FilmArray is a highly automated small instrument capable of detecting infectious agents using PCR technology. Due to its simplicity the tests could be performed in a rapid-response core laboratory by general medical technologists. This operational model has demonstrated achievements in reducing turn-around-time and thus improved patient care.
by Dr M. Xu, Dr X. Qin, Dr M. L. Astion and Dr J. C. Rutledge
Acute respiratory infection and the importance of early diagnosis
Acute respiratory infection is one of the major causes of outpatient visits and hospitalization in young children and older patients with chronic respiratory diseases. Most acute respiratory infections are caused by viral agents, whereas bacterial infections occur much less frequently. Occasionally, patients with viral infection, but without a definitive diagnosis, are given antibiotics unnecessarily. Viral respiratory infection in immunocompromised patients has significant morbidity and mortality implications, and early initiation of appropriate antiviral therapy can be life-saving. In addition, isolation of patients with viral respiratory infection plays a critical role in infection prevention. Therefore, laboratory tests providing accurate and timely determination of the infectious agents associated with respiratory diseases are crucial in clinical practice.
Methods of diagnosis of acute respiratory infection
Many diagnostic tests for respiratory viral infection are available. Point-of-care tests for detecting viral antigens have the shortest turn-around-time, usually just a few minutes. These rapid antigen tests are available for only a limited number of viruses such as influenza A (Flu A), influenza B (Flu B) and respiratory syncytial virus (RSV), though the sensitivity of rapid antigen tests is low ranging from 20–80%, with a generally acceptable specificity if the tests are used during the respiratory virus season . Direct fluorescence assay (DFA) has higher sensitivity (~80%) than rapid antigen tests and reasonable turn-around-time (TAT) of a few hours . However, these are complex assays requiring specialized and experienced technologists. Viral culture has long been considered as the gold standard for detection of respiratory viral infection with the shortcoming of requiring days for the definitive identification of viral etiology.
In the past few years, several molecular tests have been developed to detect viral RNA or DNA using the polymerase chain reaction (PCR) method. One study compared the rapid antigen test, DFA, and viral culture with RT-PCR in the detection of influenza A H1N1 2009, and found sensitivities of only 18%, 39% and 46% respectively . The specificity of all methods is not significantly lower than that of realtime PCR, which is over 90%. The authors recommended that all DFA negative results should be tested with realtime PCR. Although most molecular tests using PCR technology show high sensitivity and specificity, they are technically complex, time consuming, and require specialized medical technologists to perform the tests. This type of molecular assays is usually only available in large reference laboratories or medical centres with specialized microbiology, virology, or molecular laboratories. These specialized laboratories usually do not operate during evening and night shifts and perform these tests in batches, and, therefore, the TAT for most molecular testing is relatively long, ranging from 6 to 24 hours.
Emerging new technology
FilmArray (BioFire, previously named Idaho Technologies; Salt Lake City, UT) is a newly developed small desk-top single-specimen-flow instrument with fully automated process for detection of respiratory infectious agents by real time PCR technology . The respiratory panel performed on FilmArray is able to detect 17 viral agents including adenovirus, coronavirus HKU1, coronavirus NL63, coronavirus 229E, coronavirus OC43, human metapneumovirus, rhinovirus/enterovirus, Flu A, Flu A H1, Flu A H1 2009, Flu A H3, Flu B, parainfluenza 1, 2, 3, 4, and RSV, plus Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae from respiratory specimens. The test requires only 5 minutes hands-on time of a technologist and 65 minutes total of analyser time. The testing pouch contains all the reagents for nucleic acid extraction, reverse transcription, and two steps of PCR amplification. The built-in software automatically analyses the specific melting curves of the PCR products and reports the results as positive or negative for specific infectious agents. General medical technologists with proper training are able to perform the test without any difficulties. Several comparative studies between FilmArray and other molecular tests for respiratory viral agents have shown comparable results for the detection of respiratory infectious agents [4–6].
