Setting Up a Next-Generation Microbiology Lab

By Tanuja Koppal

Gary W. Procop, MD, MS, chair of the Department of Molecular Pathology, section head of molecular microbiology, and director of mycology and parasitology at the Cleveland Clinic, talks to contributing editor Tanuja Koppal, PhD, about the clinic’s $75 million state-of-the-art medical testing laboratory that opened in 2012. The building houses microbiology, molecular pathology, cytogenetics, and immunopathology as well as administrative offices. He talks about the thinking that went into designing the building and its labs and shares some insights on what people need to consider when embarking on such initiatives, however small or large. He emphasizes that both people and laboratories should always be open to change, making way for new advancements in science and technology.

Q: What is the challenge with microbiology labs today?

A: Our mission here at the Cleveland Clinic is the diagnosis of infectious diseases in a timely manner using laboratory testing. The main challenge in microbiology is that a lot of things are still done manually, and that increases the costs. This is a very rapidly evolving field, and there is not much room for waste in the system. It is important for a lab manager to look at the introduction of new technologies that can help specimen handling or diagnostics to identify microorganisms better, faster, and cheaper. As the section head of microbiology, I oversee various groups and staff members who have various areas of expertise, and they are all continually looking to improve. Each of the areas of the laboratory has a lab coordinator who is the interface between the bench technologists and the administration. The work done is mostly all clinical, but there is some applied research going on that involves validation of tests and testing of new methods to be used in the clinic.

Q: Are the laboratories required to follow regulations and adhere to certain standards?

A: We must follow many different regulations. Being a lab that serves a hospital, we have to have a Clinical Laboratory Improvement Amendments license, which means that we have to be inspected by either a joint commission of hospital accreditation or by the American College of Pathologists. They both have very rigorous standards. So all the tests that we perform for the clinic have to undergo rigorous validation, and when the test goes into operation in the clinic it has to have a high degree of quality control and quality assurance.

Q: When and why did you move into your new facility?

A: We moved into the new facility over a year ago. The laboratory had grown in terms of volume (of activity) over the years. Much of clinical microbiology is now molecular microbiology, and so we had an opportunity to expand.

Q: Can you talk about some of the design elements of the building?

A: This new building is the first Leadership in Energy and Environmental Design (LEED) certified building on the campus. It’s a beautiful building with lots of open space and large windows all around. There is a lot of natural light, and it has been purposely designed that way. However, we have discovered that some instruments are sensitive to direct sunlight, and that can raise the instrument temperature and cause problems. So sometimes on sunny days we have to draw the shades. That was an unforeseen complication that was adequately dealt with. It was a great opportunity to be able to work on the design of a laboratory from scratch, because we could actually plan the specimen flow through the lab. In our hospital we have process engineers and a continuous improvement group, and we were able to utilize their skills to look at workflows in the lab using tools like spaghetti diagrams and such to plan the best placement of equipment for testing. In addition, all the laboratory workspace is movable, so if you ever had to redesign a workflow it would be relatively easy to do.

Q: Can you highlight some of the technologies and instruments you work with?

A: We perform all the direct examination and culture-based methods, such as growing the microorganism and identifying it, using biochemical means that are all a part of traditional microbiology. More exciting is the introduction of automation to microbiology testing. We have just finished validating an instrument called the Walk Away Specimen Processor (WASP), which is an automated specimen handler. This helps automate all the front end of microbiology to increase reproducibility and reduce the number of full-time employees required. The other major advance for a traditional microbiology lab is the use of mass spectrometry, particularly matrix-assisted laser desorption/ionization time-of-flight, for the rapid and inexpensive identification of bacteria. This is all the rage in clinical microbiology now and it’s replacing the traditional biochemical identification, which relied on the growth and metabolic activity of the bacteria or the microorganism, with a protein-based identification method. In molecular microbiology it’s common to use rapid-cycle polymerase chain reaction, both qualitative and quantitative, for detecting microbial pathogens. DNA sequencing is also commonly used for the identification of microorganisms and certain viruses in determining their susceptibility. Those are some of the major instruments and technologies we currently use. We do our best to stay up with the times and look at new and emerging technologies to see if any of them can more rapidly identify the etiologic agents of the disease.

