TLA in, volume up—micro labs take stock

Unfortunately, Clark says, not enough manufacturers are amenable to the concept of open systems that can link to other companies’ instruments. “Some major companies feel they can put their own products out there and stay a closed system. But we try being involved with manufacturers that have systems that are open and can have others linked to them, particularly in the case of TLA.” With the technology changing so fast, he says, “systems are just going to have to open up, as far as we see it.”

Even within two weeks of installation, the technologists and technicians were commenting on how uniform and standardized the streaking was, Clark says, which reduced the number of subcultures the lab needed to perform. However, as a microbiologist who had streaked thousands of his own cultures, Clark was interested in demanding that automated instruments have a flexible style of streaking.

When Alverno acquired its WASPs, Copan had 12 or 16 patterns to choose from but offered to program modifications if the laboratory wished. “About eight months into using their patterns, we wanted to modify slightly one of the streaks so it would go only two-thirds of the way down the plate instead of all the way down.” Once that modified pattern was produced, Copan added it to the stock of patterns available to new customers.

From his perspective, one of the major benefits of Alverno’s automation has been the smart incubators. “You don’t take plates in and out of the incubator to put on your counter and sort through; they stay in the incubator. And it’s been proven that with continuous incubation, you actually get colony formation faster. So instead of taking 18 to 24 hours, we actually read our first urines at 14 hours. About 60 to 70 percent of the positive cultures can be worked up at that time.”

Reducing turnaround time was particularly important for his lab because of the centralization of setups, which has added to the time lost in transport. “But we make up at least six hours per culture just because of the automation,” Clark says.

Return on investment is always a concern. “Our front end has more than paid for itself, so depending on your volume, you are probably looking at three years for ROI,” Clark says. The cost of the system varies from lab to lab, but “for the smart incubator side of the system with servers and workstations, I would say somewhere around $1 million for a single incubator system would be pretty common. The front-end processors run around $300,000 each.”

Next on the lab’s automation agenda is adding another line to take care of the remainder of the cultures it is working with. “We’re working with Copan to improve the programming of software to make the system more capable of handling multiple-day/multiple-read cultures,” Clark says. In the meantime, BD and Copan are racing to see which will come out with software that will have colony recognition and the ability to read the cultures, instead of having a technologist read them, he adds.

Clark considers workflow to be pivotal in taking advantage of all that automation can offer. “Historically, microbiology is what we would call a semi-batch process. You go to the incubators, get all the plates out on the day shift, or maybe two shifts, look at them, decide what you’re doing, set some stuff up, put them back in the incubator, wait, and then get them out to batch again.” A set of plates might be 12 hours old or 30 hours old under current professional standards.

To maximize throughput and minimize turnaround time, “you need to have a constant flow,” he emphasizes. “And the only way to do that without having a ton of incubator space is to have a computerized incubator that can produce images effectively and generate a worklist based on them that techs can scan through quickly and continuously, 24/7.”

This kind of process will allow for every plate, when it is ready to be read, to be imaged, and for that image to be available on a screen, with a dashboard listing how many plates are to be read at 2:00 and 4:00 and 6:00 and 8:00, Clark says. “That will minimize turnaround time and maximize efficiency, which will reduce some of the workforce needs, or free people up to do more manual things.”

Like NorthShore’s laboratory, the microbiology lab at University Hospitals Cleveland Medical Center had been looking into automation for a long time because of its volume increases, says Dr. Jacobs. “Our workload has gone up enormously in the last decade as University Hospitals have developed a system from the central campus that incorporates community hospitals, lots of physician offices, patient care centers, and outpatient labs,” Dr. Jacobs says. “Over the last seven years, we consolidated all microbiology from the community hospitals into the central hospital.”

In 2010, his laboratory was the first in the country to get automated specimen plating using the Copan WASP system. Also that year, Dr. Jacobs witnessed the Kiestra TLA—then available only in Europe—in action, and was impressed. When Becton Dickinson bought Kiestra two years later, University Hospitals made the jump to BD Kiestra TLA.

The Kiestra system arrived at University Hospitals’ microbiology lab in early 2016, making the laboratory the second hospital in the U.S. to acquire a Kiestra system and, when it was installed, the largest Kiestra TLA to that date. “It took two months to install; then we went live with urine specimens and did that for a year while we went through the whole process of getting staff trained and getting all the tests validated. Now all our specimens are being tested on the system.” The specifications called for the automation system, which cost $3.5 million, to be able to absorb up to 40 percent more volume; since installation, the lab has already increased its volume by 15 percent, Dr. Jacobs says.