Impact on TAT and patient care
Our rapid response core laboratory (Core Lab) is staffed by approximately 35 full-time employees (FTEs). It provides tests of general chemistry, hematology, coagulation, urinalysis, blood gas, limited therapeutic drug monitoring, and a few rapid manual tests such as monospot, pregnancy test, and sickle screen. Our Core Lab also went through a major process improvement using the Toyota production system to streamline the testing workflow , and testing was designed based on a lean, single-piece flow principle without batching . Using these principles we eliminated STAT testing. All the tests performed in core lab are standardized to meet a TAT of 1 hour, where TAT is defined as the time from sample receipt in the laboratory to the time the result is verified in laboratory information system. To provide 24-hour per day, 7-day per week (24/7) service to our emergency department (ED) and urgent care centre, we implemented the FilmArray respiratory panel in the Core Lab . Prior to implementing the FilmArray testing, we sent our respiratory samples to a regional reference laboratory performing viral testing using the DFA method. The regional reference laboratory had an on-site facility for performing DFA testing. During the first 4 months of testing using FilmArray, we tested twice as many samples as the same time period the previous year. The average TAT was reduced from 7 hours the previous year using DFA, to 1.6 hours using FilmArray. With FilmArray, 82% of the tests were completed within 2 hours, and 95% were completed within 3 hours. Previously, with DFA, none of the tests were completed within 2 hours and only 2% of time the tests were completed within 3 hours. In addition, FilmArray detected 17 viral agents, whereas DFA detected only 8. The additional viral agents detected by FilmArray include 4 types of corona virus, 3 additional types of Flu A, parainfluenza 4, and rhinovirus/enterovirus. Although no specific treatments exist for some of the above viral agents, such as corona viruses, parainfluenza virus and rhinovirus, detection of them allowed physicians to make a specific diagnosis, which gave patients reassurance and prevented further costly diagnostic work-up and unnecessary use of antibiotics.
After implementing the FilmArray respiratory panel, we also looked at the effect of shortened TAT on patients admitted to the ED. The current guidelines for treating patients of positive Flu A and Flu B with oseltamivir recommend administering the medication within 48 hours of onset of symptoms. We found that due to the fast TAT of respiratory viral testing, more than 80% of patients admitted to the ED were given the medication or prescription in the ED or within 3 hours of discharge from the ED. This practice would have been impossible previously with DFA testing at the reference lab, which had an average of 7 hours of test TAT.
Finally, the additional clinical benefit of early detection of the infectious agents is the ability to cohort the patients effectively for appropriate isolation. As part of our hospital infection prevention policy, admission of patients with respiratory symptoms is subject to FilmArray respiratory viral screening at no charge. Clearly, the early and appropriate isolation of patients with respiratory symptoms has potential positive impact on infection prevention and overall cost savings for both patients and hospitals. One such example concerns two patients with respiratory symptoms who were scheduled for surgery. The respiratory viral testing results were negative for influenza virus for both patients, and this eliminated the need for the strict isolation procedures, such as wearing masks for staff and using negative pressure for the operating room, that would have had to have been used in the absence of test results.
Although the price of FilmArray respiratory viral panel is slightly higher than that of other conventional PCR methods, the labour saving due to its simplicity is substantial and offsets the supply costs. In addition, the sample requirement for FilmArray test is a nasal swab rather than a nasal wash, which was the sample of choice for the DFA respiratory viral assay. It is much easier for nursing staff to collect a nasal swab than a nasal wash. In addition, the nasal wash creates an aerosol that mandates room cleaning and 30-minute room closure before the next use. The cost saving for a busy ED room time is difficult to calculate but is significant. One report examined the financial consequence of reducing ED boarding (the length of time a patient stays in the ED) and found that a 1-hour reduction in ED boarding time would have resulted in $9693 (~£6058) to $13,298 (~£8311) of additional daily revenue .
The simplicity of the FilmArray assay gives it the potential to expand in small general laboratories. Currently, BioFire Diagnostics Inc. is developing gastrointestinal, blood culture ID, and sepsis panels using FilmArray technology. The current major drawback of FilmArray is its restriction to single-sample throughput. The further improvement to provide higher throughput will expand its utility in high-volume clinical laboratories.
In summary, due to its simplicity and clinical utility, the FilmArray is the first multiplex molecular test that has entered the general clinical laboratory, rather than a specialized laboratory. This marks a new era in laboratory medicine. FilmArray significantly improves the diagnosis and care of patients with respiratory infections. Overall, new and emerging technologies like FilmArray will allow more infectious agents to be detected earlier and more accurately by instruments situated in general core laboratories rather than in specialized laboratories, thereby speeding results from a 7/24 operations.
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Min Xu, MD, PhD
Xuan Qin, PhD
Michael L. Astion, MD, PhD
Joe C. Rutledge, MD
Department of Laboratories, Seattle Children’s Hospital,
4800 Sand Point Way NE, A6901
Seattle, WA 98105, USA