Automated specimen processing, robotic workup, remote image analysis, digital reporting… The future for microbiology?

June 1, 2012

An impending retirement boom…increasing workloads…budget freezes….There are many factors impacting the need for innovation in automation in today’s clinical Microbiology laboratory. Statistics show that microbiology faces a labor force crisis in the United States in the years to come. According to the American Society for Microbiology Benchmarking Study Survey of Clinical Microbiology Laboratory Workloads, Productivity Rates and Staffing Vacancies, 67% of microbiology personnel are more than 40 years of age.1 The article “Medicine Needs More Like Her,” published by The Providence Journal, estimates that in the U.S. approximately 10,000 new medical technologists are needed each year, but the schools across the country graduate only half that number.2 Additionally, the workload of the Microbiology laboratory keeps rising, driven in part by the need to screen for increasingly prevalent healthcare-acquired infections (HAIs) and emerging drug-resistant bacteria.

These factors have impact around the world. For example, in 2008, the Department of Health in the United Kingdom passed a law requiring the universal MRSA screening of patients admitted to the hospital emergency department and of elective admissions to the hospital by 2011.3 Combine increasing workloads, an aging population, and the fact that fewer young people are entering the profession, and you have a perfect storm. Automation of front-end and tedious tasks in the Microbiology laboratory is needed so that current staff can be re-deployed to high value work that requires interpretational skills.

Chemistry and Hematology have enjoyed the benefits of full laboratory automation for many years. Microbiology, on the other hand, until recently, had only experienced limited basic automation on the front end of specimen processing. Front-end automation is not a new phenomenon in Microbiology, as first generation automated streakers were developed more than 20 years ago. First and second generation planters and streakers were able to do basic functions, mainly because of the specimen challenge in Microbiology. The move to standardization of containers and the liquid nature of the samples that go to Chemistry and Hematology enabled the transition of those laboratories to automation.

The challenge in Microbiology is the different types of samples received in the laboratory. As Norman Sharples, COPAN Diagnostics’ Executive VP, states, “In Microbiology there is a buffet of samples varying in container types, sizes, and viscosities.” To be able to enjoy the benefits of automating the front end of Microbiology, a radical change is needed, and it requires a move to liquid-based microbiology.

The two most commonly received samples in the laboratory are urines and swabs. Urines are already liquid, but traditional fiber swabs present a challenge when trying to automate the manual rolling of the swab onto the plated culture media. The invention of flocked swabs, swabs with no core mattress to absorb the sample, which absorb more and release more material than traditional fiber swabs, has made the concept of liquid-based microbiology a reality by putting bacteriology swab samples in liquid format and facilitating automation. Clearly, not every sample is going to be automated. There will always be the need to streak some samples by hand, such as a cerebral spinal fluid (CSF) sample that comes into the lab and requires immediate attention. But with urines and swabs in liquid form, the door for automation in pre-analytics has been opened.

There are many benefits to implementing front-end automation. Instruments able to process most samples, (including opening and closing containers, labeling, planting, and streaking), Gram slide preparation, and broth inoculation present a promising alternative to help overworked and overwhelmed staff. Consistency and quality are some of the immediate benefits seen in the lab after implementing automation. Specimen processors plant and streak, do Gram slides, and prepare enrichment broths consistently throughout the day, no matter if it is the beginning or the end of the shift. The consistency of specimen processing results in improved quality of colony isolation, easier plate read, and more homogeneous Gram slides and enrichment broth preparation. Gillian Jones, Microbiology Lead at Plymouth Hospitals NHS Trust, published a study in the Journal of Clinical Microbiology, where the Walk-Away Specimen Processor (WASP) planted 50,000 plates from ESwab samples, and she found consistent isolated colonies and no evidence of cross contamination.4

Another benefit of implementing front-end automation in the lab is reducing repetitive stress and fatigue. Opening, sampling and closing specimens numerous times each day poses a serious concern, especially as labs face an aging population. Since the technology is fairly new, more studies need to be conducted to quantify the long-term impact on ergonomics and repetitive stress reduction by implementing automated systems in the laboratory.

Traceability is another benefit of implementing front-end automation. Right now, samples are received at different times throughout the day. Sometimes, a significant amount of time elapses between when the sample is scanned as received in the lab’s receiving area and when it is actually processed. By using barcode systems and an automated specimen processor, laboratories are able to receive the sample into the hospital’s LIS using the instrument, eliminating the manual step of receiving it at a different area of the lab. Additionally, the instrument captures the exact moment when a specimen is processed, providing the laboratory full traceability of the time associated with that sample. This becomes helpful when determining true incubation times.

Automation in front-end processing is evolving at a rapid pace. Planting and streaking was the first step of a revolution in Microbiology, and now automation is moving beyond just planting and streaking. Diagnostic companies such as COPAN, BD and bioM’erieux are investing in this field. These companies are offering solutions that fully automate the Microbiology laboratory, using conveyors to continuously move samples from the planting and streaking area to automatic incubation to remote image analysis and digital workup. Robotic plate management will take culture plated media directly to the image acquisition stations. After the image acquisition station, culture media plates are placed in incubators for a predetermined amount of time (e.g., 18 hours or 24 hours). After precise incubation, images are automatically captured at the image acquisition stations. Laboratory technicians can review cultures digitally on a screen rather than physically, which opens the door for remote bacteriology. Europe has embraced this technology, and in the United States interest is growing rapidly.

Excellent patient care is the goal of every laboratory. Increasing accuracy, consistent quality, and full traceability and reducing turnaround times improve patient care by allowing labs to provide results to physicians faster, thus allowing patients to receive treatment sooner. These practices also have a direct impact on the hospital’s bottom line by shortening stays. The use of automation for managing the whole process of specimen setup and workup allows laboratories to know precisely when the sample was processed and to generate reports exactly at 18 hours or 24 hours, regardless of uneven specimen arrivals and without having to be physically in the lab. This is an exciting time for Microbiology, a time of change and collaboration and a time of converging technologies. The future of Microbiology with automation of specimen processing, robotic workup, remote image analysis, and digital reporting is now, and we will be able to witness it firsthand.


  1. Check W, ed. Survey of clinical microbiology laboratory workloads, productivity rates and staffing vacancies. Washington, DC: American Society for Microbiology; 2005.
  2. Kimball-Stanley A. “Medicine Needs More Like Her,” Providence Journal. Oct.1, 2006.
  3. Department of Health, UK. January 2008. Code of practice for the prevention and control of healthcare associated infections. Accessed March 20, 2012.
  4. Jones GA, et al. Comparison of automated processing of flocked swabs with manual processing of fiber swabs for the detection of nasal carriage of Staphylococcus aureus. J Clin Microbiol. 2011;49(7):2717-2718.

As COPAN Diagnostics’ Global Marketing Manager, Gabriela Franco has played a key role in the expansion of COPAN’s line of automation for specimen processing in the pre-analytical phase of microbiology since it was launched in 2008. Gabriela has more than 10 years experience in marketing and product management. She holds BS in Business Administration and Marketing and Master of International Management (MIM) degrees.