Putting in place a molecular panel for pneumonia

A European multicenter study of 2,476 specimens from 52 laboratories had similar findings (Ginocchio CC, et al. Eur J Clin Microbiol Infect Dis. 2021;40[8]:1609–1622). “Their results line up to ours pretty well,” Dr. Anderson said. A bacteria or virus was detected in 75 percent of specimens, and more than one pathogen was detected in 46 percent of positive specimens. “So it’s safe to say the literature confirms you will get a lot of positivity with an assay like this,” he said.

For viral targets, Dr. Anderson and colleagues found the pneumonia panel performs well compared with their standard-of-care viral testing. They did a separate analysis of remnant specimens from the 200 specimens and tested them also by the BioFire upper respiratory panel (RP2.0), “and the comparison was nearly exact,” with 96 percent concordance, he said. For something like flu or RSV, “the testing with the pneumonia panel versus the upper respiratory panel is essentially equivalent. So you don’t need both” (Hughes AEO, et al. J Clin Microbiol. 2020;58[6]:e00254-20).

The panel missed eight instances of bacterial detection by the standard-of-care method because the targets weren’t included on the panel, Dr. Anderson said, with Stenotrophomonas maltophilia accounting for about 50 percent of the misses.

There were 92 instances of unique pneumonia panel detections that were not reported from the culture-based testing; 22 were Staphylococcus aureus, and 25 were Haemophilus influenzae. “We know these are part of normal flora,” so the panel could have detected something the laboratory didn’t report out in culture but was part of normal flora, “or maybe it was detecting flora that never actually grew on the plate,” he said.

Many detections of Streptococcus pneumoniae are unique to the panel, Dr. Anderson said, noting the organism doesn’t grow well in culture if a patient has had an antimicrobial pre-culture. “And these could potentially be clinically relevant, molecular-only detections that we’re going to miss with our culture-based techniques.”

The findings of Ginocchio, et al., reported in 2021, “almost exactly mimic ours,” he said, in their many instances of unique pneumonia panel detections for S. aureus, H. influenzae, and S. pneumoniae. His own group’s data reveal these detections are linked to lower organism load. If the pneumonia panel was 10⁴ or 10⁵, “it’s far less likely that we’re going to recover that in culture. Either it’s going to be interpreted with the mix, or it just isn’t going to grow,” he said. They found, too, that for S. aureus, the unique detections are more common in potentially polymicrobic specimens, such as sputum-type specimens. “Not surprising,” he said, “because the hypothesis is that we’re detecting it in the normal flora,” and specimens that have more normal flora will have more unique detections.

Once the panel is implemented, Gram stain triage still plays an important role. “We all know garbage in, garbage out,” Dr. Anderson said. “If you have a specimen that’s loaded with squamous epithelial cells, it’s probably oral contamination. We’ve already seen those extra detections associated with sputum-like specimens,” all of which were acceptable for testing. “You can imagine it would be far worse if we had a lot of orally contaminated specimens,” which is why the triage is important. His laboratory rejects all specimen types and samples with excessive squamous epithelial cells for multiplex molecular syndromic pneumonia panel testing, and has always done the same for culture from sputum-type specimens.

Because Gram stain plays an important role, “it’s going to complicate your workflow, because unlike a lot of your molecular testing, you can’t just send it off to the molecular lab and have it tested,” he said. Gram stain triage has to come first, and “with that triage comes communication.” Even though the microbiology and molecular laboratories at Barnes-Jewish are across the hall from one another, “there are still challenges with communicating whether the testing needs to be done” and how to hand off the specimen.

Their solution: A stickered sheet with the patient’s information accompanies the specimen to the microbiology laboratory, and on it they check whether the Gram stain was acceptable. Whether the specimen will go for molecular testing and culture, or culture only, or neither is also accounted for on the sheet, “and it tells our technologists exactly what to do,” Dr. Anderson said.

Rejected specimens are reported in the EHR with a note: “Abundant squamous epithelial cells observed on Gram stain. Specimen will not be processed for molecular analysis.”

Gram stain and culture must accompany an order for panel testing, and the order set also includes SARS-CoV-2, which is absent from the panel. “There’s a lot of discussion about how these should be offered together,” he said. The panel is orderable as pneumonia PCR with aerobic culture and Gram stain. For patients with cystic fibrosis there is a special pulmonary culture order. “The bacteria included on these panels are not the same bacteria, or many of the same bacteria, that cause disease in cystic fibrosis patients,” he explained, “so it’s not an appropriate test for that patient population.”

Ordering is otherwise unrestricted, Dr. Anderson said, though a soft stop alerts providers if a repeat pneumonia panel has been ordered within three days to curb repeat testing. This extends to repeat viral testing, such as a flu-positive result from the prior day or concern about viral pneumonia. It’s redundant to test for both, “so we let them know that that testing’s already occurred and ask if they wish to proceed.”

They report all detections with semiquantitative values and use no specimen type thresholds. “We report it as it comes off. But we do not report the data in its raw form,” because a report scanned into a patient chart would be difficult for providers to interpret. For upper respiratory panels, providers are accustomed to receiving all viral and atypical bacterial targets in a listed format. “And half of this panel is the upper respiratory panel, so we want to be able to maintain that to some degree,” Dr. Anderson said. “But we also want to maintain the cultural context for those bacterial targets. They need to be interpreted with the culture, and we wanted to make sure that was linked.” The laboratory therefore reports all atypical bacteria and viruses in a list.

Bacteria and antimicrobial resistance targets are reported as a narrative within the corresponding culture report, including the presence, not absence, of Gram-negative resistance targets. “So we’re not saying, ‘It’s negative for resistance,’ because these are much better at predicting resistance than susceptibility,” he said. “We don’t want someone to look at absence as ‘Now I can use a less broad-spectrum drug.’” Interpretive notes are provided (see examples in Fig. 1).

Adding action to the results is important. “You can’t just plop this down and expect your providers to act on it,” Dr. Anderson said. Guidance is needed. At Barnes-Jewish, pharmacy, infectious disease, and laboratory leaders wrote a guide on what to do with results and distributed it electronically. “It gives our providers a road map to these results they’re not used to seeing.”

Amy Carpenter Aquino is CAP TODAY senior editor.