His laboratory has found that the continuous processing Kiestra permits brings major improvements in turnaround time. Whereas a partial automation system would automate specimen processing and then put out the plates, having laboratory workers carry on manually from there, Kiestra eliminates the manual step, Dr. Jacobs says. “It puts the plates into an incubator, which we set for 16 hours, then it takes images of the plates to be reviewed as images on a screen. If there’s no growth, then you don’t have to handle plates; the culture is flagged as negative and then it throws the plate away. Since 80 percent of urine cultures are negative, that’s a big time savings.”

This automation makes the whole process more efficient. “If a urine specimen came in at 4 PM, we would put it in the morning basket to read at 8 AM, which would be 16 hours later. First thing in the morning, we read all plates that are 16 hours old, then at 10:00 we get the next batch, and eventually we’ll be able, 24 hours a day, to read each plate as it reaches 16 hours. This puts you on continuous processing, where you’re reading plates at the right spot, not between 16 and 30 hours, which is what we would do before.”

“Even for outpatient specimens, the continuous processing can reduce your average turnaround time by a day once your system is installed,” Dr. Jacobs says. That estimate confirms studies by Kiestra, which has found that its European installations reduce the average turnaround time for all microbiology specimens by 24 hours.

The laboratory has probably doubled its specimen volumes since 2010, Dr. Jacobs says. Now it receives about 750 specimens a day, 300 of them urine and 150 to 200 blood. The footprint of the system that handles all this volume is smaller than the manual setup it replaced. “But it’s still a pretty big footprint, because we have two inoculating stations, five reading stations, and five incubators.”

Although the laboratory hasn’t yet recalculated turnaround time, he knows it is shortened. “We’ve definitely had ID physicians contact us and say they’re aware they are getting results faster.”

The laboratory has used its MALDI-TOF to help speed up the system processing of positive blood cultures. “We put a plate in the system, have it incubate for four hours, then send the plate on to the workstation. At that point, within the next 30 to 60 minutes, we do the MALDI, and on at least two-thirds of blood cultures, we have enough growth to get good identification.” With this process, Dr. Jacobs says, “we’re also getting better susceptibility results because there are more antibiotics in the tray.”

Within a couple of months, the lab will convert completely to MALDI identifications as it is phasing out the MicroScan combo plates. “We’re working on ways of speeding up the susceptibility part of the four-hour blood culture testing. We hope to have that in play by the end of the year.”

The laboratory adopted a different strategy to address initial issues with the MacConkey plates. They can be very wet and sometimes get stuck, Dr. Jacobs says. So tweaks in the process were necessary to ensure the plates are dry before they are put into the system: “Instead of taking plates directly from refrigeration, we wait until they are at room temperature before putting them in the loading stations.”

Dr. Jacobs says his laboratory justified the installation of the Kiestra system by arguing it would be able to get 40 percent more work done without an increase in staffing. That prediction has been borne out, he says, and the laboratory is finding the number of FTEs needed to run the laboratory “keeps on going down.”

“It’s really difficult to get microbiology technologists, a lot of our people are reaching retirement age, and we have people coming in who are less qualified with less experience. So we needed to simplify the processes as much as possible, and we’ve achieved a lot of those goals,” he says. There’s been a quick learning curve for staff, and the new workflow creates a more efficient division of labor. “You can have experienced people reading a lot of plates, and less experienced doing the workups, as opposed to having everyone at the bench for the whole process.”

Dr. Jacobs’ team originally calculated that the decreasing length of stay for patients with bacteremia, plus the benefits reported in the literature of getting faster definitive results on blood cultures, are sufficiently substantial that the system could pay for itself in one year.

As it turns out, it’s only been in the past three months that turnaround time has reached the speed in those calculations, he cautions. “So it’s probably going to take us two years to get to that period. But thereafter, we’re going to get the same returns every year.”

In addition to shorter hospital stays, the savings from reducing the amount of unneeded treatment will also contribute to a quick return on investment, Dr. Jacobs believes. “When you go to a physician with a urinary tract infection, you get put on treatment before the culture results come back. If the cultures are negative, and the physician finds out 24 hours sooner, then you’ve saved the cost of extra antibiotic treatment.” In fact, he says, “I think there are going to be small savings on almost every specimen we touch.”

As microbiologists make the adjustment to the era of automation, Dr. Jacobs cautions, they shouldn’t get too comfortable. “Genetic methods are going to take over everything we’re doing; it’s just a question of when that becomes affordable. And I think it will be sooner rather than later.” He estimates that the automated system his lab now has will be practical for about 10 years. “Then it will be all genetic and molecular testing.” In the meantime, he is optimistic that other microbiology labs, if they are large enough, will find they can benefit from installing TLA. n
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Anne Paxton is a writer and attorney in Seattle.