The art and science of positive blood cultures

Karen Titus

October 2022—It might be possible to tot up, using only the number of toes on an ordinary foot, how many labs are feeling full of vim and vigor these days, open to concepts like creative destruction and get those creative juices flowing and have fun with it—slogans once easily uttered but now tiring to enact.

Nevertheless, Margie Morgan, PhD, D(ABMM), would like her colleagues to at least consider the possibility of inspiration in the microbiology laboratory. In particular, Dr. Morgan, medical director of microbiology and professor of pathology and laboratory medicine, Cedars-Sinai Medical Center, Los Angeles, has some thoughts about using a new automated system to facilitate rapid microbial identification from positive blood cultures.

The Arc system, from Accelerate Diagnostics, is composed of the Arc module and blood culture kit and concentrates organisms recovered in positive blood cultures for direct testing on MALDI-TOF mass spectrometry.

Dr. Morgan and colleagues have been using the system since February. Initially, they performed comparative studies against a manual extraction method the laboratory had been using, she says.

Interest in making a change was considerable, especially among overworked laboratory staff. Prior to bringing on the Arc system, she notes, the laboratory was exploring using Bruker’s MBT Sepsityper, which uses a standardized, multistep manual protocol for the concentration of positive blood cultures to identify organisms, she says.

Ultimately, however, “We thought an automated instrument could do it in a much more time-efficient manner for our staff.” Manual methods typically require about 30 minutes of hands-on time, she says, while Arc decreases hands-on time to two to three minutes.

Unlike many labs, Dr. Morgan’s isn’t experiencing staffing shortages. Nonetheless, “We’re really busy these days,” she says, and the manual method absorbed too much of her staff’s time. “So they were wanting to try the Arc to see if it could make the process simpler with less disruption of workflow.”

As Dr. Morgan explains it, the Arc automates the concentration of a positive blood culture, making multiple manual pipetting and extraction steps unnecessary. The user vortexes the positive blood bottle, then extracts about 1.8 mLs of the blood culture, putting it into a processing capsule. The capsule and Arc test cartridge are placed in the module. About an hour and 10 minutes later, a concentrated sample is prepared for placement on the MALDI target plate for testing.

“So it’s basically hands-off,” she says, “and it does all the concentration for you.”

Another advantage: When manual pipetting and processing steps are required, it’s most efficient for labs to batch tests. With the Arc system, she says, “it is reasonable to do one specimen at a time. You don’t have to wait for specimens to accumulate.”

So far, she says, the Arc has met the lab’s efficiency goals. Some 99 percent of the time, she says, the system supplies a usable nonviable liquid pellet. “The instrument functions without problems; we’ve not had any operational issues.

“You always wish something was faster,” she continues with a laugh. “It would be great if it was five minutes instead of an hour and 10 minutes. But other than that, it has lived up to our expectations.”

It works particularly well for Gram-negative rods, with more than 95 percent identified successfully, Dr. Morgan says. The lab has also had good results with Gram-positive organisms, with identification of 80 percent.

Yeast, on the other hand, has been more problematic, though that’s not necessarily tied to issues specific to Arc, she says. “More likely due to the biomass of yeast in the positive blood culture.” Nevertheless, it has proved useful for yeast. She reports that the laboratory obtains direct identification 50 to 60 percent of the time. The remaining 40 or so percent are cultured and identified using MALDI after colony growth.

“We’re still trying to investigate methods to increase the yeast identification percentage,” Dr. Morgan says.

Yeasts can be difficult to identify on MALDI, given the potential for variability based on technique, agrees Jennifer Dien Bard, PhD, D(ABMM), director of clinical microbiology and virology, Children’s Hospital Los Angeles (CHLA). But now, “MALDI is our first and primary choice when it comes to identifying yeast. And we were able to discontinue all of our other traditional methods that we use for yeast identification.”

Dr. Dien Bard was a member of an advisory panel for the Arc system’s development. From her perspective, any new system would need to minimize hands-on time for it to pass muster in a laboratory. Turnaround times would need to be quick as well, “especially since you’re competing against molecular samples and/or technology, which can provide identification within an hour or less.” Ideally, such attributes could also help with staffing shortages.

Dr. Dien Bard’s laboratory does not use the Arc system. About nine years ago, “We developed our own lysis procedure directly from positive blood cultures that we’re still using,” says Dr. Dien Bard, who is also chief of academic and faculty development at CHLA and professor of pathology (clinical scholar), Department of Pathology, Keck School of Medicine of USC. This approach allows them to identify Gram-negative and Gram-positive organisms directly from a positive blood culture using MALDI.

But she sees the advantages to the Arc, especially since it allows labs to use the MALDI database. “Which is much more comprehensive than any molecular PCR system that’s out there,” she says. “Instead of, let’s say, 18 or so targets, you have hundreds of thousands of organisms that can be identified on a MALDI-TOF database.” That’s one of the reasons, she says, her lab developed its simplified lysis protocol rather than opt for PCR.

The real learning curve, Dr. Morgan says, has less to do with implementation or processing than answering the question of how best to use the Arc.