The efficient function of the clinical microbiology laboratory is critical in providing the best possible patient care, as it helps clinicians to quickly and accurately diagnose infectious diseases. This role is becoming more important than ever, due to the development of new and re-emerging pathogens – increasingly in forms that are resistant to traditional antibiotics – and the growing mobility of people enabling the easier spread of superbugs around the world.

The impact of the US Affordable Care Act means there will be more insured individuals, which will equate to increased testing volumes in the laboratory. With fewer licensed technologists entering the field of clinical laboratory science there will in turn be fewer people available to perform the work. It is no surprise, therefore, that more labs are seeking to automate some or indeed all of their processes in order to respond faster and maintain the quality of their output.

"Within the past ten years, healthcare institutions have been consolidating, and, therefore, so are many labs associated with these institutions. This translates into increasing volumes for the newly formed consolidated lab, making automated instrumentation desirable to streamline processes and manage high numbers of specimens," says Dr Susan Novak, director of microbiology at Southern California Permanente Medical Group (SCPMG).

"We are talking not only about processes such as specimen handling but also the capability to digitally read cultures when they are ready rather than waiting for batches to be read. Automation means less repetitive work and fewer people popping tops.

"There is a shortage of licensed clinical scientists, and it is hard to find good-quality people, so even when consolidation is not an issue, there is still a strong drive towards automation, which has already revolutionised bacteriology, and increased speed, efficiency and volume," she adds.

Laboratory workers have a commitment to do what is best for the patient, which means getting accurate results faster. It is impossible to ignore the financial constraints on the healthcare sector, so cost-efficiency is equally important, but the looming critical shortage of skilled lab technicians – more of whom are leaving the workforce than entering – makes some level of automation almost inevitable.

"The drive for hospitals to save money is in part behind the consolidation. Centralised laboratory services have to also balance lab performance with issues such as the transportation of specimens, but ultimately, the lab cannot sacrifice the quality of patient care," stresses Novak.

Novak’s colleague, medical microbiologist Dr Beth Marlowe, SCPMG’s assistant director of microbiology, has seen automation bring great improvements in throughput at the facility they work in.

"There has been a paradigm shift in thinking. Dr Novak has been involved a lot in implementing automation in the pre-analytical space in our lab since 2003, and its volume and productivity have increased a lot without any growth in lab assistant numbers," she notes.

Bridging the skills gap

In their recent co-authored report, ‘Automation in the Clinical Microbiology Laboratory’, Novak and Marlowe consider not only the drivers of lab automation but also some of the key technology that can revolutionise laboratory processes.

They eloquently highlight the need for faster lab results with the case of Andrew Speaker, who, in 2007, carried a strain of multidrug-resistant tuberculosis from the US to France, Greece, Italy, the Czech Republic, Canada and back into the US.

"Linking digital imaging to pathology allows culture plates and smears to be read from anywhere in the world, and there is a lot of power in that."

Speaker’s diagnosis relied on systems developed more than 40 years ago that took weeks to deliver results because many of the processes were manual. Traditional microbiology methods are culture-based, requiring manual plating of specimens to growth media and skilled staff to read the plates.

Today, improved techniques are within reach, and the report highlights the Xpert MTB/RIF assay from US molecular diagnostics company Cepheid, which is a fully automated molecular assay that can detect Mycobacterium tuberculosis and rifampicin resistance from a direct specimen in just two hours. The system is approved by the FDA and routinely used in the SCPMG laboratory. Any positive rifampicin Xpert result is automatically sent to the California Department of Public Health, which will produce a genetic profile for predicting antibiotic susceptibility within days.

"In the future, we can expect to see integrated laboratory automation systems that are a hybrid of full laboratory automation systems available today and sample-to-answer technology like the Cepheid GeneXpert," says Marlowe.

Automation has changed bacterial identification and susceptibility testing with the introduction of systems such as the Vitek, MicroScan and Phoenix, enabling most testing to move from away from manual processes. Automated blood culture instruments also allow continuous monitoring of incubated culture bottles and provide alerts when positive results are seen.

The history of clinical laboratory automation is replete with innovations that have made technicians’ lives easier, and improved the speed and efficiency of key processes. The latest area of innovation is the digital imaging of media and glass slides for use in culture analysis.

"Linking digital imaging to pathology allows culture plates and smears to be read from anywhere in the world, and there is a lot of power in that. The images could patients be placed in the medical chart as part of a formal report. From the perspective of telemedicine and also job flexibility, the digital microbiology piece is very important. Staff could, for example, read plates by logging on to the Laboratory Information System from a home computer when the staff member was unable to physically be present at the laboratory. That flexibility could have a huge impact on patient care and labour needs," says Marlowe.

The challenge labs now face is whether to adopt individual systems that have proven their value or to take the plunge and choose total laboratory automation (TLA) instead. Automation enables the standardisation of key tasks in the lab, and TLA involves linking automated microbiology systems for pre-analytical plating instrumentation, smart incubators with the capability to create digital images of growth on plates, track or conveyor systems to move plates, and ancillary equipment for sample work-up.

At present, bioMérieux, BD Kiestra and Copan have systems in Europe and North America. The French Company i2a also has systems in Europe and is working to place systems in the US. The track systems that load plates from specimen processors not only save time but also free up technicians from batching plates in racks and placing them in the incubator.

Furthermore, each vendor is working on additional functionality, such as the instrument in development by bioMérieux that inoculates the mass spectrometry template and McFarland tubes for susceptibility testing.

TLA – a balancing act

The cost of laboratory automation depends on the level of automation that is required, and more detailed studies are needed to get a clearer picture of the financial and clinical impact of automation on workflow and patient outcomes.

Alongside the obvious financial issues, however, there are other questions to answer for any lab considering a modular automation programme or TLA.

Volume is an important driver as to whether a laboratory should pursue TLA. Potential growth should also be considered when making any decisions regarding automation," says Novak. "It is very important to interface and consult with the various vendors regarding options and how instruments, either TLA or modular components, can fit into a specific laboratory environment

"Individuals adept at looking at analytics are crucial to developing the business case and return-on-investment proposals in order to get the backing of administrators. Most administrators will need to see a path of development in which additional processes are added, or they may look at a reduction in force if the business case supports that conclusion. Labs will always need skilled personnel, but they could be redirected to other areas that add value," she adds.

Any implementation of automation needs to have a clear road map and is, in many ways, the beginning of a process rather than the culmination of an investment strategy. Beyond the initial gains in productivity and efficiency, there is a need for vendors, administrators and technicians to know where the automation process will lead.

Collaboration is essential to the success of any modular or TLA strategy, and vendors have much to learn, as do laboratory staff. Some vendors are particularly good at the technology side, while others are better at looking at processes. Both skill sets must combine for any automation strategy to deliver on its full potential.

"Part of the problem is that there are multiple parts to it, and people need to have their processes looked at," explains Marlowe. "You need the whole package from vendors, which means a complete analysis of the current system given that all laboratories are different and cannot necessarily be compared on paper.

"We need to remain responsive. There are a lot of dynamic processes in our lab, where there is a grand total of 160 staff, because we don’t know what the next call will be; it could be Ebola or something entirely new."

"One thing is certain," believes Marlowe, "TLA will improve as more people opt to do it. TLA is a revolution, and the technology is here to make our lives easier, and improve the quality of results that we give our physicians and patients, though it is a balancing act with cost. There is a lot of untapped potential in the technology and in digital microbiology."