Sizing up ‘mega’ multiplex panels for respiratory viruses

“The core technologists were very happy to take on this responsibility. There were very few mistakes,” Dr. Qin says. The core lab typically transmits results electronically, providing limited interactions between the technologists who perform the tests and the clinicians who order them. But that has changed, at least for respiratory testing, with the introduction of FilmArray. “Now, the results become available while patients are waiting in urgent care,” Dr. Qin notes. “When [the technologists] get a positive for influenza, they enter it in and the feedback is, ‘Wow, this is great. We already know the result!’” Integration of FilmArray has made it easier for clinicians to prescribe antiviral drugs to the right patients within 48 hours of symptoms. “It has been a huge improvement in medical decisionmaking and patient management,” Dr. Qin says.

A minor drawback, Dr. Qin notes, is the lack of an interface between the FilmArray and the laboratory’s computerized data-entry system, which means that one technologist must enter the results and a second must review the information for accuracy. “Out of 4,000-plus specimens that we processed in the winter of 2011 through May or June of 2012, we had only one clerical mistake that was not picked up during the second review,” Dr. Qin notes. The mistake was quickly corrected and did not affect patient care. “Because this is such a significant clinical improvement, everybody has been very conscientious, establishing matrices for quality measurement,” she explains.

Another drawback of the Film­Array, described in the studies by Drs. Miller and Qin, is that the instrument, while fast, processes only one patient sample at a time. The tradeoff is that results for sick neonates or transplant patients can be ready in roughly an hour, but in an eight-hour day, each FilmArray can process only seven patient samples, while each of the other three multiplex panels can process 21 or more. Though most laboratories invest in multiple FilmArray systems—Dr. Miller has seen as many as 12 systems in labs with enough counter space to spare—larger laboratories that process 50 to 100 specimens a day would need an exorbitant number of FilmArray systems to keep up with the load. And every additional system adds to the cost: Labs that use three FilmArray systems—a throughput equivalent to individual Genmark or Luminex systems—spend three times as much as labs that use a single system. That’s significant, considering the FilmArray reagents are already more expensive than those of the other multiplex panels Dr. Miller and colleagues tested.

But Dr. Miller is quick to caution that the FilmArray is not necessarily more expensive than the other assays in the grand scheme of things. “Though reagents are more expensive for the FilmArray, followed by the eSensor RVP, and the Luminex RVPv1, the hands-on time is reversed so it all averages out,” she says. Each FilmArray assay requires five minutes of staff handling time—far less than the three competing multiplex systems—and can be performed by technicians who lack molecular training. The ensuing cost savings can be considerable. “The time that the technologist spends doing the testing, the time that a senior person spends reviewing the testing, the cost of overhead—all of these things factored into our cost analysis,” Dr. Miller says.

Dr. Qin, too, acknowledges that the test isn’t cheap, but cites significant savings on the clinical treatment side of the equation. “[With the FilmArray], there’s less ED time: less contemplating whether to admit or not admit, to treat or not treat, to isolate or not isolate. It improves patient turnover. The cost of ED time is very expensive, so that gives significant savings.”

With the expanded version of the FilmArray, clinicians and pathologists face an even greater dilemma: CPT coding. In the past, Dr. Qin points out, separate tests were used to detect each of the three bacterial pathogens that are now included in the expanded FilmArray, which was not available at the time of Dr. Qin’s study. Though the viral and bacterial pathogens are now tested in a single reagent pouch, some clinicians provided feedback reflecting the desire and clinical confidence to opt to use a less expensive CPT code that covers only the cost of detecting the 17 viruses, or only the cost of detecting one of the three available bacterial pathogens. However, Dr. Qin calls the option of splitting a single test panel into several pathogen-specific tests “administratively difficult and financially irrational to payers.” For example,“If we detect pertussis when it wasn’t ordered, we have to call back to the clinician and explain that in order to report the pertussis results, they need to order the viral plus pertussis panel.” To complicate matters, many of the pertussis-positive specimens often have viral co-infections. “This is an example of technology giving us enormous data that we don’t know what to do with yet,” Dr. Qin says. “The CPT coding modality has to be updated with the technology to make the cost manageable.”

Cost savings aside, Drs. Qin and Miller acknowledge the benefits of having multiple types of systems in place—not just the Film­Array or the eSensor RVP, for example. Though batch systems are adequate for routine testing, they’re far too slow when the situation is urgent. “If we’ve just started the [batch] run, it’s going to be an additional 24 hours before that sample gets resulted,” Dr. Miller theorizes. “We can get a faster result using singleplex or smaller multiplex assays, which have a quicker turnaround time, then get the full panel the next day.”

