‘Game Changer’ Mass Spectrometry for Microbiology at UNC

Academic center microbiology lab reports multiple benefits from use of MALDI-TOF system

CEO SUMMARY: Microbiologists at the University of North Carolina are using MALDI-TOF mass spectrometry to slash the time to answer and significantly cut lab costs. Their goals are to improve patient outcomes and reduce average length of stay. In a one-year study presented last month, UNC microbiologists reported that consumable costs for many microbiology tests were reduced by 92% and that, based on the performance of this new instrument system, the ROI may be as short as 24 to 36 months.

MASS SPECTROMETRY IS THE HOT NEW TECHNOLOGY in clinical laboratory testing. At one academic center, the microbiology laboratory has used mass spec to cut the cost of reagents by 92% while measurably improving patient outcomes.

This innovative work was done at the University of North Carolina School of Medicine and UNC Health Care in Chapel Hill. The gains came after the microbiology lab began to use MALDI- TOF (matrix-assisted laser desorption/ ionization–time of flight) analysis for some lab testing.

“I don’t like to use the word ‘revolutionize,’ but this MALDI-TOF technology has revolutionized our lab,” declared Peter Gilligan, Ph.D. “We can diagnose infection more efficiently and treat patients much quicker, both of which help decrease healthcare costs.”

Gilligan is the Director of Clinical Microbiology-Immunology Laboratories and Phlebotomy Services at the University of North Carolina Hospitals and a Professor of Pathology and Laboratory Medicine. Early in the fall of 2012, he and his col- leagues began to use MALDI-TOF in the microbiology laboratory.

“We have benefited in multiple ways from using MALDI-TOF in our microbiology and immunology laboratories,” stated Gilligan. “We can now identify a pathogen in about an hour, thus saving about one to two days versus the time it takes to identify such pathogens using conventional molecular methods.

“This methodology also allowed the microbiology lab to identify organisms that would previously have been disregarded,” he continued. “One such organism causes breast abscesses and another is associated with eye infections.

Equally Accurate

“This mass spec technology is more efficient and cheaper than conventional lab tests,” observed Gilligan. “It is equally accurate when identifying bacterial and fungal infections in patient samples.”

The team at UNC conducted a one-year study to assess the performance of its MALDI-TOF analyzer. The study showed that using mass spec to identify bacterial and fungal infections in patients led to a 92% reduction in the cost of reagents needed to run clinical microbiology tests. For cash-strapped clinical labs, this is a significant benefit.

After subtracting the cost of the mass spec analyzer, the cost savings from mass spec come from not using reagents, Gilligan explained.

In conventional testing, clinical microbiologists use reagents to determine which pathogens are present in a patient’s sample. Reagents require different amounts of time to identify the pathogen and that time can range from about 24 to 48 hours. In such a setting, the researchers estimated that the costs of identifying 21,930 organisms in a year would have been $84,491.

More Pathogens Were Found

Using MALDI-TOF mass spec, Gilligan’s lab identified pathogens that lab technologists would not have previously considered to be the cause of infection. One was Corynebacterium kroppenstedtii, believed to cause breast abscesses.

“This is a big deal and an important way for the lab to add value,” noted Gilligan. “Doctors would see patients with chronic infections and no one knew what caused these infections. Now we know and we can treat patients much more effectively than before.

“When we dug through the literature, we found several organisms that we didn’t know about before. One was associated with breast abscesses and another one was associated with eye infections,” he said. “Before we would just dismiss them as being a contaminant or not being significant. This technology makes us rethink the assumptions we made previously in clinical microbiology.”

Perhaps the most significant result from the study is the potential that clinical labs will adopt MALDI-TOF MS widely and the use of reagents and reagent rentals will decline sharply. If that happens, then labs may be more inclined to buy equipment outright rather than sign long-term pay-as- you-go reagent rental agreements. If that happens, labs will need to prove the return on investment for such capital expenditures to hospital finance departments.

Presenting the Findings

Gilligan and Clinical Microbiology Fellow Anthony Tran, DrPH, presented the findings from their study at the 2014 general meeting of the American Society forMicrobiology. The meeting took place in Boston on May 18.

For the study, Gilligan and Tran analyzed the costs of identifying microorganisms from 21,930 samples from patients at UNC Hospitals over the course of one year (April 1, 2013, to March 31, 2014). The specimens consisted of enteric pathogens, enterococci, gram negative non-glucose fermenters, staphylococci, streptococci, and yeast.

Using MALDI-TOF mass spec, Gilligan and Tran produced results in about an hour, depending on the organism. The cost of materials for testing the nearly 22,000 organisms was $6,469, a savings that represented 92% of the cost of traditional testing methods.

Staff Time Savings Added

Additional savings of $118,620 (or 82% of the total with conventional testing) came from cutting the time clinical laboratory scientists would need to prepare and process the samples using reagents, Gilligan and Tran said. The staff of UNC’s Clinical Microbiology Laboratories conducted the study. The labs are part of the McLendon Clinical Laboratories at UNC Hospitals in Chapel Hill.

“We estimate that, because of the reduced cost of reagents and time saved for lab technologists, the upfront cost of the MALDI-TOF instrument will be offset in less than three years from purchase,” Tran said.

In an interview with THE DARK REPORT, Gilligan outlined the potential return on investment from using MALDI- TOF MS analysis. “This relatively new technology that is not only superior to what we used previously, but once you pay for the equipment, it is a lot less expensive,” he said. “The cost of a mass spec analyzer is about $250,000. For most labs, it will probably take about two years to recoup that cost in the savings from not using reagents.

