said. For example, “the 23-test panel for cystic fibrosis screening is reimbursed by Medicare at about $400, depending on the region. You can get a contract with a commercial reference laboratory that covers all 23 mutations for the $100 to $200 range,” he noted in the article. But direct costs to perform the test in house – meaning technologist time and reagents only – total about $65. And CF screening is going to increase dramatically, he predicted.2


When it comes to rapid microbiology testing utilizing molecular methods, there is the obvious reason that restricts many and deters some – cost. While cost may not be an issue in the end, bringing on a platform can be expensive up front. Not only does it require the purchase of a platform, but all of the reagents and supplies that go along with it. Reagent cost is determined by the frequency of testing, number of samples, linear versus clinical range, assay reliability, and reagent packaging, stability, and lot variation.3 Many times the ðdiagnostic test performed per patient can be more expensive to theð ðlaboratory ðthan ðperforming a conventional culture (i.e., growing the virus in a cell culture or isolating the pathogenic bacteria on a piece of media).

Also, if the healthcare provider does not find the test clinically useful, they will not order it and may, in some instances, prefer the conventional culture methodology. This alone may cause the laboratory to suffer a loss if reagents expire or from the cost attributed to maintaining the instrument with calibrations and quality control.

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Allocating space in many microbiology laboratories for the instrumentation affiliated with the rapid assays is often a challenge. For most labs it can be difficult to find a square of “extra” benchtop to fit even the smallest piece of equipment. Many tests also require the use of a biosafety hood for test setup with a recommended cleaning process to decrease contamination possibilities. Multiple hoods may not be a possibility and utilizing one hood for multiple functions can interrupt workflow for both the routine microbiologist and technologist setting up the rapid assay.


Successfully establishing a menu of rapid microbiological assays can ultimately lead to a significant impact on disease diagnosis and patient management. Healthcare providers can be promised better results for their patients in a shorter amount of time and the hospital can eventually make a profit from reimbursements.

Rapid diagnostics allows laboratories the ability to have sensitive and specific testing available to physicians at any time of the day when they absolutely need it. These tests can provide conformational information that a patient in fact has a viral infection and not a bacterial one, which can lead to the reduced use of antibiotics. Running a drop of blood from a blood culture positive for gram positive cocci suggestive of Staphylococcus can detect the presence of methicillin-resistant Staph Aureus or Staph aureus in one hour, potentially saving a septic patient’s life. Rapid tests to diagnose aseptic meningitis on a patient suffering from Enterovirus can prevent the patient a hospital admission and the hospital the cost associated with a one-day stay for a patient suspected of having meningitis.

Frederick Kiechle, MD, PhD, stressed that laboratories creating a molecular service can start small and scale up. “You can sort of test the waters and see how it will go. I would predict most individuals ðunderestimate the volume of tests they will get, especially for microbes and virology tests, because the volume is going to be much higher due to the
improved turnaround.”2

Theresa Castellone is technologist specialist, Virology Laboratory, Rhode Island Hospital.


1. Clinical Biochemist Review. Laboratory Turnaround Time. 2007 November; 28(4): 179-194. Available here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2282400/

2. Putting Molecular Testing in Motion. CAP Today 2007 archives. Available here: http://www.cap.org/apps/cap.portal?_nfpb=true&cntvwrPtlt_actionOverride=%2Fportlets%2FcontentViewer%2Fshow&_windowLabel=cntvwrPtlt&cntvwrPtlt{actionForm.contentReference}=cap_today%2Fcover_stories%2F0907Molecular.html&_state=maximized&_pageLabel=cntvwr

3. Not Mayo? No matter – smaller labs go molecular. CAP Today 2004 archives. Available here: http://www.cap.org/apps/cap.portal?_nfpb=true&cntvwrPtlt_actionOverride=%2Fportlets%2FcontentViewer%2Fshow&_windowLabel=cntvwrPtlt&cntvwrPtlt{actionForm.contentReference}=cap_today%2Ffeature_stories%2F0704MolecLab.html&_state=maximized&_pageLabel=cntvwr

Sidebar: Rapid Microbiology Tools

VISTA: The Isoplater 180 “Automatic Petri Dish Streaking Machine” first automated microbiological streaking over 20 years ago. Pioneered by Vista Technology Inc. and noted as having a very long life, Vista machines were regularly used in numerous hospitals and private laboratories. At 180 plates per hour with 4 “S” shaped streaking elements, these instruments work quickly and are capable of handling all types of specimen, including sputums and stools, with minimal daily maintenance.

FILMARRAY SYSTEM: The FilmArray combines sample preparation, amplification, detection and analysis into a user friendly process that produces results in an hour. Training is minimal and hands-on as the FilmArray pouch stores all of the essential reagents for sample preparation, reverse transcription-PCR, PCR and detection in a freeze-dried format. Start by injecting hydration ðsolution and an unprocessed sample, and the FilmArray walks a user through the entire process-from the extraction and purification of all nucleic acids in the unprocessed sample to both multiplex and singleplex PCR reactions.

GENEXPERT W/CEPHEID CARTRIDGE: GeneXpert systems are fast, portable and can run tests just about anywhere. The self-proclaimed “cornerstone” of GeneXpert testing is the Cepheid single-use cartridge, which allows for sample extraction, amplification and detection to produce lab-grade precision carried out in a simple self-contained unit. Load a cartridge into the FilmArray system and it does the rest.

QUIDEL: Quidel Corp., manufacturer of diagnostic healthcare solutions, recently received 510(K) clearance for the C. Difficile assay, AmpliVue, the company’s first handheld molecular device for C. difficile. The new assay allows for more sensitive, rapid molecular testing, ensuring a punctual and precise diagnosis without an upfront nucleic acid extraction step. The system is portable, cost effective, and available for sale in both the U.S. and Europe.

BD DIAGNOSTIC SYSTEMS: BD Diagnostic Systems introduces a few new systems, including the BD Viper System with XTR technology. These systems are state-of-the-art, easy-to-use with little hands-on time and provide rapid results. Fully automated specimen processing machines like the BD Viper increase laboratory efficiency in the most crucial, labor-intensive steps for molecular methods, sample handing, amplification and detection. The BD Viper system includes sample processing effective at up to 736 CT/GC results in an 8.5 hour shift for assured reliability in systems, reagents, results and support.

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