Putting in place a molecular panel for pneumonia

Amy Carpenter Aquino

March 2023—When it comes to molecular syndromic panels for pneumonia, there’s both upside and downside, says Neil W. Anderson, MD, D(ABMM), associate professor, Department of Pathology and Laboratory Medicine, Washington University School of Medicine in St. Louis.

They’re fast, easy, and close to comprehensive for potential pathogens, and they can detect some culture-negative infections. On the other hand, there are gaps in the panels—particularly for novel pathogens, and a poor-quality specimen for culture is also a poor specimen for PCR. And the panels aren’t standalone tests, “no matter how you cut it,” Dr. Anderson says. “You have to still grow these organisms to confirm identification and to perform phenotypic susceptibility.”

“This isn’t the be-all and end-all, the one test for patients with pneumonia. But it’s a little closer to that,” he said in an AACC session last year, in which he described his laboratory’s implementation of a pneumonia panel. He is medical director of the molecular infectious disease laboratory and assistant medical director of the microbiology laboratory at Barnes-Jewish Hospital. “Implementation of this testing was an intricate process for us,” he said.

Clinical outcome and impact studies to date are few, he noted, but the potential value of pneumonia panel testing, which includes detection of resistance markers, is significant. In his laboratory, since he and colleagues went live with panel testing in 2021, they have seen anecdotally a potential for antimicrobial escalation and use of infection prevention measures if a carbapenemase-associated gene is detected.

Antimicrobial deescalation or avoidance is quite likely, thanks to the high negative predictive value for on-panel organisms. A study published last fall, using the Uny-vero pneumonia panel (Curetis, Germany), which is FDA cleared for tracheal aspirate and broncho-alveolar lavage samples, found the testing to decrease the duration of inappropriate antibiotic therapy of patients admitted to the hospital with pneumonia and at risk of Gram-negative rod infection (Darie AM, et al. Lancet Respir Med. 2022;10[9]:877–887). The multicenter, randomized controlled trial was conducted at two tertiary care centers in Switzerland.

“They took 208 patients and divided them into a PCR group or a conventional microbiology group. The patients then received antimicrobials per the treating physician,” Dr. Anderson said. For the PCR group, results were reported directly to pharmacy colleagues within five hours, accompanied by written guidance for appropriate therapy and considering local resistance rates, he noted. “A very active way of reporting.”

The overall duration of inappropriate antimicrobial use in the PCR arm was shorter by 38 hours (47.1 versus 85.7, P<0.0001). “Definitely showing an impact here,” Dr. Anderson said. “Interestingly, there was no difference in time to discharge.”

Multiple diagnostic tests and methods are required for a comprehensive evaluation for pneumonia, ranging from antigen-based to culture-based to molecular testing. “Sometimes even direct observation of specimens is necessary to give us a clue of the pathogen and inform downstream testing,” Dr. Anderson said. These methods by themselves have severe limitations—many are narrow. The broader methods such as culture are more time-consuming and may not provide an answer quickly enough. Direct observation and staining can identify more but be difficult to interpret. “A lot of us aren’t going to make a diagnosis of a specific pathogen based merely on the direct stain.”

Multiplex panels have been used to diagnose pneumonia for some time. “A lot of laboratories are using the upper respiratory panels that target a variety of atypical bacteria and viruses and using those in an off-label way—we validate this, of course—on lower respiratory specimens to at least have some sort of multiplex testing on these specimen types.”

With the dedicated pneumonia panels, he said, “we’re testing for what we all refer to as ‘regular’ bacteria” that could be part of normal flora, and there are two ways to do so: providing a semiquantitative result—“telling the provider how much is there”—and using positivity cutoffs that may be more applicable to relevant quantities. The resistance markers that these newer methods detect predict resistance but not necessarily susceptibility, he said.

The Unyvero lower respiratory panel is “sample to answer,” Dr. Anderson said, but a separate instrument is needed for extraction, amplification, and detection. Its run time is less than five hours—“not incredibly fast but quicker than a culture”—and it provides a qualitative detection for all targets. A CE version provides semiquantitative readouts for bacterial targets, but the FDA-cleared version is qualitative. The panel targets 20 microorganisms (19 bacterial, one fungal) and 10 resistance markers (Sun L, et al. Eur J Clin Microbiol Infect Dis. 2021;40[10]:2113–2121; Collins ME, et al. J Clin Microbiol. 2020;58[5]:e02013-19; Klein M, et al. J Clin Microbiol. 2021;59[3]:e02497-20).

For the BioFire FilmArray pneumonia panel, sputum, tracheal aspirate, and bronchoalveolar lavage specimen types have been cleared. The panel targets 15 bacteria and seven antimicrobial resistance genes. “We also have different viruses and atypical bacteria” not on the Unyvero panel, he said, many of which are common to the BioFire upper respiratory panel.

The panel’s semiquantitative reporting applies to 15 common colonizers. “There’s a comparison of the target to an internal quantified standard,” Dr. Anderson explained, “and this is used to extrapolate copies per mL, and the copies per mL are reported into semiquantitative bins.” A value of 4 × 10⁵ copies per mL would simply be reported as being in the 10⁵ bin, for example, “so you’re not getting an exact quantification,” he said, noting results are similar to those expected from culture. Antimicrobial resistance genes are tested for qualitatively and reported only if a compatible organism is present.

The Unyvero and BioFire panels “do a good job of covering the bacterial causes of community-acquired pneumonia,” and the BioFire panel also covers the common causes of community-acquired viral pneumonia, Dr. Anderson said, adding the data his laboratory reported were gathered pre-COVID (Webber DM, et al. J Clin Microbiol. 2020;58[7]:e00343–20). Both panels adequately cover the common bacteria that cause hospital-acquired pneumonia, he said, but Stenotrophomonas maltophilia, accounting for three percent of cases, is present only on the Unyvero panel.

In evaluating the BioFire panel at Barnes-Jewish Hospital, his group used 200 consecutively available lower respiratory tract specimens from ED and ICU patients submitted for standard-of-care testing. “Every one of these specimens had a lower respiratory tract culture performed, so they all had bacterial culture, but they may have had different viral testing as well.” They tested the remnant samples using the pneumonia panel and compared the results with the standard-of-care testing. They detected a bacteria or virus in 58.5 percent (117/200) of specimens. “A lot of positives,” Dr. Anderson said, “and a lot of dual positives or positive specimens with three, perhaps even four, targets.” Multiple targets were detected in 43 percent (50/116) of the positive specimens.