Total lab automation and the evolution of the clinical microbiology lab

Employee burnout rates in the healthcare sector were exceptionally high even before COVID-19. Burnout has a significant adverse influence on clinicians’ overall well-being, as well as their sense of job fulfillment, which results in higher employee turnover rates, lower-quality patient care and decreased patient satisfaction.

The surge in COVID-19 testing has shined a spotlight on the importance of hospital microbiology labs and the critical role they play in infectious disease management. However, microbiology labs are facing a growing list of challenges. As laboratories have undergone consolidation, specimen volumes have increased significantly. At the same time, microbiology labs are seeing greater demand for rapid test results so clinicians can manage their patients effectively. There has also been a tremendous shift in the types of diagnostics that labs are performing, including increased demand for molecular and point-of-care testing. In addition to these pressures, many microbiology labs are struggling with the longer-term challenge of attracting and retaining talent, as seasoned microbiology experts retire, and fewer young people enter the field.

Becker’s Hospital Review recently spoke to Patrick Murray, PhD, vice president of Medical Affairs, Microbiology, at BD Life Sciences, about the current landscape facing microbiology labs and how automation solutions can increase operational efficiency, while delivering more accurate, timely and cost-effective testing.1,2

The pandemic has exacerbated long-standing challenges within microbiology labs

Prior to joining BD Life Sciences 10 years ago, Dr. Murray directed clinical microbiologylaboratories at major academic medical centers for 25 years. He then joined the NIH as chief of microbiology and served in that role for a decade. Through his current work, Dr. Murray regularly meets with laboratory directors, hospital administrators and government officials worldwide to discuss the wide range of microbiological challenges that they confront. This experience has given Dr. Murray a deep understanding of lab operations and trends in the microbiology sector.

“We’re very focused on what’s happening in labs today,” he said. “Virtually all of the problems that microbiology labs are currently dealing with are the same problems that existed before the pandemic began. Some of these issues have become more acute due to the need for rapid turnaround with COVID-19 diagnostics in combination with all of the same work that labs were already doing before.”

A comprehensive approach to lab automation leads to improved efficiency and accuracy

Although microbiology labs have used automation to streamline discrete workflows like blood cultures, identification of organisms and antibiotic susceptibility testing, many organizations are now turning their attention to automation of all lab processes as a way to reduce variability and the need for repeat testing while increasing lab testing capacity and staff efficiency.

“I think the real transformation that’s occurring today is automating the entire microbiology laboratory, similar to what happened with chemistry, hematology and immunology laboratories,” Dr. Murray said. “We are seeing a real push to work more efficiently in the lab.”

In a traditional microbiology lab, patient specimens come in throughout the day. Between each station — from inoculation and incubation to imaging and result reporting — techs often have to complete numerous manual steps and data entries in large batches that extend turnaround times and lead to compounding inefficiencies for overall lab operations. A better approach is to take each specimen as it arrives in the laboratory and begin processing it immediately to reduce delays in reporting results.

“The BD KiestraTM total lab automation solution process specimens as they are received in a very standardized and accurate way and then moves the specimens automatically to smart incubators on mobile tracks,” Dr. Murray said. “In the incubator, plates are examined using a sophisticated imaging system. Then the imaging system applies algorithms to prepare a composite, high-resolution image to assist technologists in interpreting the results. Automation enables lab staff to focus on more complex work, such as selecting colonies for identification and susceptibility testing, rather than non-value add tasks like moving plates around in the lab or repeat testing due to human error.”

Automation alone isn’t enough; it must be combined with lean workflow practices and informatics

Although automation systems hold great promise for addressing the challenges facing microbiology laboratories, simply automating existing practices won’t deliver optimal results.

“I think it’s important to emphasize that if you simply replicate your processes using an automated platform, you won’t see the value of automation,” Dr. Murray said. “You need to combine innovative technologies with lean workflow practices. We’ve seen a real push to introduce lean practices into the laboratory and lab efficiency lean experts have become quite valuable.”

Informatics is another component that can supercharge the value of lab automation systems. Powered by BD SynapsysTM informatics, BD Kiestra solutions generate data and analytics that lab managers use to track how much work moves through a laboratory, how long that work takes and staff their labs to best optimize their workflow. 

It’s also possible to benchmark a lab’s performance against that of other hospitals in the network to see which laboratories are more efficient than average and which ones have faster turnaround times.

“We’ve seen an increase in the tools available to monitor the work done in the clinical laboratory,” Dr. Murray said. “Informatics is a good example where the impact is much greater than what was possible 10 years ago. Now lab managers can run their laboratories in a more efficient way that enables them to communicate results more rapidly for physicians.”

Lab automation and innovation require both a big-picture viewpoint and attention to detail

As microbiologists consider an investment in a laboratory automation platform, it’s important to keep the big picture in mind. This means thinking about the benefits that the technology provides at an organizational level.

“I come from the microbiology community and we can sometimes be very conservative,” Dr. Murray said. “In some ways, microbiologists work in a vacuum and our budget is considered in isolation. This can lead people to view automation solutions as too expensive. If they keep the total cost in mind, however, they see how a solution like BD Kiestra automation can amplify efficiencies. For example, your staff will have the capacity to handle an increased volume of specimens while improving the standardization, accuracy and turnaround times for results that physicians need for patient care.”

A recent study published by Thomson et al. described the improvements in lab productivity gained through the combination of BD Kiestra Total Lab Automation and Lean process improvements.2 A metric known as Laboratory Productivity Index (LPI) was used to measure the capacity of laboratory staff to process microbiological specimens. LPI is the ratio of specimens processed per day divided by thecombined fulltime equivalent (FTE) of in-scope staff. The Thomson study found that, compared to pre-automation measurements, post automation LPI increased by 41%. This increase in efficiency was achieved while managing a 17% increase in specimen volumes and a 25% decrease in lab space.

A focus on innovation

From a product roadmap perspective, BD partners with healthcare leaders to inform how the company approaches the design of automation products.

“When we start developing a product, customers work in partnership with us,” Dr. Murray said. “We need to fully appreciate the details of how they will use a product in their workflow and lab environment. For example, customers may provide us with usability feedback, such as where a knob should be located, or with input related to processing time requirements. Experts like myself can provide a broad view and general direction about where we should go, but ultimately we must work in close partnership with hospital and lab leaders as well as the lab staff to create the right product for their laboratory.”


As hospitals and health systems evaluate automation platforms, they must recognize the potential impact these technologies have on the capacity of microbiology lab operations. Automation provides laboratories with an opportunity to do things in ways that were previously impossible and to address the challenges of today while preparing for the future.

“Chemistry and other types of labs went through this same automation evolution and today they are much more efficient and accurate,” Dr. Murray said. “Microbiology is now moving in that direction. You have to ask what automation can bring you and how you can operate in the best possible way moving forward. I think at some point in the near future, we’ll look back and ask ourselves how we worked without total automation in the microbiology lab.”

1Croxatto A et al. Comparison of inoculation with the InoqulA and WASP automated systems with manual inoculation. J Clin Microbiol. 2015;53(7):2298-2307.
2Thomson RB Jr, McElvania E. Total Laboratory Automation: What Is Gained, What Is Lost, and Who Can Afford It?. Clin Lab Med. 2019;39(3):371-389. doi:10.1016/j.cll.2019.05.002.


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