Acadiana hospitals can now diagnose Covid, flu and other respiratory diseases from a single swab

Michael Thibeaux, Our Lady of Lourdes' core lab supervisor, runs test samples through Lourdes' in-house BioFire System, which can identify 22 respiratory pathogens from a single sample. Image courtesy Our Lady of Lourdes

The gist: As Covid rages and the flu season threatens to overwhelm an already-understaffed and overburdened workforce, local hospital systems are adding new tools to their arsenal to avoid delays in diagnosing and treating respiratory infections.

Acadiana’s hospitals are once again facing fast-growing Covid admissions. As of Monday, hospitalizations in the eight-parish region were at 218, and the state now has more people hospitalized than it did in August. Though better treatments mean more people are surviving Covid, little more than a dozen ICU beds remain in the region, and hospitals are again scaling back elective procedures to make room for their sickest patients, those battling Covid. 

“I’m extremely concerned where this pandemic will leave us once we reach peak point,” Dr. Henry Kaufman IV, interim chief medical officer at Our Lady of Lourdes, said at Covid-19 roundtable discussion in Carencro earlier this month. 

Expanded rapid testing is critical. “Traditionally, in the past if you came in with a respiratory illness we were limited on the testing that we could do,” says Kaufman. “We have had influenza testing available routinely in the community. However, testing for the multiple other myriad causes of viral upper respiratory infection was not routinely available and was usually not done because there was no clinical utility in it.”

This year is different. With Covid-19 more deadly and more contagious and testing still in limited supply, it’s important that healthcare providers know what they’re dealing with at the outset. And quicker turnarounds mean freeing up precious resources, like hospital beds, as physicians can more effectively determine who’s a good candidate for recovery at home. 

One swab, 22 pathogens. Both Lourdes and Ochsner Lafayette General have turned their attention — and pocketbooks — to the best available rapid testing. Molecular tests (also called PCR tests, viral RNA tests, nucleic acid tests) that use a deep nasal swab remain the gold standard, because they have fewer false negative results than other diagnostic tests or samples from throat swabs or saliva. A panel manufactured by BioFire Systems and offered exclusively in the market by Lourdes identifies 22 viral and bacterial pathogens, including SARS-CoV-2, from one nasal swab with a run time of about 45 minutes, with results in about an hour. (Lourdes previously had access to the BioFire machine at its sister hospital in Baton Rouge, Our Lady of the Lake, but logistics compounded the turnaround.) 

“[BioFire] is a very fast and reliable instrument for Covid and respiratory pathogens,” says Richard Tulley, interim lab director for LDH’s Office of Public Health Laboratory. “We use it for surveillance studies and with special requests from [OPH’s infectious disease epidemiology section]. In our situation, the only downfall would be that you cannot run a lot of samples at the same time.” 

Kaufman says Lourdes’ BioFire machine can run about 12 tests an hour, 24 hours a day. 

Removing guesswork in treatment. In the past, there was a level of guesswork, for example, in immediately treating a sick patient believed to have a bacterial infection only to get a test result days later and have to switch the antibiotic prescription mid-course to more accurately target the infection. With this panel, physicians can tailor their therapy immediately.

A number of respiratory illnesses mimic Covid symptoms, which is concerning for physicians due to the inevitability of a false negative test for Covid. 

“We have doubts and we’re not sure we should believe [the negative test], and we do additional testing, and it sometimes confounds the care of the patient,” Kaufman says. “If we can say well, you don’t have Covid but you do have one of the other coronaviruses that’s not SARS-CoV-2, or walking pneumonia, then we can say, I know you look and you sound like you have Covid, but you definitely have one of these other things and this is how we’re going to treat it.”

What’s more, Kaufman continues, it’s “absolutely possible” to have flu or another respiratory illness at the same time as Covid, noting the inevitability Lafayette hospitals will see multi-infections in a single patient this fall. Researchers don’t yet have enough evidence to know just how risky it will be for a person to harbor both viruses at the same time.  

Accuracy and cost-effectiveness are two key considerations for these investments, according to Ochsner Lafayette General spokeswoman Patricia Parks Thompson. In recent weeks, facilities within Lourdes and Ochsner LG’s system also began offering Cepheid’s nasal swab test that yields results for Influenza A and B, RSV and COVID-19 within about an hour. California-based Cepheid’s four-in-one test received emergency authorization from the FDA on Sept. 29; Utah-based BioFire was awarded emergency authorization a few days later.   

Accuracy is about as good as it gets. Both systems have sensitivity (true positive) and specificity (true negative) accuracies topping 95 percent, according to local hospital officials. “Anything that approaches 97, 98 percent in medicine is as perfect of a test you can take,” Kaufman says. 

Neither test is available for everyone. At least for now, both are utilized on inpatients and emergency admits. “This is something that we do on patients with illness severe enough to be admitted to the hospital,” Kaufman explains. “Primarily because, just like everything else, it is a limited resource. Each sample requires a kit to run.”

Multi-pathogen tests are typically more expensive. But the benefits, like shorter hospital stays (or no stay at all) and better patient satisfaction, can go a long way toward offsetting some of those costs. Insurance pays differently, so out-of-pocket costs will likely be based on a patient’s insurance. Generally, the BioFire test runs about double the cost of two respiratory tests at an urgent care clinic, but this isn’t apples to apples for a host of reasons. First off, explains Lourdes spokeswoman Elisabeth Arnold, only a doctor can decide if the BioFire test is the way to go when you’re hospitalized or sick enough to be admitted.

Some outpatient PCR testing is now being done in-house as well. A few weeks ago, Ochsner Lafayette General rolled out “a high-throughput nasal swab analyzer,” Thompson says. The machine, the Abbott m2000, is housed at Ochsner UHC, but performs testing for all local Ochsner outpatient facilities as well as the community testing sites managed by the system. The system quickly went from five days a week to seven, Thompson says. The machine can run more than 90 tests at a time, with capacity for 400 tests per day. The turnaround was initially 48 hours but has already been cut in half now that there are enough samples to run it daily.