Useful Life of Lab Analyzers

“Most labs estimate that the useful life of an analyzer is about five years,” Gilligan added. “Thus, after the first two years, your lab will have about three years of instrument use when the cost will be extremely low and that analyzer will generate tremendous cost savings during those three years.”

MALDI-TOF MS analyzes proteins and identifies pathogens by comparing the proteins it finds in patient samples to known microorganisms stored in a database. Within the past five years, the technology has been used in clinical microbiology labs and Gilligan’s lab was one of the first in the country and the first in North Carolina to do so.

Gilligan, Tran, and other researchers plan to publish their results. Doing so will require them to add in the costs of validating the instrument, a cost that was not included in the analysis so far.

“There was a cost to get to the point of using this equipment, and we need to prove that the machine will do what the manufacturer says it will do under controlled conditions in the lab,” Gilligan explained. “For the validation, we used known isolates and tested them with this system. That gave us some idea about the accuracy of the equipment.”

Once the costs of validation are added, the next step is to measure the effect of MALDI-TOF MS on patient outcomes. Melissa B. Miller, Ph.D., Director, Clinical Molecular Microbiology Laboratory, is working on that analysis.

“Melissa Miller and her collaborators are looking at specific patient outcomes as they related to coagulase-negative staphylococci to determine whether they are a contaminant in the blood culture or the cause of bloodstream infection,” Gilligan said. “Now that we’re using MALDI-TOF MS, we have better tools to identify the organism that’s causing the infection and these tools do the analysis more quickly.

“Given that MALDI-TOF MS identifies pathogens within hours instead of days, hospitals can use more targeted medications and use fewer broad-spectrum antibiotics,” commented Gilligan. “Targeted medications may allow hospitalized patients to leave the hospital sooner.”

A study published last year involving the use of MALDI-TOF MS showed that the Methodist Hospital in Houston cut more than 2.6 days from the length of stay for patients with gram-negative infections. That represented substantial savings and improved patient outcomes. (See TDR, May 6, 2013.)

Cutting Length of Stay

“With this analyzer we may be able to stop broad-spectrum antibiotics sooner or let patients go home sooner,” he added. “Those are significant outcomes. Our MALDI-TOF was a big capital commitment, which told us that the hospital had faith we could ultimately save money and most importantly improve patient care.

“We have a multi-hospital system and one strategy we are considering is to use this equipment to serve other hospitals,” explained Gilligan. “Currently all the institutions are implementing a common information system. Once that is in place, our lab can use this analyzer to identify pathogens in patients in other hospitals in the system and quickly report those results.”

New Technology Has Microbiologists Rethinking Assumptions about ROI

SPENDING $250,000 for one analyzer was the largest expenditure ever for the microbiology department at the University of North Carolina School of Medicine and UNC Health Care, said Peter Gilligan, Ph.D., the director of Clinical Microbiology-Immunology Laboratories and Phlebotomy Services at the University of North Carolina Hospitals.

In 2012, UNC Hospitals spent $250,000 to buy a MALDI-TOF mass spectrometry analyzer from bioMérieux, a company in North Durham that has previously worked with UNC Health Care. Gilligan called the investment a “game changer.”

Big Capital Expenditure

“That amount is a big number for hospitals and for our microbiology lab. It’s the most money we’ve ever spent on a piece of equipment. No question about it,” he emphasized. “But it’s a sophisticated piece of equipment that has made us rethink the way we do things in the lab and our attitudes toward equipment. Maybe the expense of this equipment will be offset by downstream benefits for patients, such as more rapid and accurate diagnosis and better targeting of antimicrobial therapy.”

Another benefit is that the MALDI-TOF MS system increases lab efficiency significantly. “I can’t stress enough that the savings are really in efficiency,” stated Gilligan. “Our lab’s work- load increases continually, yet we’re not hiring new technologists. So somehow we had to become more efficient and smarter. This technology allows us to do that.

“I predict that every hospital with more than 300 beds will want to have this technology in their laboratory,” he said. “It’s a game changer that uses new diagnostic technology to identify microorganisms in an inexpensive way that is consistently accurate.

“Besides increased speed and accuracy, what’s significant about MALDI-TOF is that diagnostics and microbiology companies have made money by selling reagents and disposables for conventional analyzers,” observed Gilligan. “There’s a substantial profit to be made from disposables.

“Now with MALDI-TOF, labs have a system that doesn’t use disposables,” he noted. “Each test uses a toothpick-sized sample and a little bit of chemical that costs pennies to identify microorganisms.

“For our MALDI-TOF system, consumable costs are basically just the slides and the chemical,” stated Gilligan. “But where it once cost our lab $4 to $5 in disposables to identify an organism, now it costs 50¢ or less!

“If a lab can run 5,500 isolates per year on this machine and the machine runs for five years, then savings will be significant over the life of the instrument,” he said. “Running 5,500 isolates annually for five years would total 27,500 isolates at $4 to $5 per isolate. That would total $110,000 to $137,500 in reagents and other disposables. Running 27,500 isolates at 50¢ each would total $13,750.

“The important clinical benefit is that our lab now identifies an organism in minutes instead of days,” he added. “This information helps physicians shorten the length of stay for hospitalized patients. It is our lab’s contribution to cutting healthcare costs.

Game-Changing Technology

“While that effect on the healthcare system is important, this technology is a game changer in microbiology for two reasons,” explained Gilligan. “First, mass spec helps us increase productivity because the lab does work with the same number of people. That’s important because our financial department wants us to be as efficient and cost effective as possible.

“Second, the aging population will increase microbiology workload even as retirement shrinks the number of microbiologists in the workforce,” he continued. “As we need to hire more microbiologists, they may not be available. This technology gives us a bit more breathing room.”

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