Dr. Qin cites another reason to keep multiple tools in the toolbox: the constant threat of outbreaks. “When we moved to FilmArray, we determined that three analyzers would do the job based on the distribution of incoming specimens. But what if there’s a huge outbreak? How would you handle the surge?” She has experienced this firsthand: Last spring and summer, a pertussis outbreak flooded the labs at Seattle Children’s Hospital with more than 5,000 specimens. At the peak of the outbreak, Dr. Qin’s lab received 160 specimens a day. “If you have three analyzers and the samples are coming out one piece at a time, you can’t possibly analyze more than 23 specimens a day.” How might a lab accommodate 160 specimens a day? The old standard, she says: batch testing. After experiencing the pertussis outbreak, Dr. Qin’s group has calculated how many specimens they must process simultaneously to accommodate different levels of surge. They’ve learned to prepare for the worst but expect the best, particularly when it comes to the threat of an influenza pandemic.

“We have to think about surge and capacity, and keep some of the rapid influenza tests in the background just in case.” Faced with a surge, even DFA batch mode is not sufficient, Dr. Qin says. “You have to spin [the sample] down, you have to smear it onto the slide and stain it, you have to have a tech read the results. You can’t read 50 specimens at a time, so DFA is still not the modality for surge. You’d need a rapid test.” During a normal flu season, however, FilmArray more than accommodates the workload at Seattle Children’s. “We rarely have two specimens waiting in line, and even that delay is not significant compared with sending out DFA tests,” Dr. Qin notes.

Even though multiplex panels can detect multiple types of respiratory infections in a single shot, not all of the pathogens—MPV, PIV, and rhinovirus, for example—can be treated. But treatment is not the only goal of detection. “These results not only impact potential therapy for some of the viruses,” Dr. Miller says, “but also the ability to implement effective infection control practices for inpatients.” Premature infants, for example, can be given a monoclonal antibody against RSV to protect against infection. Many institutions rely on the findings to cohort patients based on their influenza subtypes: Clinicians wouldn’t necessarily cohort a patient who has MPV with a patient who has influenza, or a patient with influenza H1 versus H3.

Dr. Qin notes an additional benefit from the perspective of a children’s hospital: “For pediatrics, there’s a certain comfort in going home knowing that baby has rhinovirus and it’s going to run it’s course with just rehydration and Tylenol. It’s a positive way of antibiotic stewardship. Otherwise you might think, Oh, there’s a little redness in the ear or the throat. I’m going to prescribe amoxicillin just in case.

“There’s such an enormous benefit in reducing unnecessary antibiotics and also in isolating young patients to prevent transmission.”

The ability to type influenza strains was especially useful during outbreaks of the seasonal H1 influenza, Dr. Miller recalls. The seasonal H1 was resistant to Tamiflu while H3 was susceptible. “Being able to type these gave the physician information about whether or not they could use Tamiflu,” she says. The findings are also important for sentinel labs. “I feel like it’s a very important part of our job to be able to share with our public health colleagues that we’re seeing H3, we’re seeing H1, we’re seeing influenza B. Not every lab needs to be able to do that, but I think it’s important to have labs across the country with that capability.”

Are laboratories compromising sensitivity and specificity by moving to multiplex?

“When you look at what we’ve done for decades with viral culture, with rapid antigen tests, there’s no question we’re more sensitive now, even in the higher multiplex assays,” Dr. Miller says. In fact, Dr. Qin adds, FilmArray is so sensitive that two patients at Seattle Children’s tested positive for both influenza A and B after receiving FluMist three and seven days earlier, respectively.

That said, Dr. Miller notes, the specificity question is an important one. Because multiplex assays require pipetting a post-amplified material, even the most advanced technical laboratories face the risk of cross-contamination, which potentially compromises the specificity of some multiplex tests. The issue of specificity brings home the idea that every multiplex assay has its place, Dr. Miller notes. While the UNC study found that FilmArray upheld 100 percent specificity by performing the entire reaction in a closed pouch, which eliminates the possibility of contamination, the specificity of other assays depends on the aseptic technique of skilled molecular technologists. Dr. Miller cautions that labs should focus on what works best for their patient population: “It’s not worth doing a highly complex multiplex assay if you’re a small laboratory or one with no transplant patients. All of this factors in.” Still, she says, “Multiplex is absolutely a move in the right direction.”

Ann Griswold is a writer in Annapolis, Md.