Gary W. Procop, MD, MS, is chairman of the Department of Molecular Pathology, section head of molecular microbiology, and director of mycology and parasitology at the Cleveland Clinic. He completed anatomic and clinical pathology training at Duke University Medical Center and a Clinical Microbiology Fellowship at the Mayo Clinic. He is a diplomat of the American Board of Pathology in anatomic and clinical pathology and medical microbiology. He is a fellow of the American Academy of Microbiology, the College of American Pathologists, the American Society for Clinical Pathology, the Infectious Diseases Society of America, and the Royal Society of Tropical Medicine and Hygiene. He has given more than 470 scientific presentations and has 153 published manuscripts, 29 chapters, and one book to his credit. He is an officer and trustee of the American Board of Pathology, and chair of the Microbiology Test Development Committee for the board; a member of conferences and awards committees for the American Society for Microbiology; and the chair of the Microbiology Resource Committee for the College of American Pathologists. His primary interests are the practical applications of molecular diagnostic methods for the diagnosis and treatment of infections, infectious disease pathology, mycology, and parasitology. Finally, on a personal note, Gary is a fencer, a sailor, and enjoys genealogical research.

Q: What have you done to automate processes to minimize contamination and other problems?

A: Much of the processes are still manual. The WASP, which is an automated specimen handler, has been set up for processing urine cultures. We have also automated molecular microbiology protocols such as DNA and RNA extraction. The manual extraction methods are very tedious, whereas the automated extraction robots are really good. We have certainly looked into the possibility of automation where it exists, and if the test quality remains high we will certainly automate.

Q: Did you make any mistakes along the way, and what would you do differently the next time around?

A: We did not plan the warehouse component of our lab well, and that was one of the things that we had to backtrack on a little bit. We had worked hard, as we wanted to allow medical technologists to be able to do their jobs and not spend time going around finding gloves and pipettes. We ended up having a warehouse group deliver those supplies to them daily, in a timely manner. That was decided relatively late in the planning process. It ended up finishing well, but we had to do some last-minute changes to the design, and we could have done it better. There will always be some hiccups along the way when moving into a new facility, and you have to do the best you can.

Q: What advice would you give people who are looking to redesign their labs with limited resources?

A: Over the years I have found that laboratories and hospitals are sometimes set in their ways. So my advice is to be willing to change and look at new advances that may make testing faster and better. Second, it might be worth consulting with people who have skill sets that are different from your own. The interactions that we have had with our process engineers have been very useful, and there are now companies that offer to send in their process engineers to provide workflow assessments. That is something that we, as medical and lab professionals, are not trained in, and having that modern understanding of process engineering and how to examine workflows is very important. If the lab cannot do it for budget reasons it’s still worth a consult to figure out whether the existing workflow is optimal. Laboratories should also embrace some of the lean concepts such as 5S methodology to create a sustained neat workplace in order to decrease medical errors. Continuous quality improvement to obtain better patient results is a must. We did some site visits early on, but we were fortunate to have process engineers embedded in our labs who had the expertise we needed to get the job done. At the beginning we hired a lab consultant who had designed some large reference labs, and we did get some good information from him. It all depends on the scope of the project. With a large new facility you need the architects, lab designers, process engineers, and administrative leadership at the table. If it’s a small space that you are looking to redesign, then you can make do with a lot less.

Q: Should you design a lab based on present or future needs?

A: You should try to do a little of both. The challenge with designing a lab based on tomorrow is that the technology is rapidly changing, and we don’t honestly know what’s coming down the road. So you have to address the issues at hand and plan for current optimal workflows. But it’s wise to make the workspace as versatile as possible so that you can implement new technologies as and when they come along.

Categories: Ask the Expert

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Calculating Workplace Tragedy

Published: June 1, 2013

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